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  1. Consent-Based Siting Public Meeting Holiday Inn Capitol Plaza...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Consent-Based Siting Public Meeting Holiday Inn Capitol Plaza - Sacramento 300 J Street Sacramento, CA 95814 April 26, 2016 4:00-5:00 PM Informal Open House and Poster Session ...

  2. The Committee convened in the Clark Room, Holiday Inn Capitol,

    U.S. Energy Information Administration (EIA) Indexed Site

    MEETING - - - Thursday, April 25, 1996 - - - The Committee convened in the Clark Room, Holiday Inn Capitol, 550 C Street, S.W., Washington, D.C., at 9:00 a.m., Dr. Timothy D. Mount, Chairman, presiding. PRESENT: TIMOTHY D. MOUNT, Chairman SAMPRIT CHATTERJEE BRENDA G. COX JOHN D. GRACE CALVIN KENT GRETA M. LJUNG RICHARD A. LOCKHART DANIEL A. RELLES PRESENT (Continued): BRADLEY O. SKARPNESS G. CAMPBELL WATKINS ALSO PRESENT: RENEE MILLER YVONNE BISHOP MARY HUTZLER JAY HAKES DOUGLAS HALE ART HOLLAND

  3. The Committee convened in the Clark Room of the Holiday Inn

    U.S. Energy Information Administration (EIA) Indexed Site

    - - - - - COMMITTEE ON ENERGY STATISTICS - - - - - MEETING - - - - - FRIDAY, APRIL 26, 1996 The Committee convened in the Clark Room of the Holiday Inn Capitol, 550 C Street, S.W., Washington, D.C., at 9:00 a.m., DR. TIMOTHY D. MOUNT, Chair, presiding. PRESENT: TIMOTHY D. MOUNT, Chair SAMPRIT CHATTERJEE BRENDA G. COX JOHN D. GRACE CALVIN KENT GRETA M. LJUNG RICHARD A. LOCKHART DANIEL A. RELLES BRADLEY O. SKARPNESS G. CAMPBELL WATKINS ALSO PRESENT: RENEE MILLER YVONNE M. BISHOP DIANE LIQUE L.A.

  4. The Committee met in the Columbia Room at the Holiday Inn

    U.S. Energy Information Administration (EIA) Indexed Site

    Friday, April 21, 1995 - - - The Committee met in the Columbia Room at the Holiday Inn Capitol, 550 C Street S.W., Washington, D.C., at 9:00 a.m., Timothy D. Mount, Chairman, presiding. PRESENT: TIMOTHY D. MOUNT, Chair DAVID R. BELLHOUSE CHARLES W. BISCHOFF BRENDA G. COX FAYE DUCHIN JOHN D. GRACE PHILIP HANSWER CALVIN KENT GRETA M. LJUNG JAMES L. O'BRIEN DANIEL A. RELLES BRADLEY O. SKARPNESS G. CAMPBELL WATKINS A-G-E-N-D-A Page No. Introductory Remarks, TIMOTHY MOUNT, Chairman 3 Announcement of

  5. The Committee met in the Clark Room in the Holiday Inn Capitol,

    U.S. Energy Information Administration (EIA) Indexed Site

    - - - COMMITTEE ON ENERGY STATISTICS - - - THURSDAY, APRIL 23, 1998 - - - The Committee met in the Clark Room in the Holiday Inn Capitol, 550 C Street, S.W., Washington, D.C., at 9:00 a.m., Daniel A. Relles, Chair, presiding. PRESENT: DANIEL A. RELLES Chair CHARLES W. BISCHOFF Member CAROL A. GOTWAY CRAWFORD Member PHILIP HANSER Member CALVIN KENT Member GRETA M. LJUNG Member POLLY A. PHIPPS Member SEYMOUR SUDMAN Member ROY W. WHITMORE Member DENNY ELLERMAN Guest JAMES HAMMITT Guest I N D E X

  6. The Committee met in the Clark Room in the Holiday Inn Capitol,

    U.S. Energy Information Administration (EIA) Indexed Site

    FRIDAY APRIL 24, 1998 - - - The Committee met in the Clark Room in the Holiday Inn Capitol, 550 C Street, S.W., Washington, D.C., at 9:00 a.m., Daniel Relles, Chair, presiding. PRESENT: DANIEL RELLES Chair CHARLES BISCHOFF Member CAROL CRAWFORD Member CALVIN KENT Member GRETA M. LJUNG Member POLLY PHIPPS Member SEYMOUR SUDMAN Member ROY WHITMORE Member JAMES HAMMITT Guest I N D E X Page Opening Comments from the Chair 3 Recognizing Previous Judges of the EIA Graphics 4 Contest and Announcing

  7. The Committee met in the Clark Room of the Capitol Holiday Inn,

    U.S. Energy Information Administration (EIA) Indexed Site

    PUBLIC MEETING + + + + + THURSDAY NOVEMBER 13, 1997 + + + + + WASHINGTON, D.C. The Committee met in the Clark Room of the Capitol Holiday Inn, 550 C Street, S.W., at 9:00 a.m., G. Campbell Watkins, Chair, presiding. PRESENT: G. CAMPBELL WATKINS Chair DANIEL A. RELLES Vice Chair DAVID R. BELLHOUSE R. SAMPRIT CHATTERJEE BRENDA G. COX CAROL A. GOTWAY CRAWFORD PHILIP HANSEN CALVIN KENT GRETA M. LJUNG ROY WHITMORE INVITED GUESTS: SEYMOUR SUDMAN RICHARD TABORS EIA STAFF: JAY HAKES EIA Administrator

  8. The Committee met in the Clark Room, Holiday Inn Capitol at 550

    U.S. Energy Information Administration (EIA) Indexed Site

    PUBLIC MEETING + + + THURSDAY, APRIL 10, 1997 + + + The Committee met in the Clark Room, Holiday Inn Capitol at 550 C Street, S.W., Washington, D.C., at 9:00 a.m., G. Campbell Watkins, Chairman, presiding. PRESENT: G. CAMPBELL WATKINS, Chairman DAVID R. BELLHOUSE CHARLES W. BISCHOFF BRENDA G. COX CAROL A. GOTWAY CRAWFORD CALVIN KENT GRETA M. LJUNG DANIEL A. RELLES BRADLEY O. SKARPNESS PRESENT (Continued): ROY WHITMORE C O N T E N T S PAGE Opening Remarks, Lynda Carlson 10 Update on 1997

  9. The Committee met in the Columbia Room at the Holiday Inn Capitol,

    U.S. Energy Information Administration (EIA) Indexed Site

    THURSDAY, APRIL 20, 1995 The Committee met in the Columbia Room at the Holiday Inn Capitol, 550 C Street, S.W., Washington, D.C., at 9:00 a.m., Timothy D. Mount, Chair, presiding. PRESENT: TIMOTHY D. MOUNT, Chair DAVID R. BELLHOUSE CHARLES W. BISCHOFF BRENDA G. COX FAYE DUCHIN JOHN D. GRACE PHILIP HANSER CALVIN KENT GRETA M. LJUNG JAMES L. O'BRIEN DANIEL A. RELLES BRADLEY O. SKARPNESS G. CAMPBELL WATKINS AGENDA Introductions by Committee Chair . . . . . . . . . 3 Opening Remarks by Administrator

  10. Annual Review of BPA-Funded Projects in Natural and Artificial Propagation of Salmonids, March 27-29, 1985, Holiday Inn Airport, Portland, Oregon.

    SciTech Connect (OSTI)

    United States. Bonneville Power Administration.

    1985-04-01

    The Fish and Wildlife Division of Bonneville Power Administration (BPA) hosted a meeting for contractors to present the results of fiscal year 1984 research conducted to implement the Northwest Power Planning Council's Fish and Wildlife Program. The meeting focused on those projects specifically related to natural and artificial propagation of salmonids. The presentations were held at the Holiday Inn Airport in Portland, Oregon, on March 27-29, 1985. This document contains abstracts of the presentations from that meeting. Section 1 contains abstracts on artificial propagation, fish health, and downstream migration, and Section 2 contains abstracts on natural propagation and habitat improvement. The abstracts are indexed by BPA Project Number and by Fish and Wildlife Program Measure. The registered attendees at the meeting are listed alphabetically in Appendix A and by affiliation in Appendix B.

  11. Holiday Gift Drive

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Gift Drive Holiday Gift Drive Every year, Laboratory employees help fulfill the holiday wishes of children and seniors in our communities. In 2015, our employees donated more than 1,200 gifts to 23 nonprofit organizations to help Northern New Mexico children, senior citizens, and families have a brighter holiday season. May 7, 2015 Every holiday season, employees of Los Alamos National Laboratory donate and distribute gifts to families in need throughout Northern New Mexico. Contacts Annual Food

  12. NERSC Holiday Schedule

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Holiday Schedule NERSC Holiday Schedule December 20, 2013 by Francesca Verdier All NERSC computing and storage systems will remain in full operation throughout the holiday season (Tuesday December 24 through Wednesday January 1). From Tuesday December 24 through Wednesday January 1, NERSC Consulting and Account Support services will be available *only* on Friday December 27 and Monday December 30, from 8:00 to 5:00 Pacific Time. Normal Consulting and Account Support schedules will resume on

  13. Holiday Food Drive

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Food Drive Holiday Food Drive Laboratory employees helped donate 300 boxes of nonperishable food items and 360 frozen turkeys during the 2015 annual food drive. September 16, 2013 LANL employees organize food for the Holiday Food Drive. Contacts Annual Food & Holiday Gift Drives Mike Martinez (505) 699-3388 Community Partnerships Office (505) 665-4400 Email Helping feed Northern New Mexico families During the Laboratory's 2015 Annual Food Drive, employees and subcontract workers once again

  14. Berkeley Lab Holiday Schedule

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Thursday, January 1, 2015 New Year's Holiday Monday, January 19, 2015 Martin Luther King Day Monday, February 16, 2015 Presidents Day Friday, March 27, 2015 Cesar Chavez Day**...

  15. Michelle L. Holiday

    Broader source: Energy.gov [DOE]

    Michelle Holiday, an enrolled member of the Iowa Tribe of Oklahoma, has had extensive experience in tribal affairs, government relations, and the energy industry. From 1993 to 2001, She served in...

  16. Post-Holiday Holiday Shopping | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Post-Holiday Holiday Shopping Post-Holiday Holiday Shopping January 10, 2012 - 4:31pm Addthis Elizabeth Spencer Communicator, National Renewable Energy Laboratory Ah, January. It's still cold and it's still dark all the time, but now all the cheerful Christmas lights have come down so there's nothing to break up the monotony. What's there to do? Well, while it's a little late now, you might want to go do some post-holiday holiday shopping. Yes, I know. That sounds insane. Everyone is thoroughly

  17. Museum Closed for Thanksgiving Holiday

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Museum Closed for Thanksgiving Holiday Museum Closed for Thanksgiving Holiday WHEN: Nov 26, 2015 12:00 AM - 11:59 PM WHERE: Bradbury Science Museum 1350 Central Ave, Los Alamos, NM...

  18. Museum Closed for Christmas Holiday

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Museum Closed for Christmas Holiday Museum Closed for Christmas Holiday WHEN: Dec 25, 2015 12:00 AM - 11:59 PM WHERE: Bradbury Science Museum 1350 Central Ave, Los Alamos, NM 87544, USA CATEGORY: Bradbury INTERNAL: Calendar Login Museum Closed for Christmas Holiday Event Description The Bradbury Science Museum will be CLOSED for the Christmas holiday. The Bradbury Science Museum is open to the public every day except for Thanksgiving Day, Christmas Day and New Year's Day. Admission is always

  19. Museum Closed for Thanksgiving Holiday

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Museum Closed for Thanksgiving Holiday Museum Closed for Thanksgiving Holiday WHEN: Nov 26, 2015 12:00 AM - 11:59 PM WHERE: Bradbury Science Museum 1350 Central Ave, Los Alamos, NM 87544 USA CATEGORY: Bradbury INTERNAL: Calendar Login Museum Closed for Thanksgiving Holiday Event Description The museum will be CLOSED for the Thanksgiving holiday. The Bradbury Science Museum is open to the public every day except for Thanksgiving Day, Christmas Day and New Year's Day. Admission is always free.

  20. Leveraging Holidays and Other Events

    Broader source: Energy.gov [DOE]

    Better Buildings Residential Network Driving Demand Peer Exchange Call Series: Leveraging Holidays and Other Events, Call Slides and Discussion Summary, November 7, 2013.

  1. Riverside Inn Pool & Spa Low Temperature Geothermal Facility...

    Open Energy Info (EERE)

    Inn Pool & Spa Low Temperature Geothermal Facility Jump to: navigation, search Name Riverside Inn Pool & Spa Low Temperature Geothermal Facility Facility Riverside Inn Sector...

  2. Helping make the holidays happier

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Helping Make The Holidays Happier Community Connections: Your link to news and opportunities from Los Alamos National Laboratory Latest Issue: September 1, 2016 all issues All Issues » submit Helping make the holidays happier This year's LANL food drive collected enough donations to provide 11,600 meals for those in need. January 1, 2013 dummy image Read our archives Contacts Editor Linda Anderman Email Community Programs Office Kurt Steinhaus Email The contributions by employees included 164

  3. Save Energy on Appliances this Holiday Season

    Broader source: Energy.gov [DOE]

    Before the holiday shopping mayhem begins, take a look at Energy Saver's tips for finding the most energy efficient appliances.

  4. GovCon Holiday Soiree

    Broader source: Energy.gov [DOE]

    The 6th Annual GovCon Holiday Soiree will be held at the Kennedy Center on Monday, December 8, from 5:30pm to 7:30pm. The event is expected to bring together more than 200 representatives of women-...

  5. holiday | National Nuclear Security Administration

    National Nuclear Security Administration (NNSA)

    holiday Facts About Fireworks How do fireworks work? Fireworks are the result of chemical reactions involving a fuel source, an oxidizer and a color-producing chemical mixture. Color combinations are produced in the sky when various metal elements are heated, exciting electrons and releasing excess energy in the form of light... Labor Day Weekend 2015 Labor Day is dedicated to the achievements of American workers and the contributions they made to the strength, prosperity, and well-being of our

  6. River Inn Natural Hot Spring Pool & Spa Low Temperature Geothermal...

    Open Energy Info (EERE)

    Inn Natural Hot Spring Pool & Spa Low Temperature Geothermal Facility Jump to: navigation, search Name River Inn Natural Hot Spring Pool & Spa Low Temperature Geothermal Facility...

  7. The Saratoga Inn Pool & Spa Low Temperature Geothermal Facility...

    Open Energy Info (EERE)

    Saratoga Inn Pool & Spa Low Temperature Geothermal Facility Jump to: navigation, search Name The Saratoga Inn Pool & Spa Low Temperature Geothermal Facility Facility The Saratoga...

  8. Museum Closed for New Year's Holiday

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Museum Closed for New Year's Holiday Museum Closed for New Year's Holiday WHEN: Jan 01, 2016 12:00 AM - 11:59 PM WHERE: Bradbury Science Museum 1350 Central Ave, Los Alamos, NM 87544, USA CATEGORY: Bradbury INTERNAL: Calendar Login Museum Closed for New Year's Holiday Event Description The Bradbury Science Museum will be CLOSED for the New Year's holiday. The Bradbury Science Museum is open to the public every day except for Thanksgiving Day, Christmas Day and New Year's Day. Admission is always

  9. Tips to Save Energy During the Holidays | Department of Energy

    Broader source: Energy.gov (indexed) [DOE]

    Allison Casey Senior Communicator, NREL The winter holiday season has officially begun, and with it comes the frenzy of decorating, holiday gatherings, gift buying, and errand...

  10. holiday

    National Nuclear Security Administration (NNSA)

    bloglabor-day-weekend-2015

    Labor Day is dedicated to the achievements of American workers and the contributions they made to the strength, prosperity, and well-being...

  11. Holiday

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    in society. May 5 Tue 12:00 AM Cinco de Mayo United States and Mexico Cinco de Mayo (Spanish for "fifth of May") is a celebration held on May 5. Apr 13 Mon 12:00 AM Thomas...

  12. Code of Conduct regarding holiday gifts

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    questions about a specific event or item, please contact me at 665-3104, or Michelle Cantu, Ethics and Compliance Group Leader, at 667-7506. Have an enjoyable and safe Holiday...

  13. Solar Field Powers Historic Garden Holiday Display

    Broader source: Energy.gov [DOE]

    Popular holiday attraction Longwood Gardens in Pennsylvania has commissioned an American-made 1.2 megawatt, 10.7-acre solar field as part of a goal to generate three megawatts of renewable energy by 2018.

  14. I-N-N Electric Coop, Inc | Open Energy Information

    Open Energy Info (EERE)

    I-N-N Electric Coop, Inc Jump to: navigation, search Name: I-N-N Electric Coop, Inc Place: Alaska Phone Number: 800-571-1259 (In Alaska) or Outside Alaska: 907-571-1259 ...

  15. EM Waste Isolation Pilot Plant Team's Holiday Spirit Shines ...

    Office of Environmental Management (EM)

    Waste Isolation Pilot Plant Team's Holiday Spirit Shines EM Waste Isolation Pilot Plant Team's Holiday Spirit Shines December 23, 2013 - 12:00pm Addthis Aspen Cass, a relative of ...

  16. Reduce Waste and Save Energy this Holiday Season | Department...

    Office of Environmental Management (EM)

    Reduce Waste and Save Energy this Holiday Season Reduce Waste and Save Energy this Holiday Season December 5, 2014 - 9:55am Addthis Wrap your gifts with recycled paper to reduce ...

  17. EECBG Success Story: North Pole's Holiday Wish for an Energy...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Pole's Holiday Wish for an Energy Efficient 2012 EECBG Success Story: North Pole's Holiday Wish for an Energy Efficient 2012 December 23, 2011 - 4:20pm Addthis The city of North ...

  18. North Pole's Holiday Wish for An Energy Efficient 2012 | Department...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Pole's Holiday Wish for An Energy Efficient 2012 North Pole's Holiday Wish for An Energy Efficient 2012 December 23, 2011 - 4:20pm Addthis The city of North Pole, Alaska, is hoping ...

  19. How Do Holiday Lights Work? | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Do Holiday Lights Work? How Do Holiday Lights Work? December 16, 2015 - 11:31am Addthis Daniel Wood Daniel Wood Data Visualization and Cartographic Specialist, Office of Public Affairs Sarah Gerrity Sarah Gerrity Former Multimedia Editor, Office of Public Affairs Want to learn more about Holiday Lights? Check out our recent post on the Top 5 Things You Didn't Know About Holiday Lights. Last year, we told you how incandescent holiday string lights work, but we left out an important topic: LED

  20. Fountain Inn, South Carolina: Energy Resources | Open Energy...

    Open Energy Info (EERE)

    district.12 Registered Energy Companies in Fountain Inn, South Carolina Verde Biofuels Inc References US Census Bureau Incorporated place and minor civil...

  1. Energy-Efficient Holiday Decorating Tips | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Holiday Decorating Tips Energy-Efficient Holiday Decorating Tips December 19, 2012 - 10:36am Addthis Using LED lights for your holiday decorations can save you energy and money. | Photo courtesy of ©iStockphoto.com/peterspiro Using LED lights for your holiday decorations can save you energy and money. | Photo courtesy of ©iStockphoto.com/peterspiro Erik Hyrkas Erik Hyrkas Media Relations Specialist, Office of Energy Efficiency & Renewable Energy What does this mean for me? You can save

  2. Your Holidays...Brought to You by Fuel Cells

    Broader source: Energy.gov [DOE]

    A story about how fuel cells are helping bring the holidays to you is currently posted on the Energy Department's Blog.

  3. Fuel Cell Powers Up Festivities at Secretary Chu's Holiday Party...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Employees at the Energy Department's annual holiday party were greeted with many familiar sights - festive decorations, sugar cookies, and a tree in sparkling lights. In addition ...

  4. EECBG Success Story: South Carolina Community Lights Up the Season with Energy-Efficient Holiday Lights

    Broader source: Energy.gov [DOE]

    A South Carolina community is proving that energy efficiency can improve the holidays by reducing energy and maintenance costs, thanks to its new LED holiday lights. Learn more.

  5. SEP Success Story: Solar Field Powers Historic Garden Holiday Display

    Broader source: Energy.gov [DOE]

    One of the most visited public gardens in the United States, and a popular attraction for elaborate holiday decorations, is now running on solar power thanks to help from the Energy Department. Learn more.

  6. SEP Success Story: Solar Field Powers Historic Garden Holiday...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Photo courtesy of Longwood GardensW. Hill One of the most visited public gardens in the United States, and a popular attraction for elaborate holiday decorations, is now running...

  7. How Do Holiday Lights Work? | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... While shunts serve to remedy an open circuit, fuses work to prevent damage due to a short ... of holiday lights, let's address some common problems we run into and how to remedy them. ...

  8. Tips to Save Energy During the Holidays | Department of Energy

    Energy Savers [EERE]

    Don't let your energy-saving efforts fall by the wayside amid all the festivities; the tips below will help you save energy and money even as you celebrate. Use LED Holiday Lights ...

  9. Holiday Gifts for Energy Efficiency | Department of Energy

    Broader source: Energy.gov (indexed) [DOE]

    ... Tips to Save Energy During the Holidays Giving energy-efficient gifts is an easy way to save money and energy year-round. | Photo courtesy of iStockphoto.comnano 'Tis the Season ...

  10. SRR Staff Send the Holidays to Soldiers Overseas

    Broader source: Energy.gov [DOE]

    A request for razors from a U.S. Army private serving in Afghanistan transformed into a full-scale holiday gift rescue operation by employees of the Savannah River Site’s liquid waste contractor,...

  11. Meaningful Money Gifts at Holiday Time | The Ames Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Meaningful Money Gifts at Holiday Time Give a small child a gift of money and they'll give you a sideways look and sheepish, "Thanks." They usually prefer boxes with big bows that...

  12. NREL Provides PV Holiday Lights for Christmas Tree

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Provides PV Holiday Lights for Christmas Tree For more information contact: George Douglas (303) 275-4096 Golden, Colo., December 2, 1997 -- National Renewable Energy Laboratory (NREL) engineers are showing off the power of photovoltaics in Washington, D.C. again this holiday season. They have installed an 8-kilowatt solar array on the Ellipse just south of the White House to help power lights on the National Christmas Tree. The tree lighting ceremony on Dec. 4 begins Washington's 1997 Pageant

  13. Workers Across the Nuclear Security Enterprise Give Back This Holiday

    National Nuclear Security Administration (NNSA)

    Season | National Nuclear Security Administration | (NNSA) Workers Across the Nuclear Security Enterprise Give Back This Holiday Season December 23, 2009 This holiday season, employees from across the nuclear security enterprise have found countless ways to make this time of year more cheerful by lending a helping hand to the less fortunate in their communities. The following is a short summary of some of those efforts: Kansas City Plant (KCP) off site link Through the Salvation Army's Angel

  14. Two-Dimensional Electron Gas in Monolayer InN Quantum Wells....

    Office of Scientific and Technical Information (OSTI)

    Two-Dimensional Electron Gas in Monolayer InN Quantum Wells. Citation Details In-Document Search Title: Two-Dimensional Electron Gas in Monolayer InN Quantum Wells. Abstract not...

  15. LED Holiday Lights: Festive, Safe, and Efficient! | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    LED Holiday Lights: Festive, Safe, and Efficient! LED Holiday Lights: Festive, Safe, and Efficient! November 23, 2010 - 6:30am Addthis Allison Casey Senior Communicator, NREL This week brings a day that many people look forward to all year-and I'm not talking about Thanksgiving, or Black Friday. I'm talking about that magical day when it's finally okay to drag the dusty boxes from the basement or attic, to lovingly sort and display your decorations, to untangle your light strings and set up the

  16. Geothermal heating facilities for Frontier Inn, Susanville, California

    SciTech Connect (OSTI)

    Not Available

    1982-03-01

    The Frontier Inn, located in Susanville, California, is a 38 unit motel composed of six major sections (coffee shop, A frame units, apartments, back units, two story units and office). These sections were built over a number of years and exhibit widely varying types of construction. Space heating is provided by primarily electric resistance equipment with some propane use. Domestic hot water is provided primarily by propane with some electric resistance. The coffee shop uses fuel oil for both space and domestic hot water heating. The City of Susanville is currently in the process of installing a geothermal district heating system. Although the motel site is not located in the area of present construction activity, it is expected that the pipeline will be extended in the near future. This study examines the potential of retrofitting the existing heating facilities at the Frontier Inn to geothermal.

  17. Angular-dependent Raman study of a- and s-plane InN

    SciTech Connect (OSTI)

    Filintoglou, K.; Katsikini, M. Arvanitidis, J.; Lotsari, A.; Dimitrakopulos, G. P.; Vouroutzis, N.; Ves, S.; Christofilos, D.; Kourouklis, G. A.; Ajagunna, A. O.; Georgakilas, A.; Zoumakis, N.

    2015-02-21

    Angular-dependent polarized Raman spectroscopy was utilized to study nonpolar a-plane (11{sup ¯}20) and semipolar s-plane (101{sup ¯}1) InN epilayers. The intensity dependence of the Raman peaks assigned to the vibrational modes A{sub 1}(TO), E{sub 1}(TO), and E{sub 2}{sup h} on the angle ψ that corresponds to rotation around the growth axis, is very well reproduced by using expressions taking into account the corresponding Raman tensors and the experimental geometry, providing thus a reliable technique towards assessing the sample quality. The s- and a-plane InN epilayers grown on nitridated r-plane sapphire (Al{sub 2}O{sub 3}) exhibit good crystalline quality as deduced from the excellent fitting of the experimental angle-dependent peak intensities to the theoretical expressions as well as from the small width of the Raman peaks. On the contrary, in the case of the s-plane epilayer grown on non-nitridated r-plane sapphire, fitting of the angular dependence is much worse and can be modeled only by considering the presence of two structural modifications, rotated so as their c-axes are almost perpendicular to each other. Although the presence of the second variant is verified by transmission electron and atomic force microscopies, angular dependent Raman spectroscopy offers a non-destructive and quick way for its quantification. Rapid thermal annealing of this sample did not affect the angular dependence of the peak intensities. The shift of the E{sub 1}(TO) and E{sub 2}{sup h} Raman peaks was used for the estimation of the strain state of the samples.

  18. Top 5 Things You Didn't Know About Holiday Lights | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Things You Didn't Know About Holiday Lights Top 5 Things You Didn't Know About Holiday Lights December 5, 2014 - 4:49pm Addthis With a fiery past and a bright future, here are 5 things you probably didn’t know about holiday lights. | Graphic by <a href="/node/379579">Sarah Gerrity</a>, Energy Department. With a fiery past and a bright future, here are 5 things you probably didn't know about holiday lights. | Graphic by Sarah Gerrity, Energy Department. Pat Adams Pat

  19. #tipsEnergy: How to Save Energy During the Holidays | Department...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    the Holidays December 21, 2012 - 2:20pm Addthis Rebecca Matulka Rebecca Matulka Former Digital Communications Specialist, Office of Public Affairs storify:http:storify.com...

  20. ERSUG: July 11 - 12, 1994 (Rockville, Maryland)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    - 12, 1994 (Rockville, Maryland) Dates July 11 - 12, 1994 Location Holiday Inn, Crowne Plaza Rockville, Maryland Presentations Agenda ERSUG Meeting July 11-12, 1994 Holiday Inn,...

  1. How do You Save Energy During the Holidays? | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    How do You Save Energy During the Holidays? How do You Save Energy During the Holidays? December 20, 2011 - 9:03am Addthis Between family vacations, shopping, and cooking extravagant meals, energy conservation isn't usually at the top our list of things to do during the holiday season. But there are plenty of ways to save money & energy even now by doing little - and even fun - things to reduce our utility bills and use less energy overall. This week, Amanda showed us how she saves money and

  2. Buying an Appliance this Holiday Season? ENERGY STAR Products will Save You

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Money and Energy All Year! | Department of Energy an Appliance this Holiday Season? ENERGY STAR Products will Save You Money and Energy All Year! Buying an Appliance this Holiday Season? ENERGY STAR Products will Save You Money and Energy All Year! December 12, 2012 - 11:40am Addthis When shopping for appliances or electronics for the holidays, look for the ENERGY STAR® and EnergyGuide labels. | Photo by Dennis Schroeder, NREL 22090. When shopping for appliances or electronics for the

  3. Holiday Auction raises record amount -- $5,842 | The Ames Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    loves his crisp Vince Dahl and Dave Boeke show off their holiday garb. Auctioneer Dale Meyer plies his trade. Julie Dredla looks to see who's bidding against her. What am I bid...

  4. Y-12 helps more than 600 kids for the holidays | National Nuclear...

    National Nuclear Security Administration (NNSA)

    Photo Gallery Jobs Apply for Our Jobs Our Jobs Working at NNSA Blog Home NNSA Blog Y-12 helps more than 600 kids for ... Y-12 helps more than 600 kids for the holidays WATE...

  5. Y-12 employees help make holiday merrier for many | Y-12 National Security

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Complex help make ... Y-12 employees help make holiday merrier for many Posted: December 21, 2012 - 9:00am Bicycles and helmets provided by Y-12 workers await distribution to area charitable agencies. Nearly 50 workers at the Y-12 National Security Complex served as Santa's elves in the Y-12 Employees' Society's 2012 Angel Tree program. The society collaborates with various charitable agencies to help provide holiday gifts for families deemed eligible for assistance by their county's

  6. Large area InN terahertz emitters based on the lateral photo-Dember effect

    SciTech Connect (OSTI)

    Wallauer, Jan Grumber, Christian; Walther, Markus; Polyakov, Vladimir; Iannucci, Robert; Cimalla, Volker; Ambacher, Oliver

    2015-09-14

    Large area terahertz emitters based on the lateral photo-Dember effect in InN (indium nitride) are presented. The formation of lateral photo-Dember currents is induced by laser-illumination through a microstructured metal cover processed onto the InN substrate, causing an asymmetry in the lateral photogenerated charge carrier distribution. Our design uses simple metal structures, which are produced by conventional two-dimensional micro-structuring techniques. Having favoring properties as a photo-Dember material InN is particularly well-suited as a substrate for our emitters. We demonstrate that the emission intensity of the emitters can be significantly influenced by the structure of the metal cover leaving room for improvement by optimizing the masking structures.

  7. Spectral dependence of third-order nonlinear optical properties in InN

    SciTech Connect (OSTI)

    Ahn, H. Lee, M.-T.; Chang, Y.-M.

    2014-05-19

    We report on the nonlinear optical properties of InN measured in a wide near-infrared spectral range with the femtosecond Z-scan technique. The above-bandgap nonlinear absorption in InN is found to originate from the saturation of absorption by the band-state-filling and its cross-section increases drastically near the bandgap energy. With below-bandgap excitation, the nonlinear absorption undergoes a transition from saturation absorption (SA) to reverse-SA (RSA), attributed to the competition between SA of band-tail states and two-photon-related RSA. The measured large nonlinear refractive index of the order of 10{sup −10} cm{sup 2}/W indicates InN as a potential material for all-optical switching and related applications.

  8. Lois Curfman McInnes, 2011 | U.S. DOE Office of Science (SC)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Lois Curfman McInnes, 2011 The Ernest Orlando Lawrence Award Lawrence Award Home Nomination & Selection Guidelines Award Laureates 2010's 2000's 1990's 1980's 1970's 1960's Ceremony The Life of Ernest Orlando Lawrence Contact Information The Ernest Orlando Lawrence Award U.S. Department of Energy SC-2/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-2411 E: Email Us 2010's Lois Curfman McInnes, 2011 Print Text Size: A A A FeedbackShare Page Computer,

  9. Two-dimensional electron gas in monolayer InN quantum wells

    SciTech Connect (OSTI)

    Pan, Wei; Dimakis, Emmanouil; Wang, George T.; Moustakas, Theodore D.; Tsui, Daniel C.

    2014-11-24

    We report in this letter experimental results that confirm the two-dimensional nature of the electron systems in monolayer InN quantum wells embedded in GaN barriers. The electron density and mobility of the two-dimensional electron system (2DES) in these InN quantum wells are 5×1015 cm-2 and 420 cm2 /Vs, respectively. Moreover, the diagonal resistance of the 2DES shows virtually no temperature dependence in a wide temperature range, indicating the topological nature of the 2DES.

  10. Two-dimensional electron gas in monolayer InN quantum wells

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Pan, Wei; Dimakis, Emmanouil; Wang, George T.; Moustakas, Theodore D.; Tsui, Daniel C.

    2014-11-24

    We report in this letter experimental results that confirm the two-dimensional nature of the electron systems in monolayer InN quantum wells embedded in GaN barriers. The electron density and mobility of the two-dimensional electron system (2DES) in these InN quantum wells are 5×1015 cm-2 and 420 cm2 /Vs, respectively. Moreover, the diagonal resistance of the 2DES shows virtually no temperature dependence in a wide temperature range, indicating the topological nature of the 2DES.

  11. Growth mechanism and microstructure of low defect density InN (0001) In-face thin films on Si (111) substrates

    SciTech Connect (OSTI)

    Kehagias, Th.; Dimitrakopulos, G. P.; Koukoula, T.; Komninou, Ph.; Ajagunna, A. O.; Georgakilas, A.; Physics Department, University of Crete, P.O. Box 2208, 71003 Heraklion-Crete ; Tsagaraki, K.; Adikimenakis, A.

    2013-10-28

    Transmission electron microscopy has been employed to analyze the direct nucleation and growth, by plasma-assisted molecular beam epitaxy, of high quality InN (0001) In-face thin films on (111) Si substrates. Critical steps of the heteroepitaxial growth process are InN nucleation at low substrate temperature under excessively high N-flux conditions and subsequent growth of the main InN epilayer at the optimum conditions, namely, substrate temperature 400450 C and In/N flux ratio close to 1. InN nucleation occurs in the form of a very high density of three dimensional (3D) islands, which coalesce very fast into a low surface roughness InN film. The reduced reactivity of Si at low temperature and its fast coverage by InN limit the amount of unintentional Si nitridation by the excessively high nitrogen flux and good bonding/adhesion of the InN film directly on the Si substrate is achieved. The subsequent overgrowth of the main InN epilayer, in a layer-by-layer growth mode that enhances the lateral growth of InN, reduces significantly the crystal mosaicity and the density of threading dislocations is about an order of magnitude less compared to InN films grown using an AlN/GaN intermediate nucleation/buffer layer on Si. The InN films exhibit the In-face polarity and very smooth atomically stepped surfaces.

  12. Nanostructural and electronic properties of polytypes in InN nanocolumns

    SciTech Connect (OSTI)

    Kioseoglou, J.; Koukoula, T.; Komninou, Ph.; Kehagias, Th.; Georgakilas, A.; Androulidaki, M.

    2013-08-21

    Transmission electron microscopy techniques and density functional theory calculations were employed to investigate the nanostructural and electronic properties of InN polytypes observed in InN nanocolumns, grown on Si(111) by molecular beam epitaxy. Moir fringes and alternating hexagonal and cubic lattice stacking sequences along the c-axis, observed among the wurtzite layers, implied the presence of different structures embedded in the basic 2H structure of the nanocolumns. Quantitative electron diffraction analysis and high-resolution image simulations verified the coexistence of the wurtzite structure with the 4H, 6H, and the 3C zinc-blende structural polytypes. Total energies calculations established the 2H wurtzite structure as the most stable polytype. The band gap of all polytypes was found direct with the energies and the band gaps of the 4H (E{sub g} = 0.64 eV) and 6H (E{sub g} = 0.60 eV) structures calculated between the corresponding values of the 2H (E{sub g} = 0.75 eV) and 3C (E{sub g} = 0.49 eV) basic structures. Theoretical and experimental analysis showed that at the initial stages of growth InN nanocolumns were under tensile strain along both the basal plane and growth direction. Structural polytypes were then introduced in the form of embedded inclusions to accommodate the excess tensile strain along the growth direction, allowing the entire process of polymorphism to be the dominant strain relaxation mechanism of InN nanocolumns. Moreover, the lattice and energetic properties and band gap values of InN polytypes showed a linear dependence on hexagonality, while the presence of polytypes led to a characteristic broadening of the photoluminescence emission peak toward lower emission energies.

  13. Video e-card offers holiday greetings from everyone at PPPL | Princeton

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Plasma Physics Lab Video e-card offers holiday greetings from everyone at PPPL December 22, 2014 Tweet Widget Google Plus One Share on Facebook Staff of the U.S. Department of Energy's Princeton Plasma Physics Laboratory gathered on the Lab's front lawn on the Forrestal Campus in Plainsboro, N.J., to create the facility's first holiday video e-card. Participants flashed orange placards in a wave to form the PPPL logo. Photographer and multimedia specialist Elle Starkman, who is highly

  14. Cut Gas Costs This Holiday Traveling Season with Three Easy Tips |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy Cut Gas Costs This Holiday Traveling Season with Three Easy Tips Cut Gas Costs This Holiday Traveling Season with Three Easy Tips November 26, 2013 - 9:23am Addthis Turning off your engine while waiting in the parking lot is a great way to save money on gas. | Photo courtesy of Kristy Keel-Blackmon, NREL/21196. Turning off your engine while waiting in the parking lot is a great way to save money on gas. | Photo courtesy of Kristy Keel-Blackmon, NREL/21196. Jason

  15. Sulfur passivation of surface electrons in highly Mg-doped InN

    SciTech Connect (OSTI)

    Linhart, W. M.; Veal, T. D.; Chai, J.; McConville, C. F.; Durbin, S. M.; Department of Electrical and Computer Engineering, Western Michigan University, Kalamazoo, Michigan 49008

    2013-09-14

    Electron accumulation with a sheet density greater than 10{sup 13} cm{sup −2} usually occurs at InN surfaces. Here, the effects of treatment with ammonium sulfide ((NH{sub 4}){sub 2}S{sub x}) on the surface electronic properties of highly Mg-doped InN (>4×10{sup 18} cm{sup −3}) have been investigated with high resolution x-ray photoemission spectroscopy. The valence band photoemission spectra show that the surface Fermi level decreases by approximately 0.08 eV with (NH{sub 4}){sub 2}S{sub x} treatment, resulting in a decrease of the downward band bending and up to a 70% reduction in the surface electron sheet density.

  16. Growth modes of InN(000-1) on GaN buffer layers on sapphire

    SciTech Connect (OSTI)

    Liu, Bing; Kitajima, Takeshi; Chen, Dongxue; Leone, Stephen R.

    2005-01-24

    In this work, using atomic force microscopy and scanning tunneling microscopy, we study the surface morphologies of epitaxial InN films grown by plasma-assisted molecular beam epitaxy with intervening GaN buffer layers on sapphire substrates. On smooth GaN buffer layers, nucleation and evolution of three-dimensional InN islands at various coverages and growth temperatures are investigated. The shapes of the InN islands are observed to be predominantly mesa-like with large flat (000-1) tops, which suggests a possible role of indium as a surfactant. Rough GaN buffer layers composed of dense small GaN islands are found to significantly improve uniform InN wetting of the substrates, on which atomically smooth InN films are obtained that show the characteristics of step-flow growth. Scanning tunneling microscopy imaging reveals the defect-mediated surface morphology of smooth InN films, including surface terminations of screw dislocations and a high density of shallow surface pits with depths less than 0.3 nm. The mechanisms of the three-dimensional island size and shape evolution and formation of defects on smooth surfaces are considered.

  17. Relevant Links

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Research Institiute(AMRI), UNO Area Hotels Chase Suite Hotel Baton Rouge Extended Stay America Holiday Inn South Baton Rouge Marriott Residence Inns Wyndham Garden Gulf Coast...

  18. Growth of wurtzite InN on bulk In{sub 2}O{sub 3}(111) wafers

    SciTech Connect (OSTI)

    Sadofev, Sergey; Cho, Yong Jin; Brandt, Oliver; Ramsteiner, Manfred; Calarco, Raffaella; Riechert, Henning; Erwin, Steven C.; Galazka, Zbigniew; Korytov, Maxym; Albrecht, Martin; Uecker, Reinhard; Fornari, Roberto

    2012-10-22

    A single phase InN epitaxial film is grown on a bulk In{sub 2}O{sub 3}(111) wafer by plasma-assisted molecular beam epitaxy. The InN/In{sub 2}O{sub 3} orientation relationship is found to be (0001) parallel (111) and [1100] parallel [112]. High quality of the layer is confirmed by the small widths of the x-ray rocking curves, the sharp interfaces revealed by transmission electron microscopy, the narrow spectral width of the Raman E{sub 2}{sup h} vibrational mode, and the position of the photoluminescence band close to the fundamental band gap of InN.

  19. NNMCAB Board Minutes: June 2000 Taos

    Broader source: Energy.gov [DOE]

    Minutes of the June 28, 2000 Board meeting at Holiday Inn Presentation LANL, Procurement Process, Betty Romero

  20. NNMCAB Board Minutes: November 2002 Santa Fe

    Broader source: Energy.gov [DOE]

    Minutes of the November 20, 2002 Board meeting at Holiday Inn Planning for SSAB Chairs Workshop on Transuranic Waste

  1. NNMCAB Board Minutes: July 2009 Santa Fe

    Broader source: Energy.gov [DOE]

    Minutes of the July 29, 2009 Board meeting at Holiday Inn Q&A With New Mexico Environment Department

  2. NNMCAB Board Minutes: May 2008 Santa Fe

    Broader source: Energy.gov [DOE]

    Minutes of the May 22, 2008 Board meeting at Holiday Inn Presentation San Ildefonso, Tribal Risk Assessment, Raymond Martinez

  3. Elimination of surface band bending on N-polar InN with thin GaN capping

    SciTech Connect (OSTI)

    Kuzmík, J. Haščík, Š.; Kučera, M.; Kúdela, R.; Dobročka, E.; Adikimenakis, A.; Mičušík, M.; Gregor, M.; Plecenik, A.; Georgakilas, A.

    2015-11-09

    0.5–1 μm thick InN (0001) films grown by molecular-beam epitaxy with N- or In-polarity are investigated for the presence of native oxide, surface energy band bending, and effects introduced by 2 to 4 monolayers of GaN capping. Ex situ angle-resolved x-ray photo-electron spectroscopy is used to construct near-surface (GaN)/InN energy profiles, which is combined with deconvolution of In3d signal to trace the presence of InN native oxide for different types of polarity and capping. Downwards surface energy band bending was observed on bare samples with native oxide, regardless of the polarity. It was found that the In-polar InN surface is most readily oxidized, however, with only slightly less band bending if compared with the N-polar sample. On the other hand, InN surface oxidation was effectively mitigated by GaN capping. Still, as confirmed by ultra-violet photo-electron spectroscopy and by energy band diagram calculations, thin GaN cap layer may provide negative piezoelectric polarization charge at the GaN/InN hetero-interface of the N-polar sample, in addition to the passivation effect. These effects raised the band diagram up by about 0.65 eV, reaching a flat-band profile.

  4. Structural properties of InN films grown on O-face ZnO(0001) by plasma-assisted molecular beam epitaxy

    SciTech Connect (OSTI)

    Cho, Yong Jin; Brandt, Oliver; Kaganer, Vladimir M.; Ramsteiner, Manfred; Riechert, Henning; Korytov, Maxim; Albrecht, Martin

    2012-04-09

    We study the impact of substrate temperature and layer thickness on the morphological and structural properties of InN films directly grown on O-face ZnO(0001) substrates by plasma-assisted molecular beam epitaxy. With increasing substrate temperature, an interfacial reaction between InN and ZnO takes place that eventually results in the formation of cubic In{sub 2}O{sub 3} and voids. The properties of the InN films, however, are found to be unaffected by this reaction for substrate temperatures less than 550 deg. C. In fact, both the morphological and the structural quality of InN improve with increasing substrate temperature in the range from 350 to 500 deg. C. High quality films with low threading dislocation densities are demonstrated.

  5. Microsoft Word - cf16-la-hotel-Info.docx

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Macintosh HD:Users:rebecca_j:Desktop:cf16-la-hotel-Info.docx Accommodations Info in Los Alamos There are many wonderful places to stay in Santa Fe as well as the surrounding areas but the following is a list of hotels in Los Alamos: Comfort Inn 2455 Trinity Dr. Los Alamos, NM 87544 505-661-1110 800-992-2694 Hampton Inn & Suites 124 State Rd. 4 Los Alamos, NM 87544 505-672-3838 Holiday Inn Express at Entrada Park 60 Entrada Dr. Los Alamos, NM 87544 505-661-2646 Motel 6 2175 Trinity Dr. Los

  6. Optical characterization of free electron concentration in heteroepitaxial InN layers using Fourier transform infrared spectroscopy and a 2 Multiplication-Sign 2 transfer-matrix algebra

    SciTech Connect (OSTI)

    Katsidis, C. C.; Ajagunna, A. O.; Georgakilas, A.

    2013-02-21

    Fourier Transform Infrared (FTIR) reflectance spectroscopy has been implemented as a non-destructive, non-invasive, tool for the optical characterization of a set of c-plane InN single heteroepitaxial layers spanning a wide range of thicknesses (30-2000 nm). The c-plane (0001) InN epilayers were grown by plasma-assisted molecular beam epitaxy (PAMBE) on GaN(0001) buffer layers which had been grown on Al{sub 2}O{sub 3}(0001) substrates. It is shown that for arbitrary multilayers with homogeneous anisotropic layers having their principal axes coincident with the laboratory coordinates, a 2 Multiplication-Sign 2 matrix algebra based on a general transfer-matrix method (GTMM) is adequate to interpret their optical response. Analysis of optical reflectance in the far and mid infrared spectral range has been found capable to discriminate between the bulk, the surface and interface contributions of free carriers in the InN epilayers revealing the existence of electron accumulation layers with carrier concentrations in mid 10{sup 19} cm{sup -3} at both the InN surface and the InN/GaN interface. The spectra could be fitted with a three-layer model, determining the different electron concentration and mobility values of the bulk and of the surface and the interface electron accumulation layers in the InN films. The variation of these values with increasing InN thickness could be also sensitively detected by the optical measurements. The comparison between the optically determined drift mobility and the Hall mobility of the thickest sample reveals a value of r{sub H} = 1.49 for the Hall factor of InN at a carrier concentration of 1.11 Multiplication-Sign 10{sup 19} cm{sup -3} at 300 Degree-Sign {Kappa}.

  7. 2012 BATTERIES GORDON RESEARCH CONFERENCE, MARCH 4-9, 2012

    SciTech Connect (OSTI)

    Stephen Harris

    2012-03-09

    The Gordon Research Conference on BATTERIES was held at Four Points Sheraton / Holiday Inn Express, Ventura, California, March 4-9, 2012. The Conference was well-attended with 176 participants. Gordon Research Conferences does not permit publication of meeting proceedings.

  8. Optical and structural characterization of nitrogen-rich InN: Transition from nearly intrinsic to strongly n-type degenerate with temperature

    SciTech Connect (OSTI)

    Hong Tran, Nhung; Huy Le, Binh; Fan, Shizhao; Zhao, Songrui; Mi, Zetian; Schmidt, Benjamin A.; Savard, Michel; Gervais, Guillaume; Butcher, Kenneth Scott A.

    2013-12-23

    We report on a detailed study of the structural and optical properties of nonstoichiometric nitrogen-rich InN grown on sapphire substrates, by migration enhanced afterglow deposition. The samples were polycrystalline, with the presence of InN dots. Unusually strong photoluminescence emission was measured at cryogenic temperatures, with the peak energy at ?0.68?eV. Detailed analysis further shows that the sample has very low residual electron density in the range of ?10{sup 16}?cm{sup ?3} at temperatures below 20?K.

  9. Electronic and thermoelectric properties of InN studied using ab initio density functional theory and Boltzmann transport calculations

    SciTech Connect (OSTI)

    Borges, P. D. E-mail: lscolfaro@txstate.edu; Scolfaro, L. E-mail: lscolfaro@txstate.edu

    2014-12-14

    The thermoelectric properties of indium nitride in the most stable wurtzite phase (w-InN) as a function of electron and hole concentrations and temperature were studied by solving the semiclassical Boltzmann transport equations in conjunction with ab initio electronic structure calculations, within Density Functional Theory. Based on maximally localized Wannier function basis set and the ab initio band energies, results for the Seebeck coefficient are presented and compared with available experimental data for n-type as well as p-type systems. Also, theoretical results for electric conductivity and power factor are presented. Most cases showed good agreement between the calculated properties and experimental data for w-InN unintentionally and p-type doped with magnesium. Our predictions for temperature and concentration dependences of electrical conductivity and power factor revealed a promising use of InN for intermediate and high temperature thermoelectric applications. The rigid band approach and constant scattering time approximation were utilized in the calculations.

  10. Effects of Ga on the growth of InN on O-face ZnO(0001) by plasma-assisted molecular beam epitaxy

    SciTech Connect (OSTI)

    Cho, Yong Jin; Riechert, Henning; Brandt, Oliver; Korytov, Maxim; Albrecht, Martin

    2012-07-30

    We compare the structural properties of InN and In{sub 0.95}Ga{sub 0.05}N films grown on O-face ZnO(0001) substrates at different temperatures. The small amount of Ga results in dramatic changes in the morphology and structural properties of InN. In particular, inversion domains start to appear at higher temperatures in the In{sub 0.95}Ga{sub 0.05}N film. This process is a consequence of the chemical reaction of ZnO with Ga which can be prevented by choosing the substrate temperature to be 450{sup Degree-Sign }C or below.

  11. NNMCAB Board Minutes: July 2010 Los Alamos

    Broader source: Energy.gov [DOE]

    Minutes of the July 28, 2010 Board meeting at Holiday Inn Presentation LANL, Material Disposal Area T Background and Status Update

  12. NNMCAB Board Minutes: July 2011 Los Alamos

    Broader source: Energy.gov [DOE]

    Minutes of the July 27, 2011 Board meeting at Holiday Inn Presentation LANL, Los Conchas Fire, Dave McInroy Presentation DOE, Waste Isolation Pilot Plant, John Heaton

  13. NNMCAB Board Minutes: April 2009 Santa Fe

    Broader source: Energy.gov [DOE]

    Minutes of the April 8, 2009 Board meeting at Holiday Inn Presentation Kerr Laboratory, Well Screen Analysis Report, Steven Acree, Richard Wilkin

  14. Holiday Food Drive

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Community Programs Office (505) 665-4400 Email Get Expertise Helping feed Northern New Mexico families During the Laboratory's 2015 Annual Food Drive, employees and subcontract...

  15. International Cooperation Holiday Cheer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Administration International Atomic Energy Agency Secretary Moniz awards Hutcheon memorial nonproliferation fellowship to Thomas Gray Energy Secretary Ernest Moniz (second from bottom left, clockwise) and Anne Harrington, NNSA deputy administrator for Defense Nuclear Nonproliferation (sitting next to Moniz), discuss Ian Hutcheon's legacy with his wife Nancy (across from Harrington) and daughter Dana Hutcheon Gordon. Energy... DOE/NNSA's Nonproliferation Experts Lead First Workshop on the

  16. Holiday Gift Drive

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Disabilities Espanola Valley Toy Run Las Vegas Adult Protective Services La Tierra Montessori Los Alamos Family Council Ohkay Owingeh Boys and Girls Clubs Rio ArribaLos Alamos...

  17. InGaN/GaN multiple-quantum-well light-emitting diodes with a grading InN composition suppressing the Auger recombination

    SciTech Connect (OSTI)

    Zhang, Zi-Hui; Liu, Wei; Ju, Zhengang; Tan, Swee Tiam; Ji, Yun; Kyaw, Zabu; Zhang, Xueliang; Wang, Liancheng; Sun, Xiao Wei E-mail: VOLKAN@stanfordalumni.org; Demir, Hilmi Volkan E-mail: VOLKAN@stanfordalumni.org

    2014-07-21

    In conventional InGaN/GaN light-emitting diodes (LEDs), thin InGaN quantum wells are usually adopted to mitigate the quantum confined Stark effect (QCSE), caused due to strong polarization induced electric field, through spatially confining electrons and holes in small recombination volumes. However, this inevitably increases the carrier density in quantum wells, which in turn aggravates the Auger recombination, since the Auger recombination scales with the third power of the carrier density. As a result, the efficiency droop of the Auger recombination severely limits the LED performance. Here, we proposed and showed wide InGaN quantum wells with the InN composition linearly grading along the growth orientation in LED structures suppressing the Auger recombination and the QCSE simultaneously. Theoretically, the physical mechanisms behind the Auger recombination suppression are also revealed. The proposed LED structure has experimentally demonstrated significant improvement in optical output power and efficiency droop, proving to be an effective solution to this important problem of Auger recombination.

  18. Hydrogen and Fuel Cell Technical Advisory Committee Meeting

    Broader source: Energy.gov [DOE]

    The Hydrogen and Fuel Cell Technical Advisory Committee (HTAC) will hold its next meeting October 27–28, 2015, at the Holiday Inn Capitol in Washington, D.C.

  19. Agenda CBS Public Meeting-Sacramento

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    David Ballard, Ph.D., Professor of Sociology CONSENT- BASED SITING CONSENT-BASED SITING PUBLIC MEETING Holiday Inn Capitol Plaza-Sacramento 300 J Street Sacramento, CA 95814 April ...

  20. NNMCAB Board Minutes: January 2009 Santa Fe

    Broader source: Energy.gov [DOE]

    Minutes of the January 28, 2009 Board meeting at Holiday Inn Presentation DOE, Implementation on NNMCAB Recommendations, Jeff Casalina Presentation LANL, Well Network Analysis and Characterization of Groundwater at LANL Site, Danny Katzman

  1. Notices

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... July 15, 2015, 6:00 p.m ...... 870 Williston Road, South Burlington, Vermont 05403. Holiday Inn, Rutland, Vermont ...... July 16, 2015, 6:00 p.m ...

  2. Department of Energy Seeks Public Comment on Designation of Energy...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    MT Holiday Inn 22 North Last Chance Gulch Helena, MT 59601 November 1, 2005 Boise, ID Harrison Plaza Suite Hotel 409 S. Cole Road Boise, ID 83709 November 1, 2005 Sacramento, CA ...

  3. Northern New Mexico Citizens Advisory Board Meeting

    Office of Environmental Management (EM)

    bi-monthly meeting of the Northern New Mexico Citizens' Advisory Board (NNMCAB or CAB) meeting was held on September 30, 2009 at the Holiday Inn, 4048 Cerrillos Road Santa...

  4. NNMCAB Board Minutes: January 2010 Santa Fe

    Broader source: Energy.gov [DOE]

    Minutes of the January 27, 2010 Board meeting at Holiday Inn Presentation LANL, Status of Corrective Actions, Dave McInroy Presentation DOE, Natural Resource Damage Assessment, Nancy Werdel

  5. NNMCAB Board Minutes: November 2009 Santa Fe

    Broader source: Energy.gov [DOE]

    Minutes of the November 18, 2009 Board meeting at Holiday Inn Presentation LANL, Groundwater Monitoring System, Danny Katzman Presentation NNMCAB, Remote Handled 33 Shafts at Area G, Robert Villarreal

  6. Agenda

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Agenda Agenda ERSUG Meeting July 11-12, 1994 Holiday Inn, Crowne Plaza Rockville, MD The Energy Research Supercomputer Users' Group (ERSUG) will meet at the Holiday Inn, Crowne Plaza in Rockville, MD on July 11-12, 1994. In the past, this meeting has combined presentations describing work-in-progress at NERSC with lively user discussions in the areas of the services and capabilities provided by NERSC. For this particular meeting, however, the focus will change somewhat. First, more emphasis will

  7. The Express

    Alternative Fuels and Advanced Vehicles Data Center [Office of Energy Efficiency and Renewable Energy (EERE)]

    site. We will let you know what is new through this newsletter. As you will find in this issue, briefs of various alternative fuels information are provided by category. We will also begin an addi- tional service, the AFDC Express. The Express will provide impor- tant information on late-breaking issues via e-mail and fax. If you would like to receive these, you should ensure that the Center has your correct information. For those of you who have finished this editorial of sorts, fear not, it is

  8. Save Money with LED Holiday Light Strings

    Broader source: Energy.gov [DOE]

    LED (or light emitting diode) light strings can use 90% less energy than regular incandescent light strings. They also last about ten times longer, are cooler than incandescents (reducing fire hazards), and are more durable.

  9. A Factsheet on Holiday Fire Prevention

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    fall off, the tree has been cut too long, has probably dried out, and is a fire hazard. caring for your tree Do not place your tree close to a heat source, including a fireplace...

  10. Fourth Friday Cancelled due to Thanksgiving Holidays

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Fourth Annual Post Competition Accountability Report Fourth Annual Post Competition Accountability Report LM has completed its fourth annual Post Competition Accountability Report - Office of Legacy Management's High Performing Organization: Fiscal Year (FY) 2015 Fourth Annual Post Competition Accountability Report (279.26 KB) More Documents & Publications First Annual Post Competition Accountability Report Third Annual Post Competition Accountability Report Second Annual Post Competition

  11. Fourth Friday Cancelled due to Thanksgiving Holidays

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    open late until 6:00 PM offering access to exhibits and special activities for all ages, however it will not take place on Friday, November 27 due to the Thanksgiving...

  12. LED Holiday Lights: Festive, Safe, and Efficient!

    Broader source: Energy.gov [DOE]

    Ed. Note cross posted from the Energy Savers Blog. LED light strings may cost a little more up front, but they'll save money in the long run and probably last longer too.

  13. Today LED Holiday Lights, Tomorrow the World?

    SciTech Connect (OSTI)

    Gordon, Kelly L.

    2004-12-20

    This article for The APEM Advantage, the quarterly newsletter of the Association of Professional Energy Managers (APEM) describes the recent increase in the popularity of light emitting diode (LED) lighting and compares LED light output with that of incandescent and compact fluorescent lighting.

  14. NNMCAB Board Minutes: May 2003 Taos

    Broader source: Energy.gov [DOE]

    Minutes of the May 16, 2003 Board Retreat at Holiday Inn Don Fernando de Taos Presentation NNMCAB Fiscal Year 2003 Accomplishments Presentation DOE/LANL, Environmental Monitoring and Surveillance Groundwater and Surface Water, Ted Taylor Presentation DOE/LANL, Environmental Restoration, Ted Taylor

  15. DOE Environmental Impact Statement Public Scoping Meeting on...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... Tuesday, July 13, 2010 7:00 - 9:00 pm Albany, New York The Holiday Inn Albany at Wolf Road 205 Wolf Road Albany, NY12205 Wednesday, July 14, 2010 7:00 - 9:00 pm Glens Falls, New ...

  16. High expression Zymomonas promoters

    DOE Patents [OSTI]

    Viitanen, Paul V.; Tao, Luan; Zhang, Yuying; Caimi, Perry G.; McCole, Laura : Zhang, Min; Chou, Yat-Chen; McCutchen, Carol M.; Franden, Mary Ann

    2011-08-02

    Identified are mutants of the promoter of the Z. mobilis glyceraldehyde-3-phosphate dehydrogenase gene, which direct improved expression levels of operably linked heterologous nucleic acids. These are high expression promoters useful for expression of chimeric genes in Zymomonas, Zymobacter, and other related bacteria.

  17. TTW 12-1-05

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    , 2005 WIPP Quick Facts (As of 11-30-05) 4,110 Shipments received since opening 33,321 Cubic meters of waste disposed 72,865 Containers disposed in the underground Upcoming Holiday Parties WTS Kid's Party December 3 - 12:00 p.m. Mall Cinema Movies offered: Zathura (PG) and Harry Potter (PG-13) WTS Christmas Party December 3 - 5:30 p.m. Walter Gerrells Performing Arts & Exhibition Centre Annex CTAC Holiday Party December 12 - 6:00 p.m. Stevens Inn NMED issues draft permit The New Mexico

  18. Express Energy Efficiency Program

    Broader source: Energy.gov [DOE]

    The Express Energy Efficiency Program provides free installation of energy-saving products. This program travels around Wisconsin, community-by-community, to see if they are installing in your...

  19. WebExpress

    Energy Science and Technology Software Center (OSTI)

    1998-10-25

    WEBEXPRESS is a web interface to the Express for Unix batch scheduling product by Tidal Software. It offers web access from any client on the network and increased functionality in some areas.

  20. Sonoma Mission Inn Geothermal Area | Open Energy Information

    Open Energy Info (EERE)

    110C383.15 K 230 F 689.67 R 1 USGS Estimated Reservoir Volume: 1 km 1 USGS Mean Capacity: 6 MW 1 Click "Edit With Form" above to add content History and...

  1. Solar Express | Open Energy Information

    Open Energy Info (EERE)

    Express Place: Italy Product: A joint venture established to install some 11MW of photovoltaic generation capacity around the country. References: Solar Express1 This article...

  2. Express Power | Open Energy Information

    Open Energy Info (EERE)

    United Kingdom Zip: B1 2JB Sector: Renewable Energy Product: Express Power is a the sustainable energy company operating within the Express Park Group. It develops renewable...

  3. Consent-Based Siting Public Meeting Small Group Discussion Summary

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    26, 2016 Sacramento, California PURPOSE On April 26, 2016, the Department of Energy's consent-based siting initiative hosted a public meeting in Sacramento, California at the Holiday Inn Capitol Plaza. The purpose of this meeting was to hear from the public and stakeholders on important elements in the design of a consent-based siting process. A consent-based siting process will support the development of facilities needed to manage spent nuclear fuel and high-level radioactive waste, including

  4. Agenda12810 | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    8, 2010 Nuclear Science Advisory Committee (NSAC) NSAC Home Meetings NSAC Members Charges/Reports Charter .pdf file (78KB) NP Committees of Visitors Federal Advisory Committees NP Home Meetings December 8, 2010 Print Text Size: A A A FeedbackShare Page DOE/NSF Nuclear Science Advisory Committee Meeting December 8, 2010 Where: Holiday Inn National Airport Hotel, Shenandoah Ballroom I & II, 2650 Jefferson Davis Highway, Arlington, VA, Phone Number: 703-684-7200. Purpose/Topics: Perspectives

  5. Buying an Appliance this Holiday Season? ENERGY STAR Products...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Refrigerators Freezers Room air conditioners Televisions Clothes washers Dishwashers Battery chargers Water heaters Fluorescent lamp ballasts Incandescent reflector lamps If your ...

  6. Energy-Efficient Holiday Decorating Tips | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    In addition to using 70% less energy than traditional bulbs, they're brighter, eco-friendly, and are safer, as they are much cooler than incandescent lights. In addition, they...

  7. Your Holidays ... Brought to You by Fuel Cells | Department of...

    Office of Environmental Management (EM)

    ... Next time you're stranded, you can rest assured your cell phone will work now that telecom ... Who knows? Soon Santa may be able to give Rudolf a rest and drive his fuel cell-powered ...

  8. Reduce Waste and Save Energy this Holiday Season | Department...

    Broader source: Energy.gov (indexed) [DOE]

    Wrap your gifts with recycled paper to reduce waste and save money. | Photo courtesy of istockphotodiane555 Wrap your gifts with recycled paper to reduce waste and save money. |...

  9. ENERGY STAR Sales Tax Holiday for Energy-Efficient Products

    Broader source: Energy.gov [DOE]

    Although the eligibility of some products is limited according to their sale price, there are no limitations on the total value or number of products exempt from sales tax.

  10. Leveraging Holidays and Other Events | Department of Energy

    Energy Savers [EERE]

    for Marketing Energy Efficiency The Solarize Guidebook: A community guide to collective purchasing of residential PV systems (Book), SunShot, U.S. Department of Energy (DOE)

  11. Sales Tax Holiday for Energy-Efficient Appliances

    Broader source: Energy.gov [DOE]

    In order to qualify for the exemption, qualifying pieces of equipment must be designated as meeting or exceeding the efficiency requirements of the ENERGY STAR program. The law defines eligible...

  12. Holiday City-Berkeley, New Jersey: Energy Resources | Open Energy...

    Open Energy Info (EERE)

    City-Berkeley, New Jersey: Energy Resources Jump to: navigation, search Equivalent URI DBpedia Coordinates 39.9645797, -74.2707509 Show Map Loading map... "minzoom":false,"map...

  13. Holiday Shopping and Electric Vehicles | GE Global Research

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and it has been working with GE, Con Edison and Columbia University since 2011 on a pilot project in New York City on how to build effective vehicle charging stations. ...

  14. Sales Tax Holiday for Energy-Efficient Appliances | Department...

    Broader source: Energy.gov (indexed) [DOE]

    each year for the following appliances*: Clothes washers Clothes dryers* Water heaters Trash compactors* Dishwashers Conventional ovens, ranges, and stoves* Air conditioners...

  15. Energy Saving Holiday Kitchen Trivia | Department of Energy

    Office of Environmental Management (EM)

    In fact, there are entire books dedicated to culinary usage of the microwave. ... the number of days you use the appliance during the year for the annual consumption in kWh per year. ...

  16. Express Farms Greenhouse Low Temperature Geothermal Facility...

    Open Energy Info (EERE)

    Express Farms Greenhouse Low Temperature Geothermal Facility Jump to: navigation, search Name Express Farms Greenhouse Low Temperature Geothermal Facility Facility Express Farms...

  17. Method of controlling gene expression

    DOE Patents [OSTI]

    Peters, Norman K.; Frost, John W.; Long, Sharon R.

    1991-12-03

    A method of controlling expression of a DNA segment under the control of a nod gene promoter which comprises administering to a host containing a nod gene promoter an amount sufficient to control expression of the DNA segment of a compound of the formula: ##STR1## in which each R is independently H or OH, is described.

  18. Agenda112901 | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    29-30, 2001 Nuclear Science Advisory Committee (NSAC) NSAC Home Meetings NSAC Members Charges/Reports Charter .pdf file (78KB) NP Committees of Visitors Federal Advisory Committees NP Home Meetings November 29-30, 2001 Print Text Size: A A A FeedbackShare Page DOE/NSF Nuclear Science Advisory Committee Meeting November 29-30, 2001 Holiday Inn 550 C Street, SW Washington, D.C. Preliminary Agenda November 29, 2001 Session 1 8:30 a.m. Welcome James Symons 8:40 a.m. Report from DOE 9:05 a.m. Report

  19. Agenda CBS Public Meeting-Sacramento

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    David Ballard, Ph.D., Professor of Sociology CONSENT- BASED SITING CONSENT-BASED SITING PUBLIC MEETING Holiday Inn Capitol Plaza-Sacramento 300 J Street Sacramento, CA 95814 April 26, 2016 4:00-5:00 PM Informal Open House and Poster Session (Before Meeting Begins) 5:00-5:15 PM Welcoming Remarks Robert Weisenmiller, Chair to the California Energy Commission 5:15-5:30 PM Moving Forward with Consent-Based Siting John Kotek, Acting Assistant Secretary for Nuclear Energy, Department of Energy

  20. Report on the technical workshop on WTI incinerator risk issues. Held in Washington, DC on December 8-9, 1993

    SciTech Connect (OSTI)

    Not Available

    1993-12-01

    The report includes information and materials from a peer review workshop organized by EPA's Risk Assessment Forum (RAF) for the Office of Solid Waste and Emergency Response and Region 5. The meeting was held in Washington, DC, at the Holiday Inn Capitol on December 8-9, 1993. The subject of the peer review was a draft project plan prepared by EPA Region 5 for assessing risk at an incinerator operated by Waste Technologies Industries (WTI) in East Liverpool, Ohio. The peer review panel was convened to evaluate the project plan as the scientific foundation for a risk assessment, which will be used in setting final permit conditions for the WTI facility.

  1. PRESENT:

    U.S. Energy Information Administration (EIA) Indexed Site

    PUBLIC MEETING + + + + + FRIDAY NOVEMBER 14, 1997 + + + + + WASHINGTON, D.C. The Committee met in the Clark Room of the Capital Holiday Inn, 550 C Street, S.W., at 10:30 a.m., G. Campbell Watkins, Chair, presiding. PRESENT: G. CAMPBELL WATKINS, Chair DANIEL A. RELLES, Vice Chair DAVID R. BELLHOUSE R. SAMPRIT CHATTERJEE BRENDA G. COX CAROL A. GOTWAY CRAWFORD PHILIP HANSEN CALVIN KENT GRETA M. LJUNG ROY W. WHITMORE INVITED GUESTS: SEYMOUR SUDMAN RICHARD TABORS EIA STAFF PRESENT: JAY HAKES, EIA

  2. Microsoft Word - Consolidated Verbatim Transcript CBS Meeting Sacramento California Transcripts_Final

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Holiday Inn Capitol Plaza Sacramento 300 J Street Sacramento, CA 95814 April 26, 2016 VERBATIM TRANSCRIPT Mr. Jim Hamilton. Good afternoon. And for those in later time zones via webinar, good evening. Welcome, and thank you for being here today. My name is Jim Hamilton. I'm an advisor to the Department of Energy's Consent-Based Siting Team and my role here today is to help us all to have a good, open, productive conversation. To start off we have a few housekeeping issues I want to talk about

  3. Baculovirus expression system and method for high throughput expression of genetic material

    DOE Patents [OSTI]

    Clark, Robin; Davies, Anthony

    2001-01-01

    The present invention provides novel recombinant baculovirus expression systems for expressing foreign genetic material in a host cell. Such expression systems are readily adapted to an automated method for expression foreign genetic material in a high throughput manner. In other aspects, the present invention features a novel automated method for determining the function of foreign genetic material by transfecting the same into a host by way of the recombinant baculovirus expression systems according to the present invention.

  4. Chicago Solar Express Reduces Costs, Wait Times | Department...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Chicago Solar Express Reduces Costs, Wait Times Chicago Solar Express Reduces Costs, Wait Times October 28, 2014 - 10:48am Addthis The Solar Express program in Chicago, ...

  5. Methods for monitoring multiple gene expression

    DOE Patents [OSTI]

    Berka, Randy; Bachkirova, Elena; Rey, Michael

    2013-10-01

    The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

  6. Methods for monitoring multiple gene expression

    DOE Patents [OSTI]

    Berka, Randy; Bachkirova, Elena; Rey, Michael

    2008-06-01

    The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

  7. Methods for monitoring multiple gene expression

    DOE Patents [OSTI]

    Berka, Randy; Bachkirova, Elena; Rey, Michael

    2012-05-01

    The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

  8. PP-362 Champlain Hudson Power Express, Inc.

    Broader source: Energy.gov [DOE]

    Presidential Permit authorizing Champlain Hudson Power Express, Inc. (CHPEI) to construct, operate and maintain electric transmission facilities at the U.S. - Canada border.

  9. Express Package Shipping Services | The Ames Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Express Package Shipping Services General Information: The materials handling office's express package shipping service offers overnight domestic letter and parcel service for official business only. Express international shipments are also offered. Many hazardous and non-hazardous materials may be shipped by express. This service is provided to Ames Laboratory personnel. Hours: Monday through Friday - 7:30 a.m. to 11:50 a.m. - 12:30 p.m. through 4:00 p.m. Cutoff: for 10:30 a.m. next day

  10. Xcel Energy - Express Energy Efficiency Program | Department...

    Broader source: Energy.gov (indexed) [DOE]

    t-products-appliancesexpr... State Wisconsin Program Type Rebate Program Rebate Amount Free. Summary The Express Energy Efficiency Program provides free installation of...

  11. Materials Data on Er3InN (SG:221) by Materials Project

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kristin Persson

    2014-11-02

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  12. Materials Data on Ho3InN (SG:221) by Materials Project

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kristin Persson

    2014-11-02

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  13. Materials Data on Sc3InN (SG:221) by Materials Project

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kristin Persson

    2014-11-02

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  14. Materials Data on Dy3InN (SG:221) by Materials Project

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kristin Persson

    2014-11-02

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  15. Materials Data on InN (SG:186) by Materials Project

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kristin Persson

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  16. Materials Data on InN (SG:186) by Materials Project

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kristin Persson

    2014-11-02

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  17. Expression of eukaryotic polypeptides in chloroplasts

    SciTech Connect (OSTI)

    Mayfield, Stephen P.

    2013-06-04

    The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

  18. Expression Data Oliver Rübel

    Office of Scientific and Technical Information (OSTI)

    ... of PCX. One potential focus for future research are methods for linking other types of data, such as in vitro and in vivo binding data, with the gene expression data analysis. ...

  19. Changes in gene expression following EMF exposure

    SciTech Connect (OSTI)

    Woloschak, G.E.; Paunesku, T.; Chang-Liu, C.M.; Loberg, L.; Gauger, J.; McCormick, D.

    1997-10-01

    Experiments were designed to examine the effects of electromagnetic field (EMF) exposure on specific gene expression, an effect that can be deleterious, beneficial, or neutral, depending on the long-term consequences; however, the proof of a reproducible, quantitative biological effect (such as change in gene expression) will lead to latter experiments aimed at determining the relative contribution of these changes to cellular consequences. Past work by ourselves and by others has shown that measures of gene expression are extremely sensitive indicators of the cellular and biological effects of ionizing radiation, with transcriptional changes being detected by exposure of cells to doses of {gamma}-rays as low as 0.01 cGy that have no pronounced cellular consequences. On the basis of this work, the authors hypothesized that measures of gene expression will be equally sensitive to EMF effects on cells.

  20. Coevolution of gene expression among interacting proteins

    SciTech Connect (OSTI)

    Fraser, Hunter B.; Hirsh, Aaron E.; Wall, Dennis P.; Eisen,Michael B.

    2004-03-01

    Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well documented and has been used to predict interacting proteins, domains, and amino acids. Interacting proteins are also often precisely coexpressed with one another, presumably to maintain proper stoichiometry among interacting components. Here, we show that the expression levels of physically interacting proteins coevolve. We estimate average expression levels of genes from four closely related fungi of the genus Saccharomyces using the codon adaptation index and show that expression levels of interacting proteins exhibit coordinated changes in these different species. We find that this coevolution of expression is a more powerful predictor of physical interaction than is coevolution of amino acid sequence. These results demonstrate previously uncharacterized coevolution of gene expression, adding a different dimension to the study of the coevolution of interacting proteins and underscoring the importance of maintaining coexpression of interacting proteins over evolutionary time. Our results also suggest that expression coevolution can be used for computational prediction of protein protein interactions.

  1. What Do You Think of Your LED Holiday Lights? | Department of...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    savings, but some folks have also discovered that the lights have a slightly different color or reflect off of ornaments in a different way. Change can be difficult, especially...

  2. EECBG Success Story: North Pole's Holiday Wish for an Energy Efficient 2012

    Broader source: Energy.gov [DOE]

    Up in the iconic community of North Pole, Alaska, the city leaders have made their energy efficiency upgrade wish list, and now state auditors are “checking it twice” to see which projects the city will be able to complete in 2012 using funds from the state’s Energy Efficiency and Conservation Block Grant (EECBG) as part of the American Recovery and Reinvestment Act. This can be critical in a city that sees winter temperatures as cold as -67F. Learn more.

  3. Whimsical SRS Relay Race Brings Joy to those in Need this Holiday...

    National Nuclear Security Administration (NNSA)

    race, which has raised 25,000 for the Savannah River Site's Toys for Tots campaign. Dozens of contractor employees at the Savannah River Site (SRS) recently combined zany fun ...

  4. Food and gift drives help make holidays brighter for regional families

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Food and Beverage (2010 MECS) Food and Beverage (2010 MECS) Manufacturing Energy and Carbon Footprint for Food and Beverage Sector (NAICS 311, 312) Energy use data source: 2010 EIA MECS (with adjustments) Footprint Last Revised: February 2014 View footprints for other sectors here. Manufacturing Energy and Carbon Footprint Food and Beverage (126.07 KB) More Documents & Publications MECS 2006 - Food and Beverage All Manufacturing (2010 MECS) Cement

    STEM skills Community Connections: Your

  5. Sales Tax Exemption for Energy-Efficient Products (Sales Tax Holiday)

    Broader source: Energy.gov [DOE]

    Virginia allows a four-day sales tax* exemption for dishwashers, clothes washers, air conditioners, ceiling fans, light bulb, dehumidifiers, programmable thermostat and refrigerators that meet fe...

  6. They're Here! Winter, Holidays, and the New Year. How Will You...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    This entry from last year will help you make SMART energy-saving resolutions that last longer than the average new-year gym membership, so check it out and tell us in the comments ...

  7. It's Finally Time to Think about the Holidays! | Department of Energy

    Broader source: Energy.gov (indexed) [DOE]

    Islands can use the tools below to gather data for decision makers and run scenarios on potential energy investments. Tailored trainings provide in-person, onsite guidance and best practices for implementing clean energy solutions. Tools Island Energy Scenario Tool The ETI Energy Scenario Tool helps communities analyze different pathways to meet a given energy transition goal by modeling the levelized cost of electricity for custom, user-defined scenarios of supply and demand. Download the tool

  8. They're Here! Winter, Holidays, and the New Year. How Will You Save Energy?

    Broader source: Energy.gov (indexed) [DOE]

    02 DEER Conference Presentation: Cummins Inc. 2002_deer_fang.pdf (173.64 KB) More Documents & Publications Recent Advances and Future Challenges in the Modeling and Simulations of the injection of Urea-Water-Solution for Automotive SCR Systems An Experimental Study of PM Emission Characteristics of Commercial Diesel Engine with Urea-SCR System SCR Performance Optimization Through Advancements in Aftertreatment Packaging | Department of Energy

    Winter officially hit this week, and those

  9. Sales Tax Exemption for Energy-Efficient Products (Sales Tax Holiday)

    Broader source: Energy.gov [DOE]

    In the past few years, the Georgia legislature has traditionally allowed an annual state and local sales tax exemption on Energy Star products of $1,500 or less per product, purchased for non...

  10. How Do You Save Money on Summer Holidays? | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    the 4th of July. She mentioned several ways you can save energy by doing the things you probably did anyway -- like leaving the house or barbequing. But now that the 4th...

  11. Visualization and Analysis of 3D Gene Expression Data (Technical...

    Office of Scientific and Technical Information (OSTI)

    Technical Report: Visualization and Analysis of 3D Gene Expression Data Citation Details In-Document Search Title: Visualization and Analysis of 3D Gene Expression Data Recent...

  12. V-188: Apache XML Security XPointer Expressions Processing Buffer...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    8: Apache XML Security XPointer Expressions Processing Buffer Overflow Vulnerability V-188: Apache XML Security XPointer Expressions Processing Buffer Overflow Vulnerability June...

  13. Global Profiling of Shewanella oneidensis MR-1: Expression of...

    Office of Scientific and Technical Information (OSTI)

    Global expression studies were conducted using RNA and protein expression profiling of ... transduction, ion transport, secondary metabolism, and transcription, as well as ...

  14. The low noise limit in gene expression

    SciTech Connect (OSTI)

    Dar, Roy D.; Weinberger, Leor S.; Cox, Chris D.; Simpson, Michael L.; Razooky, Brandon S.

    2015-10-21

    Protein noise measurements are increasingly used to elucidate biophysical parameters. Unfortunately noise analyses are often at odds with directly measured parameters. Here we show that these inconsistencies arise from two problematic analytical choices: (i) the assumption that protein translation rate is invariant for different proteins of different abundances, which has inadvertently led to (ii) the assumption that a large constitutive extrinsic noise sets the low noise limit in gene expression. While growing evidence suggests that transcriptional bursting may set the low noise limit, variability in translational bursting has been largely ignored. We show that genome-wide systematic variation in translational efficiency can-and in the case of E. coli does-control the low noise limit in gene expression. Therefore constitutive extrinsic noise is small and only plays a role in the absence of a systematic variation in translational efficiency. Lastly, these results show the existence of two distinct expression noise patterns: (1) a global noise floor uniformly imposed on all genes by expression bursting; and (2) high noise distributed to only a select group of genes.

  15. The low noise limit in gene expression

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Dar, Roy D.; Weinberger, Leor S.; Cox, Chris D.; Simpson, Michael L.; Razooky, Brandon S.

    2015-10-21

    Protein noise measurements are increasingly used to elucidate biophysical parameters. Unfortunately noise analyses are often at odds with directly measured parameters. Here we show that these inconsistencies arise from two problematic analytical choices: (i) the assumption that protein translation rate is invariant for different proteins of different abundances, which has inadvertently led to (ii) the assumption that a large constitutive extrinsic noise sets the low noise limit in gene expression. While growing evidence suggests that transcriptional bursting may set the low noise limit, variability in translational bursting has been largely ignored. We show that genome-wide systematic variation in translational efficiencymore » can-and in the case of E. coli does-control the low noise limit in gene expression. Therefore constitutive extrinsic noise is small and only plays a role in the absence of a systematic variation in translational efficiency. Lastly, these results show the existence of two distinct expression noise patterns: (1) a global noise floor uniformly imposed on all genes by expression bursting; and (2) high noise distributed to only a select group of genes.« less

  16. Gene expression profiles in irradiated cancer cells

    SciTech Connect (OSTI)

    Minafra, L.; Bravat, V.; Russo, G.; Ripamonti, M.; Gilardi, M. C.

    2013-07-26

    Knowledge of the molecular and genetic mechanisms underlying cellular response to radiation may provide new avenues to develop innovative predictive tests of radiosensitivity of tumours and normal tissues and to improve individual therapy. Nowadays very few studies describe molecular changes induced by hadrontherapy treatments, therefore this field has to be explored and clarified. High-throughput methodologies, such as DNA microarray, allow us to analyse mRNA expression of thousands of genes simultaneously in order to discover new genes and pathways as targets of response to hadrontherapy. Our aim is to elucidate the molecular networks involved in the sensitivity/resistance of cancer cell lines subjected to hadrontherapy treatments with a genomewide approach by using cDNA microarray technology to identify gene expression profiles and candidate genes responsible of differential cellular responses.

  17. Stress Tolerant Plants Expressing Mannosylglcerate Enzymes - Energy

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Innovation Portal Stress Tolerant Plants Expressing Mannosylglcerate Enzymes Lawrence Berkeley National Laboratory Contact LBL About This Technology Technology Marketing SummaryHenrik Scheller of the Joint BioEnergy Institute (JBEI) and researchers from the University of Copenhagen and Aarhus University have identified genes in eukaryotes encoding mannosylglycerate synthases. Mannosylglycerate, a thermoprotectant compound, had been thought to occur only in archaea and eubacteria.

  18. Visualization and Analysis of 3D Gene Expression Data (Technical...

    Office of Scientific and Technical Information (OSTI)

    Technical Report: Visualization and Analysis of 3D Gene Expression Data Citation Details In-Document Search Title: Visualization and Analysis of 3D Gene Expression Data You are...

  19. Ice Particle Projected Area- and Mass-dimension Expressions

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    m-D and A-D expressions in BMPs is described in this paper. Figure 1. The m-D expression (black curve) for synoptic ice clouds between -20C and -40C based on SCPP m-D...

  20. Induction of gene expression using a high concentration sugar mixture

    DOE Patents [OSTI]

    England, George R.; Kelley, Aaron; Mitchinson, Colin

    2015-05-19

    Described herein is a composition useful for inducing expression of genes whose expression is under control of an inducible promoter sequence and methods for the compositions preparation and use.

  1. Induction of gene expression using a high concentration sugar mixture

    DOE Patents [OSTI]

    England, George R.; Kelley, Aaron; Mitchinson, Colin

    2010-05-11

    Described herein is a composition useful for inducing expression of genes whose expression is under control of an inducible promoter sequence and methods for the compositions preparation and use.

  2. Application of multidisciplinary analysis to gene expression.

    SciTech Connect (OSTI)

    Wang, Xuefel; Kang, Huining; Fields, Chris; Cowie, Jim R.; Davidson, George S.; Haaland, David Michael; Sibirtsev, Valeriy; Mosquera-Caro, Monica P.; Xu, Yuexian; Martin, Shawn Bryan; Helman, Paul; Andries, Erik; Ar, Kerem; Potter, Jeffrey; Willman, Cheryl L.; Murphy, Maurice H.

    2004-01-01

    Molecular analysis of cancer, at the genomic level, could lead to individualized patient diagnostics and treatments. The developments to follow will signal a significant paradigm shift in the clinical management of human cancer. Despite our initial hopes, however, it seems that simple analysis of microarray data cannot elucidate clinically significant gene functions and mechanisms. Extracting biological information from microarray data requires a complicated path involving multidisciplinary teams of biomedical researchers, computer scientists, mathematicians, statisticians, and computational linguists. The integration of the diverse outputs of each team is the limiting factor in the progress to discover candidate genes and pathways associated with the molecular biology of cancer. Specifically, one must deal with sets of significant genes identified by each method and extract whatever useful information may be found by comparing these different gene lists. Here we present our experience with such comparisons, and share methods developed in the analysis of an infant leukemia cohort studied on Affymetrix HG-U95A arrays. In particular, spatial gene clustering, hyper-dimensional projections, and computational linguistics were used to compare different gene lists. In spatial gene clustering, different gene lists are grouped together and visualized on a three-dimensional expression map, where genes with similar expressions are co-located. In another approach, projections from gene expression space onto a sphere clarify how groups of genes can jointly have more predictive power than groups of individually selected genes. Finally, online literature is automatically rearranged to present information about genes common to multiple groups, or to contrast the differences between the lists. The combination of these methods has improved our understanding of infant leukemia. While the complicated reality of the biology dashed our initial, optimistic hopes for simple answers from

  3. Expression of multiple proteins in transgenic plants

    DOE Patents [OSTI]

    Vierstra, Richard D.; Walker, Joseph M.

    2002-01-01

    A method is disclosed for the production of multiple proteins in transgenic plants. A DNA construct for introduction into plants includes a provision to express a fusion protein of two proteins of interest joined by a linking domain including plant ubiquitin. When the fusion protein is produced in the cells of a transgenic plant transformed with the DNA construction, native enzymes present in plant cells cleave the fusion protein to release both proteins of interest into the cells of the transgenic plant. Since the proteins are produced from the same fusion protein, the initial quantities of the proteins in the cells of the plant are approximately equal.

  4. Reduced expression of Autographa californica nucleopolyhedrovirus ORF34, an essential gene, enhances heterologous gene expression

    SciTech Connect (OSTI)

    Salem, Tamer Z.; Department of Microbial Molecular Biology, AGERI, Agricultural Research Center, Giza 12619; Division of Biomedical Sciences, Zewail University, Zewail City of Science and Technology, Giza 12588 ; Zhang, Fengrui; Thiem, Suzanne M.

    2013-01-20

    Autographa californica multiple nucleopolyhedrovirus ORF34 is part of a transcriptional unit that includes ORF32, encoding a viral fibroblast growth factor (FGF) and ORF33. We identified ORF34 as a candidate for deletion to improve protein expression in the baculovirus expression system based on enhanced reporter gene expression in an RNAi screen of virus genes. However, ORF34 was shown to be an essential gene. To explore ORF34 function, deletion (KO34) and rescue bacmids were constructed and characterized. Infection did not spread from primary KO34 transfected cells and supernatants from KO34 transfected cells could not infect fresh Sf21 cells whereas the supernatant from the rescue bacmids transfection could recover the infection. In addition, budded viruses were not observed in KO34 transfected cells by electron microscopy, nor were viral proteins detected from the transfection supernatants by western blots. These demonstrate that ORF34 is an essential gene with a possible role in infectious virus production.

  5. Repressor-mediated tissue-specific gene expression in plants

    DOE Patents [OSTI]

    Meagher, Richard B.; Balish, Rebecca S.; Tehryung, Kim; McKinney, Elizabeth C.

    2009-02-17

    Plant tissue specific gene expression by way of repressor-operator complexes, has enabled outcomes including, without limitation, male sterility and engineered plants having root-specific gene expression of relevant proteins to clean environmental pollutants from soil and water. A mercury hyperaccumulation strategy requires that mercuric ion reductase coding sequence is strongly expressed. The actin promoter vector, A2pot, engineered to contain bacterial lac operator sequences, directed strong expression in all plant vegetative organs and tissues. In contrast, the expression from the A2pot construct was restricted primarily to root tissues when a modified bacterial repressor (LacIn) was coexpressed from the light-regulated rubisco small subunit promoter in above-ground tissues. Also provided are analogous repressor operator complexes for selective expression in other plant tissues, for example, to produce male sterile plants.

  6. Express Primer Tool for high-throughput gene cloning and expression

    Energy Science and Technology Software Center (OSTI)

    2002-12-01

    A tool to assist in the design of primers for DNA amplification. The Express Primer web-based tool generates primer sequences specifically for the generation of expression clones for both lab scale and high-throughput projects. The application is designed not only to allow the user complete flexibility to specify primer design parameters but also to minimize the amount of manual intervention needed to generate a large number of primers for simultaneous amplification of multiple target genes.more » The Express Primer Tool enables the user to specify various experimental parameters (e.g. optimal Tm, Tm range, maximum Tm difference) for single or multiple candidate sequence(s) in FASTA format input as a flat text (ASCII) file. The application generates condidate primers, selects optimal primer pairs, and writes the forward and reverse primers pairs to an Excel file that is suitable for electronic submission to a synthesis facility. The program parameters emphasize high-throughput but allow for target atrition at various stages of the project.« less

  7. Alternative Fuels Data Center: Massachusetts Fleet Braun's Express

    Alternative Fuels and Advanced Vehicles Data Center [Office of Energy Efficiency and Renewable Energy (EERE)]

    Celebrates 10 Years of Petroleum Reduction Success Massachusetts Fleet Braun's Express Celebrates 10 Years of Petroleum Reduction Success to someone by E-mail Share Alternative Fuels Data Center: Massachusetts Fleet Braun's Express Celebrates 10 Years of Petroleum Reduction Success on Facebook Tweet about Alternative Fuels Data Center: Massachusetts Fleet Braun's Express Celebrates 10 Years of Petroleum Reduction Success on Twitter Bookmark Alternative Fuels Data Center: Massachusetts Fleet

  8. Small, Fast S-Expression Library, Version 1.0

    Energy Science and Technology Software Center (OSTI)

    2004-12-02

    This software is a library for C and C++ programmers to use for fast and efficient parsing and processing of symbolic expressions, or s-expressions. An s-expression is a text-representation of a tree data structure, and is the basis for the syntax of the LISP and Scheme programming languages. Multiple similar libraries exist, but this one was designed from the ground up for speed, efficiency, and simplicity.

  9. DOE Seeks Expression of Interest for Carlsbad Technical Support Services |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy Expression of Interest for Carlsbad Technical Support Services DOE Seeks Expression of Interest for Carlsbad Technical Support Services July 10, 2014 - 12:00pm Addthis Media Contact Lynette Chafin, 513-246-0461, Lynette.Chafin@emcbc.doe.gov Cincinnati - The U.S. Department of Energy (DOE) Environmental Management Consolidated Business Center (EMCBC) today issued a Sources Sought Synopsis/Expression of Interest seeking small business concerns with the capabilities to

  10. Estrogen induced {beta}-1,4-galactosyltransferase 1 expression...

    Office of Scientific and Technical Information (OSTI)

    cancer MCF-7 cells Citation Details In-Document Search Title: Estrogen induced beta-1,4-galactosyltransferase 1 expression regulates proliferation of human breast cancer ...

  11. Final EIS for Champlain Hudson Power Express Transmission Project...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    DOE Environmental Impact Statement Public Scoping Meeting on Champlain Hudson Power Express Transmission Line Project CEQ Releases Two Handbooks on Improving Efficiency of Federal ...

  12. High level expression of Acidothermus cellulolyticus β-1, 4...

    Office of Scientific and Technical Information (OSTI)

    The expression of the bacterial gene in rice was driven by the constitutive Mac promoter, a hybrid promoter of Ti plasmid mannopine synthetase promoter and cauliflower mosaic virus ...

  13. ANALYTIC EXPRESSIONS FOR THE LIGHT-SCATTERING CROSS SECTION

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of r and m, with many "wiggles" on many scales, and its computation, though straightforward, is time intensive. A simple expression for Q sp would simplify calculation of...

  14. U-058: Apache Struts Conversion Error OGNL Expression Injection...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    in Apache Struts. A remote user can execute arbitrary commands on the target system. PLATFORM: Apache Struts 2.x ABSTRACT: Apache Struts Conversion Error OGNL Expression...

  15. Workshop on Program for Elimination of Requirements Marginal to Safety: Proceedings

    SciTech Connect (OSTI)

    Dey, M.; Arsenault, F.; Patterson, M.; Gaal, M.

    1993-09-01

    These are the proceedings of the Public Workshop on the US Nuclear Regulatory Commission`s Program for Elimination of Requirements Marginal to Safety. The workshop was held at the Holiday Inn, Bethesda, on April 27 and 28, 1993. The purpose of the workshop was to provide an opportunity for public and industry input to the program. The workshop addressed the institutionalization of the program to review regulations with the purpose of eliminating those that are marginal. The objective is to avoid the dilution of safety efforts. One session was devoted to discussion of the framework for a performance-based regulatory approach. In addition, panelists and attendees discussed scope, schedules and status of specific regulatory items: containment leakage testing requirements, fire protection requirements, requirements for environmental qualification of electrical equipment, requests for information under 10CFR50.54(f), requirements for combustible gas control systems, and quality assurance requirements.

  16. Rhodobacter System for the Expression of Membrane Proteins | Argonne

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    National Laboratory Rhodobacter System for the Expression of Membrane Proteins Technology available for licensing: A unique system for membrane protein expression makes it possible to obtain reasonable yields of functional membrane protein. Lower production costs Yields a higher fraction of proteins in soluble form PDF icon rhodobacter

  17. Massively parallel processor networks with optical express channels

    DOE Patents [OSTI]

    Deri, R.J.; Brooks, E.D. III; Haigh, R.E.; DeGroot, A.J.

    1999-08-24

    An optical method for separating and routing local and express channel data comprises interconnecting the nodes in a network with fiber optic cables. A single fiber optic cable carries both express channel traffic and local channel traffic, e.g., in a massively parallel processor (MPP) network. Express channel traffic is placed on, or filtered from, the fiber optic cable at a light frequency or a color different from that of the local channel traffic. The express channel traffic is thus placed on a light carrier that skips over the local intermediate nodes one-by-one by reflecting off of selective mirrors placed at each local node. The local-channel-traffic light carriers pass through the selective mirrors and are not reflected. A single fiber optic cable can thus be threaded throughout a three-dimensional matrix of nodes with the x,y,z directions of propagation encoded by the color of the respective light carriers for both local and express channel traffic. Thus frequency division multiple access is used to hierarchically separate the local and express channels to eliminate the bucket brigade latencies that would otherwise result if the express traffic had to hop between every local node to reach its ultimate destination. 3 figs.

  18. Massively parallel processor networks with optical express channels

    DOE Patents [OSTI]

    Deri, Robert J.; Brooks, III, Eugene D.; Haigh, Ronald E.; DeGroot, Anthony J.

    1999-01-01

    An optical method for separating and routing local and express channel data comprises interconnecting the nodes in a network with fiber optic cables. A single fiber optic cable carries both express channel traffic and local channel traffic, e.g., in a massively parallel processor (MPP) network. Express channel traffic is placed on, or filtered from, the fiber optic cable at a light frequency or a color different from that of the local channel traffic. The express channel traffic is thus placed on a light carrier that skips over the local intermediate nodes one-by-one by reflecting off of selective mirrors placed at each local node. The local-channel-traffic light carriers pass through the selective mirrors and are not reflected. A single fiber optic cable can thus be threaded throughout a three-dimensional matrix of nodes with the x,y,z directions of propagation encoded by the color of the respective light carriers for both local and express channel traffic. Thus frequency division multiple access is used to hierarchically separate the local and express channels to eliminate the bucket brigade latencies that would otherwise result if the express traffic had to hop between every local node to reach its ultimate destination.

  19. Combined hairpin-antisense compositions and methods for modulating expression

    DOE Patents [OSTI]

    Shanklin, John; Nguyen, Tam

    2014-08-05

    A nucleotide construct comprising a nucleotide sequence that forms a stem and a loop, wherein the loop comprises a nucleotide sequence that modulates expression of a target, wherein the stem comprises a nucleotide sequence that modulates expression of a target, and wherein the target modulated by the nucleotide sequence in the loop and the target modulated by the nucleotide sequence in the stem may be the same or different. Vectors, methods of regulating target expression, methods of providing a cell, and methods of treating conditions comprising the nucleotide sequence are also disclosed.

  20. Combined hairpin-antisense compositions and methods for modulating expression

    SciTech Connect (OSTI)

    Shanklin, John; Nguyen, Tam Huu

    2015-11-24

    A nucleotide construct comprising a nucleotide sequence that forms a stem and a loop, wherein the loop comprises a nucleotide sequence that modulates expression of a target, wherein the stem comprises a nucleotide sequence that modulates expression of a target, and wherein the target modulated by the nucleotide sequence in the loop and the target modulated by the nucleotide sequence in the stem may be the same or different. Vectors, methods of regulating target expression, methods of providing a cell, and methods of treating conditions comprising the nucleotide sequence are also disclosed.

  1. DOE - Office of Legacy Management -- American Railway Express Office - NY

    Office of Legacy Management (LM)

    0-03 Railway Express Office - NY 0-03 FUSRAP Considered Sites Site: American Railway Express Office (NY.0-03 ) Eliminated from consideration under FUSRAP Designated Name: Not Designated Alternate Name: None Location: American Railway Express (Downtown) , New York , New York NY.0-03-1 Evaluation Year: 1987 NY.0-03-1 Site Operations: None - Involved with a fire during transport of uranium scrap. NY.0-03-2 Site Disposition: Eliminated - Potential for contamination remote NY.0-03-1 NY.0-03-2

  2. Array design and expression evaluation in POOMA II

    SciTech Connect (OSTI)

    Karmesin, S.; Crotinger, J.; Cummings, J.; Haney, S.; Humphrey, W.; Reynders, J.; Smith, S.; Williams, T.J.

    1998-12-31

    POOMA is a templated C++ class library for use in the development of large-scale scientific simulations on serial and parallel computers. POOMA II is a new design and implementation of POOMA intended to add richer capabilities and greater flexibility to the framework. The new design employs a generic Array class that acts as an interface to, or view on, a wide variety of data representation objects referred to as engines. This design separates the interface and the representation of multidimensional arrays. The separation is achieved using compile-time techniques rather than virtual functions, and thus code efficiency is maintained. POOMA II uses PETE, the Portable Expression Template Engine, to efficiently represent complex mathematical expressions involving arrays and other objects. The representation of expressions is kept separate from expression evaluation, allowing the use of multiple evaluator mechanisms that can support nested where-block constructs, hardware-specific optimizations and different run-time environments.

  3. American Express OPEN has teamed up with Women Impacting Public...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    American Express OPEN has teamed up with Women Impacting Public Policy (WIPP) and the U.S. Small Business Administration (SBA) to offer a ChallengeHER event with an OPEN for ...

  4. Visually Relating Gene Expression and in vivo DNA Binding Data

    SciTech Connect (OSTI)

    Huang, Min-Yu; Mackey, Lester; Ker?; nen, Soile V. E.; Weber, Gunther H.; Jordan, Michael I.; Knowles, David W.; Biggin, Mark D.; Hamann, Bernd

    2011-09-20

    Gene expression and in vivo DNA binding data provide important information for understanding gene regulatory networks: in vivo DNA binding data indicate genomic regions where transcription factors are bound, and expression data show the output resulting from this binding. Thus, there must be functional relationships between these two types of data. While visualization and data analysis tools exist for each data type alone, there is a lack of tools that can easily explore the relationship between them. We propose an approach that uses the average expression driven by multiple of ciscontrol regions to visually relate gene expression and in vivo DNA binding data. We demonstrate the utility of this tool with examples from the network controlling early Drosophila development. The results obtained support the idea that the level of occupancy of a transcription factor on DNA strongly determines the degree to which the factor regulates a target gene, and in some cases also controls whether the regulation is positive or negative.

  5. FedEx Express Gasoline Hybrid Electric Delivery Truck Evaluation...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ... Hemrick, Raquel Moreno - FedEx Express * Jim Mancuso, Dave Alef - Azure Dynamics, Inc. * ... Note: the coast downs provide by Azure and those taken at ReFUEL are not directly ...

  6. Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides

    SciTech Connect (OSTI)

    Pena-Castillo, Lourdes; Mercer, Ryan; Gurinovich, Anastasia; Callister, Stephen J.; Wright, Aaron T.; Westbye, Alexander; Beatty, J. T.; Lang, Andrew S.

    2014-08-28

    The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully sequenced and both have been the subject of transcriptional profiling studies. Gene co-expression networks can be used to identify modules of genes with similar expression profiles. Functional analysis of gene modules can then associate co-expressed genes with biological pathways, and network statistics can determine the degree of module preservation in related networks. In this paper, we constructed an R. capsulatus gene co-expression network, performed functional analysis of identified gene modules, and investigated preservation of these modules in R. capsulatus proteomics data and in R. sphaeroides transcriptomics data. Results: The analysis identified 40 gene co-expression modules in R. capsulatus. Investigation of the module gene contents and expression profiles revealed patterns that were validated based on previous studies supporting the biological relevance of these modules. We identified two R. capsulatus gene modules preserved in the protein abundance data. We also identified several gene modules preserved between both Rhodobacter species, which indicate that these cellular processes are conserved between the species and are candidates for functional information transfer between species. Many gene modules were non-preserved, providing insight into processes that differentiate the two species. In addition, using Local Network Similarity (LNS), a recently proposed metric for expression divergence, we assessed the expression conservation of between-species pairs of orthologs, and within-species gene-protein expression profiles. Conclusions: Our analyses provide new sources of information for functional annotation in R. capsulatus because uncharacterized genes in modules are now connected with groups of genes that constitute a joint functional

  7. Assessment of Normal Variability in Peripheral Blood Gene Expression

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Campbell, Catherine; Vernon, Suzanne D.; Karem, Kevin L.; Nisenbaum, Rosane; Unger, Elizabeth R.

    2002-01-01

    Peripheral blood is representative of many systemic processes and is an ideal sample for expression profiling of diseases that have no known or accessible lesion. Peripheral blood is a complex mixture of cell types and some differences in peripheral blood gene expression may reflect the timing of sample collection rather than an underlying disease process. For this reason, it is important to assess study design factors that may cause variability in gene expression not related to what is being analyzed. Variation in the gene expression of circulating peripheral blood mononuclear cells (PBMCs) from three healthy volunteers sampled three times onemore » day each week for one month was examined for 1,176 genes printed on filter arrays. Less than 1% of the genes showed any variation in expression that was related to the time of collection, and none of the changes were noted in more than one individual. These results suggest that observed variation was due to experimental variability.« less

  8. DOE Seeks Public-Private Sector Expressions of Interest for Global...

    Office of Environmental Management (EM)

    Public-Private Sector Expressions of Interest for Global Nuclear Energy Partnership Initiative DOE Seeks Public-Private Sector Expressions of Interest for Global Nuclear Energy ...

  9. Recombinant cells that highly express chromosomally-integrated heterologous genes

    DOE Patents [OSTI]

    Ingram, Lonnie O.; Ohta, Kazuyoshi; Wood, Brent E.

    1998-01-01

    Recombinant host cells are obtained that comprise (A) a heterologous, polypeptide-encoding polynucleotide segment, stably integrated into a chromosome, which is under transcriptional control of an endogenous promoter and (B) a mutation that effects increased expression of the heterologous segment, resulting in enhanced production by the host cells of each polypeptide encoded by that segment, relative to production of each polypeptide by the host cells in the absence of the mutation. The increased expression thus achieved is retained in the absence of conditions that select for cells displaying such increased expression. When the integrated segment comprises, for example, ethanol-production genes from an efficient ethanol producer like Zymomonas mobilis, recombinant Escherichia coli and other enteric bacterial cells within the present invention are capable of converting a wide range of biomass-derived sugars efficiently to ethanol.

  10. Recombinant cells that highly express chromosomally-integrated heterologous genes

    DOE Patents [OSTI]

    Ingram, L.O.; Ohta, Kazuyoshi; Wood, B.E.

    1998-10-13

    Recombinant host cells are obtained that comprise (A) a heterologous, polypeptide-encoding polynucleotide segment, stably integrated into a chromosome, which is under transcriptional control of an endogenous promoter and (B) a mutation that effects increased expression of the heterologous segment, resulting in enhanced production by the host cells of each polypeptide encoded by that segment, relative to production of each polypeptide by the host cells in the absence of the mutation. The increased expression thus achieved is retained in the absence of conditions that select for cells displaying such increased expression. When the integrated segment comprises, for example, ethanol-production genes from an efficient ethanol producer like Zymomonas mobilis, recombinant Escherichia coli and other enteric bacterial cells within the present invention are capable of converting a wide range of biomass-derived sugars efficiently to ethanol. 13 figs.

  11. Recombinant cells that highly express chromosomally-integrated heterologous gene

    DOE Patents [OSTI]

    Ingram, Lonnie O.; Ohta, Kazuyoshi; Wood, Brent E.

    2007-03-20

    Recombinant host cells are obtained that comprise (A) a heterologous, polypeptide-encoding polynucleotide segment, stably integrated into a chromosome, which is under transcriptional control of an endogenous promoter and (B) a mutation that effects increased expression of the heterologous segment, resulting in enhanced production by the host cells of each polypeptide encoded by that segment, relative to production of each polypeptide by the host cells in the absence of the mutation. The increased expression thus achieved is retained in the absence of conditions that select for cells displaying such increased expression. When the integrated segment comprises, for example, ethanol-production genes from an efficient ethanol producer like Zymomonas mobilis, recombinant Escherichia coli and other enteric bacterial cells within the present invention are capable of converting a wide range of biomass-derived sugars efficiently to ethanol.

  12. Recombinant cells that highly express chromosomally-integrated heterologous genes

    DOE Patents [OSTI]

    Ingram, Lonnie O.; Ohta, Kazuyoshi; Wood, Brent E.

    2000-08-22

    Recombinant host cells are obtained that comprise (A) a heterologous, polypeptide-encoding polynucleotide segment, stably integrated into a chromosome, which is under transcriptional control of an endogenous promoter and (B) a mutation that effects increased expression of the heterologous segment, resulting in enhanced production by the host cells of each polypeptide encoded by that segment, relative to production of each polypeptide by the host cells in the absence of the mutation. The increased expression thus achieved is retained in the absence of conditions that select for cells displaying such increased expression. When the integrated segment comprises, for example, ethanol-production genes from an efficient ethanol producer like Zymomonas mobilis, recombinant Escherichia coli and other enteric bacterial cells within the present invention are capable of converting a wide range of biomass-derived sugars efficiently to ethanol.

  13. Explicit Expressions for 3D Boundary Integrals in Potential Theory

    SciTech Connect (OSTI)

    Nintcheu Fata, Sylvain

    2009-01-01

    On employing isoparametric, piecewise linear shape functions over a flat triangular domain, exact expressions are derived for all surface potentials involved in the numerical solution of three-dimensional singular and hyper-singular boundary integral equations of potential theory. These formulae, which are valid for an arbitrary source point in space, are represented as analytic expressions over the edges of the integration triangle. They can be used to solve integral equations defined on polygonal boundaries via the collocation method or may be utilized as analytic expressions for the inner integrals in the Galerkin technique. Also, the constant element approximation can be directly obtained with no extra effort. Sample problems solved by the collocation boundary element method for the Laplace equation are included to validate the proposed formulae.

  14. Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts

    SciTech Connect (OSTI)

    Kleiner, Manuel; Young, Jacque C; Shah, Manesh B; Verberkmoes, Nathan C; Dubilier, Nicole

    2013-01-01

    Transposases, enzymes that catalyze the movement of mobile genetic elements, are the most abundant genes in nature. While many bacteria encode an abundance of transposases in their genomes, the current paradigm is that transposase gene expression is tightly regulated and generally low due to its severe mutagenic effects. In the current study, we detected the highest number of transposase proteins ever reported in bacteria, in symbionts of the gutless marine worm Olavius algarvensis using metaproteomics. At least 26 different transposases from 12 different families were detected and genomic and proteomic analyses suggest many of these are active. This high expression of transposases indicates that the mechanisms for their tight regulation have been disabled or destroyed. Based on recent studies on other symbionts and pathogens that showed high transposase transcription, we speculate that abundant transposase expression might be common in symbionts and pathogens.

  15. Robust expression of a bioactive mammalian protein in Chlamydomonas chloroplast

    DOE Patents [OSTI]

    Mayfield, Stephen P

    2015-01-13

    Methods and compositions are disclosed to engineer chloroplast comprising heterologous mammalian genes via a direct replacement of chloroplast Photosystem II (PSII) reaction center protein coding regions to achieve expression of recombinant protein above 5% of total protein. When algae is used, algal expressed protein is produced predominantly as a soluble protein where the functional activity of the peptide is intact. As the host algae is edible, production of biologics in this organism for oral delivery of proteins/peptides, especially gut active proteins, without purification is disclosed.

  16. Robust expression of a bioactive mammalian protein in chlamydomonas chloroplast

    DOE Patents [OSTI]

    Mayfield, Stephen P.

    2010-03-16

    Methods and compositions are disclosed to engineer chloroplast comprising heterologous mammalian genes via a direct replacement of chloroplast Photosystem II (PSII) reaction center protein coding regions to achieve expression of recombinant protein above 5% of total protein. When algae is used, algal expressed protein is produced predominantly as a soluble protein where the functional activity of the peptide is intact. As the host algae is edible, production of biologics in this organism for oral delivery or proteins/peptides, especially gut active proteins, without purification is disclosed.

  17. Sugarcane transgenics expressing MYB transcription factors show improved glucose release

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Poovaiah, Charleson R.; Bewg, William P.; Lan, Wu; Ralph, John; Coleman, Heather D.

    2016-07-15

    In this study, sugarcane, a tropical C4 perennial crop, is capable of producing 30-100 tons or more of biomass per hectare annually. The lignocellulosic residue remaining after sugar extraction is currently underutilized and can provide a significant source of biomass for the production of second-generation bioethanol. As a result, MYB31 and MYB42 were cloned from maize and expressed in sugarcane with and without the UTR sequences. The cloned sequences were 98 and 99 % identical to the published nucleotide sequences. The inclusion of the UTR sequences did not affect any of the parameters tested. There was little difference in plantmore » height and the number of internodes of the MYB-overexpressing sugarcane plants when compared with controls. MYB transgene expression determined by qPCR exhibited continued expression in young and maturing internodes. MYB31 downregulated more genes within the lignin biosynthetic pathway than MYB42. MYB31 and MYB42 expression resulted in decreased lignin content in some lines. All MYB42 plants further analyzed showed significant increases in glucose release by enzymatic hydrolysis in 72 h, whereas only two MYB31 plants released more glucose than control plants. This correlated directly with a significant decrease in acid-insoluble lignin. Soluble sucrose content of the MYB42 transgenic plants did not vary compared to control plants. In conclusion, this study demonstrates the use of MYB transcription factors to improve the production of bioethanol from sugarcane bagasse remaining after sugar extraction.« less

  18. Multiclass cancer diagnosis using tumor gene expression signatures

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ramaswamy, S.; Tamayo, P.; Rifkin, R.; Mukherjee, S.; Yeang, C. -H.; Angelo, M.; Ladd, C.; Reich, M.; Latulippe, E.; Mesirov, J. P.; et al

    2001-12-11

    The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is difficult or impossible because of atypical clinical presentation or histopathology. To determine whether the diagnosis of multiple common adult malignancies could be achieved purely by molecular classification, we subjected 218 tumor samples, spanning 14 common tumor types, and 90 normal tissue samples to oligonucleotide microarray gene expression analysis. The expression levels of 16,063 genes and expressed sequence tags were used to evaluate the accuracy of a multiclass classifier based on a supportmore » vector machine algorithm. Overall classification accuracy was 78%, far exceeding the accuracy of random classification (9%). Poorly differentiated cancers resulted in low-confidence predictions and could not be accurately classified according to their tissue of origin, indicating that they are molecularly distinct entities with dramatically different gene expression patterns compared with their well differentiated counterparts. Taken together, these results demonstrate the feasibility of accurate, multiclass molecular cancer classification and suggest a strategy for future clinical implementation of molecular cancer diagnostics.« less

  19. Heterologous expression of xylanase enzymes in lipogenic yeast Yarrowia lipolytica

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wang, Wei; Wei, Hui; Alahuhta, Markus; Chen, Xiaowen; Hyman, Deborah; Johnson, David K.; Zhang, Min; Himmel, Michael E.

    2014-12-02

    In order to develop a direct microbial sugar conversion platform for the production of lipids, drop-in fuels and chemicals from cellulosic biomass substrate, we chose Yarrowia lipolytica as a viable demonstration strain. Y. lipolytica is known to accumulate lipids intracellularly and is capable of metabolizing sugars to produce lipids; however, it lacks the lignocellulose-degrading enzymes needed to break down biomass directly. While research is continuing on the development of a Y. lipolytica strain able to degrade cellulose, in this study, we present successful expression of several xylanases in Y. lipolytica. The XynII and XlnD expressing Yarrowia strains exhibited an abilitymore » to grow on xylan mineral plates. This was shown by Congo Red staining of halo zones on xylan mineral plates. Enzymatic activity tests further demonstrated active expression of XynII and XlnD in Y. lipolytica. Furthermore, synergistic action in converting xylan to xylose was observed when XlnD acted in concert with XynII. Finally, the successful expression of these xylanases in Yarrowia further advances us toward our goal to develop a direct microbial conversion process using this organism.« less

  20. Consolidated pretreatment and hydrolysis of plant biomass expressing cell wall degrading enzymes

    DOE Patents [OSTI]

    Raab, R. Michael; Zhang, Dongcheng; Bougri, Oleg

    2016-02-02

    Methods for consolidated pretreatment and hydrolysis of genetically engineered plants expressing cell wall degrading enzymes are provided. Expression cassettes and vectors for making transgenic plants are described. Plants engineered to express one or more cell wall degrading enzymes using expression cassettes and vectors of the invention are also provided.

  1. Gene expression analysis of precision-cut human liver slices indicates stable expression of ADME-Tox related genes

    SciTech Connect (OSTI)

    Elferink, M.G.L., E-mail: m.g.l.elferink@rug.nl [Department of Pharmacokinetics, Toxicology and Targeting, Groningen Research Institute for Pharmacy, University of Groningen (Netherlands); Olinga, P. [Department of Pharmacokinetics, Toxicology and Targeting, Groningen Research Institute for Pharmacy, University of Groningen (Netherlands); van Leeuwen, E.M.; Bauerschmidt, S.; Polman, J. [Molecular Design and Informatics, MSD, Oss (Netherlands); Schoonen, W.G. [Toxicology and Drug Disposition, MSD, Oss (Netherlands); Heisterkamp, S.H. [Biostatistics and Research Decision Sciences MSD, Oss (Netherlands); Bioinformatics Centre, University of Groningen (Netherlands); Groothuis, G.M.M. [Department of Pharmacokinetics, Toxicology and Targeting, Groningen Research Institute for Pharmacy, University of Groningen (Netherlands)

    2011-05-15

    In the process of drug development it is of high importance to test the safety of new drugs with predictive value for human toxicity. A promising approach of toxicity testing is based on shifts in gene expression profiling of the liver. Toxicity screening based on animal liver cells cannot be directly extrapolated to humans due to species differences. The aim of this study was to evaluate precision-cut human liver slices as in vitro method for the prediction of human specific toxicity by toxicogenomics. The liver slices contain all cell types of the liver in their natural architecture. This is important since drug-induced toxicity often is a multi-cellular process. Previously we showed that toxicogenomic analysis of rat liver slices is highly predictive for rat in vivo toxicity. In this study we investigated the levels of gene expression during incubation up to 24 h with Affymetrix microarray technology. The analysis was focused on a broad spectrum of genes related to stress and toxicity, and on genes encoding for phase-I, -II and -III metabolizing enzymes and transporters. Observed changes in gene expression were associated with cytoskeleton remodeling, extracellular matrix and cell adhesion, but for the ADME-Tox related genes only minor changes were observed. PCA analysis showed that changes in gene expression were not associated with age, sex or source of the human livers. Slices treated with acetaminophen showed patterns of gene expression related to its toxicity. These results indicate that precision-cut human liver slices are relatively stable during 24 h of incubation and represent a valuable model for human in vitro hepatotoxicity testing despite the human inter-individual variability.

  2. Emerging Use of Gene Expression Microarrays in Plant Physiology

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wullschleger, Stan D.; Difazio, Stephen P.

    2003-01-01

    Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology weremore » selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.« less

  3. Transgenic rabbit that expresses a functional human lipoprotein (a)

    DOE Patents [OSTI]

    Rouy, Didier; Duverger, Nicolas; Emmanuel, Florence; Denefle, Patrice; Houdebine, Louis-Marie; Viglietta, Celine; Rubin, Edward M.; Hughes, Steven D.

    2003-01-01

    A transgenic rabbit which has in its genomic DNA sequences that encode apolipoprotein (a) and apolipoprotein B polypeptides which are capable of combining to produce lipoprotein (a), a process for creating such a rabbit, and the use of the rabbit to identify compounds which are effective in the treatment of human diseases which are associated with, induced and/or exacerbated by Lp(a) expression.

  4. MicroRNAs expression in ox-LDL treated HUVECs: MiR-365 modulates apoptosis and Bcl-2 expression

    SciTech Connect (OSTI)

    Qin, Bing; Xiao, Bo; Liang, Desheng; Xia, Jian; Li, Ye; Yang, Huan

    2011-06-24

    Highlights: {yields} We evaluated the role of miRNAs in ox-LDL induced apoptosis in ECs. {yields} We found 4 up-regulated and 11 down-regulated miRNAs in apoptotic ECs. {yields} Target genes of the dysregulated miRNAs regulate ECs apoptosis and atherosclerosis. {yields} MiR-365 promotes ECs apoptosis via suppressing Bcl-2 expression. {yields} MiR-365 inhibitor alleviates ECs apoptosis induced by ox-LDL. -- Abstract: Endothelial cells (ECs) apoptosis induced by oxidized low-density lipoprotein (ox-LDL) is thought to play a critical role in atherosclerosis. MicroRNAs (miRNAs) are a class of noncoding RNAs that posttranscriptionally regulate the expression of genes involved in diverse cell functions, including differentiation, growth, proliferation, and apoptosis. However, whether miRNAs are associated with ox-LDL induced apoptosis and their effect on ECs is still unknown. Therefore, this study evaluated potential miRNAs and their involvement in ECs apoptosis in response to ox-LDL stimulation. Microarray and qRT-PCR analysis performed on human umbilical vein endothelial cells (HUVECs) exposed to ox-LDL identified 15 differentially expressed (4 up- and 11 down-regulated) miRNAs. Web-based query tools were utilized to predict the target genes of the differentially expressed miRNAs, and the potential target genes were classified into different function categories with the gene ontology (GO) term and KEGG pathway annotation. In particular, bioinformatics analysis suggested that anti-apoptotic protein B-cell CLL/lymphoma 2 (Bcl-2) is a target gene of miR-365, an apoptomir up-regulated by ox-LDL stimulation in HUVECs. We further showed that transfection of miR-365 inhibitor partly restored Bcl-2 expression at both mRNA and protein levels, leading to a reduction of ox-LDL-mediated apoptosis in HUVECs. Taken together, our findings indicate that miRNAs participate in ox-LDL-mediated apoptosis in HUVECs. MiR-365 potentiates ox-LDL-induced ECs apoptosis by regulating the

  5. Protein Co-Expression Network Analysis (ProCoNA)

    SciTech Connect (OSTI)

    Gibbs, David L.; Baratt, Arie; Baric, Ralph; Kawaoka, Yoshihiro; Smith, Richard D.; Orwoll, Eric S.; Katze, Michael G.; Mcweeney, Shannon K.

    2013-06-01

    Biological networks are important for elucidating disease etiology due to their ability to model complex high dimensional data and biological systems. Proteomics provides a critical data source for such models, but currently lacks robust de novo methods for network construction, which could bring important insights in systems biology. We have evaluated the construction of network models using methods derived from weighted gene co-expression network analysis (WGCNA). We show that approximately scale-free peptide networks, composed of statistically significant modules, are feasible and biologically meaningful using two mouse lung experiments and one human plasma experiment. Within each network, peptides derived from the same protein are shown to have a statistically higher topological overlap and concordance in abundance, which is potentially important for inferring protein abundance. The module representatives, called eigenpeptides, correlate significantly with biological phenotypes. Furthermore, within modules, we find significant enrichment for biological function and known interactions (gene ontology and protein-protein interactions). Biological networks are important tools in the analysis of complex systems. In this paper we evaluate the application of weighted co-expression network analysis to quantitative proteomics data. Protein co-expression networks allow novel approaches for biological interpretation, quality control, inference of protein abundance, a framework for potentially resolving degenerate peptide-protein mappings, and a biomarker signature discovery.

  6. Simvastatin enhances bone morphogenetic protein receptor type II expression

    SciTech Connect (OSTI)

    Hu Hong; Sung, Arthur; Zhao, Guohua; Shi, Lingfang; Qiu Daoming; Nishimura, Toshihiko; Kao, Peter N. . E-mail: peterkao@stanford.edu

    2006-01-06

    Statins confer therapeutic benefits in systemic and pulmonary vascular diseases. Bone morphogenetic protein (BMP) receptors serve essential signaling functions in cardiovascular development and skeletal morphogenesis. Mutations in BMP receptor type II (BMPR2) are associated with human familial and idiopathic pulmonary arterial hypertension, and pathologic neointimal proliferation of vascular endothelial and smooth muscle cells within small pulmonary arteries. In severe experimental pulmonary hypertension, simvastatin reversed disease and conferred a 100% survival advantage. Here, modulation of BMPR2 gene expression by simvastatin is characterized in human embryonic kidney (HEK) 293T, pulmonary artery smooth muscle, and lung microvascular endothelial cells (HLMVECs). A 1.4 kb BMPR2 promoter containing Egr-1 binding sites confers reporter gene activation in 293T cells which is partially inhibited by simvastatin. Simvastatin enhances steady-state BMPR2 mRNA and protein expression in HLMVEC, through posttranscriptional mRNA stabilization. Simvastatin induction of BMPR2 expression may improve BMP-BMPR2 signaling thereby enhancing endothelial differentiation and function.

  7. Imaging gene expression in real-time using aptamers

    SciTech Connect (OSTI)

    Shin, Il Chung

    2011-01-01

    Signal transduction pathways are usually activated by external stimuli and are transient. The downstream changes such as transcription of the activated genes are also transient. Real-time detection of promoter activity is useful for understanding changes in gene expression, especially during cell differentiation and in development. A simple and reliable method for viewing gene expression in real time is not yet available. Reporter proteins such as fluorescent proteins and luciferase allow for non-invasive detection of the products of gene expression in living cells. However, current reporter systems do not provide for real-time imaging of promoter activity in living cells. This is because of the long time period after transcription required for fluorescent protein synthesis and maturation. We have developed an RNA reporter system for imaging in real-time to detect changes in promoter activity as they occur. The RNA reporter uses strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags), which can be expressed from a promoter of choice. The tobramycin, neomycin and PDC RNA aptamers have been utilized for this system and expressed in yeast from the GAL1 promoter. The IMAGEtag RNA kinetics were quantified by RT-qPCR. In yeast precultured in raffinose containing media the GAL1 promoter responded faster than in yeast precultured in glucose containing media. IMAGEtag RNA has relatively short half-life (5.5 min) in yeast. For imaging, the yeast cells are incubated with their ligands that are labeled with fluorescent dyes. To increase signal to noise, ligands have been separately conjugated with the FRET (Förster resonance energy transfer) pairs, Cy3 and Cy5. With these constructs, the transcribed aptamers can be imaged after activation of the promoter by galactose. FRET was confirmed with three different approaches, which were sensitized emission, acceptor photobleaching and donor lifetime by FLIM (fluorescence lifetime imaging

  8. Population genetic variation in gene expression is associated withphenotypic variation in Saccharomyces cerevisiae

    SciTech Connect (OSTI)

    Fay, Justin C.; McCullough, Heather L.; Sniegowski, Paul D.; Eisen, Michael B.

    2004-02-25

    The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits. Results: We compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown either in the presence or absence of copper sulfate. Of the nine strains, two show a reduced growth rate and two others are rust colored in the presence of copper sulfate. We identified 633 genes that show significant differences in expression among strains. Of these genes,20 were correlated with resistance to copper sulfate and 24 were correlated with rust coloration. The function of these genes in combination with their expression pattern suggests the presence of both correlative and causative expression differences. But the majority of differentially expressed genes were not correlated with either phenotype and showed the same expression pattern both in the presence and absence of copper sulfate. To determine whether these expression differences may contribute to phenotypic variation under other environmental conditions, we examined one phenotype, freeze tolerance, predicted by the differential expression of the aquaporin gene AQY2. We found freeze tolerance is associated with the expression of AQY2. Conclusions: Gene expression differences provide substantial insight into the molecular basis of naturally occurring traits and can be used to predict environment dependent phenotypic variation.

  9. Methods and constructs for expression of foreign proteins in photosynthetic organisms

    DOE Patents [OSTI]

    Laible, Philip D.; Hanson, Deborah K.

    2002-01-01

    A method for expressing and purifying foreign proteins in photosynthetic organisms comprising the simultaneous expression of both the heterologous protein and a means for compartmentalizing or sequestering of the protein.

  10. Advanced radioisotope power source options for Pluto Express

    SciTech Connect (OSTI)

    Underwood, M.L.

    1995-12-31

    In the drive to reduce mass and cost, Pluto Express is investigating using an advanced power conversion technology in a small Radioisotope Power Source (RPS) to deliver the required mission power of 74 W(electric) at end of mission. Until this year the baseline power source under consideration has been a Radioisotope Thermoelectric Generator (RTG). This RTG would be a scaled down GPHS RTG with an inventory of 6 General Purpose Heat Sources (GPHS) and a mass of 17.8 kg. High efficiency, advanced technology conversion options are being examined to lower the power source mass and to reduce the amount of radioisotope needed. Three technologies are being considered as the advanced converter technology: the Alkali Metal Thermal-to-Electric Converter (AMTEC), Thermophotovoltaic (TPV) converters, and Stirling Engines. Conceptual designs for each of these options have been prepared. Each converter would require only 2 GPHSs to provide the mission power and would have a mass of 6.1, 7.2, and 12.4 kg for AMTEC, TPV, and Stirling Engines respectively. This paper reviews the status of each technology and the projected performance of an advanced RPS based on each technology. Based on the projected performance and spacecraft integration issues, Pluto Express would prefer to use the AMTEC based RPS. However, in addition to technical performance, selection of a power technology will be based on many other factors.

  11. Computational expressions for signals in frequency-modulation spectroscopy

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Di Rosa, Michael D.; Reiten, M. T.

    2015-05-25

    In this study, general expressions for the signals in frequency-modulation spectroscopy (FMS) appear in the literature but are often reduced to simple analytical equations following the assumption of a weak modulation index. This is little help to the experimentalist who wants to predict signals for modulation depths of the order of unity or greater, where strong FMS signals reside. Here, we develop general formulas for FMS signals in the case of an absorber with a Voigt line shape and then link these expressions to an example and existing numerical code for the line shape. The resulting computational recipe is easymore » to implement and exercised here to show where the larger FMS signals are found over the coordinates of modulation index and modulation frequency. One can also estimate from provided curves the in-phase FMS signal over a wide range of modulation parameters at either the Lorentzian-broadening or Doppler-broadening limit, or anywhere in between by interpolation.« less

  12. Human AZU-1 gene, variants thereof and expressed gene products

    DOE Patents [OSTI]

    Chen, Huei-Mei; Bissell, Mina

    2004-06-22

    A human AZU-1 gene, mutants, variants and fragments thereof. Protein products encoded by the AZU-1 gene and homologs encoded by the variants of AZU-1 gene acting as tumor suppressors or markers of malignancy progression and tumorigenicity reversion. Identification, isolation and characterization of AZU-1 and AZU-2 genes localized to a tumor suppressive locus at chromosome 10q26, highly expressed in nonmalignant and premalignant cells derived from a human breast tumor progression model. A recombinant full length protein sequences encoded by the AZU-1 gene and nucleotide sequences of AZU-1 and AZU-2 genes and variant and fragments thereof. Monoclonal or polyclonal antibodies specific to AZU-1, AZU-2 encoded protein and to AZU-1, or AZU-2 encoded protein homologs.

  13. Simple and compact expressions for neutrino oscillation probabilities in matter

    SciTech Connect (OSTI)

    Minakata, Hisakazu; Parke, Stephen J.

    2015-05-07

    We reformulate perturbation theory for neutrino oscillations in matter with an expansion parameter related to the ratio of the solar to the atmospheric ?m2 scales. Unlike previous works, use a renormalized basis in which certain first-order effects are taken into account in the zeroth-order Hamiltonian. Using this perturbation theory we derive extremely compact expressions for the neutrino oscillations probabilities in matter. We find, for example, that the ?e disappearance probability at this order is of a simple two flavor form with an appropriately identified mixing angle and ?m2. Furthermore, despite exceptional simplicity in their forms they accommodate all order effects ?13 and the matter potential.

  14. Bioluminescent reporters for catabolic gene expression and pollutant bioavailability

    SciTech Connect (OSTI)

    Heitzer, A.; DiGrazia, P.M.; Sayler, G.S. . Center for Environmental Biotechnology); Burlage, R.S. )

    1991-01-01

    The application of visualized catabolic nah-gene expression using a luxCDABE gene fusion provides a valuable method to measure quantitatively and specifically naphthalene and salicylate bioavailability. It has been demonstrated that the physiological state of the test culture together with the intrinsic regulation mechanisms of the naphthalene degradation pathway as well as the physiological aspects of the lux gene fusion have to be taken into account. The method presented provides a high potential for in situ bioprocess monitoring. In addition, the results obtained with immobilized cells provide a basis for the development of biosensors for environmental applications in specific pollutant monitoring in waste streams and soil slurry systems but, as a general method, also for more conventional biotechnological process control. 8 refs., 2 figs., 1 tab.

  15. Expression of hPNAS-4 Radiosensitizes Lewis Lung Cancer

    SciTech Connect (OSTI)

    Zeng Hui; Yuan Zhu; Zhu Hong; Li Lei; Shi Huashan; Wang Zi; Fan Yu; Deng Qian; Zeng Jianshuang; He Yinbo; Xiao Jianghong; Li Zhiping

    2012-11-15

    Purpose: This study aimed to transfer the hPNAS-4 gene, a novel apoptosis-related human gene, into Lewis lung cancer (LL2) and observe its radiosensitive effect on radiation therapy in vitro and in vivo. Methods and Materials: The hPNAS-4 gene was transfected into LL2 cells, and its expression was detected via western blot. Colony formation assay and flow cytometry were used to detect the growth and apoptosis of cells treated with irradiation/PNAS-4 in vitro. The hPNAS-4 gene was transferred into LL2-bearing mice through tail vein injection of the liposome/gene complex. The tumor volumes were recorded after radiation therapy. Proliferating cell nuclear antigen (PCNA) immunohistochemistry staining and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assay were performed to detect the tumor cell growth and apoptosis in vivo. Results: The hPNAS-4 gene was successfully transferred into LL2 cells and tumor tissue, and its overexpressions were confirmed via western blot analysis. Compared with the control, empty plasmid, hPNAS-4, radiation, and empty plasmid plus radiation groups, the hPNAS-4 plus radiation group more significantly inhibited growth and enhanced apoptosis of LL2 cells in vitro and in vivo (P<.05). Conclusions: The hPNAS-4 gene was successfully transferred into LL2 cells and tumor tissue and was expressed in both LL2 cell and tumor tissue. The hPNAS-4 gene therapy significantly enhanced growth inhibition and apoptosis of LL2 tumor cells by radiation therapy in vitro and in vivo. Therefore, it may be a potential radiosensitive treatment of radiation therapy for lung cancer.

  16. We've Got Saving Energy All Wrapped Up | Department of Energy

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ... Save Energy this Holiday Season How do You Save Energy During the Holidays? Energy-efficient light bulbs can make great energy-saving stocking stuffers. Holiday Gifts for Energy ...

  17. Jefferson Lab Activities Group Invites Young and Not-So-Young...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Holiday Events Holiday Party on Dec. 12 for Jefferson Lab Children and the Young at Heart The JAG Holiday Party is scheduled for Saturday, Dec. 12, 10 a.m.-1 p.m. in the CEBAF...

  18. Metformin suppresses CYP1A1 and CYP1B1 expression in breast cancer cells by down-regulating aryl hydrocarbon receptor expression

    SciTech Connect (OSTI)

    Do, Minh Truong; Kim, Hyung Gyun; Tran, Thi Thu Phuong; Khanal, Tilak; Choi, Jae Ho; Chung, Young Chul; Jeong, Tae Cheon; Jeong, Hye Gwang

    2014-10-01

    Induction of cytochrome P450 (CYP) 1A1 and CYP1B1 by environmental xenobiotic chemicals or endogenous ligands through the activation of the aryl hydrocarbon receptor (AhR) has been implicated in a variety of cellular processes related to cancer, such as transformation and tumorigenesis. Here, we investigated the effects of the anti-diabetes drug metformin on expression of CYP1A1 and CYP1B1 in breast cancer cells under constitutive and inducible conditions. Our results indicated that metformin down-regulated the expression of CYP1A1 and CYP1B1 in breast cancer cells under constitutive and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced conditions. Down-regulation of AhR expression was required for metformin-mediated decreases in CYP1A1 and CYP1B1 expression, and the metformin-mediated CYP1A1 and CYP1B1 reduction is irrelevant to estrogen receptor α (ERα) signaling. Furthermore, we found that metformin markedly down-regulated Sp1 protein levels in breast cancer cells. The use of genetic and pharmacological tools revealed that metformin-mediated down-regulation of AhR expression was mediated through the reduction of Sp1 protein. Metformin inhibited endogenous AhR ligand-induced CYP1A1 and CYP1B1 expression by suppressing tryptophan-2,3-dioxygenase (TDO) expression in MCF-7 cells. Finally, metformin inhibits TDO expression through a down-regulation of Sp1 and glucocorticoid receptor (GR) protein levels. Our findings demonstrate that metformin reduces CYP1A1 and CYP1B1 expression in breast cancer cells by down-regulating AhR signaling. Metformin would be able to act as a potential chemopreventive agent against CYP1A1 and CYP1B1-mediated carcinogenesis and development of cancer. - Graphical abstract: Schematic of the CYP1A1 and CYP1B1 gene regulation by metformin. - Highlights: • Metformin inhibits CYP1A1 and CYP1B1 expression. • Metformin down-regulates the AhR signaling. • Metformin reduces Sp1 protein expression. • Metformin suppresses TDO expression.

  19. Analytical expression for the electric potential in the plasma sheath near an arc-cathode

    SciTech Connect (OSTI)

    Askari, S.; Minoo, H.

    2008-04-15

    An expression for the spatial dependence of the electric potential in a collisionless plasma sheath near an electron-emitting cathode is presented. The applicability of this expression for an arc cathode is demonstrated. Comparison with the numerical solutions of the model equations indicates that the sheath thickness and potential variation predicted by this expression are accurate in a wide range of the electron-emission yield.

  20. Using Rhodobacter Bacteria to Express Membrane Proteins (ANL-IN-99-089) -

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Energy Innovation Portal Biomass and Biofuels Biomass and Biofuels Find More Like This Return to Search Using Rhodobacter Bacteria to Express Membrane Proteins (ANL-IN-99-089) Argonne National Laboratory Contact ANL About This Technology <p> A strategy to express heterologous membrane proteins by using photosynthetic bacteria</p> A strategy to express heterologous membrane proteins by using photosynthetic bacteria Technology Marketing Summary Cell membranes serve as the

  1. DOE Seeks Public-Private Sector Expressions of Interest for Global Nuclear

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Energy Partnership Initiative | Department of Energy Public-Private Sector Expressions of Interest for Global Nuclear Energy Partnership Initiative DOE Seeks Public-Private Sector Expressions of Interest for Global Nuclear Energy Partnership Initiative March 17, 2006 - 3:46pm Addthis WASHINGTON, DC - U.S. Secretary of Energy Samuel Bodman today announced that the Department of Energy (DOE) is seeking expressions of interest from the public and private sectors by March 31, 2006, to propose

  2. Compact perturbative expressions for neutrino oscillations in matter

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Denton, Peter B.; Minakata, Hisakazu; Parke, Stephen J.

    2016-06-08

    We further develop and extend a recent perturbative framework for neutrino oscillations in uniform matter density so that the resulting oscillation probabilities are accurate for the complete matter potential versus baseline divided by neutrino energy plane. This extension also gives the exact oscillation probabilities in vacuum for all values of baseline divided by neutrino energy. The expansion parameter used is related to the ratio of the solar to the atmosphericmore » $$\\Delta m^2$$ scales but with a unique choice of the atmospheric $$\\Delta m^2$$ such that certain first-order effects are taken into account in the zeroth-order Hamiltonian. Using a mixing matrix formulation, this framework has the exceptional feature that the neutrino oscillation probability in matter has the same structure as in vacuum, to all orders in the expansion parameter. It also contains all orders in the matter potential and $$\\sin\\theta_{13}$$. It facilitates immediate physical interpretation of the analytic results, and makes the expressions for the neutrino oscillation probabilities extremely compact and very accurate even at zeroth order in our perturbative expansion. Furthermore, the first and second order results are also given which improve the precision by approximately two or more orders of magnitude per perturbative order.« less

  3. Bio-Derived Liquids to Hydrogen Distributed Reforming Working Group (BILIWG) Kick-Off Meeting Proceedings Hilton Garden Inn-BWI,Baltimore, MD October 24, 2006

    Broader source: Energy.gov [DOE]

    Proceedings from the October 24, 2006 Bio-Derived Liquids to Hydrogen Distributed Reforming Working Group Kick-Off Meeting.

  4. Enhanced memory effect via quantum confinement in 16?nm InN nanoparticles embedded in ZnO charge trapping layer

    SciTech Connect (OSTI)

    El-Atab, Nazek; Nayfeh, Ammar; Cimen, Furkan; Alkis, Sabri; Orta, Blend; Alevli, Mustafa; Dietz, Nikolaus; Okyay, Ali K.

    2014-06-23

    In this work, the fabrication of charge trapping memory cells with laser-synthesized indium-nitride nanoparticles (InN-NPs) embedded in ZnO charge trapping layer is demonstrated. Atomic layer deposited Al{sub 2}O{sub 3} layers are used as tunnel and blocking oxides. The gate contacts are sputtered using a shadow mask which eliminates the need for any lithography steps. High frequency C-V{sub gate} measurements show that a memory effect is observed, due to the charging of the InN-NPs. With a low operating voltage of 4?V, the memory shows a noticeable threshold voltage (V{sub t}) shift of 2?V, which indicates that InN-NPs act as charge trapping centers. Without InN-NPs, the observed memory hysteresis is negligible. At higher programming voltages of 10?V, a memory window of 5?V is achieved and the V{sub t} shift direction indicates that electrons tunnel from channel to charge storage layer.

  5. High density growth of T7 expression strains with auto-induction option

    DOE Patents [OSTI]

    Studier, F. William

    2010-04-27

    Methods for promoting and suppressing auto-induction of transcription of cloned DNA in cultures of T7 expression strains are disclosed.

  6. Application for presidential permit OE Docket No. PP-362 Champlain Hudson Power Express Inc

    Office of Energy Efficiency and Renewable Energy (EERE)

    Application from Champlain Hudson Power Express Inc to construct, operate, and maintain electric transmission facilities at the U.S. - Canada Border.

  7. Calibration Model Assignments expressed as U3O8, Summary Table ES-1 |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy Model Assignments expressed as U3O8, Summary Table ES-1 Calibration Model Assignments expressed as U3O8, Summary Table ES-1 Calibration Model Assignments expressed as U3O8, Summary Table ES-1 Calibration Model Assignments expressed as U3O8, Summary Table ES-1 (25.9 KB) More Documents & Publications Field Calibration Facilities for Environmental Measurement of Radium, Thorium, and Potassium (October 2013) Offshore Wind Market and Economic Analysis Report 2013 Natural

  8. T cells stimulate catabolic gene expression by the stromal cells from giant cell tumor of bone

    SciTech Connect (OSTI)

    Cowan, Robert W.; Juravinski Cancer Centre, 699 Concession St., Hamilton, ON, Canada L8V 5C2 ; Ghert, Michelle; Department of Surgery, McMaster University, 1280 Main St. W., Hamilton, ON, Canada L8S 4L8 ; Singh, Gurmit; Juravinski Cancer Centre, 699 Concession St., Hamilton, ON, Canada L8V 5C2

    2012-03-23

    Highlights: Black-Right-Pointing-Pointer Two T cell lines stimulate PTHrP, RANKL, MMP13 gene expression in GCT cell cultures. Black-Right-Pointing-Pointer CD40 expressed by stromal cells; CD40L detected in whole tumor but not cultures. Black-Right-Pointing-Pointer Effect of CD40L treatment on GCT cells increased PTHrP and MMP13 gene expression. Black-Right-Pointing-Pointer PTHrP treatment increased MMP13 expression, while inhibition decreased expression. Black-Right-Pointing-Pointer T cells may stimulate GCT stromal cells and promote the osteolysis of the tumor. -- Abstract: The factors that promote the localized bone resorption by giant cell tumor of bone (GCT) are not fully understood. We investigated whether T cells could contribute to bone resorption by stimulating expression of genes for parathyroid hormone-related protein (PTHrP), matrix metalloproteinase (MMP)-13, and the receptor activator of nuclear-factor {kappa}B ligand (RANKL). Two cell lines, Jurkat clone E6-1 and D1.1, were co-cultured with isolated GCT stromal cells. Real-time PCR analyses demonstrated a significant increase of all three genes following 48 h incubation, and PTHrP and MMP-13 gene expression was also increased at 24 h. Further, we examined the expression of CD40 ligand (CD40L), a protein expressed by activated T cells, and its receptor, CD40, in GCT. Immunohistochemistry results revealed expression of the CD40 receptor in both the stromal cells and giant cells of the tumor. RNA collected from whole GCT tissues showed expression of CD40LG, which was absent in cultured stromal cells, and suggests that CD40L is expressed within GCT. Stimulation of GCT stromal cells with CD40L significantly increased expression of the PTHrP and MMP-13 genes. Moreover, we show that inhibition of PTHrP with neutralizing antibodies significantly decreased MMP13 expression by the stromal cells compared to IgG-matched controls, whereas stimulation with PTHrP (1-34) increased MMP-13 gene expression. These

  9. Weatherization and Intergovernmental Program Success Stories...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    can improve the holidays by reducing energy and maintenance costs, thanks to its new LED holiday lights. Learn more. December 16, 2011 Cows like these in Skagit County,...

  10. Fermilab Office of General Counsel - Ethics Program - Ask the...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Ask the Ethicist Questions & Answers Submit a Question Annual Reminders Reporting Fraud Holiday Parties Holidays and contractor gratuities From Fermilab Today, December 18,...

  11. Seismic expressions of Monterey Formation diagenesis: examples from offshore California

    SciTech Connect (OSTI)

    Roy, M.B.

    1988-03-01

    Diagenesis of the diatomaceous rocks in the Monterey Formation in California coastal and offshore basins involves changes from amorphous biogenic silica to a stable crystalline quartz facies. In the intermediate stage, the transformation undergoes passage from the Opal-A to the Opal-CT phase. Associated with this diagenetic process is a marked increase in bulk densities between the different silica phases, owing to loss of porosity from compaction and solution recrystallization caused by increase in burial load and other physical factors. The sharp density contrast between the silica phases is manifested by an acoustic impedance boundary that may be expressed on seismic records. This seismic event can be distinct and independent of structural configuration, and in many places cuts through stratigraphic boundaries. Several examples of seismic records from offshore California demonstrate the diagenetically caused reflection cutting through Monterey and post-Monterey formations. Current and future exploration efforts in offshore California will continue to center on the widespread Monterey Formation. In addition to being the main source rock, the Monterey is also the reservoir rock. Recent discoveries indicate that oil production is mainly from the highly permeable, fractured, silica-rich sections. It is therefore important to recognize the diagenetic boundaries on seismic records and to delineate the more brittle quartz-rich facies where the reservoir quality is expected to be better than the intermediate Opal-A or Opal-CT facies. Furthermore, these boundaries could also provide good diagenetic traps off the flanks of structures where updip unaltered impermeable rocks hinder fluid migration.

  12. Transcriptomic analysis in the developing zebrafish embryo after compound exposure: Individual gene expression and pathway regulation

    SciTech Connect (OSTI)

    Hermsen, Sanne A.B.; Pronk, Tessa E.; Brandhof, Evert-Jan van den; Ven, Leo T.M. van der; Piersma, Aldert H.

    2013-10-01

    The zebrafish embryotoxicity test is a promising alternative assay for developmental toxicity. Classically, morphological assessment of the embryos is applied to evaluate the effects of compound exposure. However, by applying differential gene expression analysis the sensitivity and predictability of the test may be increased. For defining gene expression signatures of developmental toxicity, we explored the possibility of using gene expression signatures of compound exposures based on commonly expressed individual genes as well as based on regulated gene pathways. Four developmental toxic compounds were tested in concentration-response design, caffeine, carbamazepine, retinoic acid and valproic acid, and two non-embryotoxic compounds, D-mannitol and saccharin, were included. With transcriptomic analyses we were able to identify commonly expressed genes, which were mostly development related, after exposure to the embryotoxicants. We also identified gene pathways regulated by the embryotoxicants, suggestive of their modes of action. Furthermore, whereas pathways may be regulated by all compounds, individual gene expression within these pathways can differ for each compound. Overall, the present study suggests that the use of individual gene expression signatures as well as pathway regulation may be useful starting points for defining gene biomarkers for predicting embryotoxicity. - Highlights: • The zebrafish embryotoxicity test in combination with transcriptomics was used. • We explored two approaches of defining gene biomarkers for developmental toxicity. • Four compounds in concentration-response design were tested. • We identified commonly expressed individual genes as well as regulated gene pathways. • Both approaches seem suitable starting points for defining gene biomarkers.

  13. Cul4A overexpression associated with Gli1 expression in malignant pleural mesothelioma

    SciTech Connect (OSTI)

    Yang, Yi -Lin; Ni, Jian; Hsu, Ping -Chih; Mao, Jian -Hua; Hsieh, David; Xu, Angela; Chan, Geraldine; Au, Alfred; Xu, Zhidong; Jablons, David M.; You, Liang

    2015-07-27

    Malignant pleural mesothelioma (mesothelioma) is a highly aggressive cancer without an effective treatment. Cul4A, a scaffold protein that recruits substrates for degradation, is amplified in several human cancers, including mesothelioma. We have recently shown that Cul4A plays an oncogenic role in vitro and in a mouse model. In this study, we analysed clinical mesothelioma tumours and found moderate to strong expression of Cul4A in 70.9% (51/72) of these tumours, as shown by immunohistochemistry. In 72.2% mesothelioma tumours with increased Cul4A copy number identified by fluorescence in situ hybridization analysis, Cul4A protein expression was moderate to strong. Similarly, Cul4A was overexpressed and Cul4A copy number was increased in human mesothelioma cell lines. Because Gli1 is highly expressed in human mesothelioma cells, we compared Cul4A and Gli1 expression in mesothelioma tumours and found their expression associated (P < 0.05, chi-square). In mesothelioma cell lines, inhibiting Cul4A by siRNA decreased Gli1 expression, suggesting that Gli1 expression is, at least in part, regulated by Cul4A in mesothelioma cells. Our results suggest a linkage between Cul4A and Gli1 expression in human mesothelioma.

  14. Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

    SciTech Connect (OSTI)

    Dey, Siddharth S.; Foley, Jonathan E.; Limsirichai, Prajit; Schaffer, David V.; Arkin, Adam P.

    2015-05-05

    While gene expression noise has been shown to drive dramatic phenotypic variations, the molecular basis for this variability in mammalian systems is not well understood. Gene expression has been shown to be regulated by promoter architecture and the associated chromatin environment. However, the exact contribution of these two factors in regulating expression noise has not been explored. Using a dual-reporter lentiviral model system, we deconvolved the influence of the promoter sequence to systematically study the contribution of the chromatin environment at different genomic locations in regulating expression noise. By integrating a large-scale analysis to quantify mRNA levels by smFISH and protein levels by flow cytometry in single cells, we found that mean expression and noise are uncorrelated across genomic locations. Furthermore, we showed that this independence could be explained by the orthogonal control of mean expression by the transcript burst size and noise by the burst frequency. Finally, we showed that genomic locations displaying higher expression noise are associated with more repressed chromatin, thereby indicating the contribution of the chromatin environment in regulating expression noise.

  15. Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Dey, Siddharth S.; Foley, Jonathan E.; Limsirichai, Prajit; Schaffer, David V.; Arkin, Adam P.

    2015-05-05

    While gene expression noise has been shown to drive dramatic phenotypic variations, the molecular basis for this variability in mammalian systems is not well understood. Gene expression has been shown to be regulated by promoter architecture and the associated chromatin environment. However, the exact contribution of these two factors in regulating expression noise has not been explored. Using a dual-reporter lentiviral model system, we deconvolved the influence of the promoter sequence to systematically study the contribution of the chromatin environment at different genomic locations in regulating expression noise. By integrating a large-scale analysis to quantify mRNA levels by smFISH andmore » protein levels by flow cytometry in single cells, we found that mean expression and noise are uncorrelated across genomic locations. Furthermore, we showed that this independence could be explained by the orthogonal control of mean expression by the transcript burst size and noise by the burst frequency. Finally, we showed that genomic locations displaying higher expression noise are associated with more repressed chromatin, thereby indicating the contribution of the chromatin environment in regulating expression noise.« less

  16. Cul4A overexpression associated with Gli1 expression in malignant pleural mesothelioma

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Yang, Yi -Lin; Ni, Jian; Hsu, Ping -Chih; Mao, Jian -Hua; Hsieh, David; Xu, Angela; Chan, Geraldine; Au, Alfred; Xu, Zhidong; Jablons, David M.; et al

    2015-07-27

    Malignant pleural mesothelioma (mesothelioma) is a highly aggressive cancer without an effective treatment. Cul4A, a scaffold protein that recruits substrates for degradation, is amplified in several human cancers, including mesothelioma. We have recently shown that Cul4A plays an oncogenic role in vitro and in a mouse model. In this study, we analysed clinical mesothelioma tumours and found moderate to strong expression of Cul4A in 70.9% (51/72) of these tumours, as shown by immunohistochemistry. In 72.2% mesothelioma tumours with increased Cul4A copy number identified by fluorescence in situ hybridization analysis, Cul4A protein expression was moderate to strong. Similarly, Cul4A was overexpressedmore » and Cul4A copy number was increased in human mesothelioma cell lines. Because Gli1 is highly expressed in human mesothelioma cells, we compared Cul4A and Gli1 expression in mesothelioma tumours and found their expression associated (P < 0.05, chi-square). In mesothelioma cell lines, inhibiting Cul4A by siRNA decreased Gli1 expression, suggesting that Gli1 expression is, at least in part, regulated by Cul4A in mesothelioma cells. Our results suggest a linkage between Cul4A and Gli1 expression in human mesothelioma.« less

  17. Interleukin-2 (IL-2) dependent expression of biologically relevant IL-2 receptors: uncoupling of anti-T3 induced receptor expression with cyclosporin

    SciTech Connect (OSTI)

    Gitter, A.B.D.; Labus, J.M.; Butler, L.D.

    1986-03-01

    Human peripheral blood T cell expression of IL-2 receptors (IL-2R), detected by both immunocytofluorometry and /sup 125/I-IL-2 binding, was studied using lymphocytes stimulated with monoclonal anti-T3 antibodies (Leu-4, OKT3). Lymphocytes, isolated from healthy individuals, were prescreened and classified as Leu-4 responders or non-responders according to 72 h /sup 3/H-thymidine incorporation experiments. Leu-4 non-responder lymphocytes, though capable of normal IL-2R expression and IL-2 secretion when cultured with OKT3 (IgG2a), expressed little to no IL-2R nor secreted IL-2 when stimulated with Leu-4 (IgG1). In addition, the amount of IL-2 secreted by Leu-4 stimulated, Leu-4 responder cells, was one-third- to one-fifth of that detected when OKT3 was used as the stimulant. The addition of recombinant IL-2 (rIL-2) to a Leu-4 stimulated, Leu-4 non-responder lymphocyte culture, resulted in the expression of IL-2R and cellular proliferation, indicating that IL-2 upregulated its biologically relevant receptor. As expected, cyclosporin-A (CSA) inhibited the secretion of IL-2 and subsequent proliferation of Leu-4 stimulated, Leu-4 responder cells. Unexpectedly, however, the expression of IL-2R was also blocked. Exogenous rIL-2 partially reversed the effect of CSA on IL-2R expression and proliferation. The results indicate that IL-2 may provide an additional, required signal for optimal IL-2R expression.

  18. SPARCL1 Expression Increases With Preoperative Radiation Therapy and Predicts Better Survival in Rectal Cancer Patients

    SciTech Connect (OSTI)

    Kotti, Angeliki Holmqvist, Annica; Albertsson, Maria; Sun, Xiao-Feng

    2014-04-01

    Purpose: The secreted protein acidic and rich in cysteine-like 1 (SPARCL1) is expressed in various normal tissues and many types of cancers. The function of SPARCL1 and its relationship to a patient's prognosis have been studied, whereas its relationship to radiation therapy (RT) is not known. Our aim was to investigate the expression of SPARCL1 in rectal cancer patients who participated in a clinical trial of preoperative RT. Methods and Materials: The study included 136 rectal cancer patients who were randomized to undergo preoperative RT and surgery (n=63) or surgery alone (n=73). The expression levels of SPARCL1 in normal mucosa (n=29), primary tumor (n=136), and lymph node metastasis (n=35) were determined by immunohistochemistry. Results: Tumors with RT had stronger SPARCL1 expression than tumors without RT (P=.003). In the RT group, strong SPARCL1 expression was related to better survival than weak expression in patients with stage III tumors, independent of sex, age, differentiation, and margin status (P=.022; RR = 18.128; 95% confidence interval, 1.512-217.413). No such relationship was found in the non-RT group (P=.224). Further analysis of interactions among SPARCL1 expression, RT, and survival showed statistical significance (P=.024). In patients with metastases who received RT, strong SPARCL1 expression was related to better survival compared to weak expression (P=.041) but not in the non-RT group (P=.569). Conclusions: SPARCL1 expression increases with RT and is related to better prognosis in rectal cancer patients with RT but not in patients without RT. This result may help us to select the patients best suited for preoperative RT.

  19. Sodium arsenite represses the expression of myogenin in C2C12 mouse myoblast cells through histone modifications and altered expression of Ezh2, Glp, and Igf-1

    SciTech Connect (OSTI)

    Hong, Gia-Ming; Present address: The University of Chicago, Section of Hematology Bain, Lisa J.

    2012-05-01

    Arsenic is a toxicant commonly found in water systems and chronic exposure can result in adverse developmental effects including increased neonatal death, stillbirths, and miscarriages, low birth weight, and altered locomotor activity. Previous studies indicate that 20 nM sodium arsenite exposure to C2C12 mouse myocyte cells delayed myoblast differentiation due to reduced myogenin expression, the transcription factor that differentiates myoblasts into myotubes. In this study, several mechanisms by which arsenic could alter myogenin expression were examined. Exposing differentiating C2C12 cells to 20 nM arsenic increased H3K9 dimethylation (H3K9me2) and H3K9 trimethylation (H3K9me3) by 3-fold near the transcription start site of myogenin, which is indicative of increased repressive marks, and reduced H3K9 acetylation (H3K9Ac) by 0.5-fold, indicative of reduced permissive marks. Protein expression of Glp or Ehmt1, a H3-K9 methyltransferase, was also increased by 1.6-fold in arsenic-exposed cells. In addition to the altered histone remodeling status on the myogenin promoter, protein and mRNA levels of Igf-1, a myogenic growth factor, were significantly repressed by arsenic exposure. Moreover, a 2-fold induction of Ezh2 expression, and an increased recruitment of Ezh2 (3.3-fold) and Dnmt3a (? 2-fold) to the myogenin promoter at the transcription start site (? 40 to + 42), were detected in the arsenic-treated cells. Together, we conclude that the repressed myogenin expression in arsenic-exposed C2C12 cells was likely due to a combination of reduced expression of Igf-1, enhanced nuclear expression and promoter recruitment of Ezh2, and altered histone remodeling status on myogenin promoter (? 40 to + 42). -- Highlights: ? Igf-1 expression is decreased in C2C12 cells after 20 nM arsenite exposure. ? Arsenic exposure alters histone remodeling on the myogenin promoter. ? Glp expression, a H3K9 methyltransferase, was increased in arsenic-exposed cells. ? Ezh2 and Dnmt3a

  20. Sex-based differences in gene expression in hippocampus following postnatal lead exposure

    SciTech Connect (OSTI)

    Schneider, J.S. Anderson, D.W.; Sonnenahalli, H.; Vadigepalli, R.

    2011-10-15

    The influence of sex as an effect modifier of childhood lead poisoning has received little systematic attention. Considering the paucity of information available concerning the interactive effects of lead and sex on the brain, the current study examined the interactive effects of lead and sex on gene expression patterns in the hippocampus, a structure involved in learning and memory. Male or female rats were fed either 1500 ppm lead-containing chow or control chow for 30 days beginning at weaning.Blood lead levels were 26.7 {+-} 2.1 {mu}g/dl and 27.1 {+-} 1.7 {mu}g/dl for females and males, respectively. The expression of 175 unique genes was differentially regulated between control male and female rats. A total of 167 unique genes were differentially expressed in response to lead in either males or females. Lead exposure had a significant effect without a significant difference between male and female responses in 77 of these genes. In another set of 71 genes, there were significant differences in male vs. female response. A third set of 30 genes was differentially expressed in opposite directions in males vs. females, with the majority of genes expressed at a lower level in females than in males. Highly differentially expressed genes in males and females following lead exposure were associated with diverse biological pathways and functions. These results show that a brief exposure to lead produced significant changes in expression of a variety of genes in the hippocampus and that the response of the brain to a given lead exposure may vary depending on sex. - Highlights: > Postnatal lead exposure has a significant effect on hippocampal gene expression patterns. > At least one set of genes was affected in opposite directions in males and females. > Differentially expressed genes were associated with diverse biological pathways.

  1. Differential expression of nanog1 and nanogp8 in colon cancer cells

    SciTech Connect (OSTI)

    Ishiguro, Tatsuya; Sato, Ai; Ohata, Hirokazu; Sakai, Hiroaki; Nakagama, Hitoshi; Okamoto, Koji

    2012-02-10

    Highlights: Black-Right-Pointing-Pointer Nanog is expressed in a majority of colon cancer cell lines examined. Black-Right-Pointing-Pointer Both nanog1 and nanogp8 are expressed in colon cancer cells with varying ratios. Black-Right-Pointing-Pointer Nanog mediates cell proliferation of colon cancer cells. Black-Right-Pointing-Pointer Nanog predominantly localizes in cytoplasm of colon cancer cells. -- Abstract: Nanog, a homeodomain transcription factor, is an essential regulator for promotion of self-renewal of embryonic stem cells and inhibition of their differentiation. It has been demonstrated that nanog1 as well as nanogp8, a retrogene of nanog1, is preferentially expressed in advanced stages of several types of cancer, suggesting their involvement during cancer progression. Here, we investigated the expression of Nanog in well-characterized colon cancer cell lines. Expression of Nanog was detectable in 5 (HCT116, HT29, RKO, SW48, SW620) out of seven cell lines examined. RNA expression analyses of nanog1 and nanogp8 indicated that, while nanog1 was a major form in SW620 as well as in teratoma cells Tera-2, nanogp8 was preferentially expressed in HT29 and HCT116. In accordance with this, shRNA-mediated knockdown of nanog1 caused the reduction of Nanog in SW620 but not in HT29. Inhibition of Nanog in SW620 cells negatively affected cell proliferation and tumor formation in mouse xenograft. Biochemical subcellular fractionation and immunostaining analyses revealed predominant localization of Nanog in cytoplasm in SW620 and HT29, while it was mainly localized in nucleus in Tera-2. Our data indicate that nanog1 and nanogp8 are differentially expressed in colon cancer cells, and suggest that their expression contributes to proliferation of colon cancer cells.

  2. Redox Protein Expression Predicts Radiotherapeutic Response in Early-Stage Invasive Breast Cancer Patients

    SciTech Connect (OSTI)

    Woolston, Caroline M.; Al-Attar, Ahmad; Storr, Sarah J.; Ellis, Ian O.; Morgan, David A.L.; Martin, Stewart G.

    2011-04-01

    Purpose: Early-stage invasive breast cancer patients have commonly undergone breast-conserving surgery and radiotherapy. In a large majority of these patients, the treatment is effective; however, a proportion will develop local recurrence. Deregulated redox systems provide cancer cells protection from increased oxidative stress, such as that induced by ionizing radiation. Therefore, the expression of redox proteins was examined in tumor specimens from this defined cohort to determine whether such expression could predict response. Methods and Materials: The nuclear and cytoplasmic expression of nine redox proteins (glutathione, glutathione reductase, glutaredoxin, glutathione peroxidase 1, 3, and 4, and glutathione S-transferase-{theta}, -{pi}, and -{alpha}) was assessed using conventional immunohistochemistry on a tissue microarray of 224 tumors. Results: A high cytoplasmic expression of glutathione S-transferase-{theta} significantly correlated with a greater risk of local recurrence (p = .008) and, when combined with a low nuclear expression (p = .009), became an independent predictive factor (p = .002) for local recurrence. High cytoplasmic expression of glutathione S-transferase-{theta} also correlated with a worse overall survival (p = .009). Low nuclear and cytoplasmic expression of glutathione peroxidase 3 (p = .002) correlated with a greater risk of local recurrence and was an independent predictive factor (p = .005). These proteins did not correlate with tumor grade, suggesting their function might be specific to the regulation of oxidative stress rather than alterations of tumor phenotype. Only nuclear (p = .005) and cytoplasmic (p = .001) expression of glutathione peroxidase 4 correlated with the tumor grade. Conclusions: Our results support the use of redox protein expression, namely glutathione S-transferase-{theta} and glutathione peroxidase 3, to predict the response to radiotherapy in early-stage breast cancer patients. If incorporated into

  3. RNA binding protein and binding site useful for expression of recombinant molecules

    DOE Patents [OSTI]

    Mayfield, Stephen P.

    2006-10-17

    The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

  4. RNA binding protein and binding site useful for expression of recombinant molecules

    DOE Patents [OSTI]

    Mayfield, Stephen

    2000-01-01

    The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

  5. Ethanol increases matrix metalloproteinase-12 expression via NADPH oxidase-dependent ROS production in macrophages

    SciTech Connect (OSTI)

    Kim, Mi Jin; Nepal, Saroj; Lee, Eung-Seok; Jeong, Tae Cheon; Kim, Sang-Hyun; Park, Pil-Hoon

    2013-11-15

    Matrix metalloproteinase-12 (MMP-12), an enzyme responsible for degradation of extracellular matrix, plays an important role in the progression of various diseases, including inflammation and fibrosis. Although most of those are pathogenic conditions induced by ethanol ingestion, the effect of ethanol on MMP-12 has not been explored. In the present study, we investigated the effect of ethanol on MMP-12 expression and its potential mechanisms in macrophages. Here, we demonstrated that ethanol treatment increased MMP-12 expression in primary murine peritoneal macrophages and RAW 264.7 macrophages at both mRNA and protein levels. Ethanol treatment also significantly increased the activity of nicotinamide adenine dinucleotide (NADPH) oxidase and the expression of NADPH oxidase-2 (Nox2). Pretreatment with an anti-oxidant (N-acetyl cysteine) or a selective inhibitor of NADPH oxidase (diphenyleneiodonium chloride (DPI)) prevented ethanol-induced MMP-12 expression. Furthermore, knockdown of Nox2 by small interfering RNA (siRNA) prevented ethanol-induced ROS production and MMP-12 expression in RAW 264.7 macrophages, indicating a critical role for Nox2 in ethanol-induced intracellular ROS production and MMP-12 expression in macrophages. We also showed that ethanol-induced Nox2 expression was suppressed by transient transfection with dominant negative IκB-α plasmid or pretreatment with Bay 11-7082, a selective inhibitor of NF-κB, in RAW 264.7 macrophages. In addition, ethanol-induced Nox2 expression was also attenuated by treatment with a selective inhibitor of p38 MAPK, suggesting involvement of p38 MAPK/NF-κB pathway in ethanol-induced Nox2 expression. Taken together, these results demonstrate that ethanol treatment elicited increase in MMP-12 expression via increase in ROS production derived from Nox2 in macrophages. - Highlights: • Ethanol increases ROS production through up-regulation of Nox2 in macrophages. • Enhanced oxidative stress contributes to ethanol

  6. EERE Success Story-Chicago Solar Express Reduces Costs, Wait Times |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy Chicago Solar Express Reduces Costs, Wait Times EERE Success Story-Chicago Solar Express Reduces Costs, Wait Times October 28, 2014 - 10:48am Addthis The Solar Express program in Chicago, Illinois-funded through a SunShot Initiative Rooftop Solar Challenge (RSC) I award of $750,000-is making it faster, easier, and cheaper for residents to go solar by cutting long wait times and fees for solar permits. Residents of Chicago can now acquire permits for their residential

  7. U-116: IBM Tivoli Provisioning Manager Express for Software Distribution Multiple Vulnerabilities

    Broader source: Energy.gov [DOE]

    Multiple vulnerabilities have been reported in IBM Tivoli Provisioning Manager Express for Software Distribution, which can be exploited by malicious people to conduct SQL injection attacks and compromise a user's system

  8. Isolated yeast promoter sequence and a method of regulated heterologous expression

    DOE Patents [OSTI]

    Gao, Johnway; Skeen, Rodney S.; Hooker, Brian S.; Anderson, Daniel B.

    2005-05-31

    The present invention provides the promoter clone discovery of a glucoamylase gene of a starch utilizing yeast strain Schwanniomyces castellii. The isolated glucoamylase promoter is an inducible promoter, which can regulate strong gene expression in starch culture medium.

  9. Uncertainty Estimation of Radiometric Data using a Guide to the Expression of Uncertainty in Measurement (GUM) Method

    SciTech Connect (OSTI)

    Habte, Aron

    2015-06-25

    This presentation summarizes uncertainty estimation of radiometric data using the Guide to the Expression of Uncertainty (GUM) method.

  10. Radiation-Induced Micro-RNA Expression Changes in Peripheral Blood Cells of Radiotherapy Patients

    SciTech Connect (OSTI)

    Templin, Thomas; Paul, Sunirmal; Amundson, Sally A.; Young, Erik F.; Barker, Christopher A.; Wolden, Suzanne L.; Smilenov, Lubomir B.

    2011-06-01

    Purpose: MicroRNAs (miRNAs), a class of noncoding small RNAs that regulate gene expression, are involved in numerous physiologic processes in normal and malignant cells. Our in vivo study measured miRNA and gene expression changes in human blood cells in response to ionizing radiation, to develop miRNA signatures that can be used as biomarkers for radiation exposure. Methods and Materials: Blood from 8 radiotherapy patients in complete remission 1 or 2 was collected immediately before and 4 hours after total body irradiation with 1.25 Gy x-rays. Both miRNA and gene expression changes were measured by means of quantitative polymerase chain reaction and microarray hybridization, respectively. Hierarchic clustering, multidimensional scaling, class prediction, and gene ontology analysis were performed to investigate the potential of miRNAs to serve as radiation biomarkers and to elucidate their likely physiologic roles in the radiation response. Results: The expression levels of 45 miRNAs were statistically significantly upregulated 4 hours after irradiation with 1.25 Gy x-rays, 27 of them in every patient. Nonirradiated and irradiated samples form separate clusters in hierarchic clustering and multidimensional scaling. Out of 223 differentially expressed genes, 37 were both downregulated and predicted targets of the upregulated miRNAs. Paired and unpaired miRNA-based classifiers that we developed can predict the class membership of a sample with unknown irradiation status, with accuracies of 100% when all 45 upregulated miRNAs are included. Both miRNA control of and gene involvement in biologic processes such as hemopoiesis and the immune response are increased after irradiation, whereas metabolic processes are underrepresented among all differentially expressed genes and the genes controlled by miRNAs. Conclusions: Exposure to ionizing radiation leads to the upregulation of the expression of a considerable proportion of the human miRNAome of peripheral blood cells

  11. P70S6K 1 regulation of angiogenesis through VEGF and HIF-1{alpha} expression

    SciTech Connect (OSTI)

    Bian, Chuan-Xiu; Shi, Zhumei; Meng, Qiao; Jiang, Yue; Liu, Ling-Zhi; Jiang, Bing-Hua; Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107

    2010-07-30

    Research highlights: {yields} P70S6K1 regulates VEGF expression; {yields} P70S6K1 induces transcriptional activation through HIF-1{alpha} binding site; {yields} P70S6K1 regulates HIF-1{alpha}, but not HIF-1{beta} protein expression; {yields} P70S6K1 mediates tumor growth and angiogenesis through HIF-1{alpha} and VEGF expression. -- Abstract: The 70 kDa ribosomal S6 kinase 1 (p70S6K1), a downstream target of phosphoinositide 3-kinase (PI3K) and ERK mitogen-activated protein kinase (MAPK), is an important regulator of cell cycle progression, and cell proliferation. Recent studies indicated an important role of p70S6K1 in PTEN-negative and AKT-overexpressing tumors. However, the mechanism of p70S6K1 in tumor angiogenesis remains to be elucidated. In this study, we specifically inhibited p70S6K1 activity in ovarian cancer cells using vector-based small interfering RNA (siRNA) against p70S6K1. We found that knockdown of p70S6K1 significantly decreased VEGF protein expression and VEGF transcriptional activation through the HIF-1{alpha} binding site at its enhancer region. The expression of p70S6K1 siRNA specifically inhibited HIF-1{alpha}, but not HIF-1{beta} protein expression. We also found that p70S6K1 down-regulation inhibited ovarian tumor growth and angiogenesis, and decreased cell proliferation and levels of VEGF and HIF-1{alpha} expression in tumor tissues. Our results suggest that p70S6K1 is required for tumor growth and angiogenesis through HIF-1{alpha} and VEGF expression, providing a molecular mechanism of human ovarian cancer mediated by p70S6K1 signaling.

  12. ADAM15 expression is downregulated in melanoma metastasis compared to primary melanoma

    SciTech Connect (OSTI)

    Ungerer, Christopher; Doberstein, Kai; Boehm, Beate; Pfeilschifter, Josef; Mihic-Probst, Daniela; Gutwein, Paul

    2010-10-22

    Research highlights: {yields} Strong ADAM15 expression is found in normal melanocytes. {yields} ADAM15 expression is significantly downregulated in patients with melanoma metastasis. {yields} TGF-{beta} can downregulate ADAM15 expression in melanoma cells. {yields} Overexpression of ADAM15 in melanoma cells inhibits migration, proliferation and invasion of melanoma cells. {yields} Conclusion: ADAM15 represents an tumor suppressor protein in melanoma. -- Abstract: In a mouse melanoma metastasis model it has been recently shown that ADAM15 overexpression in melanoma cells significantly reduced the number of metastatic nodules on the lung. Unfortunately, the expression of ADAM15 in human melanoma tissue has not been determined so far. In our study, we characterized the expression of ADAM15 in tissue micro-arrays of patients with primary melanoma with melanoma metastasis. ADAM15 was expressed in melanocytes and endothelial cells of benign nevi and melanoma tissue. Importantly, ADAM15 was significantly downregulated in melanoma metastasis compared to primary melanoma. We further demonstrate that IFN-{gamma} and TGF-{beta} downregulate ADAM15 protein levels in melanoma cells. To investigate the role of ADAM15 in melanoma progression, we overexpressed ADAM15 in melanoma cells. Importantly, overexpression of ADAM15 in melanoma cells reduced the migration, invasion and the anchorage dependent and independent cell growth of melanoma cells. In summary, the downregulation of ADAM15 plays an important role in melanoma progression and ADAM15 act as a tumorsuppressor in melanoma.

  13. Temporal Changes in Gene Expression in Rainbow Trout Exposed to Ethynyl Estradiol

    SciTech Connect (OSTI)

    Hook, Sharon E.; Skillman, Ann D.; Small, Jack A.; Schultz, Irv R.

    2006-11-25

    We examined changes in the genomic response during continuous exposure to the xenoestrogen ethynylestradiol. Isogenic rainbow trout Onorhyncus mykiss were exposed to nominal concentrations of 100 ng/L ethynyl estradiol (EE2) for a period 3 weeks. At fixed time points within the exposure fish were euthanized, livers harvested and RNA extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Salmonid array (GRASP project, University of Victoria) spotted with 16,000 cDNA's. The slides were scanned to measure abundance of a given transcript in each sample relative to controls. Data were analyzed via Genespring (Silicon Genetics) to identify a list of up and down regulated genes, and to determine gene clustering patterns that can be used as ''expression signatures''. Gene ontology was determined using the annotation available from the GRASP website. Our analysis indicates each exposure time period generated specific gene expression profiles. Changes in gene expression were best understood by grouping genes by their gene expression profiles rather than examining fold change at a particular time point. Many of the genes commonly used as biomarkers of exposure to xenoestrogens were not induced initially and did not have gene expression profiles typical of the majority of genes with altered expression.

  14. Knockdown of p53 suppresses Nanog expression in embryonic stem cells

    SciTech Connect (OSTI)

    Abdelalim, Essam Mohamed; Tooyama, Ikuo

    2014-01-10

    Highlights: We investigate the role of p53 in ESCs in the absence of DNA damage. p53 knockdown suppresses ESC proliferation. p53 knockdown downregulates Nanog expression. p53 is essential for mouse ESC self-renewal. -- Abstract: Mouse embryonic stem cells (ESCs) express high levels of cytoplasmic p53. Exposure of mouse ESCs to DNA damage leads to activation of p53, inducing Nanog suppression. In contrast to earlier studies, we recently reported that chemical inhibition of p53 suppresses ESC proliferation. Here, we confirm that p53 signaling is involved in the maintenance of mouse ESC self-renewal. RNA interference-mediated knockdown of p53 induced downregulation of p21 and defects in ESC proliferation. Furthermore, p53 knockdown resulted in a significant downregulation in Nanog expression at 24 and 48 h post-transfection. p53 knockdown also caused a reduction in Oct4 expression at 48 h post-transfection. Conversely, exposure of ESCs to DNA damage caused a higher reduction of Nanog expression in control siRNA-treated cells than in p53 siRNA-treated cells. These data show that in the absence of DNA damage, p53 is required for the maintenance of mouse ESC self-renewal by regulating Nanog expression.

  15. Enhanced human papillomavirus type 8 oncogene expression levels are crucial for skin tumorigenesis in transgenic mice

    SciTech Connect (OSTI)

    Hufbauer, M.; Lazic, D.; Akguel, B.; Brandsma, J.L.; Pfister, H.; Weissenborn, S.J.

    2010-08-01

    Human papillomavirus 8 (HPV8) is involved in skin cancer development in epidermodysplasia verruciformis patients. Transgenic mice expressing HPV8 early genes (HPV8-CER) developed papillomas, dysplasias and squamous cell carcinomas. UVA/B-irradiation and mechanical wounding of HPV8-CER mouse skin led to prompt papilloma induction in about 3 weeks. The aim of this study was to analyze the kinetics and level of transgene expression in response to skin irritations. Transgene expression was already enhanced 1 to 2 days after UVA/B-irradiation or tape-stripping and maintained during papilloma development. The enhanced transgene expression could be assigned to UVB and not to UVA. Papilloma development was thus always paralleled by an increased transgene expression irrespective of the type of skin irritation. A knock-down of E6 mRNA by tattooing HPV8-E6-specific siRNA led to a delay and a lower incidence of papilloma development. This indicates that the early increase of viral oncogene expression is crucial for induction of papillomatosis.

  16. A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

    SciTech Connect (OSTI)

    Shakoor, N; Nair, R; Crasta, O; Morris, G; Feltus, A; Kresovich, S

    2014-01-23

    Background: Effective improvement in sorghum crop development necessitates a genomics-based approach to identify functional genes and QTLs. Sequenced in 2009, a comprehensive annotation of the sorghum genome and the development of functional genomics resources is key to enable the discovery and deployment of regulatory and metabolic genes and gene networks for crop improvement. Results: This study utilizes the first commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast, and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e. g., microRNAs), and confirmed functional small RNAs in related species (maize and sugarcane) were also included in our array design. We generated expression data for 78 samples with a combination of four different tissue types (shoot, root, leaf and stem), two dissected stem tissues (pith and rind) and six diverse genotypes, which included 6 public sorghum lines (R159, Atlas, Fremont, PI152611, AR2400 and PI455230) representing grain, sweet, forage, and high biomass ideotypes. Conclusions: Here we present a summary of the microarray dataset, including analysis of tissue-specific gene expression profiles and associated expression profiles of relevant metabolic pathways. With an aim to enable identification and functional characterization of genes in sorghum, this expression atlas presents a new and valuable resource to the research community.

  17. Proceedings of the 1996 spring technical conference of the ASME Internal Combustion Engine Division. Volume 2: Engine design and engine systems; ICE-Volume 26-2

    SciTech Connect (OSTI)

    Uzkan, T.

    1996-12-31

    Although the cost of the petroleum crude has not increased much within the last decade, the drive to develop internal combustion engines is still continuing. The basic motivation of this drive is to reduce both emissions and costs. Recent developments in computer chip production and information management technology have opened up new applications in engine controls and monitoring. The development of new information is continuing at a rapid pace. Some of these research and development results were presented at the 1996 Spring Technical Conference of the ASME Internal Combustion Engine Division in Youngstown, Ohio, April 21--24, 1996. The papers presented covered various aspects of the design, development, and application of compression ignition and spark ignition engines. The conference was held at the Holiday Inn Metroplex Complex and hosted by Altronic Incorporated of Girard, Ohio. The written papers submitted to the conference have been published in three conference volumes. Volume 2 includes the papers on the topics of engine design, engine systems, and engine user experience.

  18. Chemoresistance of CD133{sup +} colon cancer may be related with increased survivin expression

    SciTech Connect (OSTI)

    Lee, Mi-Ra; Ji, Sun-Young; Mia-Jan, Khalilullah; Cho, Mee-Yon

    2015-07-31

    CD133, putative cancer stem cell marker, deemed to aid chemoresistance. However, this claim has been challenged recently and we previously reported that patients with CD133{sup +} colon cancer have benefit from 5-fluorouracil (5-FU) chemotherapy incontrast to no benefit in patients with CD133{sup −} cancer. To elucidate the role of CD133 expression in chemoresistance, we silenced the CD133 expression in a colon cancer cell line and determined its effect on the biological characteristics downstream. We comparatively analyzed the sequential changes of MDR1, ABCG2, AKT1 and survivin expression and the result of proliferation assay (WST-1 assay) with 5-FU treatment in CD133{sup +} and siRNA-induced CD133{sup −} cells, derived from Caco-2 colon cancer cell line. 5-FU treatment induced significantly increase of the mRNA expression of MDR1, ABCG2 and AKT1genes, but not protein level. CD133 had little to no effect on the mRNA and protein expression of these genes. However, survivin expression at mRNA and protein level were significantly increased in CD133{sup +} cells compared with siRNA-induced CD133-cells and Mock (not sorted CD133{sup +} cells) at 96 h after siRNA transfection. The cytotoxicity assay demonstrated notable increase of chemoresistance to 5-FU treatment (10 μM) in CD133{sup +} cells at 96 h after siRNA transfection. From this study, we conclude that CD133{sup +} cells may have chemoresistance to 5-FU through the mechanism which is related with survivin expression, instead of MDR1, ABCG2 and AKT1 expression. Therefore a survivin inhibitor can be a new target for effective treatment of CD133{sup +} colon cancer. - Highlights: • We evaluate the role of CD133 in chemoresistance of colon cancer. • We compared the chemoresistance of CD133{sup +} cells and siRNA-induced CD133{sup −} cells. • CD133 had little to no effect on MDR1, ABCG2 and AKT1 expression. • Survivin expression and chemoresistance were increased in CD133{sup +} colon cancer cells.

  19. Gene expression patterns in Rainbow Trout, Oncorhynchus mykiss, exposed to a suite of model toxicants

    SciTech Connect (OSTI)

    Hook, Sharon E.; Skillman, Ann D.; Small, Jonathan A.; Schultz, Irv R.

    2006-05-25

    The increased availability and use of DNA microarrays has allowed the characterization of gene expression patterns associated with different toxicants. An important question is whether toxicant induced changes in gene expression in fish are sufficiently diverse to allow for identification of specific modes of action and/or specific contaminants. In theory, each class of toxicant may generate a gene expression profile unique to its mode of toxic action. We exposed isogenic (cloned) rainbow trout Oncorhyncus mykiss, to sublethal levels of a series of model toxicants with varying modes of action, including ethynylestradiol (xeno-estrogen), trenbolone (anabolic steroid; model androgen), 2,2,4,4´tetrabromodiphenyl ether (BDE-47, thyroid active), diquat (oxidant stressor), chromium VI, and benzo[a]pyrene (BaP) for a period of 1-3 weeks. Following exposure, fish were euthanized, livers harvested and RNA extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon / Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNA’s. The slides were scanned to measure abundance of a given transcript in each sample relative to controls. Data were analyzed via Genespring (Silicon Genetics) to identify a list of up and down regulated genes, as well as to determine gene clustering patterns that can be used as “expression signatures”. Our analysis indicates each toxicant generated specific gene expression profiles. Most genes exhibiting altered expression responded to only one of the toxicants. Relatively few genes are co-expressed in multiple treatments. For example, BaP and Diquat, both of which exert toxicity via oxidative stress, up-regulated 28 of the same genes, of over 100 genes altered by ether treatment. Other genes associated with steroidogenesis, p450 and estrogen responsive genes appear to be useful for selectively identifying toxicant mode of in fish, suggesting a link between gene expression

  20. JAZF1 can regulate the expression of lipid metabolic genes and inhibit lipid accumulation in adipocytes

    SciTech Connect (OSTI)

    Ming, Guang-feng; Xiao, Di; Gong, Wei-jing; Liu, Hui-xia; Liu, Jun; Zhou, Hong-hao; Liu, Zhao-qian

    2014-03-14

    Highlights: • JAZF1 was significantly upregulated during the differentiation of 3T3-L1 preadipocytes. • JAZF1 overexpression inhibited lipid accumulation in differentiated mature 3T3-L1 adipocytes. • JAZF1 overexpression inhibited the expression of SREBP1, ACC, and FAS. • JAZF1 overexpression upregulated the expression of HSL and ATGL. • SREBP1 and JAZF1 could regulate each other in adipocytes. - Abstract: JAZF1 is a newly identified gene with unknown functions. A recent genome-wide association study showed that JAZF1 is associated with type 2 diabetes and is highly expressed in liver and adipose tissue. Studies have demonstrated that JAZF1 is the co-repressor for nuclear orphan receptor TAK1, whereas most nuclear orphan receptor family members are involved in the regulation of lipid metabolism. Therefore, JAZF1 could be closely related to glycolipid metabolism. In this study, JAZF1 was significantly upregulated during the induced differentiation process of 3T3-L1 preadipocytes. The overexpression of JAZF1 inhibited lipid accumulation in differentiated mature 3T3-L1 adipocytes and significantly inhibited the expression of SREBPl, ACC, and FAS, which were important in lipid synthesis, while upregulating the expression of key enzyme hormone-sensitive lipase in lipoclasis. Moreover, SREBPl exhibited an inhibitory function on the expression of JAZF1. SREBP1 reversed the inhibitory action on lipid accumulation of JAZF1. SREBP1 and JAZF1 were observed to regulate each other in adipocytes. Therefore, JAZF1 could regulate the expression of particular genes related to lipid metabolism and inhibit lipid accumulation in adipocytes. This result suggests that JAZF1 may be a potential target for the treatment of diseases, such as obesity and lipid metabolism disorders.

  1. Prominin-2 expression increases protrusions, decreases caveolae and inhibits Cdc42 dependent fluid phase endocytosis

    SciTech Connect (OSTI)

    Singh, Raman Deep Schroeder, Andreas S.; Scheffer, Luana; Holicky, Eileen L.; Wheatley, Christine L.; Marks, David L. Pagano, Richard E.

    2013-05-10

    Highlights: Prominin-2 expression induced protrusions that co-localized with lipid raft markers. Prominin-2 expression decreased caveolae, caveolar endocytosis and increased pCav1. Prominin-2 expression inhibited fluid phase endocytosis by inactivation of Cdc42. These endocytic effects can be reversed by adding exogenous cholesterol. Caveolin1 knockdown restored fluid phase endocytosis in Prominin2 expressing cells. -- Abstract: Background: Membrane protrusions play important roles in biological processes such as cell adhesion, wound healing, migration, and sensing of the external environment. Cell protrusions are a subtype of membrane microdomains composed of cholesterol and sphingolipids, and can be disrupted by cholesterol depletion. Prominins are pentaspan membrane proteins that bind cholesterol and localize to plasma membrane (PM) protrusions. Prominin-1 is of great interest as a marker for stem and cancer cells, while Prominin-2 (Prom2) is reportedly restricted to epithelial cells. Aim: To characterize the effects of Prom-2 expression on PM microdomain organization. Methods: Prom2-fluorescent protein was transfected in human skin fibroblasts (HSF) and Chinese hamster ovary (CHO) cells for PM raft and endocytic studies. Caveolae at PM were visualized using transmission electron microscopy. Cdc42 activation was measured and caveolin-1 knockdown was performed using siRNAs. Results: Prom2 expression in HSF and CHO cells caused extensive Prom2-positive protrusions that co-localized with lipid raft markers. Prom2 expression significantly decreased caveolae at the PM, reduced caveolar endocytosis and increased caveolin-1 phosphorylation. Prom2 expression also inhibited Cdc42-dependent fluid phase endocytosis via decreased Cdc42 activation. Effects on endocytosis were reversed by addition of cholesterol. Knockdown of caveolin-1 by siRNA restored Cdc42 dependent fluid phase endocytosis in Prom2-expressing cells. Conclusions: Prom2 protrusions primarily localize

  2. Investigating the Correspondence Between Transcriptomic and Proteomic Expression Profiles Using Coupled Cluster Models.

    SciTech Connect (OSTI)

    Rogers, Simon; Girolami, Mark; Kolch, Walter; Waters, Katrina M.; Liu, Tao; Thrall, Brian D.; Wiley, H. S.

    2008-12-01

    Modern transcriptomics and proteomics enable us to survey the expression of RNAs and proteins at large scales. While these data are usually generated and analysed separately, there is an increasing interest in comparing and co-analysing transcriptome and proteome expression data. A major open question is whether transcriptome and proteome expression is linked and how it is coordinated. Results: Here we have developed a probabilistic clustering model that permits analysis of the links between transcriptomic and proteomic profiles in a sensible and flexible manner. Our coupled mixture model defines a prior probability distribution over the component to which a protein profile should be assigned conditioned on which component the associated mRNA profile belongs to. By providing probabilistic assignments this approach sits between the two extremes of concatenating the data on the assumption that mRNA and protein clusters would have a one-to-one relationship, and independent clustering where the mRNA profile provides no information on the protein profile and vice-versa. We apply this approach to a large dataset of quantitative transcriptomic and proteomic expression data obtained from a human breast epithelial cell line (HMEC) stimulated by epidermal growth factor (EGF) over a series of timepoints corresponding to one cell cycle. The results reveal a complex relationship between transcriptome and proteome with most mRNA clusters linked to at least two protein clusters, and vice versa. A more detailed analysis incorporating information on gene function from the gene ontology database shows that a high correlation of mRNA and protein expression is limited to the components of some molecular machines, such as the ribosome, cell adhesion complexes and the TCP-1 chaperonin involved in protein folding. Conclusions: The dynamic regulation of the transcriptome and proteome in mammalian cells in response to an acute mitogenic stimulus appears largely independent with very little

  3. Catalog of gene expression in adult neural stem cells and their in vivo microenvironment

    SciTech Connect (OSTI)

    Williams, Cecilia; Wirta, Valtteri; Meletis, Konstantinos; Wikstroem, Lilian; Carlsson, Leif; Frisen, Jonas; Lundeberg, Joakim . E-mail: joakim.lundeberg@biotech.kth.se

    2006-06-10

    Stem cells generally reside in a stem cell microenvironment, where cues for self-renewal and differentiation are present. However, the genetic program underlying stem cell proliferation and multipotency is poorly understood. Transcriptome analysis of stem cells and their in vivo microenvironment is one way of uncovering the unique stemness properties and provides a framework for the elucidation of stem cell function. Here, we characterize the gene expression profile of the in vivo neural stem cell microenvironment in the lateral ventricle wall of adult mouse brain and of in vitro proliferating neural stem cells. We have also analyzed an Lhx2-expressing hematopoietic-stem-cell-like cell line in order to define the transcriptome of a well-characterized and pure cell population with stem cell characteristics. We report the generation, assembly and annotation of 50,792 high-quality 5'-end expressed sequence tag sequences. We further describe a shared expression of 1065 transcripts by all three stem cell libraries and a large overlap with previously published gene expression signatures for neural stem/progenitor cells and other multipotent stem cells. The sequences and cDNA clones obtained within this framework provide a comprehensive resource for the analysis of genes in adult stem cells that can accelerate future stem cell research.

  4. Knowledge-based analysis of microarray gene expression data by using support vector machines

    SciTech Connect (OSTI)

    William Grundy; Manuel Ares, Jr.; David Haussler

    2001-06-18

    The authors introduce a method of functionally classifying genes by using gene expression data from DNA microarray hybridization experiments. The method is based on the theory of support vector machines (SVMs). SVMs are considered a supervised computer learning method because they exploit prior knowledge of gene function to identify unknown genes of similar function from expression data. SVMs avoid several problems associated with unsupervised clustering methods, such as hierarchical clustering and self-organizing maps. SVMs have many mathematical features that make them attractive for gene expression analysis, including their flexibility in choosing a similarity function, sparseness of solution when dealing with large data sets, the ability to handle large feature spaces, and the ability to identify outliers. They test several SVMs that use different similarity metrics, as well as some other supervised learning methods, and find that the SVMs best identify sets of genes with a common function using expression data. Finally, they use SVMs to predict functional roles for uncharacterized yeast ORFs based on their expression data.

  5. Performance Optimization of Tensor Contraction Expressions for Many Body Methods in Quantum Chemistry

    SciTech Connect (OSTI)

    Krishnamoorthy, Sriram; Bernholdt, David E; Pitzer, R. M.; Sadayappan, Ponnuswamy

    2009-01-01

    Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to significantly decrease the number of arithmetic operations required for evaluation of these expressions. The identification of common subexpressions among a set of tensor contraction expressions can result in a reduction of the total number of operations required to evaluate the tensor contractions. The first part of the paper describes an effective algorithm for operation minimization with common subexpression identification and demonstrates its effectiveness on tensor contraction expressions for coupled cluster equations. The second part of the paper highlights the importance of data layout transformation in the optimization of tensor contraction computations on modern processors. A number of considerations, such as minimization of cache misses and utilization of multimedia vector instructions, are discussed. A library for efficient index permutation of multidimensional tensors is described, and experimental performance data is provided that demonstrates its effectiveness.

  6. Performance Optimization of Tensor Contraction Expressions for Many Body Methods in Quantum Chemistry

    SciTech Connect (OSTI)

    Hartono, Albert; Lu, Qingda; henretty, thomas; Krishnamoorthy, Sriram; zhang, huaijian; Baumgartner, Gerald; Bernholdt, David E.; Nooijen, Marcel; Pitzer, Russell M.; Ramanujam, J.; Sadayappan, Ponnuswamy

    2009-11-12

    Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to significantly decrease the number of arithmetic operations required for evaluation of these expressions. The identification of common subexpressions among a set of tensor contraction expressions can result in a reduction of the total number of operations required to evaluate the tensor contractions. The first part of the paper describes an effective algorithm for operation minimization with common subexpression identification and demonstrates its effectiveness on tensor contraction expressions for coupled cluster equations. The second part of the paper highlights the importance of data layout transformation in the optimization of tensor contraction computations on modern processors. A number of considerations such as minimization of cache misses and utilization of multimedia vector instructions are discussed. A library for efficient index permutation of multi-dimensional tensors is described and experimental performance data is provided that demonstrates its effectiveness.

  7. Cloning and expression of autogenes encoding RNA polymerases of T7-like bacteriophages

    DOE Patents [OSTI]

    Studier, F. William; Dubendorff, John W.

    1998-01-01

    This invention relates to the cloning and expression of autogenes encoding RNA polymerases of T7 and T7-like bacteriophages, in which the RNA polymerase gene is transcribed from a promoter which is recognized by the encoded RNA polymerase. Cloning of T7 autogenes was achieved by reducing the activity of the RNA polymerase sufficiently to permit host cell growth. T7 RNA polymerase activity was controlled by combining two independent methods: lac-repression of the recombinant lac operator-T7 promoter in the autogene and inhibition of the polymerase by T7 lysozyme. Expression systems for producing the RNA polymerases of T7 and other T7-like bacteriophages, and expression systems for producing selected gene products are described, as well as other related materials and methods.

  8. Cloning and expression of autogenes encoding RNA poly,erases of T7-like bacteriophages

    DOE Patents [OSTI]

    Studier, F. William; Dubendorff, John W.

    1998-01-01

    This invention relates to the cloning and expression of autogenes encoding RNA polymerases of T7 and T7-like bacteriophages, in which the RNA polymerase gene is transcribed from a promoter which is recognized by the encoded RNA polymerase. Cloning of T7 autogenes was achieved by reducing the activity of the RNA polymerase sufficiently to permit host cell growth. T7 RNA polymerase activity was controlled by combining two independent methods: lac-repression of the recombinant lac operator-T7 promoter in the autogene and inhibition of the polymerase by T7 lysozyme. Expression systems for producing the RNA polymerases of T7 and other T7-like bacteriophages, and expression systems for producing selected gene products are described, as well as other related materials and methods.

  9. Cloning and expression of autogenes encoding RNA polymerases of T7-like bacteriophages

    DOE Patents [OSTI]

    Studier, F.W.; Dubendorff, J.W.

    1998-10-20

    This invention relates to the cloning and expression of autogenes encoding RNA polymerases of T7 and T7-like bacteriophages, in which the RNA polymerase gene is transcribed from a promoter which is recognized by the encoded RNA polymerase. Cloning of T7 autogenes was achieved by reducing the activity of the RNA polymerase sufficiently to permit host cell growth. T7 RNA polymerase activity was controlled by combining two independent methods: lac-repression of the recombinant lac operator-T7 promoter in the autogene and inhibition of the polymerase by T7 lysozyme. Expression systems for producing the RNA polymerases of T7 and other T7-like bacteriophages, and expression systems for producing selected gene products are described, as well as other related materials and methods. 12 figs.

  10. Cloning and expression of autogenes encoding RNA polymerases of T7-like bacteriophages

    DOE Patents [OSTI]

    Studier, F.W.; Dubendorff, J.W.

    1998-11-03

    This invention relates to the cloning and expression of autogenes encoding RNA polymerases of T7 and T7-like bacteriophages, in which the RNA polymerase gene is transcribed from a promoter which is recognized by the encoded RNA polymerase. Cloning of T7 autogenes was achieved by reducing the activity of the RNA polymerase sufficiently to permit host cell growth. T7 RNA polymerase activity was controlled by combining two independent methods: lac-repression of the recombinant lac operator-T7 promoter in the autogene and inhibition of the polymerase by T7 lysozyme. Expression systems for producing the RNA polymerases of T7 and other T7-like bacteriophages, and expression systems for producing selected gene products are described, as well as other related materials and methods. 12 figs.

  11. Protocol for Uniformly Measuring and Expressing the Performance of Energy Storage Systems

    SciTech Connect (OSTI)

    Conover, David R.; Crawford, Aladsair J.; Viswanathan, Vilayanur V.; Ferreira, Summer; Schoenwald, David

    2014-06-01

    The Protocol for Uniformly Measuring and Expressing the Performance of Energy Storage Systems (PNNL-22010) was first issued in November 2012 as a first step toward providing a foundational basis for developing an initial standard for the uniform measurement and expression of energy storage system (ESS) performance. Its subsequent use in the field and review by the protocol working group and most importantly the users’ subgroup and the thermal subgroup has led to the fundamental modifications reflected in this update of the 2012 Protocol. As an update of the 2012 Protocol, this document (the June 2014 Protocol) is intended to supersede its predecessor and be used as the basis for measuring and expressing ESS performance. The foreword provides general and specific details about what additions, revisions, and enhancements have been made to the 2012 Protocol and the rationale for them in arriving at the June 2014 Protocol.

  12. Femtosecond spectroscopy probes the folding quality of antibody fragments expressed as GFP fusions in the cytoplasm

    SciTech Connect (OSTI)

    Didier, P. [Faculte de Pharmacie, UMR 7175, 74, route du Rhin, 67412 Illkirch (France); Weiss, E.; Sibler, A.-P. [Ecole Superieure de Biotechnologie de Strasbourg, UMR 7175, Boulevard Sebastien Brant, F-67412 Illkirch (France); Philibert, P.; Martineau, P. [Centre de recherche en cancerologie de Montpellier, UMR 5160, Val d'Aurelle-Paul Lamarque, 34298 Montpellier cedex 5 (France); Bigot, J.-Y. [Institut de Physique et Chimie des Materiaux de Strasbourg, UMR 7504, 23, rue du Loess, F-67037 Strasbourg (France); Guidoni, L. [Institut de Physique et Chimie des Materiaux de Strasbourg, UMR 7504, 23, rue du Loess, F-67037 Strasbourg (France); Laboratoire Materiaux et Phenomenes Quantiques, UMR 7162, Batiment Condorcet, 10 rue Alice Domon et Leonie Duquet, 75205 Paris cedex 13 (France)], E-mail: luca.guidoni@univ-paris-diderot.fr

    2008-02-22

    Time-resolved femtosecond spectroscopy can improve the application of green fluorescent proteins (GFPs) as protein-folding reporters. The study of ultrafast excited-state dynamics (ESD) of GFP fused to single chain variable fragment (scFv) antibody fragments, allowed us to define and measure an empirical parameter that only depends on the folding quality (FQ) of the fusion. This method has been applied to the analysis of genetic fusions expressed in the bacterial cytoplasm and allowed us to distinguish folded and thus functional antibody fragments (high FQ) with respect to misfolded antibody fragments. Moreover, these findings were strongly correlated to the behavior of the same scFvs expressed in animal cells. This method is based on the sensitivity of the ESD to the modifications in the tertiary structure of the GFP induced by the aggregation state of the fusion partner. This approach may be applicable to the study of the FQ of polypeptides over-expressed under reducing conditions.

  13. Genetic analysis of the regulation of TCH gene expression, Final Report

    SciTech Connect (OSTI)

    Braam, Janet

    2008-10-28

    The Arabidopsis TCH genes, originally isolated as a consequence of their upregulation in response to the mechanical stimulus of touch, are also upregulated by a variety of seemingly disparate environmental and hormonal stimuli. To gain insight into the complexities of TCH gene regulation, a number of approaches were taken. Regulatory elements responsible for regulation were identified and characteristics of the regulation were evaluated. Reporter genes were used to monitor expression localization and dynamics. Microarray analyses of genome-wide expression behavior indicated that touch-inducible gene expression is more widespread than generally appreciated. Identification of all touch-regulated genes shed light on the types of cellular processes that may be altered in response to mechanical stress perturbations. Expression of the TCH2 gene, also called CML24, encoding a calmodulin (CaM)-like (CML) protein, was evaluated. CML24 shares over 40% amino acid sequence identity with CaM, has 4 EF hands and undergoes a Ca2+-dependent change in migration rate through denaturing gel electrophoresis, indicating that CML24 binds Ca2+ and, as a consequence, undergoes conformational changes. CML24 expression occurs in all major organs and is induced from 2- to 15-fold in plants subjected to touch, darkness, heat, cold, hydrogen peroxide, abscisic acid (ABA) and indole-3-acetic acid. The putative CML24 regulatory region confers reporter expression at sites of predicted mechanical stress, in regions undergoing growth, in vascular tissues and various floral organs and in stomata, trichomes and hydathodes. CML24 underexpressing transgenics are resistant to ABA inhibition of germination and seedling growth, defective in long-day induction of flowering, and have enhanced tolerance to CoCl2, molybdic acid, ZnSO4 and MgCl2. These data present evidence that CML24 encodes a potential Ca2+ sensor that may function to enable responses to ABA, day length and presence of various salts. Further

  14. Regulation of bcl-2 proto-oncogene expression during normal human lymphocyte proliferation

    SciTech Connect (OSTI)

    Reed, J.C.; Tsujimoto, Y.; Alpers, J.D.; Croce, C.M.; Nowell, P.C.

    1987-06-05

    The bcl-2 and c-myc proto-oncogenes are brought into juxtaposition with the immuno-globulin heavy chain locus in particular B-cell lymphomas, resulting in high levels of constitutive accumulation of their messenger RNAs. Precisely how the products of the bcl-2 and c-myc genes contribute to tumorigenesis is unknown, but observations that c-myc expression is rapidly induced in nonneoplastic lymphocytes upon stimulation of proliferation raise the possibility that this proto-oncogene is involved in the control of normal cellular growth. In addition to c-myc, the bcl-2 proto-oncogene also was expressed in normal human B and T lymphocytes after stimulation with appropriate mitogens. Comparison of the regulation of the expression of these proto-oncogenes demonstrated marked differences and provided evidence that, in contrast to c-myc, levels of bcl-2 messenger RNA are regulated primarily though transcriptional mechanisms. 10 references, 3 figures.

  15. Analysis of FBN1 allele expression by dermal fibroblasts from Marfan syndrome patients

    SciTech Connect (OSTI)

    Putman, E.A.; Cao, S.N.; Milewicz, D.M.

    1994-09-01

    Screening for mutations in the FBN1 cDNA from Marfan patient cell strains has detected mutations in only 10-15% of patients. In an attempt to explain this poor detection rate, we examined FBN1 allele expression and fibrillin synthesis by 26 cell strains from Marfan patients. DNA from the patients and 10 controls was assessed for the presence of a polymorphic Rsa I restriction site in the 3{prime} untranslated region of the FBN1 gene. Twelve of 26 patient and 5 of 10 control DNAs were heterozygous. Fibroblast RNA from the heterozygous cell strains was reverse-transcribed and subsequently PCR amplified using a [{sup 32}P]-labelled primer, digested with Rsa I and analyzed. Although 3 samples showed no transcript from one allele by ethidium bromide staining, a Betagen scanner detected low levels (10-15%) of that allele. In addition, there was unequal expression of the two alleles in three other patients; for example, only 30% expression from one allele. The remaining patients and the controls had equal expression of each allele. Fibrillin protein synthesis by fibroblasts from these heterozygous patients was also examined. After a 30 minute pulse with [{sup 35}S]-cysteine, cell lysates were collected and proteins analyzed by SDS-PAGE. The amount of fibrillin produced relative to a reference protein was determined using a Betagen scanner. Fibrillin protein synthesis was reduced in 2 of the 3 patients with very low RNA production from one of the FBN1 alleles. All other Marfan and control cell strains showed normal amounts of fibrillin synthesized. The low expression levels from one allele may contribute to, but not fully account for, the low detection rate of FBN1 mutations. Interestingly, protein synthesis levels were not affected in 4 of 6 cell strains demonstrating low levels of RNA expression.

  16. A Framework for Load Balancing of Tensor Contraction Expressions via Dynamic Task Partitioning

    SciTech Connect (OSTI)

    Lai, Pai-Wei; Stock, Kevin; Rajbhandari, Samyam; Krishnamoorthy, Sriram; Sadayappan, Ponnuswamy

    2013-11-17

    In this paper, we introduce the Dynamic Load-balanced Tensor Contractions (DLTC), a domain-specific library for efficient task parallel execution of tensor contraction expressions, a class of computation encountered in quantum chemistry and physics. Our framework decomposes each contraction into smaller unit of tasks, represented by an abstraction referred to as iterators. We exploit an extra level of parallelism by having tasks across independent contractions executed concurrently through a dynamic load balancing run- time. We demonstrate the improved performance, scalability, and flexibility for the computation of tensor contraction expressions on parallel computers using examples from coupled cluster methods.

  17. Matrigel Basement Membrane Matrix influences expression of microRNAs in cancer cell lines

    SciTech Connect (OSTI)

    Price, Karina J.; School of Medicine and Pharmacology, University of Western Australia, Nedlands, WA 6008 ; Tsykin, Anna; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005 ; Giles, Keith M.; Sladic, Rosemary T.; Epis, Michael R.; Ganss, Ruth; Goodall, Gregory J.; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005; Department of Medicine, University of Adelaide, Adelaide, SA 5005 ; Leedman, Peter J.

    2012-10-19

    Highlights: Black-Right-Pointing-Pointer Matrigel alters cancer cell line miRNA expression relative to culture on plastic. Black-Right-Pointing-Pointer Many identified Matrigel-regulated miRNAs are implicated in cancer. Black-Right-Pointing-Pointer miR-1290, -210, -32 and -29b represent a Matrigel-induced miRNA signature. Black-Right-Pointing-Pointer miR-32 down-regulates Integrin alpha 5 (ITGA5) mRNA. -- Abstract: Matrigel is a medium rich in extracellular matrix (ECM) components used for three-dimensional cell culture and is known to alter cellular phenotypes and gene expression. microRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression and have roles in cancer. While miRNA profiles of numerous cell lines cultured on plastic have been reported, the influence of Matrigel-based culture on cancer cell miRNA expression is largely unknown. This study investigated the influence of Matrigel on the expression of miRNAs that might facilitate ECM-associated cancer cell growth. We performed miRNA profiling by microarray using two colon cancer cell lines (SW480 and SW620), identifying significant differential expression of miRNAs between cells cultured in Matrigel and on plastic. Many of these miRNAs have previously been implicated in cancer-related processes. A common Matrigel-induced miRNA signature comprised of up-regulated miR-1290 and miR-210 and down-regulated miR-29b and miR-32 was identified using RT-qPCR across five epithelial cancer cell lines (SW480, SW620, HT-29, A549 and MDA-MB-231). Experimental modulation of these miRNAs altered expression of their known target mRNAs involved in cell adhesion, proliferation and invasion, in colon cancer cell lines. Furthermore, ITGA5 was identified as a novel putative target of miR-32 that may facilitate cancer cell interactions with the ECM. We propose that culture of cancer cell lines in Matrigel more accurately recapitulates miRNA expression and function in cancer than culture on plastic and thus is a

  18. Engineering of living cells for the expression of holo-phycobiliprotein-based constructs

    DOE Patents [OSTI]

    Glazer, Alexander N.; Tooley, Aaron J.; Cai, Yuping

    2004-05-25

    Recombinant cells which express a fluorescent holo-phycobiliprotein fusion protein and methods of use are described. The cells comprises a bilin, a recombinant bilin reductase, an apo-phycobiliprotein fusion protein precursor of the fusion protein comprising a corresponding apo-phycobiliprotein domain, and a recombinant phycobiliprotein domain-bilin lyase, which components react to form the holo-phycobiliprotein fusion protein. Also described are holo-phycobiliprotein based transcription reporter cells and assays, which cells conditionally express a heterologous-to-the-cell, fluorescent, first holo-phycobiliprotein domain.

  19. Analysis of differential protein expression in normal and neoplastic human breast epithelial cell lines

    SciTech Connect (OSTI)

    Williams, K.; Chubb, C.; Huberman, E.; Giometti, C.S.

    1997-07-01

    High resolution two dimensional get electrophoresis (2DE) and database analysis was used to establish protein expression patterns for cultured normal human mammary epithelial cells and thirteen breast cancer cell lines. The Human Breast Epithelial Cell database contains the 2DE protein patterns, including relative protein abundances, for each cell line, plus a composite pattern that contains all the common and specifically expressed proteins from all the cell lines. Significant differences in protein expression, both qualitative and quantitative, were observed not only between normal cells and tumor cells, but also among the tumor cell lines. Eight percent of the consistently detected proteins were found in significantly (P < 0.001) variable levels among the cell lines. Using a combination of immunostaining, comigration with purified protein, subcellular fractionation, and amino-terminal protein sequencing, we identified a subset of the differentially expressed proteins. These identified proteins include the cytoskeletal proteins actin, tubulin, vimentin, and cytokeratins. The cell lines can be classified into four distinct groups based on their intermediate filament protein profile. We also identified heat shock proteins; hsp27, hsp60, and hsp70 varied in abundance and in some cases in the relative phosphorylation levels among the cell lines. Finally, we identified IMP dehydrogenase in each of the cell lines, and found the levels of this enzyme in the tumor cell lines elevated 2- to 20-fold relative to the levels in normal cells.

  20. Use of CYP52A2A promoter to increase gene expression in yeast

    DOE Patents [OSTI]

    Craft, David L.; Wilson, C. Ron; Eirich, Dudley; Zhang, Yeyan

    2004-01-06

    A nucleic acid sequence including a CYP promoter operably linked to nucleic acid encoding a heterologous protein is provided to increase transcription of the nucleic acid. Expression vectors and host cells containing the nucleic acid sequence are also provided. The methods and compositions described herein are especially useful in the production of polycarboxylic acids by yeast cells.

  1. Cellulase variants with improved expression, activity and stability, and use thereof

    DOE Patents [OSTI]

    Aehle, Wolfgang; Bott, Richard R; Bower, Benjamin; Caspi, Jonathan; Estell, David A; Goedegebuur, Frits; Hommes, Ronaldus W.J.; Kaper, Thijs; Kelemen, Bradley; Kralj, Slavko; Van Lieshout, Johan; Nikolaev, Igor; Van Stigt Thans, Sander; Wallace, Louise; Vogtentanz, Gudrun; Sandgren, Mats

    2014-03-25

    The present disclosure relates to cellulase variants. In particular the present disclosure relates to cellulase variants having improved expression, activity and/or stability. Also described are nucleic acids encoding the cellulase variants, compositions comprising the cellulase variants, and methods of use thereof.

  2. Liver X Receptor (LXR) activation negatively regulates visfatin expression in macrophages

    SciTech Connect (OSTI)

    Mayi, Therese Hervee; Rigamonti, Elena; INSERM UR1011, F-59000 Lille; UDSL, F-59000 Lille; Institut Pasteur de Lille, F-59019 Lille ; Pattou, Francois; Department of Endocrine Surgery, University Hospital, Lille; U859 Biotherapies for Diabetes, INSERM, Lille ; Staels, Bart; INSERM UR1011, F-59000 Lille; UDSL, F-59000 Lille; Institut Pasteur de Lille, F-59019 Lille ; Chinetti-Gbaguidi, Giulia; INSERM UR1011, F-59000 Lille; UDSL, F-59000 Lille; Institut Pasteur de Lille, F-59019 Lille

    2011-01-07

    Research highlights: {yields} Synthetic LXR ligands decreased visfatin expression in human macrophages. {yields} LXR activation leads to a modest and transient decrease of NAD{sup +} concentration. {yields} LXR activation decreased PPAR{gamma}-induced visfatin in human macrophages. -- Abstract: Adipose tissue macrophages (ATM) are the major source of visfatin, a visceral fat adipokine upregulated during obesity. Also known to play a role in B cell differentiation (pre-B cell colony-enhancing factor (PBEF)) and NAD biosynthesis (nicotinamide phosphoribosyl transferase (NAMPT)), visfatin has been suggested to play a role in inflammation. Liver X Receptor (LXR) and Peroxisome Proliferator-Activated Receptor (PPAR){gamma} are nuclear receptors expressed in macrophages controlling the inflammatory response. Recently, we reported visfatin as a PPAR{gamma} target gene in human macrophages. In this study, we examined whether LXR regulates macrophage visfatin expression. Synthetic LXR ligands decreased visfatin gene expression in a LXR-dependent manner in human and murine macrophages. The decrease of visfatin mRNA was paralleled by a decrease of protein secretion. Consequently, a modest and transient decrease of NAD{sup +} concentration was observed. Interestingly, LXR activation decreased the PPAR{gamma}-induced visfatin gene and protein secretion in human macrophages. Our results identify visfatin as a gene oppositely regulated by the LXR and PPAR{gamma} pathways in human macrophages.

  3. Comparative analysis of gene {beta}Est2 expression in ontogenesis of Drosophila group virilis

    SciTech Connect (OSTI)

    Polyakova, E.V.; Ambrosova, S.V.; Korochkin, L.I.

    1995-01-01

    Expression of gene {beta}Est2 controlling synthesis of nonspecific carboxylesterase (EC 3.1.1.1) in ontogenesis of Drosophila group virilis was studied. It was established that, in all sibling species of this group, except D. lummei, {beta}-esterase is found at all developmental stages: in larvae, pupae, and imago. In D. lummei, {beta}-esterase is found at the imago stage only. Analysis of 17 laboratory strains of D. lummei of various geographical origins has shown that the absence of the gene {beta}Est2 expression in larvae and pupae can be considered a species-specific diagnostic feature. Comparison of esterase phenotypes in the progeny of crosses between D. lummei and other species has shown that the D. lummei gene is not expressed in hybrid larvae and pupae. Thus, species-specific expression of gene {beta}Est2 in ontogenesis of D. lummei is due to a cis-acting regulatory system. 22 refs., 4 figs., 1 tab.

  4. EIS-0447: Champlain Hudson Power Express Transmission Line Project, New York

    Broader source: Energy.gov [DOE]

    This EIS evaluated the potential environmental impacts of a DOE proposal to grant a Presidential permit to Champlain Hudson Power Express, Inc., to construct, operate, maintain, and connect a new 1000-megawatt (MW) electric transmission system across the U.S.-Canada border in northeastern New York State. The proposed transmission line would run from the Canadian Province of Quebec to New York City.

  5. Final EIS for Champlain Hudson Power Express Transmission Project Now Available

    Broader source: Energy.gov [DOE]

    The U.S. Department of Energy (DOE) has prepared a Final Environmental Impact Statement (EIS) to evaluate the potential environmental impacts in the United States of the proposed action to issue a Presidential permit to the Applicant, Champlain Hudson Power Express, Inc. (CHPEI), and the range of reasonable alternatives.

  6. An EGF receptor inhibitor induces RAR-{beta} expression in breast and ovarian cancer cells

    SciTech Connect (OSTI)

    Grunt, Thomas W. . E-mail: thomas.grunt@meduniwien.ac.at; Puckmair, Klaudia; Tomek, Katharina; Kainz, Birgit; Gaiger, Alexander

    2005-04-22

    Inhibition of the epidermal growth factor (EGF)-receptor (EGFR) has become a promising anticancer treatment strategy. In addition, application of retinoids yields encouraging results for cancer prevention and therapy. Many tumors express no or low amounts of retinoic acid receptor-{beta}2 (RAR-{beta}2) due to epigenetic silencing via DNA hypermethylation. RAR-{beta}2 is the main mediator of the antiproliferative effect of retinoids. RAR-{beta}2 re-expression causes reversal of transformation, cell cycle arrest, and restoration of retinoid sensitivity. RAR-{beta}2 is thus a tumor suppressor. Western blotting, colorimetric in vitro cell proliferation assays, and reverse transcription-polymerase chain reaction demonstrated that the EGFR inhibitor PD153035 not only blocked activation of EGFR and inhibited cell growth, but also stimulated RAR-{beta} expression in MDA-MB-468 breast and OVCAR-3 ovarian carcinoma cells. Upregulation of RAR-{beta} by PD153035 was confirmed by real-time reverse transcription-polymerase chain reaction. In contrast, expression of other retinoid receptors and of estrogen receptor-{alpha} was not affected. PD153035-mediated re-induction of RAR-{beta} was associated with demethylation of the RAR-{beta}2 gene promoter P2 as demonstrated by methylation-specific polymerase chain reaction. These novel results on the ErbB/retinoid receptor cross-talk may be useful for designing future anticancer combination regimens.

  7. Systems for the expression of orthogonal translation components eubacterial host cells

    DOE Patents [OSTI]

    Ryu, Youngha; Schultz, Peter G.

    2012-06-12

    The invention relates to compositions and methods for the in vivo production of polypeptides comprising one or more unnatural amino acids. Specifically, the invention provides plasmid systems for the efficient eubacterial expression of polypeptides comprising one or more unnatural amino acids at genetically-programmed positions.

  8. Systems for the expression of orthogonal translation components in eubacterial host cells

    DOE Patents [OSTI]

    Ryu, Youngha; Schultz, Peter G.

    2013-01-22

    The invention related to compositions and methods for the in vivo production of polypeptides comprising one or more unnatural amino acids. Specifically, the invention provides plasmid systems for the efficient eubacterial expression of polypeptides comprising one or more unnatural acids at genetically-programmed positions.

  9. Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis

    SciTech Connect (OSTI)

    Yamamoto, Miki L.; Clark, Tyson A.; Gee, Sherry L.; Kang, Jeong-Ah; Schweitzer, Anthony C.; Wickrema, Amittha; Conboy, John G.

    2009-02-03

    Differentiating erythroid cells execute a unique gene expression program that insures synthesis of the appropriate proteome at each stage of maturation. Standard expression microarrays provide important insight into erythroid gene expression but cannot detect qualitative changes in transcript structure, mediated by RNA processing, that alter structure and function of encoded proteins. We analyzed stage-specific changes in the late erythroid transcriptome via use of high-resolution microarrays that detect altered expression of individual exons. Ten differentiation-associated changes in erythroblast splicing patterns were identified, including the previously known activation of protein 4.1R exon 16 splicing. Six new alternative splicing switches involving enhanced inclusion of internal cassette exons were discovered, as well as 3 changes in use of alternative first exons. All of these erythroid stage-specific splicing events represent activated inclusion of authentic annotated exons, suggesting they represent an active regulatory process rather than a general loss of splicing fidelity. The observation that 3 of the regulated transcripts encode RNA binding proteins (SNRP70, HNRPLL, MBNL2) may indicate significant changes in the RNA processing machinery of late erythroblasts. Together, these results support the existence of a regulated alternative pre-mRNA splicing program that is critical for late erythroid differentiation.

  10. Systems for the expression of orthogonal translation components in eubacterial host cells

    DOE Patents [OSTI]

    Ryu, Youngha; Schultz, Peter G.

    2011-06-14

    The invention relates to compositions and methods for the in vivo production of polypeptides comprising one or more unnatural amino acids. Specifically, the invention provides plasmid systems for the efficient eubacterial expression of polypeptides comprising one or more unnatural amino acids at genetically-programmed positions.

  11. Cloning of a yeast alpha-amylase promoter and its regulated heterologous expression

    DOE Patents [OSTI]

    Gao, Johnway [Richland, WA; Skeen, Rodney S [Pendleton, OR; Hooker, Brian S [Kennewick, WA; Anderson, Daniel B [Pasco, WA

    2003-04-01

    The present invention provides the promoter clone discovery of an alpha-amylase gene of a starch utilizing yeast strain Schwanniomyces castellii. The isolated alpha-amylase promoter is an inducible promoter, which can regulate strong gene expression in starch culture medium.

  12. Pre- and post-exposure safety and efficacy of attenuated rabies virus vaccines are enhanced by their expression of IFNγ

    SciTech Connect (OSTI)

    Barkhouse, Darryll A.; Faber, Milosz; Hooper, D. Craig

    2015-01-01

    Consistent with evidence of a strong correlation between interferon gamma (IFNγ) production and rabies virus (RABV) clearance from the CNS, we recently demonstrated that engineering a pathogenic RABV to express IFNγ highly attenuates the virus. Reasoning that IFNγ expression by RABV vaccines would enhance their safety and efficacy, we reverse-engineered two proven vaccine vectors, GAS and GASGAS, to express murine IFNγ. Mortality and morbidity were monitored during suckling mice infection, immunize/challenge experiments and mixed intracranial infections. We demonstrate that GASγ and GASγGAS are significantly attenuated in suckling mice compared to the GASGAS vaccine. GASγ better protects mice from lethal DRV4 RABV infection in both pre- and post-exposure experiments compared to GASGAS. Finally, GASγGAS reduces post-infection neurological sequelae, compared to control, during mixed intracranial infection with DRV4. These data show IFNγ expression by a vaccine vector can enhance its safety while increasing its efficacy as pre- and post-exposure treatment. - Highlights: • IFNγ expression improves attenuated rabies virus safety and immunogenicity. • IFNγ expression is safer and more immunogenic than doubling glycoprotein expression. • Co-infection with IFNγ-expressing RABV prevents wild-type rabies virus lethality. • Vaccine safety and efficacy is additive for IFNγ and double glycoprotein expression.

  13. Expression of transforming growth factor alpha in plutonium-239-induced lung neoplasms in dogs: investigations of autocrine mechanisms of growth

    SciTech Connect (OSTI)

    Gillett, N.A.; Stegelmeier, B.L.; Chang, I.Y.; Kelly, G. )

    1991-06-01

    We have previously shown that 47% of radiation-induced lung neoplasms in dogs exhibit increased expression of epidermal growth factor receptor (EGFR). In this study, we investigated the expression of transforming growth factor alpha (TGF-alpha), a ligand for EGFR, to determine if an autocrine mechanism for growth stimulation was present in these tumors. As determined by immunohistochemistry, 59% (26/44) of the lung neoplasms examined had increased expression of TGF-alpha. Expression of TGF-alpha was not related to the etiology of the tumor, e.g., spontaneous or plutonium-induced; however, it was related to the phenotype of the tumor. Statistical analysis of the correlation of EGFR and TGF-alpha expression within the same tumor did not show a positive association; however, specific phenotypes did have statistically significant expression of EGFR or TGF-alpha, suggesting that overexpression of either the ligand or its receptor conferred a growth advantage to the neoplasm. Twenty-seven percent (32/117) of radiation-induced proliferative epithelial foci expressed TGF-alpha, and a portion of those foci (8/32) expressed both EGFR and TGF-alpha. This supports the hypothesis that these foci represent preneoplastic lesions, and suggests that those foci exhibiting increased expression of the growth factor or its receptor are at greater risk for progressing to neoplasia.

  14. Nicotine induces fibrogenic changes in human liver via nicotinic acetylcholine receptors expressed on hepatic stellate cells

    SciTech Connect (OSTI)

    Soeda, Junpei; Morgan, Maelle; McKee, Chad; Mouralidarane, Angelina; Lin, ChingI; Roskams, Tania; Oben, Jude A.

    2012-01-06

    Highlights: Black-Right-Pointing-Pointer Cigarette smoke may induce liver fibrosis via nicotine receptors. Black-Right-Pointing-Pointer Nicotine induces proliferation of hepatic stellate cells (HSCs). Black-Right-Pointing-Pointer Nicotine activates hepatic fibrogenic pathways. Black-Right-Pointing-Pointer Nicotine receptor antagonists attenuate HSC proliferation. Black-Right-Pointing-Pointer Nicotinic receptor antagonists may have utility as novel anti-fibrotic agents. -- Abstract: Background and aims: Cigarette smoke (CS) may cause liver fibrosis but possible involved mechanisms are unclear. Among the many chemicals in CS is nicotine - which affects cells through nicotinic acetylcholine receptors (nAChR). We studied the effects of nicotine, and involved pathways, on human primary hepatic stellate cells (hHSCs), the principal fibrogenic cells in the liver. We then determined possible disease relevance by assaying nAChR in liver samples from human non-alcoholic steatohepatitis (NASH). Methods: hHSC were isolated from healthy human livers and nAChR expression analyzed - RT-PCR and Western blotting. Nicotine induction of hHSC proliferation, upregulation of collagen1-{alpha}2 and the pro-fibrogenic cytokine transforming growth factor beta 1 (TGF-{beta}1) was determined along with involved intracellular signaling pathways. nAChR mRNA expression was finally analyzed in whole liver biopsies obtained from patients diagnosed with non-alcoholic steatohepatitis (NASH). Results: hHSCs express muscle type ({alpha}1, {beta}1, delta and epsilon) and neuronal type ({alpha}3, {alpha}6, {alpha}7, {beta}2 and {beta}4) nAChR subunits at the mRNA level. Among these subunits, {alpha}3, {alpha}7, {beta}1 and {epsilon} were predominantly expressed as confirmed by Western blotting. Nicotine induced hHSC proliferation was attenuated by mecamylamine (p < 0.05). Additionally, collagen1-{alpha}2 and TGF-{beta}1 mRNA expression were significantly upregulated by nicotine and inhibited by

  15. Expression and potential role of the peptide orexin-A in prostate cancer

    SciTech Connect (OSTI)

    Valiante, Salvatore; Liguori, Giovanna; Tafuri, Simona; Pavone, Luigi Michele; Campese, Roberto; Monaco, Roberto; Iachetta, Giuseppina; Assisi, Loredana; Mirabella, Nicola; Forte, Maurizio; Costagliola, Anna; Vittoria, Alfredo

    2015-09-04

    The peptides orexin-A and orexin-B and their G protein-coupled OX1 and OX2 receptors are involved in multiple physiological processes in the central nervous system and peripheral organs. Altered expression or signaling dysregulation of orexins and their receptors have been associated with a wide range of human diseases including narcolepsy, obesity, drug addiction, and cancer. Although orexin-A, its precursor molecule prepro-orexin and OX1 receptor have been detected in the human normal and hyperplastic prostate tissues, their expression and function in the prostate cancer (PCa) remains to be addressed. Here, we demonstrate for the first time the immunohistochemical localization of orexin-A in human PCa specimens, and the expression of prepro-orexin and OX1 receptor at both protein and mRNA levels in these tissues. Orexin-A administration to the human androgen-dependent prostate carcinoma cells LNCaP up-regulates OX1 receptor expression resulting in a decrease of cell survival. Noteworthy, nanomolar concentrations of the peptide counteract the testosterone-induced nuclear translocation of the androgen receptor in the cells: the orexin-A action is prevented by the addition of the OX1 receptor antagonist SB-408124 to the test system. These findings indicate that orexin-A/OX1 receptor interaction interferes with the activity of the androgen receptor which regulates PCa onset and progression, thus suggesting that orexin-A and its receptor might represent novel therapeutic targets to challenge this aggressive cancer. - Highlights: • Orexin-A and OX1 receptor are present in human cancer prostate tissues. • Orexin-A up-regulates OX1 receptor expression in LNCaP cells. • Orexin-A inhibits testosterone-induced nuclear translocation of androgen receptor.

  16. Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency

    SciTech Connect (OSTI)

    Eudes, Aymerick; Sathitsuksanoh, Noppadon; Baidoo, Edward E. K.; George, Anthe; Liang, Yan; Yang, Fan; Singh, Seema; Keasling, Jay D.; Simmons, Blake A.; Loqué, Dominique

    2015-01-13

    Lignin confers recalcitrance to plant biomass used as feedstocks in agro-processing industries or as source of renewable sugars for the production of bioproducts. The metabolic steps for the synthesis of lignin building blocks belong to the shikimate and phenylpropanoid pathways. Genetic engineering efforts to reduce lignin content typically employ gene knockout or gene silencing techniques to constitutively repress one of these metabolic pathways. Recently, new strategies have emerged offering better spatiotemporal control of lignin deposition, including the expression of enzymes that interfere with the normal process for cell wall lignification. In this study, we report that expression of a 3-dehydroshikimate dehydratase (QsuB from Corynebacterium glutamicum) reduces lignin deposition in Arabidopsis cell walls. QsuB was targeted to the plastids to convert 3-dehydroshikimate – an intermediate of the shikimate pathway – into protocatechuate. Compared to wild-type plants, lines expressing QsuB contain higher amounts of protocatechuate, p-coumarate, p-coumaraldehyde and p-coumaryl alcohol, and lower amounts of coniferaldehyde, coniferyl alcohol, sinapaldehyde and sinapyl alcohol. 2D-NMR spectroscopy and pyrolysis-gas chromatography/mass spectrometry (pyro-GC/MS) reveal an increase of p-hydroxyphenyl units and a reduction of guaiacyl units in the lignin of QsuB lines. Size-exclusion chromatography indicates a lower degree of lignin polymerization in the transgenic lines. Therefore, our data show that the expression of QsuB primarily affects the lignin biosynthetic pathway. Finally, biomass from these lines exhibits more than a twofold improvement in saccharification efficiency. We conclude that the expression of QsuB in plants, in combination with specific promoters, is a promising gain-of-function strategy for spatiotemporal reduction of lignin in plant biomass.

  17. Nucleic and amino acid sequences relating to a novel transketolase, and methods for the expression thereof

    DOE Patents [OSTI]

    Croteau, Rodney Bruce; Wildung, Mark Raymond; Lange, Bernd Markus; McCaskill, David G.

    2001-01-01

    cDNAs encoding 1-deoxyxylulose-5-phosphate synthase from peppermint (Mentha piperita) have been isolated and sequenced, and the corresponding amino acid sequences have been determined. Accordingly, isolated DNA sequences (SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7) are provided which code for the expression of 1-deoxyxylulose-5-phosphate synthase from plants. In another aspect the present invention provides for isolated, recombinant DXPS proteins, such as the proteins having the sequences set forth in SEQ ID NO:4, SEQ ID NO:6 and SEQ ID NO:8. In other aspects, replicable recombinant cloning vehicles are provided which code for plant 1-deoxyxylulose-5-phosphate synthases, or for a base sequence sufficiently complementary to at least a portion of 1-deoxyxylulose-5-phosphate synthase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding a plant 1-deoxyxylulose-5-phosphate synthase. Thus, systems and methods are provided for the recombinant expression of the aforementioned recombinant 1-deoxyxylulose-5-phosphate synthase that may be used to facilitate its production, isolation and purification in significant amounts. Recombinant 1-deoxyxylulose-5-phosphate synthase may be used to obtain expression or enhanced expression of 1-deoxyxylulose-5-phosphate synthase in plants in order to enhance the production of 1-deoxyxylulose-5-phosphate, or its derivatives such as isopentenyl diphosphate (BP), or may be otherwise employed for the regulation or expression of 1-deoxyxylulose-5-phosphate synthase, or the production of its products.

  18. Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Eudes, Aymerick; Sathitsuksanoh, Noppadon; Baidoo, Edward E. K.; George, Anthe; Liang, Yan; Yang, Fan; Singh, Seema; Keasling, Jay D.; Simmons, Blake A.; Loqué, Dominique

    2015-01-13

    Lignin confers recalcitrance to plant biomass used as feedstocks in agro-processing industries or as source of renewable sugars for the production of bioproducts. The metabolic steps for the synthesis of lignin building blocks belong to the shikimate and phenylpropanoid pathways. Genetic engineering efforts to reduce lignin content typically employ gene knockout or gene silencing techniques to constitutively repress one of these metabolic pathways. Recently, new strategies have emerged offering better spatiotemporal control of lignin deposition, including the expression of enzymes that interfere with the normal process for cell wall lignification. In this study, we report that expression of a 3-dehydroshikimatemore » dehydratase (QsuB from Corynebacterium glutamicum) reduces lignin deposition in Arabidopsis cell walls. QsuB was targeted to the plastids to convert 3-dehydroshikimate – an intermediate of the shikimate pathway – into protocatechuate. Compared to wild-type plants, lines expressing QsuB contain higher amounts of protocatechuate, p-coumarate, p-coumaraldehyde and p-coumaryl alcohol, and lower amounts of coniferaldehyde, coniferyl alcohol, sinapaldehyde and sinapyl alcohol. 2D-NMR spectroscopy and pyrolysis-gas chromatography/mass spectrometry (pyro-GC/MS) reveal an increase of p-hydroxyphenyl units and a reduction of guaiacyl units in the lignin of QsuB lines. Size-exclusion chromatography indicates a lower degree of lignin polymerization in the transgenic lines. Therefore, our data show that the expression of QsuB primarily affects the lignin biosynthetic pathway. Finally, biomass from these lines exhibits more than a twofold improvement in saccharification efficiency. We conclude that the expression of QsuB in plants, in combination with specific promoters, is a promising gain-of-function strategy for spatiotemporal reduction of lignin in plant biomass.« less

  19. Mixed lineage kinase 3 is required for matrix metalloproteinase expression and invasion in ovarian cancer cells

    SciTech Connect (OSTI)

    Zhan, Yu; Abi Saab, Widian F.; Modi, Nidhi; Stewart, Amanda M.; Liu, Jinsong; Chadee, Deborah N.

    2012-08-15

    Mixed lineage kinase 3 (MLK3) is a mitogen-activated protein kinase kinase kinase (MAP3K) that activates MAPK signaling pathways and regulates cellular responses such as proliferation, migration and apoptosis. Here we report high levels of total and phospho-MLK3 in ovarian cancer cell lines in comparison to immortalized nontumorigenic ovarian epithelial cell lines. Using small interfering RNA (siRNA)-mediated gene silencing, we determined that MLK3 is required for the invasion of SKOV3 and HEY1B ovarian cancer cells. Furthermore, mlk3 silencing substantially reduced matrix metalloproteinase (MMP)-1, -2, -9 and -12 gene expression and MMP-2 and -9 activities in SKOV3 and HEY1B ovarian cancer cells. MMP-1, -2, -9 and-12 expression, and MLK3-induced activation of MMP-2 and MMP-9 requires both extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK) activities. In addition, inhibition of activator protein-1 (AP-1) reduced MMP-1, MMP-9 and MMP-12 gene expression. Collectively, these findings establish MLK3 as an important regulator of MMP expression and invasion in ovarian cancer cells. -- Highlights: Black-Right-Pointing-Pointer Ovarian cancer cell lines have high levels of total and phosphorylated MLK3. Black-Right-Pointing-Pointer MLK3 is required for MMP expression and activity in ovarian cancer cells. Black-Right-Pointing-Pointer MLK3 is required for invasion of SKOV3 and HEY1B ovarian cancer cells. Black-Right-Pointing-Pointer MLK3-dependent regulation of MMP-2 and MMP-9 activities requires ERK and JNK.

  20. Cancer Associated Fibroblasts express pro-inflammatory factors in human breast and ovarian tumors

    SciTech Connect (OSTI)

    Erez, Neta; Glanz, Sarah; Raz, Yael; Avivi, Camilla; Barshack, Iris

    2013-08-02

    Highlights: •CAFs in human breast and ovarian tumors express pro-inflammatory factors. •Expression of pro-inflammatory factors correlates with tumor invasiveness. •Expression of pro-inflammatory factors is associated with NF-κb activation in CAFs. -- Abstract: Inflammation has been established in recent years as a hallmark of cancer. Cancer Associated Fibroblasts (CAFs) support tumorigenesis by stimulating angiogenesis, cancer cell proliferation and invasion. We previously demonstrated that CAFs also mediate tumor-enhancing inflammation in a mouse model of skin carcinoma. Breast and ovarian carcinomas are amongst the leading causes of cancer-related mortality in women and cancer-related inflammation is linked with both these tumor types. However, the role of CAFs in mediating inflammation in these malignancies remains obscure. Here we show that CAFs in human breast and ovarian tumors express high levels of the pro-inflammatory factors IL-6, COX-2 and CXCL1, previously identified to be part of a CAF pro-inflammatory gene signature. Moreover, we show that both pro-inflammatory signaling by CAFs and leukocyte infiltration of tumors are enhanced in invasive ductal carcinoma as compared with ductal carcinoma in situ. The pro-inflammatory genes expressed by CAFs are known NF-κB targets and we show that NF-κB is up-regulated in breast and ovarian CAFs. Our data imply that CAFs mediate tumor-promoting inflammation in human breast and ovarian tumors and thus may be an attractive target for stromal-directed therapeutics.

  1. Long-term in vitro, cell-type-specific genome-wide reprogramming of gene expression

    SciTech Connect (OSTI)

    Hakelien, Anne-Mari; Gaustad, Kristine G.; Taranger, Christel K.; Skalhegg, Bjorn S.; Kuentziger, Thomas; Collas, Philippe . E-mail: philippe.collas@medisin.uio.no

    2005-09-10

    We demonstrate a cell extract-based, genome-wide and heritable reprogramming of gene expression in vitro. Kidney epithelial 293T cells have previously been shown to take on T cell properties following a brief treatment with an extract of Jurkat T cells. We show here that 293T cells exposed for 1 h to a Jurkat cell extract undergo genome-wide, target cell-type-specific and long-lasting transcriptional changes. Microarray analyses indicate that on any given week after extract treatment, {approx}2500 genes are upregulated >3-fold, of which {approx}900 are also expressed in Jurkat cells. Concomitantly, {approx}1500 genes are downregulated or repressed, of which {approx}500 are also downregulated in Jurkat cells. Gene expression changes persist for over 30 passages ({approx}80 population doublings) in culture. Target cell-type specificity of these changes is shown by the lack of activation or repression of Jurkat-specific genes by extracts of 293T cells or carcinoma cells. Quantitative RT-PCR analysis confirms the long-term transcriptional activation of genes involved in key T cell functions. Additionally, growth of cells in suspended aggregates, expression of CD3 and CD28 T cell surface markers, and interleukin-2 secretion by 293T cells treated with extract of adult peripheral blood T cells illustrate a functional nuclear reprogramming. Therefore, target cell-type-specific and heritable changes in gene expression, and alterations in cell function, can be promoted by extracts derived from transformed cells as well as from adult primary cells.

  2. CDKN2B expression and subcutaneous adipose tissue expandability: Possible influence of the 9p21 atherosclerosis locus

    SciTech Connect (OSTI)

    Svensson, Per-Arne; Wahlstrand, Björn; Olsson, Maja; Froguel, Philippe; Falchi, Mario; Bergman, Richard N.; McTernan, Philip G.; Hedner, Thomas; Carlsson, Lena M.S.; Jacobson, Peter

    2014-04-18

    Highlights: • The tumor suppressor gene CDKN2B is highly expressed in human adipose tissue. • Risk alleles at the 9p21 locus modify CDKN2B expression in a BMI-dependent fashion. • There is an inverse relationship between expression of CDKN2B and adipogenic genes. • CDKN2B expression influences to postprandial triacylglycerol clearance. • CDKN2B expression in adipose tissue is linked to markers of hepatic steatosis. - Abstract: Risk alleles within a gene desert at the 9p21 locus constitute the most prevalent genetic determinant of cardiovascular disease. Previous research has demonstrated that 9p21 risk variants influence gene expression in vascular tissues, yet the biological mechanisms by which this would mediate atherosclerosis merits further investigation. To investigate possible influences of this locus on other tissues, we explored expression patterns of 9p21-regulated genes in a panel of multiple human tissues and found that the tumor suppressor CDKN2B was highly expressed in subcutaneous adipose tissue (SAT). CDKN2B expression was regulated by obesity status, and this effect was stronger in carriers of 9p21 risk alleles. Covariation between expression of CDKN2B and genes implemented in adipogenesis was consistent with an inhibitory effect of CDKN2B on SAT proliferation. Moreover, studies of postprandial triacylglycerol clearance indicated that CDKN2B is involved in down-regulation of SAT fatty acid trafficking. CDKN2B expression in SAT correlated with indicators of ectopic fat accumulation, including markers of hepatic steatosis. Among genes regulated by 9p21 risk variants, CDKN2B appears to play a significant role in the regulation of SAT expandability, which is a strong determinant of lipotoxicity and therefore might contribute to the development of atherosclerosis.

  3. DNA sequence and spatial expression pattern of a drought- and ABA-induced gene in tomato

    SciTech Connect (OSTI)

    Plant, A.L.; Cohen, A.; Moses, M.S.; Bray, E.A. )

    1991-05-01

    The genomic and cDNA sequence for the previously characterized drought- and ABA-induced gene pLE16 are presented. The single open reading frame contained within the gene has the capacity to encode a polypeptide of 12.7 kD with a predicted pI of 8.73. The amino-terminus is highly hydrophobic and is characteristic of signal sequences which target polypeptides for export from the cytoplasm. There is considerable homology (51.3% identity) between the amino-terminus of pLE16 and the amino-terminal domains of a group of proteins that comprise the phospholipid transfer proteins. Although this homology breaks down at the carboxy-terminal half of pLE16, the homology that exists suggests that pLE16 may be associated with membranes and may therefore play a role in maintaining membrane integrity during drought-stress. pLE16 is expressed in drought-stressed leaf, petiole and stem tissue and to a much lower extent in the seeds and pericarp of mature green tomato fruit. No expression was detected in the seeds or pericarp of red fruit or drought-stressed roots. Expression of pLE16 is induced in leaf tissue by a variety of other environmental stresses including PEG-mediated water deficit, salt, cold stress and heat stress. These stresses did not however induce expression of pLE16 in the roots. Examination of the 5{prime} flanking DNA sequences for this gene did not reveal the presence of the consensus ABA responsive element (ABRE), implicated in ABA induction of gene expression and so far common to the 5{prime} flanking DNA sequences of many genes that are ABA responsive. The expression of pLE16 in response to drought-stress and other environmental stresses in vegetative tissue, together with the lack of a consensus ABRE, suggests that the regulation of this gene by ABA may differ from those that are seed-specific.

  4. Trps1 deficiency inhibits the morphogenesis of secondary hair follicles via decreased Noggin expression

    SciTech Connect (OSTI)

    Sun, Yujing; Nakanishi, Masako; Sato, Fuyuki; Oikawa, Kosuke; Muragaki, Yasuteru; Zhou, Gengyin

    2015-01-16

    Highlights: • The number of secondary hair follicles is reduced by half in Trps1 KO embryonic skin compared to wild-type skin. • Noggin expression is significantly decreased and BMP signaling is promoted in Trps1 KO embryonic skin. • Treatment with a Noggin or BMP inhibitor rescued the decreased number of hair follicles in Trps1 KO skin graft cultures. • Cell proliferation and apoptosis of the epidermis were normalized by Noggin treatment. - Abstract: A representative phenotype of patients with tricho-rhino-phalangeal syndrome (TRPS) is sparse hair. To understand the developmental defects of these patient’s hair follicles, we analyzed the development of hair follicles histologically and biochemically using Trps1 deficient (KO) mice. First, we compared the numbers of primary hair follicles in wild-type (WT) and KO embryos at different developmental stages. No differences were observed in the E14.5 skins of WT and KO mice. However, at later time points, KO fetal skin failed to properly develop secondary hair follicles, and the number of secondary hair follicles present in E18.5 KO skin was approximately half compared to that of WT skin. Sonic hedgehog expression was significantly decreased in E17.5 KO skin, whereas no changes were observed in Eda/Edar expression in E14.5 or E17.5 skins. In addition, Noggin expression was significantly decreased in E14.5 and E17.5 KO skin compared to WT skin. In parallel with the suppression of Noggin expression, BMP signaling was promoted in the epidermal cells of KO skins compared to WT skins as determined by immunohistochemistry for phosphorylated Smad1/5/8. The reduced number of secondary hair follicles was restored in skin graft cultures treated with a Noggin and BMP inhibitor. Furthermore, decreased cell proliferation, and increased apoptosis in KO skin was rescued by Noggin treatment. Taken together, we conclude that hair follicle development in Trps1 KO embryos is impaired directly or indirectly by decreased Noggin

  5. Modulation of keratinocyte expression of antioxidants by 4-hydroxynonenal, a lipid peroxidation end product

    SciTech Connect (OSTI)

    Zheng, Ruijin; Heck, Diane E.; Mishin, Vladimir; Black, Adrienne T.; Shakarjian, Michael P.; Kong, Ah-Ng Tony; Laskin, Debra L.; Laskin, Jeffrey D.

    2014-03-01

    4-Hydroxynonenal (4-HNE) is a lipid peroxidation end product generated in response to oxidative stress in the skin. Keratinocytes contain an array of antioxidant enzymes which protect against oxidative stress. In these studies, we characterized 4-HNE-induced changes in antioxidant expression in mouse keratinocytes. Treatment of primary mouse keratinocytes and PAM 212 keratinocytes with 4-HNE increased mRNA expression for heme oxygenase-1 (HO-1), catalase, NADPH:quinone oxidoreductase (NQO1) and glutathione S-transferase (GST) A1-2, GSTA3 and GSTA4. In both cell types, HO-1 was the most sensitive, increasing 8698 fold within 6 h. Further characterization of the effects of 4-HNE on HO-1 demonstrated concentration- and time-dependent increases in mRNA and protein expression which were maximum after 6 h with 30 ?M. 4-HNE stimulated keratinocyte Erk1/2, JNK and p38 MAP kinases, as well as PI3 kinase. Inhibition of these enzymes suppressed 4-HNE-induced HO-1 mRNA and protein expression. 4-HNE also activated Nrf2 by inducing its translocation to the nucleus. 4-HNE was markedly less effective in inducing HO-1 mRNA and protein in keratinocytes from Nrf2 ?/? mice, when compared to wild type mice, indicating that Nrf2 also regulates 4-HNE-induced signaling. Western blot analysis of caveolar membrane fractions isolated by sucrose density centrifugation demonstrated that 4-HNE-induced HO-1 is localized in keratinocyte caveolae. Treatment of the cells with methyl-?-cyclodextrin, which disrupts caveolar structure, suppressed 4-HNE-induced HO-1. These findings indicate that 4-HNE modulates expression of antioxidant enzymes in keratinocytes, and that this can occur by different mechanisms. Changes in expression of keratinocyte antioxidants may be important in protecting the skin from oxidative stress. - Highlights: Lipid peroxidation generates 4-hydroxynonenal, a reactive aldehyde. 4-HNE induces antioxidant proteins in mouse keratinocytes. Induction of antioxidant proteins

  6. A constitutive expression system for glycosyl hydrolase family 7 cellobiohydrolases in Hypocrea jecorina

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Linger, Jeffrey G.; Taylor, II, Larry E.; Baker, John O.; Vander Wall, Todd; Hobdey, Sarah E.; Podkaminer, Kara; Himmel, Michael E.; Decker, Stephen R.

    2015-03-18

    One of the primary industrial-scale cellulase producers is the ascomycete fungus, Hypocrea jecorina, which produces and secretes large quantities of diverse cellulolytic enzymes. Perhaps the single most important biomass degrading enzyme is cellobiohydrolase I (cbh1or Cel7A) due to its enzymatic proficiency in cellulose depolymerization. However, production of Cel7A with native-like properties from heterologous expression systems has proven difficult. In this study, we develop a protein expression system in H. jecorina (Trichoderma reesei) useful for production and secretion of heterologous cellobiohydrolases from glycosyl hydrolase family 7. Building upon previous work in heterologous protein expression in filamentous fungi, we have integrated amore » native constitutive enolase promoter with the native cbh1 signal sequence. The results are the following: The constitutive eno promoter driving the expression of Cel7A allows growth on glucose and results in repression of the native cellulase system, severely reducing background endo- and other cellulase activity and greatly simplifying purification of the recombinant protein. Coupling this system to a Δcbh1 strain of H. jecorina ensures that only the recombinant Cel7A protein is produced. Two distinct transformant colony morphologies were observed and correlated with high and null protein production. Production levels in ‘fast’ transformants are roughly equivalent to those in the native QM6a strain of H. jecorina, typically in the range of 10 to 30 mg/L when grown in continuous stirred-tank fermenters. ‘Slow’ transformants showed no evidence of Cel7A production. Specific activity of the purified recombinant Cel7A protein is equivalent to that of native protein when assayed on pretreated corn stover, as is the thermal stability and glycosylation level. Purified Cel7A produced from growth on glucose demonstrated remarkably consistent specific activity. Purified Cel7A from the same strain grown on lactose

  7. Wnt/{beta}-catenin signaling changes C2C12 myoblast proliferation and differentiation by inducing Id3 expression

    SciTech Connect (OSTI)

    Zhang, Long; Shi, Songting; Zhang, Juan; Zhou, Fangfang; Dijke, Peter ten

    2012-03-02

    Highlights: Black-Right-Pointing-Pointer Expression of Id3 but not Id1 is induced by Wnt3a stimulation in C2C12 cells. Black-Right-Pointing-Pointer Wnt3a induces Id3 expression via canonical Wnt/{beta}-catenin pathway. Black-Right-Pointing-Pointer Wnt3a-induced Id3 expression does not depend on BMP signaling activation. Black-Right-Pointing-Pointer Induction of Id3 expression is critical determinant in Wnt3a-induced cell proliferation and differentiation. -- Abstract: Canonical Wnt signaling plays important roles in regulating cell proliferation and differentiation. In this study, we report that inhibitor of differentiation (Id)3 is a Wnt-inducible gene in mouse C2C12 myoblasts. Wnt3a induced Id3 expression in a {beta}-catenin-dependent manner. Bone morphogenetic protein (BMP) also potently induced Id3 expression. However, Wnt-induced Id3 expression occurred independent of the BMP/Smad pathway. Functional studies showed that Id3 depletion in C2C12 cells impaired Wnt3a-induced cell proliferation and alkaline phosphatase activity, an early marker of osteoblast cells. Id3 depletion elevated myogenin induction during myogenic differentiation and partially impaired Wnt3a suppressed myogenin expression in C2C12 cells. These results suggest that Id3 is an important Wnt/{beta}-catenin induced gene in myoblast cell fate determination.

  8. Irreversible inhibition of RANK expression as a possible mechanism for IL-3 inhibition of RANKL-induced osteoclastogenesis

    SciTech Connect (OSTI)

    Khapli, Shruti M.; Tomar, Geetanjali B.; Barhanpurkar, Amruta P.; Gupta, Navita; Yogesha, S.D.; Pote, Satish T.; Wani, Mohan R.

    2010-09-03

    Research highlights: {yields} IL-3 inhibits receptor activator of NF-{kappa}B ligand (RANKL)-induced osteoclastogenesis. {yields} IL-3 inhibits RANKL-induced JNK activation. {yields} IL-3 down-regulates expression of c-Fos and NFATc1 transcription factors. {yields} IL-3 down-regulates RANK expression posttranscriptionally and irreversibly. {yields} IL-3 inhibits in vivo RANK expression. -- Abstract: IL-3, a cytokine secreted by activated T lymphocytes, stimulates the proliferation, differentiation and survival of pluripotent hematopoietic stem cells. In this study, we investigated the mechanism of inhibitory action of IL-3 on osteoclast differentiation. We show here that IL-3 significantly inhibits receptor activator of NF-{kappa}B (RANK) ligand (RANKL)-induced activation of c-Jun N-terminal kinase (JNK). IL-3 down-regulates expression of c-Fos and nuclear factor of activated T cells (NFATc1) transcription factors. In addition, IL-3 down-regulates RANK expression posttranscriptionally in both purified osteoclast precursors and whole bone marrow cells. Furthermore, the inhibitory effect of IL-3 on RANK expression was irreversible. Interestingly, IL-3 inhibits in vivo RANK expression in mice. Thus, we provide the first evidence that IL-3 irreversibly inhibits RANK expression that results in inhibition of important signaling molecules induced by RANKL.

  9. Process and genes for expression and overexpression of active [FeFe] hydrogenases

    DOE Patents [OSTI]

    Seibert, Michael; King, Paul W; Ghirardi, Maria Lucia; Posewitz, Matthew C; Smolinski, Sharon L

    2014-09-16

    A process for expression of active [FeFe]-hydrogenase in a host organism that does not contain either the structural gene(s) for [FeFe]-hydrogenases and/or homologues for the maturation genes HydE, HydF and HyG, comprising: cloning the structural hydrogenase gene(s) and/or the maturation genes HydE, HydF and HydG from an organisms that contains these genes into expression plasmids; transferring the plasmids into an organism that lacks a native [FeFe]-hydrogenase or that has a disrupted [FeFe]-hydrogenase and culturing it aerobically; and inducing anaerobiosis to provide [FeFe] hydrogenase biosynthesis and H?2#191 production.

  10. In silico method for modelling metabolism and gene product expression at genome scale

    SciTech Connect (OSTI)

    Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem; Portnoy, Vasiliy A.; Lewis, Nathan E.; Orth, Jeffrey D.; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Zengler, Karsten; Palsson, Bernard O.

    2012-07-03

    Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.

  11. A Hybrid Approach to Protein Differential Expression in Mass Spectrometry-Based Proteomics

    SciTech Connect (OSTI)

    Wang, Xuan; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.

    2012-04-19

    Motivation: Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein's associated spectral peaks. However, typical MS-based proteomics data sets have substantial proportions of missing observations, due at least in part to censoring of low intensities. This complicates intensity-based differential expression analysis. Results: We outline a statistical method for protein differential expression, based on a simple Binomial likelihood. By modeling peak intensities as binary, in terms of 'presence/ absence,' we enable the selection of proteins not typically amendable to quantitative analysis; e.g., 'one-state' proteins that are present in one condition but absent in another. In addition, we present an analysis protocol that combines quantitative and presence/ absence analysis of a given data set in a principled way, resulting in a single list of selected proteins with a single associated FDR.

  12. Explicit expressions for three-dimensional boundary integrals in linear elasticity

    SciTech Connect (OSTI)

    Nintcheu Fata, Sylvain

    2011-01-01

    On employing isoparametric, piecewise linear shape functions over a flat triangle, exact formulae are derived for all surface potentials involved in the numerical treatment of three-dimensional singular and hyper-singular boundary integral equations in linear elasticity. These formulae are valid for an arbitrary source point in space and are represented as analytical expressions along the edges of the integration triangle. They can be employed to solve integral equations defined on triangulated surfaces via a collocation method or may be utilized as analytical expressions for the inner integrals in a Galerkin technique. A numerical example involving a unit triangle and a source point located at various distances above it, as well as sample problems solved by a collocation boundary element method for the Lame equation are included to validate the proposed formulae.

  13. Expression of POTE protein in human testis detected by novel monoclonal antibodies

    SciTech Connect (OSTI)

    Ise, Tomoko; Das, Sudipto; Nagata, Satoshi; Maeda, Hiroshi; Lee, Yoomi; Onda, Masanori; Anver, Miriam R.; Pastan, Ira

    2008-01-25

    The POTE gene family is composed of 13 highly homologous paralogs preferentially expressed in prostate, ovary, testis, and placenta. We produced 10 monoclonal antibodies (MAbs) against three representative POTE paralogs: POTE-21, POTE-2{gamma}C, and POTE-22. One reacted with all three paralogs, six MAbs reacted with POTE-2{gamma}C and POTE-22, and three MAbs were specific to POTE-21. Epitopes of all 10 MAbs were located in the cysteine-rich repeats (CRRs) motifs located at the N-terminus of each POTE paralog. Testing the reactivity of each MAb with 12 different CRRs revealed slight differences among the antigenic determinants, which accounts for differences in cross-reactivity. Using MAbs HP8 and PG5 we were able to detect a POTE-actin fusion protein in human testis by immunoprecipitation followed by Western blotting. By immunohistochemistry we demonstrated that the POTE protein is expressed in primary spermatocytes, implying a role in spermatogenesis.

  14. Microsoft Word - IARC_Expression of interest_Rev5_Nov2012.doc

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Rev.01/13/2012 Fermilab Technology Applications Program Expression of Interest Project/Proposal Name: Company/Institution Street Address Phone Company URL City, State, Zip Code Fax Contact Person Name Street Address Phone Title City, State, Zip Code Email Do you wish to have information in this EOI treated as proprietary? Yes No (please circle one) Provide additional comments if desired. Comments: Is your interest in the Fermilab Technology Applications Program "general" in nature or

  15. EIS-0450: TransWest Express Transmission Project; Wyoming, Colorado, Utah, and Nevada

    Broader source: Energy.gov [DOE]

    This EIS, prepared jointly by DOE's Western Area Power Administration and the Department of the Interior's Bureau of Land Management (Wyoming State Office), evaluates the potential environmental impacts of granting a right-of-way for the TransWest Express Transmission Project and amending a land use plan. The project consists of an overhead transmission line that would extend approximately 725 miles from south-central Wyoming, through Colorado and Utah. Western proposes to be a joint owner of the project.

  16. Homologous Expression of the Caldicellulosiruptor bescii CelA Reveals that the Extracellular Protein Is Glycosylated

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Chung, Daehwan; Young, Jenna; Bomble, Yannick J.; Vander Wall, Todd A.; Groom, Joseph; Himmel, Michael E.; Westpheling, Janet

    2015-03-23

    Members of the bacterial genus Caldicellulosiruptor are the most thermophilic cellulolytic microbes described with ability to digest lignocellulosic biomass without conventional pretreatment. The cellulolytic ability of different species varies dramatically and correlates with the presence of the multimodular cellulase CelA, which contains both a glycoside hydrolase family 9 endoglucanase and a glycoside hydrolase family 48 exoglucanase known to be synergistic in their activity, connected by three cellulose-binding domains via linker peptides. This architecture exploits the cellulose surface ablation driven by its general cellulase processivity as well as excavates cavities into the surface of the substrate, revealing a novel paradigm formore » cellulase activity. We recently reported that a deletion of celA in C. bescii had a significant effect on its ability to utilize complex biomass. To analyze the structure and function of CelA and its role in biomass deconstruction, we constructed a new expression vector for C. bescii and were able, for the first time, to express significant quantities of full-length protein in vivo in the native host. The protein, which contains a Histidine tag, was active and excreted from the cell. Expression of CelA protein with and without its signal sequence allowed comparison of protein retained intracellularly to protein transported extracellularly. Analysis of protein in culture supernatants revealed that the extracellular CelA protein is glycosylated whereas the intracellular CelA is not, suggesting that either protein transport is required for this post-translational modification or that glycosylation is required for protein export. The mechanism and role of protein glycosylation in bacteria is poorly understood and the ability to express CelA in vivo in C. bescii will allow the study of the mechanism of protein glycosylation in this thermophile. Finally, it will also allow the study of glycosylation of CelA itself and its role

  17. Expression analysis and prognostic significance of the SRA1 gene, in ovarian cancer

    SciTech Connect (OSTI)

    Leoutsakou, Theoni; Talieri, Maroulio; Scorilas, Andreas . E-mail: ascorilas@biol.uoa.gr

    2006-06-02

    The SR-related-CTD-associated-factors (SCAFs) have the ability to interact with the C-terminal domain of the RNA polymerase II, linking this way transcription to splicing. SRA1 (SR-A1) gene, encoding for a human high-molecular weight SCAF protein, is located on chromosome 19, between the IRF3 and the R-RAS oncogene and it has been demonstrated from members of our group that SRA1 is constitutively expressed in most of the human tissues, while it is overexpressed in a subset of ovarian tumors. In this study, we examine the expression of SRA1 gene in 111 ovarian malignant tissues and in the human ovarian carcinoma cell lines OVCAR-3, TOV21-G, and ES-2, using a semi-quantitative RT-PCR method. SRA1 gene was overexpressed in 61/111 (55%) of ovarian carcinomas. This higher expression was positively associated to the size of the tumor (p < 0.001), the grade and the stage of the disease (p = 0.003 and p = 0.006, respectively), and the debulking success (p < 0.001). Kaplan-Meier survival analysis revealed that lower SRA1 expression increases the probability of both the longer overall and the progression free survival of the patients. Multivariate Cox regression analysis revealed that SRA1 may be used as an independent prognostic biomarker in ovarian cancer. Our results suggest that SRA1 is associated with cancer progression and may possibly be characterized as a new marker of unfavorable prognosis for ovarian cancer.

  18. DOE Environmental Impact Statement Public Scoping Meeting on Champlain Hudson Power Express Transmission Line Project

    Broader source: Energy.gov [DOE]

    The Department of Energy (DOE) is hosting seven meetings for public participation as part of its Environmental Impact Statement (EIS) preparation process pursuant to the National Environmental Policy Act (NEPA) to assess the potential environmental impacts from its proposed action of granting a Presidential permit to Champlain Hudson Power Express, Inc., to construct, operate, maintain, and connect a new electric transmission line across the U.S.- Canada border in northeastern New York.

  19. Microsoft Word - CafeExpressSecurityFormFinal June 2012 v2.doc

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Café Systems Express Access Form Version: 06/2012 Page 1 of 2 Applicant Information □ New User □ School or Department Transfer □ Inactivate *Date *NetID *Name (Last, First MI) *EMPLID Title NU Email Department Work Phone * indicates required field NUFinancials - Data Entry and Inquiry OPTIONAL: Model an existing user's access: Name: ____________________________ NetID: _________ □ Expense Entry and iBuyNU Shopper □ Budget Journal Entry □ CRT Entry □ CRT Inquiry □ Expense Entry,

  20. Stabilization of gene expression and cell morphology after explant recycling during fin explant culture in goldfish

    SciTech Connect (OSTI)

    Chenais, Nathalie; Lareyre, Jean-Jacques; Le Bail, Pierre-Yves; Labbe, Catherine

    2015-07-01

    The development of fin primary cell cultures for in vitro cellular and physiological studies is hampered by slow cell outgrowth, low proliferation rate, poor viability, and sparse cell characterization. Here, we investigated whether the recycling of fresh explants after a first conventional culture could improve physiological stability and sustainability of the culture. The recycled explants were able to give a supplementary cell culture showing faster outgrowth, cleaner cell layers and higher net cell production. The cells exhibited a highly stabilized profile for marker gene expression including a low cytokeratin 49 (epithelial marker) and a high collagen 1a1 (mesenchymal marker) expression. Added to the cell spindle-shaped morphology, motility behavior, and actin organization, this suggests that the cells bore stable mesenchymal characteristics. This contrast with the time-evolving expression pattern observed in the control fresh explants during the first 2 weeks of culture: a sharp decrease in cytokeratin 49 expression was concomitant with a gradual increase in col1a1. We surmise that such loss of epithelial features for the benefit of mesenchymal ones was triggered by an epithelial to mesenchymal transition (EMT) process or by way of a progressive population replacement process. Overall, our findings provide a comprehensive characterization of this new primary culture model bearing mesenchymal features and whose stability over culture time makes those cells good candidates for cell reprogramming prior to nuclear transfer, in a context of fish genome preservation. - Highlights: • Recycled fin explants outgrow cells bearing stable mesenchymal traits. • Cell production and quality is enhanced in the recycled explant culture system. • Fresh fin primary culture is highly variable and loose epithelial traits over time.

  1. AG490 inhibits NFATc1 expression and STAT3 activation during RANKL induced osteoclastogenesis

    SciTech Connect (OSTI)

    Li, Chang-hong; Zhao, Jin-xia; Sun, Lin; Yao, Zhong-qiang; Deng, Xiao-li; Liu, Rui; Liu, Xiang-yuan

    2013-06-14

    Highlights: AG490 inhibits RANKL-induced osteoclastogenesis in RAW264.7 cells. AG490 affects cell proliferation and cell cycle distribution. AG490 reduces NFATc1 expression during RANKL-induced osteoclastogenesis. AG490 disrupts the activation of RANKL-mediated JAK2/STAT3 signaling pathway. STAT3 depletion partly mimics the effect of AG490 on RANKL-induced osteoclastogenesis. -- Abstract: Commonly, JAK/STAT relays cytokine signals for cell activation and proliferation, and recent studies have shown that the elevated expression of JAK/STAT is associated with the immune rejection of allografts and the inflammatory processes of autoimmune disease. However, the role which JAK2/STAT3 signaling plays in the receptor activator of nuclear factor-?B ligand (RANKL)-mediated osteoclastogenesis is unknown. In this study, we investigated the effects of AG490, specific JAK2 inhibitor, on osteoclast differentiation in vitro. AG490 significantly inhibited osteoclastogenesis in murine osteoclast precursor cell line RAW264.7 induced by RANKL. AG490 suppressed cell proliferation and delayed the G1 to S cell cycle transition. Furthermore, AG490 also suppressed the expression of nuclear factor of activated T cells (NFAT) c1 but not c-Fos in RAW264.7. Subsequently, we investigated various intracellular signaling components associated with osteoclastogenesis. AG490 had no effects on RANKL-induced activation of Akt, ERK1/2. Interestingly, AG490 partly inhibited RANKL-induced phosphorylation of Ser{sup 727} in STAT3. Additionally, down-regulation of STAT3 using siRNA resulted in suppression of TRAP, RANK and NFATc1 expression. In conclusion, we demonstrated that AG490 inhibited RANKL-induced osteoclastogenesis by suppressing NFATc1 production and cell proliferation via the STAT3 pathway. These results suggest that inhibition of JAK2 may be useful for the treatment of bone diseases characterized by excessive osteoclastogenesis.

  2. Tigutcystatin, a cysteine protease inhibitor from Triatoma infestans midgut expressed in response to Trypanosoma cruzi

    SciTech Connect (OSTI)

    Buarque, Diego S.; Spindola, Leticia M.N.; Martins, Rafael M.; Braz, Gloria R.C.; Tanaka, Aparecida S.

    2011-09-23

    Highlights: {yields} Tigutcystatin inhibits Trypanosoma cruzi cysteine proteases with high specificity. {yields} Tigutcystatin expression is up-regulated in response to T. cruzi infection. {yields} It is the first cysteine proteases inhibitor characterized from a triatomine insect. -- Abstract: The insect Triatoma infestans is a vector of Trypanosoma cruzi, the etiological agent of Chagas disease. A cDNA library was constructed from T. infestans anterior midgut, and 244 clones were sequenced. Among the EST sequences, an open reading frame (ORF) with homology to a cystatin type 2 precursor was identified. Then, a 288-bp cDNA fragment encoding mature cystatin (lacking signal peptide) named Tigutcystatin was cloned fused to a N-terminal His tag in pET-14b vector, and the protein expressed in Escherichia coli strain Rosetta gami. Tigutcystatin purified and cleaved by thrombin to remove His tag presented molecular mass of 11 kDa and 10,137 Da by SDS-PAGE and MALDI-TOF mass spectrometry, respectively. Purified Tigutcystatin was shown to be a tight inhibitor towards cruzain, a T. cruzi cathepsin L-like enzyme (K{sub i} = 3.29 nM) and human cathepsin L (K{sub i} = 3.78 nM). Tissue specific expression analysis showed that Tigutcystatin was mostly expressed in anterior midgut, although amplification in small intestine was also detected by semi quantitative RT-PCR. qReal time PCR confirmed that Tigutcystatin mRNA is significantly up-regulated in anterior midgut when T. infestans is infected with T. cruzi. Together, these results indicate that Tigutcystatin may be involved in modulation of T. cruzi in intestinal tract by inhibiting parasite cysteine proteases, which represent the virulence factors of this protozoan.

  3. Head and Neck Squamous Cell Carcinomas Do Not Express EGFRvIII

    SciTech Connect (OSTI)

    Melchers, Lieuwe J.; Clausen, Martijn J.A.M.; Mastik, Mirjam F.; Slagter-Menkema, Lorian; Laan, Bernard F.A.M. van der; Roodenburg, Jan L.N.; Schuuring, Ed

    2014-10-01

    Purpose: To assess the prevalence of EGFRvIII, a specific variant of EGFR (epidermal growth factor receptor), in 3 well-defined cohorts of head and neck squamous cell carcinoma (HNSCC). Methods and Materials: Immunohistochemistry for the specific detection of EGFRvIII using the L8A4 antibody was optimized on formalin-fixed, paraffin-embedded tissue using glioblastoma tissue. It was compared with EGFR and EGFRvIII RNA expression using a specific reverse transcription–polymerase chain reaction also optimized for formalin-fixed, paraffin-embedded tissue. Tissue microarrays including 531 HNSCCs of various stages with complete clinicopathologic and follow-up data were tested for the presence of EGFRvIII. Results: None of the 531 cases showed EGFRvIII protein expression. Using an immunohistochemistry protocol reported by others revealed cytoplasmic staining in 8% of cases. Reverse transcription–polymerase chain reaction for the EGFRvIII transcript of the 28 highest cytoplasmic staining cases, as well as 69 negative cases, did not show expression in any of the tested cases, suggesting aspecific staining by a nonoptimal protocol. Conclusions: The EGFRvIII mutation is not present in HNSCC. Therefore, EGFRvIII does not influence treatment response in HNSCC and is not a usable clinical prognostic marker.

  4. Adult rat bone marrow stromal cells express genes associated with dopamine neurons

    SciTech Connect (OSTI)

    Kramer, Brian C.; Woodbury, Dale . E-mail: WOODBURYDL@AOL.COM; Black, Ira B.

    2006-05-19

    An intensive search is underway to identify candidates to replace the cells that degenerate in Parkinson's disease (PD). To date, no suitable substitute has been found. We have recently found that adult rat bone marrow stromal cells (MSCs) can be induced to assume a neuronal phenotype in vitro. These findings may have particular relevance to the treatment of PD. We now report that adult MSCs express multiple dopaminergic genes, suggesting that they are potential candidates for cell therapy. Using RT-PCR, we have examined families of genes that are associated with the development and/or survival of dopaminergic neurons. MSCs transcribe a variety of dopaminergic genes including patched and smoothened (components of the Shh receptor), Gli-1 (downstream mediator of Shh), and Otx-1, a gene associated with formation of the mesencephalon during development. Furthermore, Shh treatment elicits a 1.5-fold increase in DNA synthesis in cultured MSCs, suggesting the presence of a functional Shh receptor complex. We have also found that MSCs transcribe and translate Nurr-1, a nuclear receptor essential for the development of dopamine neurons. In addition, MSCs express a variety of growth factor receptors including the glycosyl-phosphatidylinositol-anchored ligand-binding subunit of the GDNF receptor, GFR{alpha}1, as well as fibroblast growth factor receptors one and four. The expression of genes that are associated with the development and survival of dopamine neurons suggests a potential role for these cells in the treatment of Parkinson's disease.

  5. Nutlin-3 down-regulates retinoblastoma protein expression and inhibits muscle cell differentiation

    SciTech Connect (OSTI)

    Walsh, Erica M.; Niu, MengMeng; Bergholz, Johann; Jim Xiao, Zhi-Xiong

    2015-05-29

    The p53 tumor suppressor gene plays a critical role in regulation of proliferation, cell death and differentiation. The MDM2 oncoprotein is a major negative regulator for p53 by binding to and targeting p53 for proteasome-mediated degradation. The small molecule inhibitor, nutlin-3, disrupts MDM2-p53 interaction resulting in stabilization and activation of p53 protein. We have previously shown that nutlin-3 activates p53, leading to MDM2 accumulation as concomitant of reduced retinoblastoma (Rb) protein stability. It is well known that Rb is important in muscle development and myoblast differentiation and that rhabdomyosarcoma (RMS), or cancer of the skeletal muscle, typically harbors MDM2 amplification. In this study, we show that nutlin-3 inhibited myoblast proliferation and effectively prevented myoblast differentiation, as evidenced by lack of expression of muscle differentiation markers including myogenin and myosin heavy chain (MyHC), as well as a failure to form multinucleated myotubes, which were associated with dramatic increases in MDM2 expression and decrease in Rb protein levels. These results indicate that nutlin-3 can effectively inhibit muscle cell differentiation. - Highlights: • Nutlin-3 inhibits myoblast proliferation and prevents differentiation into myotubes. • Nutlin-3 increases MDM2 expression and down-regulates Rb protein levels. • This study has implication in nutlin-3 treatment of rhabdomyosarcomas.

  6. Gene expression profiling--Opening the black box of plant ecosystem responses to global change

    SciTech Connect (OSTI)

    Leakey, A.D.B.; Ainsworth, E.A.; Bernard, S.M.; Markelz, R.J.C.; Ort, D.R.; Placella, S.A.P.; Rogers, A.; Smith, M.D.; Sudderth, E.A.; Weston, D.J.; Wullschleger, S.D.; Yuan, S.

    2009-11-01

    The use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Since the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the 'black box' of unknown mechanism. Various tools and approaches are available for assessing gene expression in model and non-model species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.

  7. Expression of HPV16 E5 produces enlarged nuclei and polyploidy through endoreplication

    SciTech Connect (OSTI)

    Hu Lulin; Potapova, Tamara A.; Li Shibo; Rankin, Susannah; Gorbsky, Gary J.; Angeletti, Peter C.; Ceresa, Brian P.

    2010-09-30

    Anogenital cancers and head and neck cancers are causally associated with infection by high-risk human papillomavirus (HPV). The mechanism by which high-risk HPVs contribute to oncogenesis is poorly understood. HPV16 encodes three genes (HPV16 E5, E6, and E7) that can transform cells when expressed independently. HPV16 E6 and E7 have well-described roles causing genomic instability and unregulated cell cycle progression. The role of HPV16 E5 in cell transformation remains to be elucidated. Expression of HPV16 E5 results in enlarged, polyploid nuclei that are dependent on the level and duration of HPV16 E5 expression. Live cell imaging data indicate that these changes do not arise from cell-cell fusion or failed cytokinesis. The increase in nuclear size is a continual process that requires DNA synthesis. We conclude that HPV16 E5 produces polyploid cells by endoreplication. These findings provide insight into how HPV16 E5 can contribute to cell transformation.

  8. Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes

    SciTech Connect (OSTI)

    Wang, Xuting; Tomso, Daniel J.; Liu Xuemei; Bell, Douglas A. . E-mail: BELL1@niehs.nih.gov

    2005-09-01

    Single nucleotide polymorphisms (SNPs) in the human genome are DNA sequence variations that can alter an individual's response to environmental exposure. SNPs in gene coding regions can lead to changes in the biological properties of the encoded protein. In contrast, SNPs in non-coding gene regulatory regions may affect gene expression levels in an allele-specific manner, and these functional polymorphisms represent an important but relatively unexplored class of genetic variation. The main challenge in analyzing these SNPs is a lack of robust computational and experimental methods. Here, we first outline mechanisms by which genetic variation can impact gene regulation, and review recent findings in this area; then, we describe a methodology for bioinformatic discovery and functional analysis of regulatory SNPs in cis-regulatory regions using the assembled human genome sequence and databases on sequence polymorphism and gene expression. Our method integrates SNP and gene databases and uses a set of computer programs that allow us to: (1) select SNPs, from among the >9 million human SNPs in the NCBI dbSNP database, that are similar to cis-regulatory element (RE) consensus sequences; (2) map the selected dbSNP entries to the human genome assembly in order to identify polymorphic REs near gene start sites; (3) prioritize the candidate polymorphic RE containing genes by searching the existing genotype and gene expression data sets. The applicability of this system has been demonstrated through studies on p53 responsive elements and is being extended to additional pathways and environmentally responsive genes.

  9. Thymosin beta 4 expression and nuclear transport are regulated by hMLH1

    SciTech Connect (OSTI)

    Brieger, Angela Plotz, Guido; Zeuzem, Stefan; Trojan, Joerg

    2007-12-28

    For hMLH1, a key enzyme of DNA mismatch repair and frequently mutated in human cancers, several additional functions have been suggested. We now identified Thymosin {beta}{sub 4} (T{beta}{sub 4}), an actin-binding and cell motility regulating protein, by bacterial two-hybrid screening. Interaction was confirmed by coimmunoprecipitation. T{beta}{sub 4} was weakly expressed in the hMLH1-deficient cell lines 293T and HCT-116. Reconstitution of hMLH1 resulted in strong expression of T{beta}{sub 4}. Confocal laser microscopy revealed nuclear colocalization of both proteins. Reconstitution with hMLH1 mutants lacking a functional nuclear localization sequence resulted in cytoplasmatic retention of both proteins. After T{beta}{sub 4}- or hMLH1-siRNA treatment, cell migration of hMLH1-proficient cells was markedly decreased. Our results show that hMLH1 interacts with T{beta}{sub 4} and regulates its expression and nuclear transport. Moreover, loss of hMLH1 causes T{beta}{sub 4} deprivation and results in reduced migratory activity in vitro. These data give insight into novel functions of hMLH1 and probably disease related dysregulated mechanisms.

  10. Claudin-3 expression in radiation-exposed rat models: A potential marker for radiation-induced intestinal barrier failure

    SciTech Connect (OSTI)

    Shim, Sehwan; Lee, Jong-geol; Bae, Chang-hwan; Lee, Seung Bum; Jang, Won-Suk; Lee, Sun-Joo; Lee, Seung-Sook; Park, Sunhoo

    2015-01-02

    Highlights: • Irradiation increased intestinal bacterial translocation, accompanied by claudin protein expression in rats. • Neurotensin decreased the bacterial translocation and restored claudin-3 expression. • Claudin-3 can be used as a marker in evaluating radiation induced intestinal injury. - Abstract: The molecular events leading to radiation-induced intestinal barrier failure are not well known. The influence of the expression of claudin proteins in the presence and absence of neurotensin was investigated in radiation-exposed rat intestinal epithelium. Wistar rats were randomly divided into control, irradiation, and irradiation + neurotensin groups, and bacterial translocation to the mesenteric lymph node and expression of claudins were determined. Irradiation led to intestinal barrier failure as demonstrated by significant bacterial translocation. In irradiated terminal ilea, expression of claudin-3 and claudin-4 was significantly decreased, and claudin-2 expression was increased. Administration of neurotensin significantly reduced bacterial translocation and restored the structure of the villi as seen by histologic examination. Among the three subtype of claudins, only claudin-3 expression was restored. These results suggest that the therapeutic effect of neurotensin on the disruption of the intestinal barrier is associated with claudin-3 alteration and that claudin-3 could be used as a marker in evaluating radiation-induced intestinal injury.

  11. Thalidomide induced early gene expression perturbations indicative of human embryopathy in mouse embryonic stem cells

    SciTech Connect (OSTI)

    Gao, Xiugong Sprando, Robert L.; Yourick, Jeffrey J.

    2015-08-15

    Developmental toxicity testing has traditionally relied on animal models which are costly, time consuming, and require the sacrifice of large numbers of animals. In addition, there are significant disparities between human beings and animals in their responses to chemicals. Thalidomide is a species-specific developmental toxicant that causes severe limb malformations in humans but not in mice. Here, we used microarrays to study transcriptomic changes induced by thalidomide in an in vitro model based on differentiation of mouse embryonic stem cells (mESCs). C57BL/6 mESCs were allowed to differentiate spontaneously and RNA was collected at 24, 48, and 72 h after exposure to 0.25 mM thalidomide. Global gene expression analysis using microarrays revealed hundreds of differentially expressed genes upon thalidomide exposure that were enriched in gene ontology (GO) terms and canonical pathways associated with embryonic development and differentiation. In addition, many genes were found to be involved in small GTPases-mediated signal transduction, heart development, and inflammatory responses, which coincide with clinical evidences and may represent critical embryotoxicities of thalidomide. These results demonstrate that transcriptomics in combination with mouse embryonic stem cell differentiation is a promising alternative model for developmental toxicity assessment. - Highlights: • Studied genomic changes in mouse embryonic stem cells upon thalidomide exposure • Identified gene expression changes that may represent thalidomide embryotoxicity • The toxicogenomic changes coincide well with known thalidomide clinical outcomes. • The mouse embryonic stem cell model is suitable for developmental toxicity testing. • The model has the potential for high-throughput screening of a multitude of compounds.

  12. A bacterial model for expression of mutations in the human ornithine transcarbamylase (OTC) gene

    SciTech Connect (OSTI)

    Tuchman, M.; McCann, M.T.; Qureshi, A.A.

    1994-09-01

    OTC is a mitochondrial enzyme catalyzing the formation of citrulline from carbamyl phosphate and ornithine. X-linked deficiency of OTC is the most prevalent genetic defect of ureagenesis. Mutations and polymorphisms in the OTC gene identified in deficient patients have indicated the occurrence of many family-specific, unique alleles. Due to the low frequency of recurrent mutations, distinguishing between deleterious mutations and polymorphisms is difficult. Using a human OTC gene containing plasmid driven by a tac promoter, we have devised a simple and efficient method for expressing mutations in the mature human OTC enzyme. To demonstrate this method, PCR engineered site-directed mutagenesis was employed to generated cDNA fragments which contained either the R151Q or R277W known mutations found in patients with neonatal and late-onset OTC deficiency, respectively. The normal allele for each mutation was also generated by an identical PCR procedure. Digestion with Bgl II- and Sty I-generated mutant and normal replacement cassettes containing the respective mutant and wild type sequences. Upon transformation of JM109 E.coli cells, OTC enzymatic activity was measured at log and stationary phases of growth using a radiochromatographic method. The R141Q mutation abolished enzymatic activity (<0.02% of normal), whereas the R277W mutation expressed partial activity (2.3% of normal). In addition, a PCR-generated mutation, A280V, resulted in 73% loss of catalytic activity. This OTC expression system is clinically applicable for distinguishing between mutations and polymorphisms, and it can be used to investigate the effects of mutations on various domains of the OTC gene.

  13. The effects of deoxynivalenol on gene expression in the murine thymus

    SciTech Connect (OSTI)

    Kol, Sandra W.M. van; Hendriksen, Peter J.M.; Loveren, Henk van; Peijnenburg, Ad

    2011-02-01

    Deoxynivalenol (DON) is a mycotoxin produced by several Fusarium species and is often detected in grains. Because of its high abundance, there has been a large interest in the effects of DON in animals and humans. DON is known to be immunosuppressive at high concentrations and immunostimulatory at low concentrations. The present study aimed to acquire insight into the modes of action of DON. For this, C57Bl6 mice were orally exposed to 5, 10, or 25 mg/kg bw DON for 3, 6, or 24 h and thymuses were subjected to genome-wide expression microarray analysis. Gene set enrichment analysis (GSEA) demonstrated that DON downregulated genes involved in proliferation, mitochondria, protein synthesis, and ribosomal proteins. Furthermore, GSEA showed a selective downregulation of genes highly expressed at the early precursor thymocytes stage. This indicates that early precursor thymocytes, particularly at the double-positive CD4+CD8+ stage, are more vulnerable to DON than very early or late precursor thymocytes. There was a large overlap of genes upregulated by DON with genes previously reported to be either upregulated during T cell activation or upregulated during negative selection of thymocytes that recognize 'self-antigens'. This indicates that DON induces cellular events that also occur after activation of the T cell receptor, for example, release of calcium from the endoplasmatic reticulum. This T cell activation in the thymus then evokes negative selection and depletion of thymocytes, which provides a plausible explanation for the high sensitivity of the thymus for DON exposure. The expression patterns of four genes indicative for some of the processes that were affected after DON treatment were confirmed using real-time PCR. Immunocytological experiments with primary mouse thymocytes demonstrated the translocation of NFAT from the cytoplasm into the nucleus upon exposure top DON, thus providing further evidence for the involvement of T cell activation.

  14. Influence of heart failure on nucleolar organization and protein expression in human hearts

    SciTech Connect (OSTI)

    Rosello-Lleti, Esther; Rivera, Miguel; Cortes, Raquel; Azorin, Inmaculada; Sirera, Rafael; Martinez-Dolz, Luis; Hove, Leif; Cinca, Juan; Lago, Francisca; Gonzalez-Juanatey, Jose R.; Salvador, Antonio; Portoles, Manuel

    2012-02-10

    Highlights: Black-Right-Pointing-Pointer Heart failure alters nucleolar morphology and organization. Black-Right-Pointing-Pointer Nucleolin expression is significant increased in ischemic and dilated cardiomyopathy. Black-Right-Pointing-Pointer Ventricular function of heart failure patients was related with nucleolin levels. -- Abstract: We investigate for the first time the influence of heart failure (HF) on nucleolar organization and proteins in patients with ischemic (ICM) or dilated cardiomyopathy (DCM). A total of 71 human hearts from ICM (n = 38) and DCM (n = 27) patients, undergoing heart transplantation and control donors (n = 6), were analysed by western-blotting, RT-PCR and cell biology methods. When we compared protein levels according to HF etiology, nucleolin was increased in both ICM (117%, p < 0.05) and DCM (141%, p < 0.01). Moreover, mRNA expression were also upregulated in ICM (1.46-fold, p < 0.05) and DCM (1.70-fold, p < 0.05. Immunofluorescence studies showed that the highest intensity of nucleolin was into nucleolus (p < 0.0001), and it was increased in pathological hearts (p < 0.0001). Ultrastructure analysis by electron microscopy showed an increase in the nucleus and nucleolus size in ICM (17%, p < 0.05 and 131%, p < 0.001) and DCM (56%, p < 0.01 and 69%, p < 0.01). Nucleolar organization was influenced by HF irrespective of etiology, increasing fibrillar centers (p < 0.001), perinucleolar chromatin (p < 0.01) and dense fibrillar components (p < 0.01). Finally, left ventricular function parameters were related with nucleolin levels in ischemic hearts (p < 0.0001). The present study demonstrates that HF influences on morphology and organization of nucleolar components, revealing changes in the expression and in the levels of nucleolin protein.

  15. Oxidative stress/reactive metabolite gene expression signature in rat liver detects idiosyncratic hepatotoxicants

    SciTech Connect (OSTI)

    Leone, Angelique; Nie, Alex; Brandon Parker, J.; Sawant, Sharmilee; Piechta, Leigh-Anne; Kelley, Michael F. Mark Kao, L.; Jim Proctor, S.; Verheyen, Geert; Johnson, Mark D.; Lord, Peter G.; McMillian, Michael K.

    2014-03-15

    Previously we reported a gene expression signature in rat liver for detecting a specific type of oxidative stress (OS) related to reactive metabolites (RM). High doses of the drugs disulfiram, ethinyl estradiol and nimesulide were used with another dozen paradigm OS/RM compounds, and three other drugs flutamide, phenacetin and sulindac were identified by this signature. In a second study, antiepileptic drugs were compared for covalent binding and their effects on OS/RM; felbamate, carbamazepine, and phenobarbital produced robust OS/RM gene expression. In the present study, liver RNA samples from drug-treated rats from more recent experiments were examined for statistical fit to the OS/RM signature. Of all 97 drugs examined, in addition to the nine drugs noted above, 19 more were identified as OS/RM-producing compounds—chlorpromazine, clozapine, cyproterone acetate, dantrolene, dipyridamole, glibenclamide, isoniazid, ketoconazole, methapyrilene, naltrexone, nifedipine, sulfamethoxazole, tamoxifen, coumarin, ritonavir, amitriptyline, valproic acid, enalapril, and chloramphenicol. Importantly, all of the OS/RM drugs listed above have been linked to idiosyncratic hepatotoxicity, excepting chloramphenicol, which does not have a package label for hepatotoxicity, but does have a black box warning for idiosyncratic bone marrow suppression. Most of these drugs are not acutely toxic in the rat. The OS/RM signature should be useful to avoid idiosyncratic hepatotoxicity of drug candidates. - Highlights: • 28 of 97 drugs gave a positive OS/RM gene expression signature in rat liver. • The specificity of the signature for human idiosyncratic hepatotoxicants was 98%. • The sensitivity of the signature for human idiosyncratic hepatotoxicants was 75%. • The signature can help eliminate hepatotoxicants from drug development.

  16. Heat flux expressions that satisfy the conservation laws in atomistic system involving multibody potentials

    SciTech Connect (OSTI)

    Fu, Yao Song, Jeong-Hoon

    2015-08-01

    Heat flux expressions are derived for multibody potential systems by extending the original Hardy's methodology and modifying Admal & Tadmor's formulas. The continuum thermomechanical quantities obtained from these two approaches are easy to compute from molecular dynamics (MD) results, and have been tested for a constant heat flux model in two distinctive systems: crystalline iron and polyethylene (PE) polymer. The convergence criteria and affecting parameters, i.e. spatial and temporal window size, and specific forms of localization function are found to be different between the two systems. The conservation of mass, momentum, and energy are discussed and validated within this atomistic–continuum bridging.

  17. Compositions and methods for the expression of selenoproteins in eukaryotic cells

    DOE Patents [OSTI]

    Gladyshev, Vadim; Novoselov, Sergey

    2012-09-25

    Recombinant nucleic acid constructs for the efficient expression of eukaryotic selenoproteins and related methods for production of recombinant selenoproteins are provided. The nucleic acid constructs comprise novel selenocysteine insertion sequence (SECIS) elements. Certain novel SECIS elements of the invention contain non-canonical quartet sequences. Other novel SECIS elements provided by the invention are chimeric SECIS elements comprising a canonical SECIS element that contains a non-canonical quartet sequence and chimeric SECIS elements comprising a non-canonical SECIS element that contains a canonical quartet sequence. The novel SECIS elements of the invention facilitate the insertion of selenocysteine residues into recombinant polypeptides.

  18. Suppression of Tla1 gene expression for improved solar conversion efficiency and photosynthetic productivity in plants and algae

    DOE Patents [OSTI]

    Melis, Anastasios; Mitra, Mautusi

    2010-06-29

    The invention provides method and compositions to minimize the chlorophyll antenna size of photosynthesis by decreasing TLA1 gene expression, thereby improving solar conversion efficiencies and photosynthetic productivity in plants, e.g., green microalgae, under bright sunlight conditions.

  19. miR-208-3p promotes hepatocellular carcinoma cell proliferation and invasion through regulating ARID2 expression

    SciTech Connect (OSTI)

    Yu, Peng; Wu, Dingguo; You, Yu; Sun, Jing; Lu, Lele; Tan, Jiaxing; Bie, Ping

    2015-08-15

    MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate gene expression at post-transcriptional level. miRNA dysregulation plays a causal role in cancer progression. In this study, miR-208-3p was highly expressed and directly repressed ARID2 expression. As a result, ARID2 expression in hepatocellular carcinoma (HCC) was decreased. In vitro, miR-208-3p down-regulation and ARID2 over-expression elicited similar inhibitory effects on HCC cell proliferation and invasion. In vivo test results revealed that miR-208-3p down-regulation inhibited HCC tumorigenesis in Hep3B cells. Moreover, ARID2 was possibly a downstream element of transforming growth factor beta1 (TGFβ1)/miR-208-3p/ARID2 regulatory pathway. These findings suggested that miR-208-3p up-regulation is associated with HCC cell progression and may provide a new target for liver cancer treatment. - Highlights: • miR-208-3p was highly expressed and directly repressed the expression of ARID2 in HCC. • miR-208-3p contributed to HCC cell progression both in vitro and in vivo. • Over-expression of ARID2 inhibited the HCC cell proliferation and invasion. • Restoration of ARID2 partly reversed the the effect of miR-208-3p down-regulation on HCC cells. • Newly regulatory pathway: miR-208-3p mediated the repression of ARID2 by TGFβ1 in HCC cells.

  20. 27-Oxygenated cholesterol induces expression of CXCL8 in macrophages via NF-κB and CD88

    SciTech Connect (OSTI)

    Kim, Sun-Mi; Lee, Chung Won; Kim, Bo-Young; Jung, Young-Suk; Eo, Seong-Kug; Park, Young Chul; Kim, Koanhoi

    2015-08-07

    We attempted to determine the effects of a milieu rich in cholesterol molecules on expression of chemokine CXCL8. A high-cholesterol diet led to an increased transcription of the IL-8 gene in the arteries and elevated levels of CXCL8 in sera of ApoE{sup −/−} mice, compared with those of wild-type C57BL/6 mice. Treatment of THP-1 monocyte/macrophage cells with 27-hydroxycholesterol (27OHChol) resulted in transcription of the IL-8 gene and increased secretion of its corresponding gene product whereas cholesterol did not induce expression of CXCL8 in THP-1 cells. 27OHChol-induced transcription of the IL-8 gene was blocked by cycloheximide, but not by polymyxin B. Treatment of THP-1 cells with 27OHChol caused translocation of p65 NF-κB subunit into the nucleus and up-regulation of CD88. Inhibition of NF-κB and CD88 using SN50 and W-54011, respectively, resulted in reduced transcription of the IL-8 gene and attenuated secretion of CXCL8 induced by 27OHChol. We propose that oxidatively modified cholesterol like 27OHChol, rather than cholesterol, is responsible for sustained expression of CXCL8 in monocytes/macrophages in atherosclerotic arteries. - Highlights: • Consumption of a high-cholesterol diet leads to increased CXCL8 expression in ApoE{sup −/−} mice. • 27OHChol, but not cholesterol, up-regulates expression of CXCL8 in macrophages. • 27OHChol enhances nuclear translocation of NF-κB and expression of CD88 in macrophages. • Inhibition of NF-κB or CD88 results in decreased CXCL8 expression induced by 27OHChol. • 27OHChol up-regulates CXCL8 expression via NF-κB and CD88 in macrophages.

  1. Loss of expression of miR-335 is implicated in hepatic stellate cell migration and activation

    SciTech Connect (OSTI)

    Chen, Chao; Wu, Chao-Qun; Zhang, Zong-Qi; Yao, Ding-Kang; Zhu, Liang

    2011-07-15

    Activation and migration of resident stellate cells (HSCs) within the hepatic space of Disse play an important role in hepatic fibrosis, which accounts for the increased numbers of activated HSCs in areas of inflammation during hepatic fibrosis. Currently, microRNAs have been found to play essential roles in HSC differentiation, proliferation, apoptosis, fat accumulation and collagen production. However, little is known about microRNA mediated HSC activation and migration. In this study, the miRNA expression profiles of quiescent HSCs, partially activated HSCs and fully activated HSCs were compared in pairs. Gene ontology (GO) and GO-Map network analysis indicated that the activation of HSCs was regulated by microRNAs. Among them miR-335 was confirmed to be significantly reduced during HSC activation by qRT-PCR, and restoring expression of miR-335 inhibited HSC migration and reduced {alpha}-SMA and collagen type I. Previous study revealed that tenascin-C (TNC), an extracellular matrix glycoprotein involved in cell migration, might be a target of miR-335. Therefore, we further studied the TNC expression in miR-335 over-expressed HSCs. Our data showed that exogenous TNC could enhance HSC migration in vitro and miR-335 restoration resulted in a significant inhibition of TNC expression. These results demonstrated that miR-335 restoration inhibited HSC migration, at least in part, via downregulating the TNC expression.

  2. Kinetics of expression of interleukin 2 receptors on class I and class II restricted murine T cell clones

    SciTech Connect (OSTI)

    Churilla, A.; Braciale, V.; Braciale, T.

    1986-03-05

    The kinetics of interleukin 2 receptor (IL-2R) expression has been examined on various class I and class II restricted, influenza specific murine T cell clones. Expression and relative levels of IL-2R were examined by Fluorescence Activated Cell Sorter analysis utilizing 3 anti-murine IL-2R monoclonal antibodies. Receptor expression was analyzed by scatchard analysis using radiolabeled recombinant human interleukin 2 to access the number of high and low affinity IL-2R per cell as well as the affinity of binding. The clones tested bound all 3 monoclonal antibodies and were inhibited in an IL-2 dependent proliferation assay by the addition of the antibodies to the culture. There was, however, differing degrees of inhibition ranging up to 99%, depending on the clone and the antibody used. IL-2R expression was detectable as early as 4-6 hours after antigenic stimulation of quiescent cells. After maximal levels of receptors were expressed, which was about 24 hours after stimulation, expression of IL-2R decreased with time on all clones examined (both class I and class II restricted). Differing rates of receptor loss is seen however, with some class II restricted clones retaining relatively high levels of receptors.

  3. Radiation-Induced Upregulation of Gene Expression From Adenoviral Vectors Mediated by DNA Damage Repair and Regulation

    SciTech Connect (OSTI)

    Nokisalmi, Petri; Rajecki, Maria; Pesonen, Sari; Escutenaire, Sophie; Soliymani, Rabah; Tenhunen, Mikko; Ahtiainen, Laura; Hemminki, Akseli

    2012-05-01

    Purpose: In the present study, we evaluated the combination of replication-deficient adenoviruses and radiotherapy in vitro. The purpose of the present study was to analyze the mechanism of radiation-mediated upregulation of adenoviral transgene expression. Methods and Materials: Adenoviral transgene expression (luciferase or green fluorescent protein) was studied with and without radiation in three cell lines: breast cancer M4A4-LM3, prostate cancer PC-3MM2, and lung cancer LNM35/enhanced green fluorescent protein. The effect of the radiation dose, modification of the viral capsid, and five different transgene promoters were studied. The cellular responses were studied using mass spectrometry and immunofluorescence analysis. Double strand break repair was modulated by inhibitors of heat shock protein 90, topoisomerase-I, and DNA protein kinase, and transgene expression was measured. Results: We found that a wide range of radiation doses increased adenoviral transgene expression regardless of the cell line, transgene, promoter, or viral capsid modification. Treatment with adenovirus, radiation, and double strand break repair inhibitors resulted in persistence of double strand breaks and subsequent increases in adenovirus transgene expression. Conclusions: Radiation-induced enhancement of adenoviral transgene expression is linked to DNA damage recognition and repair. Radiation induces a global cellular response that results in increased production of RNA and proteins, including adenoviral transgene products. This study provides a mechanistic rationale for combining radiation with adenoviral gene delivery.

  4. NFAT5 promotes proliferation and migration of lung adenocarcinoma cells in part through regulating AQP5 expression

    SciTech Connect (OSTI)

    Guo, Kai; Jin, Faguang

    2015-09-25

    The osmoregulated transcription factor nuclear factor of activated T-cells 5(NFAT5), has been found to play important roles in the development of many kinds of human cancers, including breast cancer, colon carcinoma, renal cell carcinoma and melanoma. The aim of the present study was to determine whether NFAT5 is involved in the proliferation and migration of lung adenocarcinoma cells. We found that NFAT5 was upregulated in lung adenocarcinoma cells and knockdown of NFAT5 decreased proliferation and migration of the cells, accompanied by a significant reduction in the expression of AQP5. AQP5 was upregulated in lung adenocarcinoma cells and knockdown of AQP5 also inhibited proliferation and migration of the cells as knockdown of NFAT5 did. Moreover, overexpression of NFAT5 promoted proliferation and migration of lung adenocarcinoma cells, accompanied by a significant increase in the expression of AQP5. These results indicate that NFAT5 plays important roles in proliferation and migration of human lung adenocarcinoma cells through regulating AQP5 expression, providing a new therapeutic option for lung adenocarcinoma therapy. - Highlights: • NFAT5 expression is higher in lung adenocarcinoma cells compared with normal cells. • NFAT5 knockdown decreases proliferation and migration of lung adenocarcinoma cells. • Knockdown of NFAT5 reduces AQP5 expression in human lung adenocarcinoma cells. • Overexpression of NFAT5 promotes proliferation and migration of lung adenocarcinoma cells. • Overexpression of NFAT5 increases AQP5 expression in human lung adenocarcinoma cells.

  5. A replication-deficient rabies virus vaccine expressing Ebola virus glycoprotein is highly attenuated for neurovirulence

    SciTech Connect (OSTI)

    Papaneri, Amy B.; Wirblich, Christoph; Cann, Jennifer A.; Cooper, Kurt; Jahrling, Peter B.; Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick MD, 21702 ; Schnell, Matthias J.; Blaney, Joseph E.

    2012-12-05

    We are developing inactivated and live-attenuated rabies virus (RABV) vaccines expressing Ebola virus (EBOV) glycoprotein for use in humans and endangered wildlife, respectively. Here, we further characterize the pathogenesis of the live-attenuated RABV/EBOV vaccine candidates in mice in an effort to define their growth properties and potential for safety. RABV vaccines expressing GP (RV-GP) or a replication-deficient derivative with a deletion of the RABV G gene (RV{Delta}G-GP) are both avirulent after intracerebral inoculation of adult mice. Furthermore, RV{Delta}G-GP is completely avirulent upon intracerebral inoculation of suckling mice unlike parental RABV vaccine or RV-GP. Analysis of RV{Delta}G-GP in the brain by quantitative PCR, determination of virus titer, and immunohistochemistry indicated greatly restricted virus replication. In summary, our findings indicate that RV-GP retains the attenuation phenotype of the live-attenuated RABV vaccine, and RV{Delta}G-GP would appear to be an even safer alternative for use in wildlife or consideration for human use.

  6. The effect of retinal pigment epithelial cell patch size on growth factor expression

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Vargis, Elizabeth A.; Peterson, Cristen B.; Morrell-Falvey, Jennifer L.; Retterer, Scott T.; Collier, Charles Patrick

    2014-01-30

    The spatial organization of retinal pigment epithelial (RPE) cells grown in culture was controlled using micropatterning techniques in order to examine the effect of patch size on cell health and differentiation. Understanding this effect is a critical step in the development of multiplexed high throughput fluidic assays and provides a model for replicating disease states associated with the deterioration of retinal tissue during age-related macular degeneration (AMD). Microcontact printing of fibronectin on polystyrene and glass substrates was used to promote cell attachment, forming RPE patches of controlled size and shape. These colonies mimic the effect of atrophy and loss-of-function thatmore » occurs in the retina during degenerative diseases such as AMD. After 72 hours of cell growth, levels of vascular endothelial growth factor (VEGF), an important biomarker of AMD, were measured. Cells were counted and morphological indicators of cell viability and tight junction formation were assessed via fluorescence microscopy. As a result, up to a twofold increase of VEGF expression per cell was measured as colony size decreased, suggesting that the local microenvironment of, and connections between, RPE cells influences growth factor expression leading to the initiation and progression of diseases such as AMD.« less

  7. Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis

    SciTech Connect (OSTI)

    Merkley, Eric D.; Wrighton, Kelly C.; Castelle, Cindy; Anderson, Brian J.; Wilkins, Michael J.; Shah, Vega; Arbour, Tyler; Brown, Joseph N.; Singer, Steven W.; Smith, Richard D.; Lipton, Mary S.

    2015-03-06

    Bacterial extracellular metal respiration, as carried out by members of the genus Geobacter, is of interest for applications including microbial fuel cells and bioremediation. Geobacter bemidjiensis is the major species whose growth is stimulated during groundwater amendment with acetate. We have carried out label-free proteomics studies of Geobacter bemidjiensis grown with acetate as the electron donor and either fumarate, ferric citrate, or one of two hydrous ferric oxide mineral types as electron acceptor. The major class of proteins whose expression changes across these conditions is c-type cytochromes, many of which are known to be involved in extracellular metal reduction in other, better-characterized Geobacter species. Some proteins with multiple homologues in G. bemidjiensis (OmcS, OmcB) had different expression patterns than observed for their G. sulfurreducens homologues under similar growth conditions. We also compared the proteome from our study to a prior proteomics study of biomass recovered from an aquifer in Colorado, where the microbial community was dominated by strains closely-related to G. bemidjiensis. We detected an increased number of proteins with functions related to motility and chemotaxis in the Colorado field samples compared to the laboratory samples, suggesting the importance of motility for in situ extracellular metal respiration.

  8. Novel, highly expressed late nodulin gene (LjNOD16) from Lotus japonicus

    SciTech Connect (OSTI)

    Kapranov, P.; Bruijn, F.J. de; Szczyglowski, K.

    1997-04-01

    We have isolated a Lotus japonicus cDNA corresponding to a highly abundant, late nodule-specific RNA species that encodes a polypeptide with a predicted molecular mass of 15.6 kD. The protein and its corresponding gene were designated NIj16 and LjNOD16, respectively. LjNOD16 was found to be expressed only in the infected cells of L. japonicus nodules. Related DNA sequences could be identified in the genomes of both Glycine max and Medicago sativa. In the latter, a homologous mRNA species was detected in the nodules. Unlike LiNOD16, its alfalfa homologs appear to represent low-abundance mRNA species. However, the proteins corresponding to the LjNOD16 and its alfalfa homolog could be detected at similar levels in nodules but not in roots of both legume species. The predicted amino acid sequence analysis of nodulin NIj16 revealed the presence of a long {alpha}-helical region and a positively charged C terminus. The former domain has a very high propensity to form a coiled-coil type structure, indicating that nodulin NIj16 may interact with an as-yet-unidentified protein target(s) in the nodule-infected cells. Homology searches revealed no significant similarities to any known sequences in the databases, with the exception of two related, anonymous Arabidopsis expressed sequence tags.

  9. Methods for transforming and expression screening of filamentous fungal cells with a DNA library

    DOE Patents [OSTI]

    Teter, Sarah; Lamsa, Michael; Cherry, Joel; Ward, Connie

    2015-06-02

    The present invention relates to methods for expression screening of filamentous fungal transformants, comprising: (a) isolating single colony transformants of a DNA library introduced into E. coli; (b) preparing DNA from each of the single colony E. coli transformants; (c) introducing a sample of each of the DNA preparations of step (b) into separate suspensions of protoplasts of a filamentous fungus to obtain transformants thereof, wherein each transformant contains one or more copies of an individual polynucleotide from the DNA library; (d) growing the individual filamentous fungal transformants of step (c) on selective growth medium, thereby permitting growth of the filamentous fungal transformants, while suppressing growth of untransformed filamentous fungi; and (e) measuring activity or a property of each polypeptide encoded by the individual polynucleotides. The present invention also relates to isolated polynucleotides encoding polypeptides of interest obtained by such methods, to nucleic acid constructs, expression vectors, and recombinant host cells comprising the isolated polynucleotides, and to methods of producing the polypeptides encoded by the isolated polynucleotides.

  10. Expression of lectin-like oxidized LDL receptor-1 in smooth muscle cells after vascular injury

    SciTech Connect (OSTI)

    Eto, Hideyuki; Miyata, Masaaki . E-mail: miyatam@m3.kufm.kagoshima-u.ac.jp; Kume, Noriaki; Minami, Manabu; Itabe, Hiroyuki; Orihara, Koji; Hamasaki, Shuichi; Biro, Sadatoshi; Otsuji, Yutaka; Kita, Toru; Tei, Chuwa

    2006-03-10

    Lectin-like oxidized LDL receptor-1 (LOX-1) is an oxidized LDL receptor, and its role in restenosis after angioplasty remains unknown. We used a balloon-injury model of rabbit aorta, and reverse transcription-polymerase chain reaction revealed that LOX-1 mRNA expression was modest in the non-injured aorta, reached a peak level 2 days after injury, and remained elevated until 24 weeks after injury. Immunohistochemistry and in situ hybridization showed that LOX-1 was not detected in the media of non-injured aorta but expressed in both medial and neointimal smooth muscle cells (SMC) at 2 and 24 weeks after injury. Low concentrations of ox-LDL (10 {mu}g/mL) stimulated the cultured SMC proliferation, which was inhibited by antisense oligonucleotides of LOX-1 mRNA. Double immunofluorescense staining showed the colocalization of LOX-1 and proliferating cell nuclear antigen in human restenotic lesion. These results suggest that LOX-1 mediates ox-LDL-induced SMC proliferation and plays a role in neointimal formation after vascular injury.

  11. Deficient expression of the small proteoglycan decorin in a case of severe/lethal osteogenesis imperfecta

    SciTech Connect (OSTI)

    Dyne, K.M.; Valli, M.; Forlino, A.; Cetta, G.; Mottes, M.; Kresse, H.

    1996-05-03

    In osteogenesis imperfecta (OI) the effects of mutations in type I collagen genes generally reflect their nature and localization. Unrelated individuals sharing identical mutations present, in general, similar clinical phenotypes. However, in some such cases the clinical phenotype differs. This variable clinical expression could be the result of abnormalities in other connective tissue proteins. Since decorin is a component of connective tissue, binds to type I collagen fibrils and plays a role in matrix assembly, we studied decorin production in skin fibroblasts from OI patients. Cultured fibroblasts from one patient with extremely severe osteogenesis imperfecta (classified as type II/III) who has an {alpha}1(I)gly415ser mutation were found to secrete barely detectable amounts of decorin into culture medium. Western blotting using antibodies raised against decorin confirmed the reduction of the decorin core protein and Northern blot analysis showed decorin mRNA levels below the limit of detection. Cells from a patient, with a less severe phenotype, bearing a mutation in the same position of the triple helix ({alpha}1(1)gly415) expressed decorin normally. The different clinical phenotypes could be due to the differing genetic backgrounds of the patients, so it is tempting to conclude that in our most severely affected patient, the absence of decorin aggravates the clinical phenotype. 34 refs., 4 figs., 1 tab.

  12. Controlling Retinal Pigment Epithelial Cell Patch Size Influences Growth Factor Expression

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Vargis, Elizabeth A; Peterson, Cristen B; Morrell-Falvey, Jennifer L; Retterer, Scott T; Collier, Pat

    2014-01-01

    The spatial organization of retinal pigment epithelial (RPE) cells grown in culture was controlled using micropatterning techniques in order to examine the effect of patch size on cell health and differentiation. Understanding this effect is a critical step in the development of multiplexed high throughput fluidic assays and provides a model for replicating disease states associated with the deterioration of retinal tissue during age-related macular degeneration (AMD). Microcontact printing of fibronectin on polystyrene and glass substrates was used to promote cell attachment, forming RPE patches of controlled size and shape. These colonies mimic the effect of atrophy and loss-of-function thatmore » occurs in the retina during degenerative diseases such as AMD. After 72 hours of cell growth, levels of vascular endothelial growth factor (VEGF), an important biomarker of AMD, were measured. Cells were counted and morphological indicators of cell viability and tight junction formation were assessed via fluorescence microscopy. Up to a twofold increase of VEGF expression per cell was measured as colony size decreased, suggesting that the local microenvironment of, and connections between, RPE cells influences growth factor expression leading to the initiation and progression of diseases such as AMD.« less

  13. miR-17 inhibitor suppressed osteosarcoma tumor growth and metastasis via increasing PTEN expression

    SciTech Connect (OSTI)

    Gao, Yong; Luo, Ling-hui; Li, Shuai; Yang, Cao

    2014-02-07

    Highlights: • miR-17 was increased in OS tissues and cell lines. • Inhibition of miR-17 suppressed OS cell proliferation. • Inhibition of miR-17 suppressed OS cell migration and invasion. • PTEN was a target of miR-17. • miR-17 was negatively correlated with PTEN in OS tissues. - Abstract: MicroRNAs (miRNAs) play essential roles in cancer development and progression. Here, we investigated the role of miR-17 in the progression and metastasis of osteosarcoma (OS). miR-17 was frequently increased in OS tissues and cell lines. Inhibition of miR-17 in OS cell lines substantially suppressed cell proliferation, migration, and invasion. Phosphatase and tensin homolog (PTEN) was identified as a target of miR-17, and ectopic expression of miR-17 inhibited PTEN by direct binding to its 3′-untranslated region (3′-UTR). Expression of miR-17 was negatively correlated with PTEN in OS tissues. Together, these findings indicate that miR-17 acts as an oncogenic miRNA and may contribute to the progression and metastasis of OS, suggesting miR-17 as a potential novel diagnostic and therapeutic target of OS.

  14. Functional Heterologous Expression of an Engineered Full Length CipA from Clostridium thermocellum in Thermoanaerobacterium saccharolyticum

    SciTech Connect (OSTI)

    Currie, Devin; Herring, Christopher; Guss, Adam M; Olson, Daniel G.; Hogsett, David; Lynd, Lee R

    2013-01-01

    BACKGROUND: Cellulose is highly recalcitrant and thus requires a specialized suite of enzymes to solubilize it into fermentable sugars. In C. thermocellum, these extracellular enzymes are present as a highly active multi-component system known as the cellulosome. This study explores the expression of a critical C. thermocellum cellulosomal component in T. saccharolyticum as a step toward creating a thermophilic bacterium capable of consolidated bioprocessing by employing heterologously expressed cellulosomes. RESULTS: We developed an inducible promoter system based on the native T. saccharolyticum xynA promoter, which was shown to be induced by xylan and xylose. The promoter was used to express the cellulosomal component cipA*, an engineered form of the wild-type cipA from C. thermocellum. Expression and localization to the supernatant were both verified for CipA*. When a cipA mutant C. thermocellum strain was cultured with a CipA*-expressing T. saccharolyticum strain, hydrolysis and fermentation of 10 grams per liter SigmaCell 101, a highly crystalline cellulose, were observed. This trans-species complementation of a cipA deletion demonstrated the ability for CipA* to assemble a functional cellulosome. CONCLUSION: This study is the first example of an engineered thermophile heterologously expressing a structural component of a cellulosome. To achieve this goal we developed and tested an inducible promoter for controlled expression in T. saccharolyticum as well as a synthetic cipA. In addition, we demonstrate a high degree of hydrolysis (up to 93%) on microcrystalline cellulose.

  15. Expression and subcellular localization of the Qa-SNARE syntaxin17 in human eosinophils

    SciTech Connect (OSTI)

    Carmo, Lívia A.S.; Dias, Felipe F.; Malta, Kássia K.; Amaral, Kátia B.; Shamri, Revital; Weller, Peter F.; Melo, Rossana C.N.

    2015-10-01

    Background: SNARE members mediate membrane fusion during intracellular trafficking underlying innate and adaptive immune responses by different cells. However, little is known about the expression and function of these proteins in human eosinophils, cells involved in allergic, inflammatory and immunoregulatory responses. Here, we investigate the expression and distribution of the Qa-SNARE syntaxin17 (STX17) within human eosinophils isolated from the peripheral blood. Methods: Flow cytometry and a pre-embedding immunonanogold electron microscopy (EM) technique that combines optimal epitope preservation and secondary Fab-fragments of antibodies linked to 1.4 nm gold particles for optimal access to microdomains, were used to investigate STX17. Results: STX17 was detected within unstimulated eosinophils. Immunogold EM revealed STX17 on secretory granules and on granule-derived vesiculotubular transport carriers (Eosinophil Sombrero Vesicles-EoSVs). Quantitative EM analyses showed that 77.7% of the granules were positive for STX17 with a mean±SEM of 3.9±0.2 gold particles/granule. Labeling was present on both granule outer membranes and matrices while EoSVs showed clear membrane-associated labeling. STX17 was also present in secretory granules in eosinophils stimulated with the cytokine tumor necrosis factor alpha (TNF-α) or the CC-chemokine ligand 11 CCL11 (eotaxin-1), stimuli that induce eosinophil degranulation. The number of secretory granules labeled for STX17 was significantly higher in CCL11 compared with the unstimulated group. The level of cell labeling did not change when unstimulated cells were compared with TNF-α-stimulated eosinophils. Conclusions: The present study clearly shows by immunanonogold EM that STX17 is localized in eosinophil secretory granules and transport vesicles and might be involved in the transport of granule-derived cargos. - Highlights: • First demonstration of the Qa-SNARE syntaxin-17 (STX17) in human eosinophils. • High

  16. Sandia National Laboratories: MTEM 2014: Malware Technical Exchange

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Meeting: Registration Hotels in Albuquerque ABQ Marriott ABQ Marriott Pyramid North Andaluz Hotel (downtown ABQ) Candlewood Suites ABQ Courtyard Albuquerque Airport Embassy Suites ABQ Hilton Garden Inn Uptown Hyatt Place Uptown Residence Inn Airport

  17. Triangle Universities Nuclear Laboratory : 2011

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    every half-hour between Residence Inn by Marriott, Hilton Garden Inn, and the French Family Science Center (FFSC). Saturday, Nov. 7: 7:30 AM - 10 AM - Every half-hour...

  18. Identification and characterization of a cis-regulatory element for zygotic gene expression in Chlamydomonas reinhardtii

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Hamaji, Takashi; Lopez, David; Pellegrini, Matteo; Umen, James

    2016-03-26

    Upon fertilization Chlamydomonas reinhardtii zygotes undergo a program of differentiation into a diploid zygospore that is accompanied by transcription of hundreds of zygote-specific genes. We identified a distinct sequence motif we term a zygotic response element (ZYRE) that is highly enriched in promoter regions of C. reinhardtii early zygotic genes. A luciferase reporter assay was used to show that native ZYRE motifs within the promoter of zygotic gene ZYS3 or intron of zygotic gene DMT4 are necessary for zygotic induction. A synthetic luciferase reporter with a minimal promoter was used to show that ZYRE motifs introduced upstream are sufficient tomore » confer zygotic upregulation, and that ZYRE-controlled zygotic transcription is dependent on the homeodomain transcription factor GSP1. Furthermore, we predict that ZYRE motifs will correspond to binding sites for the homeodomain proteins GSP1-GSM1 that heterodimerize and activate zygotic gene expression in early zygotes.« less

  19. Transgenic plants expressing GLK1 and CCA1 having increased nitrogen assimilation capacity

    DOE Patents [OSTI]

    Coruzzi, Gloria; Gutierrez, Rodrigo A.; Nero, Damion C.

    2012-04-10

    Provided herein are compositions and methods for producing transgenic plants. In specific embodiments, transgenic plants comprise a construct comprising a polynucleotide encoding CCA1, GLK1 or bZIP1, operably linked to a plant-specific promote, wherein the CCA1, GLK1 or bZIP1 is ectopically overexpressed in the transgenic plants, and wherein the promoter is optionally a constitutive or inducible promoter. In other embodiments, transgenic plants in which express a lower level of CCA1, GLK1 or bZIP1 are provided. Also provided herein are commercial products (e.g., pulp, paper, paper products, or lumber) derived from the transgenic plants (e.g., transgenic trees) produced using the methods provided herein.

  20. Bone regeneration by implantation of adipose-derived stromal cells expressing BMP-2

    SciTech Connect (OSTI)

    Li Huiwu; Dai Kerong . E-mail: krdai@163.com; Tang Tingting; Zhang Xiaoling; Yan Mengning; Lou Jueren

    2007-05-18

    In this study, we reported that the adipose-derived stromal cells (ADSCs) genetically modified by bone morphogenetic protein 2 (BMP-2) healed critical-sized canine ulnar bone defects. First, the osteogenic and adipogenic differentiation potential of the ADSCs derived from canine adipose tissue were demonstrated. And then the cells were modified by the BMP-2 gene and the expression and bone-induction ability of BMP-2 were identified. Finally, the cells modified by BMP-2 gene were applied to a {beta}-tricalcium phosphate (TCP) carrier and implanted into ulnar bone defects in the canine model. After 16 weeks, radiographic, histological, and histomorphometry analysis showed that ADSCs modified by BMP-2 gene produced a significant increase of newly formed bone area and healed or partly healed all of the bone defects. We conclude that ADSCs modified by the BMP-2 gene can enhance the repair of critical-sized bone defects in large animals.

  1. Analytical Expressions for the Hard-Scattering Production of Massive Partons

    SciTech Connect (OSTI)

    Wong, Cheuk-Yin

    2016-01-01

    We obtain explicit expressions for the two-particle differential cross section $E_c E_\\kappa d\\sigma (AB \\to c\\kappa X) /d\\bb c d \\bb \\kappa$ and the two-particle angular correlation function \\break $d\\sigma(AB$$ \\to$$ c\\kappa X)/d\\Delta \\phi \\, d\\Delta y$ in the hard-scattering production of massive partons in order to exhibit the ``ridge" structure on the away side in the hard-scattering process. The single-particle production cross section $d\\sigma(AB \\to cX) /dy_c c_T dc_T $ is also obtained and compared with the ALICE experimental data for charm production in $pp$ collisions at 7 TeV at LHC.

  2. High density growth of T7 expression strains with auto-induction option

    DOE Patents [OSTI]

    Studier, F. William

    2010-07-20

    A bacterial growth medium for promoting auto-induction of transcription of cloned DNA in cultures of bacterial cells grown batchwise is disclosed. The transcription is under the control of a lac repressor. Also disclosed is a bacterial growth medium for improving the production of a selenomethionine-containing protein or polypeptide in a bacterial cell, the protein or polypeptide being produced by recombinant DNA techniques from a lac or T7lac promoter, the bacterial cell encoding a vitamin B12-dependent homocysteine methylase. Finally, disclosed is a bacterial growth medium for suppressing auto-induction of expression in cultures of bacterial cells grown batchwise, said transcription being under the control of lac repressor.

  3. Flow cytometric analysis of expression of interleukin-2 receptor beta chain (p70-75) on various leukemic cells

    SciTech Connect (OSTI)

    Hoshino, S.; Oshimi, K.; Tsudo, M.; Miyasaka, M.; Teramura, M.; Masuda, M.; Motoji, T.; Mizoguchi, H. )

    1990-08-15

    We analyzed the expression of the interleukin-2 receptor (IL-2R) beta chain (p70-75) on various leukemic cells from 44 patients by flow cytometric analysis using the IL-2R beta chain-specific monoclonal antibody, designated Mik-beta 1. Flow cytometric analysis demonstrated the expression of the IL-2R beta chain on granular lymphocytes (GLs) from all eight patients with granular lymphocyte proliferative disorders (GLPDs), on adult T-cell leukemia (ATL) cells from all three patients with ATL, and on T-cell acute lymphoblastic leukemia (T-ALL) cells from one of three patients with T-ALL. Although GLs from all the GLPD patients expressed the IL-2R beta chain alone and not the IL-2R alpha chain (Tac-antigen: p55), ATL and T-ALL cells expressing the beta chain coexpressed the alpha chain. In two of seven patients with common ALL (cALL) and in both patients with B-cell chronic lymphocytic leukemia, the leukemic cells expressed the alpha chain alone. Neither the alpha chain nor the beta chain was expressed on leukemic cells from the remaining 28 patients, including all 18 patients with acute nonlymphocytic leukemia, five of seven patients with cALL, all three patients with multiple myeloma, and two of three patients with T-ALL. These results indicate that three different forms of IL-2R chain expression exist on leukemic cells: the alpha chain alone; the beta chain alone; and both the alpha and beta chains. To examine whether the results obtained by flow cytometric analysis actually reflect functional aspects of the expressed IL-2Rs, we studied the specific binding of 125I-labeled IL-2 (125I-IL-2) to leukemic cells in 18 of the 44 patients. In addition, we performed 125I-IL-2 crosslinking studies in seven patients. The results of IL-2R expression of both 125I-IL-2 binding assay and crosslinking studies were in agreement with those obtained by flow cytometric analysis.

  4. Gene expression profiles in rainbow trout, Onchorynchus mykiss, exposed to a simple chemical mixture.

    SciTech Connect (OSTI)

    Hook, Sharon E.; Skillman, Ann D.; Gopalan, Banu; Small, Jack A.; Schultz, Irvin R.

    2008-03-01

    Among proposed uses for microarrays in environmental toxiciology is the identification of key contributors to toxicity within a mixture. However, it remains uncertain whether the transcriptomic profiles resulting from exposure to a mixture have patterns of altered gene expression that contain identifiable contributions from each toxicant component. We exposed isogenic rainbow trout Onchorynchus mykiss, to sublethal levels of ethynylestradiol, 2,2,4,4 tetrabromodiphenyl ether, and chromium VI or to a mixture of all three toxicants Fluorescently labeled cDNA were generated and hybridized against a commercially available Salmonid array spotted with 16,000 cDNAs. Data were analyzed using ANOVA (p < 0.05) with a Benjamani-Hochberg multiple test correction (Genespring (Agilent) software package) to identify up and down regulated genes. Gene clustering patterns that can be used as “expression signatures” were determined using hierarchical cluster analysis. The gene ontology terms associated with significantly altered genes were also used to identify functional groups that were associated with toxicant exposure. Cross-ontological analytics (XOA) approach was used to assign functional annotations to genes with "unknown" function. Our analysis indicates that transcriptomic profiles resulting from the mixture exposure resemble those of the individual contaminant exposures, but are not a simple additive list. However, patterns of altered genes representative of each component of the mixture are clearly discernible, and the functional classes of genes altered represent the individual components of the mixture. These findings indicate that the use of microarrays to identify transcriptomic profiles may aid in the identification of key stressors within a chemical mixture, ultimately improving environmental assessment.

  5. Subacute effects of hexabromocyclododecane (HBCD) on hepatic gene expression profiles in rats

    SciTech Connect (OSTI)

    Canton, Rocio F. [Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.177, NL-3508 TD, Utrecht (Netherlands)], E-mail: rfcanton@gmail.com; Peijnenburg, Ad A.C.M.; Hoogenboom, Ron L.A.P. [RIKILT Institute of Food Safety, Wageningen University and Research Center, P.O. Box 230, 6700 AE Wageningen (Netherlands); Piersma, Aldert H.; Ven, Leo T.M. van der [National Institute of Public Health and the Environment (RIVM), Laboratory for Heath Protection Research, P.O. Box 1, 3720 BA Bilthoven (Netherlands); Berg, Martin van den [Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.177, NL-3508 TD, Utrecht (Netherlands); Heneweer, Marjoke [RIKILT Institute of Food Safety, Wageningen University and Research Center, P.O. Box 230, 6700 AE Wageningen (Netherlands)

    2008-09-01

    Hexabromoyclododecane (HBCD), used as flame retardant (FR) mainly in textile industry and in polystyrene foam manufacture, has been identified as a contaminant at levels comparable to other brominated FRs (BFRs). HBCD levels in biota are increasing slowly and seem to reflect the local market demand. The toxicological database of HBCD is too limited to perform at present a solid risk assessment, combining data from exposure and effect studies. In order to fill in some gaps, a 28-day HBCD repeated dose study (OECD407) was done in Wistar rats. In the present work liver tissues from these animals were used for gene expression profile analysis. Results show clear gender specificity with females having a higher number of regulated genes and therefore being more sensitive to HBCD than males. Several specific pathways were found to be affected by HBCD exposure, like PPAR-mediated regulation of lipid metabolism, triacylglycerol metabolism, cholesterol biosynthesis, and phase I and II pathways. These results were corroborated with quantitative RT-PCR analysis. Cholesterol biosynthesis and lipid metabolism were especially down-regulated in females. Genes involved in phase I and II metabolism were up-regulated predominantly in males, which could explain the observed lower HBCD hepatic disposition in male rats in this 28-day study. These sex-specific differences in gene expression profiles could also underlie sex-specific differences in toxicity (e.g. decreased thyroid hormone or increased serum cholesterol levels). To our knowledge, this is the fist study that describes the changes in rat hepatic gene profiles caused by this commonly used flame retardant.

  6. Azidothymidine and cisplatin increase p14ARF expression in OVCAR-3 ovarian cancer cell line

    SciTech Connect (OSTI)

    Vaskivuo, Liisa; Rysae, Jaana; Koivuperae, Johanna; Myllynen, Paeivi; Vaskivuo, Tommi; Chvalova, Katerina; Serpi, Raisa; Savolainen, Eeva-Riitta; Puistola, Ulla; Vaehaekangas, Kirsi . E-mail: kirsi.vahakangas@uku.fi

    2006-10-01

    p14{sup ARF} tumor suppressor protein regulates p53 by interfering with mdm2-p53 interaction. p14{sup ARF} is activated in response to oncogenic stimuli but little is known of the responses of endogenous p14{sup ARF} to different types of cellular stress or DNA damage. Azidothymidine (AZT) is being tested in several clinical trials as an enhancer of anticancer chemotherapy. However, the knowledge of the relationship between AZT and cellular pathways, e.g. p53 pathway, is very limited. In this study, we show that AZT, cisplatin (CDDP) and docetaxel (DTX) all induce unique molecular responses in OVCAR-3 ovarian carcinoma cells carrying a mutated p53, while in A2780, ovarian carcinoma and MCF-7 breast carcinoma cells with wild type p53, all of these drugs cause similar p53 responses. We found that endogenous p14{sup ARF} protein in OVCAR-3 cells is down-regulated by DTX but induced by AZT and a short CDDP pulse treatment. In HT-29 colon carcinoma cells with a mutated p53, all treatments down-regulated p14{sup ARF} protein. Both CDDP and AZT increased the expression of p14ARF mRNA in OVCAR-3 cells. Differences in cell death induced by these drugs did not explain the differences in protein and mRNA expressions. No increase in the level of either c-Myc or H-ras oncoproteins was seen in OVCAR-3 cells after AZT or CDDP-treatment. These results suggest that p14{sup ARF} can respond to DNA damage without oncogene activation in cell lines without functional p53.

  7. Effect of 1918 PB1-F2 expression on influenza A virus infection kinetics

    SciTech Connect (OSTI)

    Ribeiro, Ruy; Perelson, Alan S; Smith, Amber M; Adler, Frederick R; Mcauley, Julie L; Mccullers, Jonathan A

    2009-01-01

    Relatively little is known about the viral factors contributing to the lethality of the 1918 pandemic, although its unparalleled virulence was likely due in part to the newly discovered PB1-F2 protein. This protein, while unnecessary for replication, increases apoptosis in monocytes, alters viral polymerase activity in vitro, and produces enhanced inflammation and increased secondary pneumonia in vivo. However, the effects the PB1-F2 protein have in vivo remain unclear. To address the mechanisms involved, we intranasally infected groups of mice with either influenza A virus PR8 or a genetically engineered virus that expresses the 1918 PB1-F2 protein on a PR8 background, PR8-PB1-F2(1918). Mice inoculated with PR8 had viral concentrations peaking at 72 hours, while those infected with PR8-PB1-F2(1918) reached peak concentrations earlier, 48 hours. Mice given PR8-PB1-F2(1918) also showed a faster decline in viral loads. We fit a mathematical model to these data to estimate parameter values and select the best model. This model supports a lower viral clearance rate and higher infected cell death rate with the PR8-PB1-F2(1918) virus, although the viral production rate may also be higher. We hypothesize that the higher PR8-PB1-F2(1918) viral titers early in an infection are due to both an increase in viral production with decreased viral clearance, and that the faster decline in the later stages of infection result from elevated cell death rates. We discuss the implications these mechanisms have during an infection with a virus expressing a virulent PBI-F2 on the possibility of a pandemic and on the importance of antiviral treatments.

  8. K-Ras4B proteins are expressed in the nucleolus: Interaction with nucleolin

    SciTech Connect (OSTI)

    Birchenall-Roberts, Maria C. . E-mail: birchena@mail.ncifcrf.gov; Fu, Tao; Kim, Soo-Gyung; Huang, Ying K.; Dambach, Michael; Resau, James H.; Ruscetti, Francis W.

    2006-09-22

    Kirsten Ras4B (K-Ras4B) is a potent onco-protein that is expressed in the majority of human cell types and is frequently mutated in carcinomas. K-Ras4B, like other members of the Ras family of proteins, is considered to be a cytoplasmic protein that must be localized to the plasma membrane for activation. Here, using confocal microscopy and biochemical analysis, we show that K-Ras4B, but not H-Ras or the closely related K-Ras4A, is also present in the nucleoli of normal and transformed cells. Subcellular fractionation and immunostaining show that K-Ras4B is located not only in the cytoplasm, but also in the nucleolar compartment. Modification of a C-terminal hexa-lysine motif unique to K-Ras4B results in exclusively cytoplasmic forms of the protein. Nucleolin, a pleiotropic regulator of cellular processes, including transcriptional regulation, is also characterized by a nucleolar-like nuclear appearance. We show that K-Ras4B and nucleolin co-localize within the nucleus and that nucleolin physically associates with K-Ras4B. Inhibition of K-Ras4B/nucleolin association blocked nucleolar localization of K-Ras4B. Using siRNA to knockdown the expression of nucleolin eliminated the nucleolar localization of K-Ras4B and significantly repressed the activation of the well-characterized K-Ras4B transcriptional target Ap-1, but stimulated Elk1. These data provide evidence of a nucleolar localization of K-Ras4B and describe a functional association between K-Ras4B and nucleolin.

  9. Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Schwessinger, Benjamin; Bahar, Ofir; Thomas, Nicolas; Holton, Nicolas; Nekrasov, Vladimir; Ruan, Deling; Canlas, Patrick E.; Daudi, Arsalan; Petzold, Christopher J.; Singan, Vasanth R.; et al

    2015-03-30

    Plant plasma membrane localized pattern recognition receptors (PRRs) detect extracellular pathogen-associated molecules. PRRs such as Arabidopsis EFR and rice XA21 are taxonomically restricted and are absent from most plant genomes. Here we show that rice plants expressing EFR or the chimeric receptor EFR::XA21, containing the EFR ectodomain and the XA21 intracellular domain, sense both Escherichia coli- and Xanthomonas oryzae pv. oryzae (Xoo)-derived elf18 peptides at sub-nanomolar concentrations. Treatment of EFR and EFR::XA21 rice leaf tissue with elf18 leads to MAP kinase activation, reactive oxygen production and defense gene expression. Although expression of EFR does not lead to robust enhanced resistancemore » to fully virulent Xoo isolates, it does lead to quantitatively enhanced resistance to weakly virulent Xoo isolates. EFR interacts with OsSERK2 and the XA21 binding protein 24 (XB24), two key components of the rice XA21-mediated immune response. Rice-EFR plants silenced for OsSERK2, or overexpressing rice XB24 are compromised in elf18-induced reactive oxygen production and defense gene expression indicating that these proteins are also important for EFR-mediated signaling in transgenic rice. Taken together, our results demonstrate the potential feasibility of enhancing disease resistance in rice and possibly other monocotyledonous crop species by expression of dicotyledonous PRRs. Our results also suggest that Arabidopsis EFR utilizes at least a subset of the known endogenous rice XA21 signaling components.« less

  10. CD26-mediated regulation of periostin expression contributes to migration and invasion of malignant pleural mesothelioma cells

    SciTech Connect (OSTI)

    Komiya, Eriko; Ohnuma, Kei; Yamazaki, Hiroto; Hatano, Ryo; Iwata, Satoshi; Okamoto, Toshihiro; Dang, Nam H.; Morimoto, Chikao

    2014-05-16

    Highlights: CD26-expressing MPM cells upregulate production of periostin. The intracytoplasmic region of CD26 mediates the upregulation of periostin. CD26 expression leads to nuclear translocation of Twist1 via phosphorylation of Src. Secreted periostin enhances migration and invasion of MPM cells. - Abstract: Malignant pleural mesothelioma (MPM) is an aggressive malignancy arising from mesothelial lining of pleura. It is generally associated with a history of asbestos exposure and has a very poor prognosis, partly due to the lack of a precise understanding of the molecular mechanisms associated with its malignant behavior. In the present study, we expanded on our previous studies on the enhanced motility and increased CD26 expression in MPM cells, with a particular focus on integrin adhesion molecules. We found that expression of CD26 upregulates periostin secretion by MPM cells, leading to enhanced MPM cell migratory and invasive activity. Moreover, we showed that upregulation of periostin expression results from the nuclear translocation of the basic helix-loop-helix transcription factor Twist1, a process that is mediated by CD26-associated activation of Src phosphorylation. While providing new and profound insights into the molecular mechanisms involved in MPM biology, these findings may also lead to the development of novel therapeutic strategies for MPM.

  11. Altered microRNA expression patterns in irradiated hematopoietic tissues suggest a sex-specific protective mechanism

    SciTech Connect (OSTI)

    Ilnytskyy, Yaroslav; Zemp, Franz J.; Koturbash, Igor; Kovalchuk, Olga

    2008-12-05

    To investigate involvement of miRNAs in radiation responses we used microRNAome profiling to analyze the sex-specific response of radiation sensitive hematopoietic lymphoid tissues. We show that radiation exposure resulted in a significant and sex-specific deregulation of microRNA expression in murine spleen and thymus tissues. Among the regulated miRNAs, we found that changes in expression of miR-34a and miR-7 may be involved in important protective mechanisms counteracting radiation cytotoxicity. We observed a significant increase in the expression of tumor-suppressor miR-34a, paralleled by a decrease in the expression of its target oncogenes NOTCH1, MYC, E2F3 and cyclin D1. Additionally, we show that miR-7 targets the lymphoid-specific helicase LSH, a pivotal regulator of DNA methylation and genome stability. While miR-7 was significantly down-regulated LSH was significantly up-regulated. These cellular changes may constitute an attempt to counteract radiation-induced hypomethylation. Tissue specificity of miRNA responses and possible regulation of miRNA expression upon irradiation are discussed.

  12. Epidermal Growth Factor Receptor Expression As Prognostic Marker in Patients With Anal Carcinoma Treated With Concurrent Chemoradiation Therapy

    SciTech Connect (OSTI)

    Fraunholz, Ingeborg; Falk, Stefan

    2013-08-01

    Purpose: To investigate the prognostic value of epidermal growth factor receptor (EGFR) expression in pretreatment tumor biopsy specimens of patients with anal cancer treated with concurrent 5-fluorouracil and mitomycin C-based chemoradiation therapy (CRT). Methods and Materials: Immunohistochemical staining for EGFR was performed in pretreatment biopsy specimens of 103 patients with anal carcinoma. EGFR expression was correlated with clinical and histopathologic characteristics and with clinical endpoints, including local failure-free survival (LFFS), colostomy-free survival (CFS), distant metastases-free survival (DMFS), cancer-specific survival (CSS), and overall survival (OS). Results: EGFR staining intensity was absent in 3%, weak in 23%, intermediate in 36% and intense in 38% of the patients. In univariate analysis, the level of EGFR staining was significantly correlated with CSS (absent/weak vs intermediate/intense expression: 5-year CSS, 70% vs 86%, P=.03). As a trend, this was also observed for DMFS (70% vs 86%, P=.06) and LFFS (70% vs 87%, P=.16). In multivariate analysis, N stage, tumor differentiation, and patients’ sex were independent prognostic factors for CSS, whereas EGFR expression only reached borderline significance (hazard ratio 2.75; P=.08). Conclusion: Our results suggest that elevated levels of pretreatment EGFR expression could be correlated with favorable clinical outcome in anal cancer patients treated with CRT. Further studies are warranted to elucidate how EGFR is involved in the response to CRT.

  13. Endothelial Cell Migration and Vascular Endothelial Growth Factor Expression Are the Result of Loss of Breast Tissue Polarity

    SciTech Connect (OSTI)

    Chen, Amy; Cuevas, Ileana; Kenny, Paraic A; Miyake, Hiroshi; Mace, Kimberley; Ghajar, Cyrus; Boudreau, Aaron; Bissell, Mina; Boudreau, Nancy

    2009-05-26

    Recruiting a new blood supply is a rate-limiting step in tumor progression. In a three-dimensional model of breast carcinogenesis, disorganized, proliferative transformed breast epithelial cells express significantly higher expression of angiogenic genes compared with their polarized, growth-arrested nonmalignant counterparts. Elevated vascular endothelial growth factor (VEGF) secretion by malignant cells enhanced recruitment of endothelial cells (EC) in heterotypic cocultures. Significantly, phenotypic reversion of malignant cells via reexpression of HoxD10, which is lost in malignant progression, significantly attenuated VEGF expression in a hypoxia-inducible factor 1{alpha}-independent fashion and reduced EC migration. This was due primarily to restoring polarity: forced proliferation of polarized, nonmalignant cells did not induce VEGF expression and EC recruitment, whereas disrupting the architecture of growth-arrested, reverted cells did. These data show that disrupting cytostructure activates the angiogenic switch even in the absence of proliferation and/or hypoxia and restoring organization of malignant clusters reduces VEGF expression and EC activation to levels found in quiescent nonmalignant epithelium. These data confirm the importance of tissue architecture and polarity in malignant progression.

  14. The Y-located gonadoblastoma gene TSPY amplifies its own expression through a positive feedback loop in prostate cancer cells

    SciTech Connect (OSTI)

    Kido, Tatsuo; Lau, Yun-Fai Chris

    2014-03-28

    Highlights: • Y-encoded proto-oncoprotein TSPY amplifies its expression level via a positive feedback loop. • TSPY binds to the chromatin/DNA at exon 1 of TSPY gene. • TSPY enhances the gene expression in a TSPY exon 1 sequence dependent manner. • The conserved SET/NAP-domain is essential for TSPY transactivation. • Insights on probable mechanisms on TSPY exacerbation on cancer development in men. - Abstract: The testis-specific protein Y-encoded (TSPY) is a repetitive gene located on the gonadoblastoma region of the Y chromosome, and has been considered to be the putative gene for this oncogenic locus on the male-only chromosome. It is expressed in spermatogonial cells and spermatocytes in normal human testis, but abundantly in gonadoblastoma, testicular germ cell tumors and a variety of somatic cancers, including melanoma, hepatocellular carcinoma and prostate cancer. Various studies suggest that TSPY accelerates cell proliferation and growth, and promotes tumorigenesis. In this report, we show that TSPY could bind directly to the chromatin/DNA at exon 1 of its own gene, and greatly enhance the transcriptional activities of the endogenous gene in the LNCaP prostate cancer cells. Domain mapping analyses of TSPY have localized the critical and sufficient domain to the SET/NAP-domain. These results suggest that TSPY could efficiently amplify its expression and oncogenic functions through a positive feedback loop, and contribute to the overall tumorigenic processes when it is expressed in various human cancers.

  15. Effect of the anatomical site on telomere length and pref-1 gene expression in bovine adipose tissues

    SciTech Connect (OSTI)

    Yamada, Tomoya Higuchi, Mikito; Nakanishi, Naoto

    2015-08-07

    Adipose tissue growth is associated with preadipocyte proliferation and differentiation. Telomere length is a biological marker for cell proliferation. Preadipocyte factor-1 (pref-1) is specifically expressed in preadipocytes and acts as a molecular gatekeeper of adipogenesis. In the present study, we investigated the fat depot-specific differences in telomere length and pref-1 gene expression in various anatomical sites (subcutaneous, intramuscular and visceral) of fattening Wagyu cattle. Visceral adipose tissue expressed higher pref-1 mRNA than did subcutaneous and intramuscular adipose tissues. The telomere length in visceral adipose tissue tended to be longer than that of subcutaneous and intramuscular adipose tissues. The telomere length of adipose tissue was not associated with adipocyte size from three anatomical sites. No significant correlation was found between the pref-1 mRNA level and the subcutaneous adipocyte size. In contrast, the pref-1 mRNA level was negatively correlated with the intramuscular and visceral adipocyte size. These results suggest that anatomical sites of adipose tissue affect the telomere length and expression pattern of the pref-1 gene in a fat depot-specific manner. - Highlights: • Visceral adipose tissue express higher pref-1 mRNA than other anatomical sites. • Telomere length in visceral adipose tissue is longer than other anatomical sites. • Telomere length of adipose tissue is not associated with adipocyte size. • Pref-1 mRNA is negatively correlated with intramuscular and visceral adipocyte size.

  16. NNMCAB Board Minutes: September 2011 Taos

    Broader source: Energy.gov [DOE]

    Minutes of the September 28, 2011 Board meeting at Sagebrush Inn Conference Center Presentation DOE, Long Term Stewardship, Tom Longo

  17. cityOakRidgeWeb

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    0 miles 1 12 HIGH SCHOOL Oak Ridge Playhouse Methodist Medical Center CIVIC CENTER Art Ctr. Oak Ridge Associated Universities (ORAU) Hampton Inn DoubleTree Hotel Days Inn MUSEUM OF SCIENCE AND ENERGY Y-12 NATIONAL SECURITY COMPLEX Oak Ridge Mall Jameson Inn Numbered and unnumbered tra c lights Staybridge Suites Comfort Inn Commerce Park Jack Case Center New Hope Center Y-12 Visitor Center Children 's Museum OFFICE OF SCIENTIFIC & TECHNICAL INFORMATION Oak Ridge Marina Centennial Golf Course

  18. Fibroblast growth factor-2 up-regulates the expression of nestin through the RasRafERKSp1 signaling axis in C6 glioma cells

    SciTech Connect (OSTI)

    Chang, Kai-Wei; Huang, Yuan-Li; Wong, Zong-Ruei; Su, Peng-Han; Huang, Bu-Miin; Ju, Tsai-Kai; Technology Commons, College of Life Science, National Taiwan University, Taipei 106, Taiwan ; Yang, Hsi-Yuan

    2013-05-17

    Highlights: Nestin expression in C6 glioma cells is induced by FGF-2. Nestin expression is induced by FGF-2 via de novo RNA and protein synthesis. The FGFR inhibitor SU5402 blocks the FGF-2-induced nestin expression. The mRNA of FGFR1 and 3 are detected in C6 glioma cells. RasRafERKSp1 signaling pathway is responsibe for FGF-2-induced nestin expression. -- Abstract: Nestin is a 240-kDa intermediate filament protein expressed mainly in neural and myogenic stem cells. Although a substantial number of studies have focused on the expression of nestin during development of the central nervous system, little is known about the factors that induce and regulate its expression. Fibroblast growth factor-2 (FGF-2) is an effective mitogen and stimulates the proliferation and differentiation of a subset of nestin-expressing cells, including neural progenitor cells, glial precursor cells, and smooth muscle cells. To assess whether FGF-2 is a potent factor that induces the expression of nestin, C6 glioma cells were used. The results showed that nestin expression was up-regulated by FGF-2 via de novo RNA and protein synthesis. Our RT-PCR results showed that C6 glioma cells express FGFR1/3, and FGFRs is required for FGF-2-induced nestin expression. Further signaling analysis also revealed that FGF-2-induced nestin expression is mediated through FGFRMAPKERK signaling axis and the transcriptional factor Sp1. These findings provide new insight into the regulation of nestin in glial system and enable the further studies on the function of nestin in glial cells.

  19. Expression of WNT genes in cervical cancer-derived cells: Implication of WNT7A in cell proliferation and migration

    SciTech Connect (OSTI)

    Ramos-Solano, Moisés; Meza-Canales, Ivan D.; Torres-Reyes, Luis A.; Alvarez-Zavala, Monserrat; and others

    2015-07-01

    According to the multifactorial model of cervical cancer (CC) causation, it is now recognized that other modifications, in addition to Human papillomavirus (HPV) infection, are necessary for the development of this neoplasia. Among these, it has been proposed that a dysregulation of the WNT pathway might favor malignant progression of HPV-immortalized keratinocytes. The aim of this study was to identify components of the WNT pathway differentially expressed in CC vs. non-tumorigenic, but immortalized human keratinocytes. Interestingly, WNT7A expression was found strongly downregulated in cell lines and biopsies derived from CC. Restoration of WNT7A in CC-derived cell lines using a lentiviral gene delivery system or after adding a recombinant human protein decreases cell proliferation. Likewise, WNT7A silencing in non-tumorigenic cells markedly accelerates proliferation. Decreased WNT7A expression was due to hypermethylation at particular CpG sites. To our knowledge, this is the first study reporting reduced WNT7A levels in CC-derived cells and that ectopic WNT7A restoration negatively affects cell proliferation and migration. - Highlights: • WNT7A is expressed in normal keratinocytes or cervical cells without lesion. • WNT7A is significantly reduced in cervical cancer-derived cells. • Restoration of WNT7A expression in HeLa decreases proliferation and cell migration. • Silencing of WNT7A in HaCaT induces an increased proliferation and migration rate. • Decreased WNT7A expression in this model is due to hypermethylation.

  20. Gene expression profiles in the cerebellum and hippocampus following exposure to a neurotoxicant, Aroclor 1254: Developmental effects

    SciTech Connect (OSTI)

    Royland, Joyce E.; Wu, Jinfang; Zawia, Nasser H.; Kodavanti, Prasada Rao S.

    2008-09-01

    The developmental consequences of exposure to the polychlorinated biphenyls (PCBs) have been widely studied, making PCBs a unique model to understand issues related to environmental mixture of persistent chemicals. PCB exposure in humans adversely affects neurocognitive development, causes psychomotor difficulties, and contributes to attention deficits in children, all of which seem to be associated with altered patterns of neuronal connectivity. In the present study, we examined gene expression profiles in the rat nervous system following PCB developmental exposure. Pregnant rats (Long-Evans) were dosed perinatally with 0 or 6 mg/kg/day of Aroclor 1254 from gestation day 6 through postnatal day (PND) 21. Gene expression in cerebellum and hippocampus from PND7 and PND14 animals was analyzed with an emphasis on developmental aspects. Changes in gene expression ({>=} 1.5 fold) in control animals identified normal developmental changes. These basal levels of expression were compared to data from Aroclor 1254-treated animals to determine the impact of gestational PCB exposure on developmental parameters. The results indicate that the expression of a number of developmental genes related to cell cycle, synaptic function, cell maintenance, and neurogenesis is significantly altered from PND7 to PND14. Aroclor 1254 treatment appears to dampen the overall growth-related gene expression levels in both regions with the effect being more pronounced in the cerebellum. Functional analysis suggests that Aroclor 1254 delays maturation of the developing nervous system, with the consequences dependent on the ontological state of the brain area and the functional role of the individual gene. Such changes may underlie learning and memory deficits observed in PCB exposed animals and humans.

  1. In vivo expression of the lacY gene in two segments leads to functional lac permease

    SciTech Connect (OSTI)

    Bibi, E.; Kaback, H.R. )

    1990-06-01

    The lacY gene of Escherichia coli was cut into two approximately equal-size fragments with Afl II and subcloned individually or together under separate lac operator/promoters in plasmid pT7-5. Under these conditions, lac permease is expressed in two portions: (i) the N-terminal portion (the N terminus, the first six putative transmembrane helices, and most of putative loop 7) and (ii) the C-terminal portion (the last six putative transmembrane helices and the C terminus). Cells harboring pT7-5 encoding both fragments transport lactose at about 30% the rate of cells expressing intact permease to a comparable steady-state level of accumulation. In contrast, cells expressing either half of the permease independently do not transport lactose. As judged by ({sup 35}S)methionine labeling and immunoblotting, intact permease in completely absent from the membrane of cells expressing lacY fragments either individually or together. Thus, transport activity must result from an association between independently synthesized pieces of lac permease. When the gene fragments are expressed individually, the N-terminal portion of the permease is observed inconsistently, and the C-terminal portion is not observed. When the gene fragments are expressed together, polypeptides identified as the N- and C-terminal moieties of the permease are found in the membrane. It is concluded that the N- or C-terminal halves of lac permease are proteolyzed when synthesized independently and that association between the two complementing polypeptides leads to a more stable, catalytically active complex.

  2. Age- and sex-related differences of organic anion-transporting polypeptide gene expression in livers of rats

    SciTech Connect (OSTI)

    Hou, Wei-Yu; Xu, Shang-Fu; Zhu, Qiong-Ni; Lu, Yuan-Fu; Cheng, Xing-Guo; Liu, Jie

    2014-10-15

    Organic anion-transporting polypeptides (Oatps) play important roles in transporting endogenous substances and xenobiotics into the liver and are implicated in drug-drug interactions. Many factors could influence their expression and result in alterations in drug disposition, efficacy and toxicity. This study was aimed to examine the development-, aging-, and sex-dependent Oatps expression in livers of rats. The livers from SD rats during development (− 2, 1, 7, 14, 21, 28, 35, and 60 d) and aging (60, 180, 540 and/or 800 d) were collected and total RNAs were extracted, purified, and subjected to real-time PCR analysis. Total proteins were extracted for western-blot analysis. Results showed that Oatp1a1, Oatp1a4, Oatp1a5 and Oatp1b2 were all hardly detectable in fetal rat livers, low at birth, rapidly increased after weaning (21 d), and reached the peak at 60 d. The Oatps remained stable during the age between 60–180 d, and decreased at elderly (540 and/or 800 d). After birth, Oatp1a1, Oatp1a4, and Oatp1b2 were all highly expressed in liver, in contrast, Oatp1a5 expression was low. Oatp expressions are male-predominant in rat livers. In the livers of aged rats, the Oatp expression decreased and shared a consistent ontogeny pattern at the mRNA and protein level. In conclusion, this study showed that in rat liver, Oatp1a1, Oatp1a4, Oatp1a5 and Oatp1b2 gene expressions are influenced by age and gender, which could provide a basis of individual variation in drug transport, metabolism and toxicity in children, elderly and women. - Highlights: • Oatp1a1, Oatp1a4, Oatp1a5 and Oatp1b2 expression in livers of rats. • Ontogenic changes of Oatps at − 2, 1, 7, 14, 21, 28, 35, and 60 days. • Age-related changes of Oatps at 60, 180, 540, and 800 days. • Sex-difference of Oatps at the both mRNA and protein levels.

  3. Human metastatic melanoma cell lines express high levels of growth hormone receptor and respond to GH treatment

    SciTech Connect (OSTI)

    Sustarsic, Elahu G.; Department of Biological Sciences, Ohio University, Athens, OH ; Junnila, Riia K.; Kopchick, John J.

    2013-11-08

    Highlights: Most cancer types of the NCI60 have sub-sets of cell lines with high GHR expression. GHR is highly expressed in melanoma cell lines. GHR is elevated in advanced stage IV metastatic tumors vs. stage III. GH treatment of metastatic melanoma cell lines alters growth and cell signaling. -- Abstract: Accumulating evidence implicates the growth hormone receptor (GHR) in carcinogenesis. While multiple studies show evidence for expression of growth hormone (GH) and GHR mRNA in human cancer tissue, there is a lack of quantification and only a few cancer types have been investigated. The National Cancer Institutes NCI60 panel includes 60 cancer cell lines from nine types of human cancer: breast, CNS, colon, leukemia, melanoma, non-small cell lung, ovarian, prostate and renal. We utilized this panel to quantify expression of GHR, GH, prolactin receptor (PRLR) and prolactin (PRL) mRNA with real-time RT qPCR. Both GHR and PRLR show a broad range of expression within and among most cancer types. Strikingly, GHR expression is nearly 50-fold higher in melanoma than in the panel as a whole. Analysis of human metastatic melanoma biopsies confirmed GHR gene expression in melanoma tissue. In these human biopsies, the level of GHR mRNA is elevated in advanced stage IV tumor samples compared to stage III. Due to the novel finding of high GHR in melanoma, we examined the effect of GH treatment on three NCI60 melanoma lines (MDA-MB-435, UACC-62 and SK-MEL-5). GH increased proliferation in two out of three cell lines tested. Further analysis revealed GH-induced activation of STAT5 and mTOR in a cell line dependent manner. In conclusion, we have identified cell lines and cancer types that are ideal to study the role of GH and PRL in cancer, yet have been largely overlooked. Furthermore, we found that human metastatic melanoma tumors express GHR and cell lines possess active GHRs that can modulate multiple signaling pathways and alter cell proliferation. Based on this data

  4. Twenty-first workshop on geothermal reservoir engineering: Proceedings

    SciTech Connect (OSTI)

    1996-01-26

    PREFACE The Twenty-First Workshop on Geothermal Reservoir Engineering was held at the Holiday Inn, Palo Alto on January 22-24, 1996. There were one-hundred fifty-five registered participants. Participants came from twenty foreign countries: Argentina, Austria, Canada, Costa Rica, El Salvador, France, Iceland, Indonesia, Italy, Japan, Mexico, The Netherlands, New Zealand, Nicaragua, the Philippines, Romania, Russia, Switzerland, Turkey and the UK. The performance of many geothermal reservoirs outside the United States was described in several of the papers. Professor Roland N. Horne opened the meeting and welcomed visitors. The key note speaker was Marshall Reed, who gave a brief overview of the Department of Energy's current plan. Sixty-six papers were presented in the technical sessions of the workshop. Technical papers were organized into twenty sessions concerning: reservoir assessment, modeling, geology/geochemistry, fracture modeling hot dry rock, geoscience, low enthalpy, injection, well testing, drilling, adsorption and stimulation. Session chairmen were major contributors to the workshop, and we thank: Ben Barker, Bobbie Bishop-Gollan, Tom Box, Jim Combs, John Counsil, Sabodh Garg, Malcolm Grant, Marcel0 Lippmann, Jim Lovekin, John Pritchett, Marshall Reed, Joel Renner, Subir Sanyal, Mike Shook, Alfred Truesdell and Ken Williamson. Jim Lovekin gave the post-dinner speech at the banquet and highlighted the exciting developments in the geothermal field which are taking place worldwide. The Workshop was organized by the Stanford Geothermal Program faculty, staff, and graduate students. We wish to thank our students who operated the audiovisual equipment. Shaun D. Fitzgerald Program Manager.

  5. Equine cytochrome P450 2B6 Genomic identification, expression and functional characterization with ketamine

    SciTech Connect (OSTI)

    Peters, L.M.; Demmel, S.; Pusch, G.; Buters, J.T.M.; Zielinski, J.; Leeb, T.; Mevissen, M.; Schmitz, A.

    2013-01-01

    Ketamine is an anesthetic and analgesic regularly used in veterinary patients. As ketamine is almost always administered in combination with other drugs, interactions between ketamine and other drugs bear the risk of either adverse effects or diminished efficacy. Since cytochrome P450 enzymes (CYPs) play a pivotal role in the phase I metabolism of the majority of all marketed drugs, drugdrug interactions often occur at the active site of these enzymes. CYPs have been thoroughly examined in humans and laboratory animals, but little is known about equine CYPs. The characterization of equine CYPs is essential for a better understanding of drug metabolism in horses. We report annotation, cloning and heterologous expression of the equine CYP2B6 in V79 Chinese hamster fibroblasts. After computational annotation of all CYP2B genes, the coding sequence (CDS) of equine CYP2B6 was amplified by RT-PCR from horse liver total RNA and revealed an amino acid sequence identity of 77% and a similarity of 93.7% to its human ortholog. A non-synonymous variant c.226G>A in exon 2 of the equine CYP2B6 was detected in 97 horses. The mutant A-allele showed an allele frequency of 82%. Two further variants in exon 3 were detected in one and two horses of this group, respectively. Transfected V79 cells were incubated with racemic ketamine and norketamine as probe substrates to determine metabolic activity. The recombinant equine CYP2B6 N-demethylated ketamine to norketamine and produced metabolites of norketamine, such as hydroxylated norketamines and 5,6-dehydronorketamine. V{sub max} for S-/and R-norketamine formation was 0.49 and 0.45 nmol/h/mg cellular protein and K{sub m} was 3.41 and 2.66 ?M, respectively. The N-demethylation of S-/R-ketamine was inhibited concentration-dependently with clopidogrel showing an IC{sub 50} of 5.63 and 6.26 ?M, respectively. The functional importance of the recorded genetic variants remains to be explored. Equine CYP2B6 was determined to be a CYP enzyme

  6. Blog | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    your tips for saving energy and money during the holidays. December 19, 2012 Using LED lights for your holiday decorations can save you energy and money. | Photo courtesy of...

  7. South Carolina Community Lights Up the Season with Energy-Efficient...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Community Lights Up the Season with Energy-Efficient Holiday Lights South Carolina Community Lights Up the Season with Energy-Efficient Holiday Lights December 20, 2011 - 1:12pm ...

  8. Wreaths Across America

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    wreath-laying ceremonies at over 1,000 locations worldwide, including 12 locations in New Mexico. G ving Employee Giving Campaign Holiday Food Drive Holiday Gift Drive LANL Laces...

  9. January Events

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    for New Year's Holiday Bradbury Science Museum - 1350 Central Ave, Los Alamos, NM 87544, USA The Bradbury Science Museum will be CLOSED for the New Year's holiday. Jan 9 Sat 11:00...

  10. Business Operations Calendar: FY 2013

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    the official source for holiday information by shift, Holidays vary by shift The business month cut-off is the same regardless of the shift S October 12 M T W T F S 1 2 3 4 5...

  11. Business Operations Calendar: FY 2014

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    the official source for holiday information by shift, Holidays vary by shift The business month cut-off is the same regardless of the shift S October 13 M T W T F S 1 2 3 4 5...

  12. Blog | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Photo courtesy of Chris Gunn, NREL. Energy Saving Holiday Kitchen Trivia Test your energy-saving knowledge with our holiday kitchen trivia. November 19, 2012 Save time and money on...

  13. Natural Gas Weekly Update, Printer-Friendly Version

    Annual Energy Outlook [U.S. Energy Information Administration (EIA)]

    2.852 2.813 Holiday Closed January Delivery 2.996 3.041 2.991 Holiday Closed Source: Reuters Information Service Storage: Net injections into working gas storage were 15 billion...

  14. Natural Gas Weekly Update

    Annual Energy Outlook [U.S. Energy Information Administration (EIA)]

    Holiday Notice: Due to the federal holiday in observance of Martin Luther King Day on Monday, January 21, 2002, the next issue of the Natural Gas Weekly Update will be published on...

  15. Natural Gas Weekly Update, Printer-Friendly Version

    Annual Energy Outlook [U.S. Energy Information Administration (EIA)]

    Holiday Notice: Due to the federal holiday in observance of Martin Luther King Day on Monday, January 21, 2002, the next issue of the Natural Gas Weekly Update will be published on...

  16. Expression of Autoactivated Stromelysin-1 in Mammary Glands of Transgenic Mice Leads to a Reactive Stroma During Early Development

    SciTech Connect (OSTI)

    Thomasset, N.; Lochter, A.; Sympson, C.J.; Lund, L.R.; Williams, D.R.; Behrendtsen, O.; Werb, Z.; Bissell, M.J.

    1998-04-24

    Extracellular matrix and extracellular matrix-degrading matrix metalloproteinases play a key role in interactions between the epithelium and the mesenchyme during mammary gland development and disease. In patients with breast cancer, the mammary mesenchyme undergoes a stromal reaction, the etiology of which is unknown. We previously showed that targeting of an autoactivating mutant of the matrix metalloproteinase stromelysin-1 to mammary epithelia of transgenic mice resulted in reduced mammary function during pregnancy and development of preneoplastic and neoplastic lesions. Here we examine the cascade of alterations before breast tumor formation in the mammary gland stroma once the expression of the stromelysin-1 transgene commences. Beginning in postpubertal virgin animals, low levels of transgene expression in mammary epithelia led to increased expression of endogenous stromelysin-1 in stromal fibroblasts and up-regulation of other matrix metalloproteinases, without basement membrane disruption. These changes were accompanied by the progressive development of a compensatory reactive stroma, characterized by increased collagen content and vascularization in glands from virgin mice. This remodeling of the gland affected epithelial-mesenchymal communication as indicated by inappropriate expression of tenascin-C starting by day 6 of pregnancy. This, together with increased transgene expression, led to basement membrane disruption starting by day 15 of pregnancy. We propose that the highly reactive stroma provides a prelude to breast epithelial tumors observed in these animals. Epithelial development depends on an exquisite series of inductive and instructive interactions between the differentiating epithelium and the mesenchymal (stromal) compartment. The epithelium, which consists of luminal and myoepithelial cells, is separated from the stroma by a basement membrane (BM), which plays a central role in mammary gland homeostasis and gene expression. In vivo, stromal

  17. Repression of miR-17-5p with elevated expression of E2F-1 and c-MYC in non-metastatic hepatocellular carcinoma and enhancement of cell growth upon reversing this expression pattern

    SciTech Connect (OSTI)

    El Tayebi, H.M.; Omar, K.; Hegy, S.; El Maghrabi, M.; El Brolosy, M.; Hosny, K.A.; Esmat, G.; Abdelaziz, A.I.

    2013-05-10

    Highlights: The oncogenic miR-17-5p is downregulated in non-metastatic hepatocellular carcinoma patients. E2F-1 and c-MYC transcripts are upregulated in non-metastatic HCC patients. miR-17-5p forced overexpression inhibited E2F-1 and c-MYC expression in HuH-7 cells. miR-17-5p mimicking increased HuH-7 cell growth, proliferation, migration and colony formation. miR-17-5p is responsible for HCC progression among the c-MYC/E2F-1/miR-17-5p triad members. -- Abstract: E2F-1, c-MYC, and miR-17-5p is a triad of two regulatory loops: a negative and a positive loop, where c-MYC induces the expression of E2F-1 that induces the expression of miR-17-5p which in turn reverses the expression of E2F-1 to close the loop. In this study, we investigated this triad for the first time in hepatocellular carcinoma (HCC), where miR-17-5p showed a significant down-regulation in 23 non-metastatic HCC biopsies compared to 10 healthy tissues; however, E2F-1 and c-MYC transcripts were markedly elevated. Forced over-expression of miR-17-5p in HuH-7 cells resulted in enhanced cell proliferation, growth, migration and clonogenicity with concomitant inhibition of E2F-1 and c-MYC transcripts expressions, while antagomirs of miR-17-5p reversed these events. In conclusion, this study revealed a unique pattern of expression for miR-17-5p in non-metastatic HCC patients in contrast to metastatic HCC patients. In addition we show that miR-17-5p is the key player among the triad that tumor growth and spread.

  18. An Endogenous Accelerator for Viral Gene Expression Confers a Fitness Advantage

    SciTech Connect (OSTI)

    Wong, Melissa; Bolovan-Fritts, Cynthia; Dar, Roy D.; Womack, Andrew; Simpson, Michael L; Shenk, Thomas; Weinberger, Leor S.

    2012-01-01

    Signal transduction circuits have long been known to differentiate between signals by amplifying inputs to different levels. Here, we describe a novel transcriptional circuitry that dynamically converts greater input levels into faster rates, without increasing the final equilibrium level (i.e. a rate amplifier). We utilize time-lapse microscopy to study human herpesvirus (cytomegalovirus) infection of live cells in real time. Strikingly, our results show that transcriptional activators accelerate viral gene expression in single cells without amplifying the steady-state levels of gene products in these cells. Experiment and modeling show that rate amplification operates by dynamically manipulating the traditional gain-bandwidth feedback relationship from electrical circuit theory to convert greater input levels into faster rates, and is driven by highly self-cooperative transcriptional feedback encoded by the virus s essential transactivator, IE2. This transcriptional rate-amplifier provides a significant fitness advantage for the virus and for minimal synthetic circuits. In general, rate-amplifiers may provide a mechanism for signal-transduction circuits to respond quickly to external signals without increasing steady-state levels of potentially cytotoxic molecules.

  19. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Pimentel, Harold; Parra, Marilyn; Gee, Sherry L.; Mohandas, Narla; Pachter, Lior; Conboy, John G.

    2015-11-03

    Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentallydynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclearlocalized. Splicemore » site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. Finally, we conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.« less

  20. Extracellular Matrix-Regulated Gene Expression RequiresCooperation of SWI/SNF and Transcription Factors

    SciTech Connect (OSTI)

    Xu, Ren; Spencer, Virginia A.; Bissell, Mina J.

    2006-05-25

    Extracellular cues play crucial roles in the transcriptional regulation of tissue-specific genes, but whether and how these signals lead to chromatin remodeling is not understood and subject to debate. Using chromatin immunoprecipitation (ChIP) assays and mammary-specific genes as models, we show here that extracellular matrix (ECM) molecules and prolactin cooperate to induce histone acetylation and binding of transcription factors and the SWI/SNF complex to the {beta}- and ?-casein promoters. Introduction of a dominant negative Brg1, an ATPase subunit of SWI/SNF complex, significantly reduced both {beta}- and ?-casein expression, suggesting that SWI/SNF-dependent chromatin remodeling is required for transcription of mammary-specific genes. ChIP analyses demonstrated that the ATPase activity of SWI/SNF is necessary for recruitment of RNA transcriptional machinery, but not for binding of transcription factors or for histone acetylation. Coimmunoprecipitation analyses showed that the SWI/SNF complex is associated with STAT5, C/EBP{beta}, and glucocorticoid receptor (GR). Thus, ECM- and prolactin-regulated transcription of the mammary-specific casein genes requires the concerted action of chromatin remodeling enzymes and transcription factors.

  1. Receptor expression is essential for proliferation induced by dimerized Jak kinases

    SciTech Connect (OSTI)

    Fujii, Hodaka

    2008-06-13

    Two members of Jak kinases, Jak1 and Jak3, are associated with the cytoplasmic domains of the interleukin-2 (IL-2) receptor (IL-2R) {beta} chain (IL-2R{beta}) and the common cytokine receptor {gamma} chain ({gamma}c), respectively, and accumulating evidence indicates their functional importance in IL-2 signaling. Here, I showed that coumermycin-induced chemical heterodimerization of Jak1 and Jak3 but not homodimerization of Jak1 or Jak3 induces cell proliferation of an IL-2R-reconstituted cell line. In this regard, expression of IL-2R{beta} was essential for cell proliferation by chemical heterodimerization of Jak1 and Jak3, indicating that dimerized Jak1 and Jak3 induce heterodimerization of IL-2R{beta} and {gamma}c, which may activate receptor-bound signaling molecules. Previous reports using chemical dimerization suggest that dimerization of Jak kinases is sufficient to induce cell proliferation. The present study indicates that re-evaluation of this conclusion is necessary and that interpretation of functional analysis of signaling molecules using chemical dimerizers needs more careful assessment.

  2. ERK Oscillation-Dependent Gene Expression Patterns and Deregulation by Stress-Response

    SciTech Connect (OSTI)

    Waters, Katrina M.; Cummings, Brian S.; Shankaran, Harish; Scholpa, Natalie E.; Weber, Thomas J.

    2014-09-15

    Studies were undertaken to determine whether ERK oscillations regulate a unique subset of genes in human keratinocytes and subsequently, whether the p38 stress response inhibits ERK oscillations. A DNA microarray identified many genes that were unique to ERK oscillations, and network reconstruction predicted an important role for the mediator complex subunit 1 (MED1) node in mediating ERK oscillation-dependent gene expression. Increased ERK-dependent phosphorylation of MED1 was observed in oscillating cells compared to non-oscillating counterparts as validation. Treatment of keratinocytes with a p38 inhibitor (SB203580) increased ERK oscillation amplitudes and MED1 and phospho-MED1 protein levels. Bromate is a probable human carcinogen that activates p38. Bromate inhibited ERK oscillations in human keratinocytes and JB6 cells and induced an increase in phospho-p38 and decrease in phospho-MED1 protein levels. Treatment of normal rat kidney cells and primary salivary gland epithelial cells with bromate decreased phospho-MED1 levels in a reversible fashion upon treatment with p38 inhibitors (SB202190; SB203580). Our results indicate that oscillatory behavior in the ERK pathway alters homeostatic gene regulation patterns and that the cellular response to perturbation may manifest differently in oscillating vs non-oscillating cells.

  3. Protocol for Uniformly Measuring and Expressing the Performance of Energy Storage Systems

    SciTech Connect (OSTI)

    Bray, Kathryn L.; Conover, David R.; Kintner-Meyer, Michael CW; Viswanathan, Vijayganesh; Ferreira, Summer; Rose, David; Schoenwald, David

    2012-10-01

    The U.S. Department of Energy’s Energy Storage Systems (ESS) Program, through the support of Pacific Northwest National Laboratory (PNNL) and Sandia National Laboratories (SNL), facilitated the development of the protocol provided in this report. The focus of the protocol is to provide a uniform way of measuring, quantifying, and reporting the performance of EESs in various applications; something that does not exist today and, as such, is hampering the consideration and use of this technology in the market. The availability of an application-specific protocol for use in measuring and expressing performance-related metrics of ESSs will allow technology developers, power-grid operators and other end-users to evaluate the performance of energy storage technologies on a uniform and comparable basis. This will help differentiate technologies and products for specific application(s) and provide transparency in how performance is measured. It also will assist utilities and other consumers of ESSs make more informed decisions as they consider the potential application and use of ESSs, as well as form the basis for documentation that might be required to justify utility investment in such technologies.

  4. Protocol for uniformly measuring and expressing the performance of energy storage systems.

    SciTech Connect (OSTI)

    Ferreira, Summer Rhodes; Rose, David Martin; Schoenwald, David Alan; Bray, Kathy; Conover, David; Kintner-Meyer, Michael; Viswanathan, Vilayanur

    2013-08-01

    The U.S. Department of Energy's Energy Storage Systems (ESS) Program, through the support of Pacific Northwest National Laboratory (PNNL) and Sandia National Laboratories (SNL), facilitated the development of the protocol provided in this report. The focus of the protocol is to provide a uniform way of measuring, quantifying, and reporting the performance of ESSs in various applications; something that does not exist today and, as such, is hampering the consideration and use of this technology in the market. The availability of an application-specific protocol for use in measuring and expressing performance-related metrics of ESSs will allow technology developers, power-grid operators and other end-users to evaluate the performance of energy storage technologies on a uniform and comparable basis. This will help differentiate technologies and products for specific application(s) and provide transparency in how performance is measured. It also will assist utilities and other consumers of ESSs to make more informed decisions as they consider the potential application and use of ESSs, as well as form the basis for documentation that might be required to justify utility investment in such technologies.

  5. Analysis of Shewanella oneidensis Membrane Protein Expression in Response to Electron Acceptor Availability

    SciTech Connect (OSTI)

    Giometti, Carol S.; Khare, Tripti; Verberkmoes, Nathan; O'Loughlin, Ed; Lindberg, Carl; Thompson, Melissa; Hettich, Robert

    2006-04-05

    Shewanella oneidensis MR-1, a gram negative metal-reducing bacterium, can utilize a large number of electron acceptors. In the natural environment, S. oneidensis utilizes insoluble metal oxides as well as soluble terminal electron acceptors. The purpose of this ERSP project is to identify differentially expressed proteins associated with the membranes of S. oneidensis MR-1 cells grown with different electron acceptors, including insoluble metal oxides. We hypothesize that through the use of surface labeling, subcellular fractionation, and a combination of proteome analysis tools, proteins involved in the reduction of different terminal electron acceptors will be elucidated. We are comparing the protein profiles from cells grown with the soluble electron acceptors oxygen and fumarate and with those from cells grown with the insoluble iron oxides goethite, ferrihydrite and lepidocrocite. Comparison of the cell surface proteins isolated from cells grown with oxygen or anaerobically with fumarate revealed an increase in the abundance of over 25 proteins in anaerobic cells, including agglutination protein and flagellin proteins along with the several hypothetical proteins. In addition, the surface protein composition of cells grown with the insoluble iron oxides varies considerably from the protein composition observed with either soluble electron acceptor as well as between the different insoluble acceptors.

  6. Expression, purification, crystallization and crystallographic study of Lutzomyia longipalpis LJL143

    SciTech Connect (OSTI)

    Kelleher, Alan; Liu, Zhuyun; Seid, Christopher A.; Zhan, Bin; Asojo, Oluwatoyin A.

    2015-06-27

    LJL143, a salivary protein from L. longipalpis, was produced using P. pastoris and crystallized in space group P2{sub 1}2{sub 1}2{sub 1}. Leishmaniasis is a neglected vector-borne disease with a global prevalence of over 12 million cases and 59 000 annual deaths. Transmission of the parasite requires salivary proteins, including LJL143 from the New World sandfly Lutzomyia longipalpis. LJL143 is a known marker of sandfly exposure in zoonotic hosts. LJL143 was crystallized from soluble protein expressed using Pichia pastoris. X-ray data were collected to 2.6 Å resolution from orthorhombic crystals belonging to space group P2{sub 1}2{sub 1}2{sub 1}, with average unit-cell parameters a = 57.39, b = 70.24, c = 79.58 Å. The crystals are predicted to have a monomer in the asymmetric unit, with an estimated solvent content of 48.5%. LJL143 has negligible homology to any reported structures, so the phases could not be determined by molecular replacement. All attempts at S-SAD failed and future studies include experimental phase determination using heavy-atom derivatives.

  7. GIM3E: Condition-specific Models of Cellular Metabolism Developed from Metabolomics and Expression Data

    SciTech Connect (OSTI)

    Schmidt, Brian; Ebrahim, Ali; Metz, Thomas O.; Adkins, Joshua N.; Palsson, Bernard O.; Hyduke, Daniel R.

    2013-11-15

    Motivation: Genome-scale metabolic models have been used extensively to investigate alterations in cellular metabolism. The accuracy of these models to represent cellular metabolism in specific conditions has been improved by constraining the model with omics data sources. However, few practical methods for integrating metabolomics data with other omics data sources into genome-scale models of metabolism have been reported. Results: GIMMME (Gene Inactivation Moderated by Metabolism, Metabolomics, and Expression) is an algorithm that enables the development of condition-specific models based on an objective function, transcriptomics, and intracellular metabolomics data. GIMMME establishes metabolite utilization requirements with metabolomics data, uses model-paired transcriptomics data to find experimentally supported solutions, and also provides calculations of the turnover (production / consumption) flux of metabolites. GIMMME was employed to investigate the effects of integrating additional omics datasets to create increasingly constrained solution spaces of Salmonella Typhimurium metabolism during growth in both rich and virulence media. This integration proved to be informative and resulted in a requirement of additional active reactions (12 in each case) or metabolites (26 or 29, respectively). The addition of constraints from transcriptomics also impacted the allowed solution space, and the cellular metabolites with turnover fluxes that were necessarily altered by the change in conditions increased from 118 to 271 of 1397. Availability: GIMMME has been implemented in Python and requires a COBRApy 0.2.x. The algorithm and sample data described here are freely available at: http://opencobra.sourceforge.net/

  8. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

    SciTech Connect (OSTI)

    Pimentel, Harold; Parra, Marilyn; Gee, Sherry L.; Mohandas, Narla; Pachter, Lior; Conboy, John G.

    2015-11-03

    Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentallydynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclearlocalized. Splice site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. Finally, we conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.

  9. PRAD1, a candidate BCL1 oncogene: Mapping and expression in centrocytic lymphoma

    SciTech Connect (OSTI)

    Rosenberg, C.L.; Arnold, A.; Harris, N.L. (Massachusetts General Hospital, Boston, MA (United States) Harvard Medical School, Boston, MA (United States)); Wong, E.; Petty, E.M.; Bale, A.E. (Yale Univ., New Haven, CT (United States)); Tsujimoto, Yoshihide (Wistar Inst., Philadelphia, PA (United States))

    1991-11-01

    Rearrangement of the BCL1 (B-cell lymphoma 1) region on chromosome 11q13 appears to be highly characteristic of centrocytic lymphoma and also is found infrequently in other B-cell neoplasma. Rearrangement is thought to deregulate a nearby protooncogene, but transcribed sequences in the immediate vicinity of BCL1 breakpoints had not been identified. PRAD1, previously designated D11S287E, was identified on 11q13 as a chromosomal breakpoint region rearranged with the parathyroid hormone gene in a subset of parathyroid adenomas; this highly conserved putative oncogene, which encodes a novel cyclin, has been linked to BCL1 and implicated also in subsets of breast and squamous cell neoplasms with 11q13 amplification. The authors report pulsed-field gel electrophoresis data showing BCL1 and PRAD1 to be no more than 130 kilobases apart. PRAD1 mRNA is abundantly expressed in seven of seven centrocytic lymphomas (Kiel classification), in contrast to 13 closely related but noncentrocytic lymphomas. Three of the seven centrocytic lymphomas had detectable BCL1 DNA rearrangement. Also, two unusual cases of CLL and BCL1 rearrangement overexpressed PRAD1, in contrast to five CLL controls. Thus, PRAD1 is an excellent candidate BCL1 oncogene. Its overexpression may be a key consequence of rearrangement of the BCL1 vicinity in B-cell neoplasms and a unifying pathogenetic feature in centrocytic lymphoma.

  10. Plant stimulation of soil microbial community succession: how sequential expression mediates soil carbon stabilization and turnover

    SciTech Connect (OSTI)

    Firestone, Mary

    2015-03-31

    It is now understood that most plant C is utilized or transformed by soil microorganisms en route to stabilization. Hence the composition of microbial communities that mediate decomposition and transformation of root C is critical, as are the metabolic capabilities of these communities. The change in composition and function of the C-transforming microbial communities over time in effect defines the biological component of soil C stabilization. Our research was designed to test 2 general hypotheses; the first two hypotheses are discussed first; H1: Root-exudate interactions with soil microbial populations results in the expression of enzymatic capacities for macromolecular, complex carbon decomposition; and H2: Microbial communities surrounding roots undergo taxonomic succession linked to functional gene activities as roots grow, mature, and decompose in soil. Over the term of the project we made significant progress in 1) quantifying the temporal pattern of root interactions with the soil decomposing community and 2) characterizing the role of root exudates in mediating these interactions.

  11. New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes for Methanosarcina species

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Guss, Adam M.; Rother, Michael; Zhang, Jun Kai; Kulkkarni, Gargi; Metcalf, William W.

    2008-01-01

    A highly efficient method for chromosomal integration of cloned DNA into Methanosarcina spp. was developed utilizing the site-specific recombination system from the Streptomyces phage φC31. Host strains expressing the φC31 integrase gene and carrying an appropriate recombination site can be transformed with non-replicating plasmids carrying the complementary recombination site at efficiencies similar to those obtained with self-replicating vectors. We have also constructed a series of hybrid promoters that combine the highly expressed M. barkeri P mcrB promoter with binding sites for the tetracycline-responsive, bacterial TetR protein. These promoters are tightly regulated by the presence or absence of tetracycline inmore » strains that express the tetR gene. The hybrid promoters can be used in genetic experiments to test gene essentiality by placing a gene of interest under their control. Thus, growth of strains with tetR -regulated essential genes becomes tetracycline-dependent. A series of plasmid vectors that utilize the site-specific recombination system for construction of reporter gene fusions and for tetracycline regulated expression of cloned genes are reported. These vectors were used to test the efficiency of translation at a variety of start codons. Fusions using an ATG start site were the most active, whereas those using GTG and TTG were approximately one half or one fourth as active, respectively. The CTG fusion was 95% less active than the ATG fusion.« less

  12. Id1 expression promotes peripheral CD4{sup +} T cell proliferation and survival upon TCR activation without co-stimulation

    SciTech Connect (OSTI)

    Liu, Chen; Jin, Rong; Wang, Hong-Cheng; Tang, Hui; Liu, Yuan-Feng; Qian, Xiao-Ping; Sun, Xiu-Yuan; Ge, Qing; Sun, Xiao-Hong; Zhang, Yu

    2013-06-21

    Highlights: •Id1 expression enables naïve T cell proliferation without anti-CD28 co-stimulation. •Id1 expression facilitates T cells survival when stimulated with anti-CD3. •Elevation of IL-2 production by Id1 contributes increased proliferation and survival. •Id1 potentiates NF-κB activation by anti-CD3 stimulation. -- Abstract: Although the role of E proteins in the thymocyte development is well documented, much less is known about their function in peripheral T cells. Here we demonstrated that CD4 promoter-driven transgenic expression of Id1, a naturally occurring dominant-negative inhibitor of E proteins, can substitute for the co-stimulatory signal delivered by CD28 to facilitate the proliferation and survival of naïve CD4{sup +} cells upon anti-CD3 stimulation. We next discovered that IL-2 production and NF-κB activity after anti-CD3 stimulation were significantly elevated in Id1-expressing cells, which may be, at least in part, responsible for the augmentation of their proliferation and survival. Taken together, results from this study suggest an important role of E and Id proteins in peripheral T cell activation. The ability of Id proteins to by-pass co-stimulatory signals to enable T cell activation has significant implications in regulating T cell immunity.

  13. Increased Production of Fatty Acids and Triglycerides in Aspergillus oryzae by Enhancing Expressions of Fatty Acid Synthesis-Related Genes

    SciTech Connect (OSTI)

    Tamano, Koichi; Bruno, Kenneth S.; Karagiosis, Sue A.; Culley, David E.; Deng, Shuang; Collett, James R.; Umemura, Myco; Koike, Hideaki; Baker, Scott E.; Machida, Masa

    2013-01-01

    Microbial production of fats and oils is being developedas a means of converting biomass to biofuels. Here we investigate enhancing expression of enzymes involved in the production of fatty acids and triglycerides as a means to increase production of these compounds in Aspergillusoryzae. Examination of the A.oryzaegenome demonstrates that it contains twofatty acid synthases and several other genes that are predicted to be part of this biosynthetic pathway. We enhancedthe expressionof fatty acid synthesis-related genes by replacing their promoters with thepromoter fromthe constitutively highly expressedgene tef1. We demonstrate that by simply increasing the expression of the fatty acid synthasegenes we successfullyincreasedtheproduction of fatty acids and triglyceridesby more than two fold. Enhancement of expression of the fatty acid pathway genes ATP-citrate lyase and palmitoyl-ACP thioesteraseincreasedproductivity to a lesser extent.Increasing expression ofacetyl-CoA carboxylase caused no detectable change in fatty acid levels. Increases in message level for each gene were monitored usingquantitative real-time RT-PCR. Our data demonstrates that a simple increase in the abundance of fatty acid synthase genes can increase the detectable amount of fatty acids.

  14. New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes forMethanosarcinaspecies

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Guss, Adam M.; Rother, Michael; Zhang, Jun Kai; Kulkkarni, Gargi; Metcalf, William W.

    2008-01-01

    A highly efficient method for chromosomal integration of cloned DNA intoMethanosarcina spp.was developed utilizing the site-specific recombination system from theStreptomycesphage ?C31. Host strains expressing the ?C31 integrase gene and carrying an appropriate recombination site can be transformed with non-replicating plasmids carrying the complementary recombination site at efficiencies similar to those obtained with self-replicating vectors. We have also constructed a series of hybrid promoters that combine the highly expressedM. barkeriPmcrBpromoter with binding sites for the tetracycline-responsive, bacterial TetR protein. These promoters are tightly regulated by the presence or absence of tetracycline in strains that express thetetRgene. The hybrid promoters can bemoreused in genetic experiments to test gene essentiality by placing a gene of interest under their control. Thus, growth of strains withtetR-regulated essential genes becomes tetracycline-dependent. A series of plasmid vectors that utilize the site-specific recombination system for construction of reporter gene fusions and for tetracycline regulated expression of cloned genes are reported. These vectors were used to test the efficiency of translation at a variety of start codons. Fusions using an ATG start site were the most active, whereas those using GTG and TTG were approximately one half or one fourth as active, respectively. The CTG fusion was 95% less active than the ATG fusion.less

  15. Fuels Performance Technologies: Milestone FY06 9.1 -- Using IQT measurements, develop simplified kinetic expressions for ignition of fuels that could be used in HCCI engine models

    SciTech Connect (OSTI)

    Taylor, J. D.

    2006-11-01

    Discusses the development of a new fuel characterization, based on simplified kinetic expression, to quantify ignition quality for low-temperature combustion vehicle applications.

  16. Remember the Batteries – and Maybe a Charger?

    Broader source: Energy.gov [DOE]

    For the holiday gift-giving season take a look at the ENERGY STAR® list of certified rechargeable batteries.

  17. Have You Used LED Light Strings?

    Broader source: Energy.gov [DOE]

    This week, you read about LED holiday light strings, which can use 90% less energy than regular incandescent light strings.

  18. Association of brominated proteins and changes in protein expression in the rat kidney with subcarcinogenic to carcinogenic doses of bromate

    SciTech Connect (OSTI)

    Kolisetty, Narendrababu; Bull, Richard J.; Muralidhara, Srinivasa; Costyn, Leah J.; Delker, Don A.; Guo, Zhongxian; Cotruvo, Joseph A.; Fisher, Jeffrey W.; Cummings, Brian S.

    2013-10-15

    The water disinfection byproduct bromate (BrO{sub 3}{sup −}) produces cytotoxic and carcinogenic effects in rat kidneys. Our previous studies demonstrated that BrO{sub 3}{sup −} caused sex-dependent differences in renal gene and protein expression in rats and the elimination of brominated organic carbon in their urine. The present study examined changes in renal cell apoptosis and protein expression in male and female F344 rats treated with BrO{sub 3}{sup −} and associated these changes with accumulation of 3-bromotyrosine (3-BT)-modified proteins. Rats were treated with 0, 11.5, 46 and 308 mg/L BrO{sub 3}{sup −} in drinking water for 28 days and renal sections were prepared and examined for apoptosis (TUNEL-staining), 8-oxo-deoxyguanosine (8-oxoG), 3-BT, osteopontin, Kim-1, clusterin, and p-21 expression. TUNEL-staining in renal proximal tubules increased in a dose-related manner beginning at 11.5 mg BrO{sub 3}{sup −}/L in female rats and 46 mg/L in males. Increased 8-oxoG staining was observed at doses as low as 46 mg/L. Osteopontin expression also increased in a dose-related manner after treatment with 46 mg/L, in males only. In contrast, Kim-1 expression increased in a dose-related manner in both sexes, although to a greater extent in females at the highest dose. Clusterin and p21 expression also increased in a dose-related manner in both sexes. The expression of 3-BT-modified proteins only increased in male rats, following a pattern previously reported for accumulation of α-2{sub u}-globulin. Increases in apoptosis in renal proximal tubules of male and female rats at the lowest doses suggest a common mode of action for renal carcinogenesis for the two sexes that is independent of α-2{sub u}-globulin nephropathy. - Highlights: • Bromate induced nephrotoxicity in both male and female rats by similar mechanisms. • Apoptosis was seen in both male and female rats at the lowest doses tested. • Bromate-induced apoptosis correlated to 8-oxo

  19. Proton pump inhibitors suppress iNOS-dependent DNA damage in Barrett's esophagus by increasing Mn-SOD expression

    SciTech Connect (OSTI)

    Thanan, Raynoo; Ma, Ning; Iijima, Katsunori; Abe, Yasuhiko; Koike, Tomoyuki; Shimosegawa, Tooru; Pinlaor, Somchai; Hiraku, Yusuke; Oikawa, Shinji; Murata, Mariko; Kawanishi, Shosuke

    2012-05-04

    Highlights: Black-Right-Pointing-Pointer Inflammation by Barrett's esophagus (BE) is a risk factor of its adenocarcinoma (BEA). Black-Right-Pointing-Pointer 8-Nitroguanine and 8-oxodG are inflammation-related DNA lesions. Black-Right-Pointing-Pointer DNA lesions and iNOS expression were higher in the order, BEA > BE > normal tissues. Black-Right-Pointing-Pointer Proton pump inhibitors suppress DNA damage by increasing Mn-SOD via Nrf2 activation. Black-Right-Pointing-Pointer DNA lesions can be useful biomarkers to predict risk of BEA in BE patients. -- Abstract: Barrett's esophagus (BE), an inflammatory disease, is a risk factor for Barrett's esophageal adenocarcinoma (BEA). Treatment of BE patients with proton pump inhibitors (PPIs) is expected to reduce the risk of BEA. We performed an immunohistochemical study to examine the formation of nitrative and oxidative DNA lesions, 8-nitroguanine and 8-oxo-7,8-dihydro-2 Prime -deoxygaunosine (8-oxodG), in normal esophageal, BE with pre- and post-treatment by PPIs and BEA tissues. We also observed the expression of an oxidant-generating enzyme (iNOS) and its transcription factor NF-{kappa}B, an antioxidant enzyme (Mn-SOD), its transcription factor (Nrf2) and an Nrf2 inhibitor (Keap1). The immunoreactivity of DNA lesions was significantly higher in the order of BEA > BE > normal tissues. iNOS expression was significantly higher in the order of BEA > BE > normal tissues, while Mn-SOD expression was significantly lower in the order of BEA < BE < normal tissues. Interestingly, Mn-SOD expression and the nuclear localization of Nrf2 were significantly increased, and the formation of DNA lesions was significantly decreased in BE tissues after PPIs treatment for 3-6 months. Keap1 and iNOS expression was not significantly changed by the PPIs treatment in BE tissues. These results indicate that 8-nitroguanine and 8-oxodG play a role in BE-derived BEA. Additionally, PPIs treatment may trigger the activation and nuclear translocation

  20. Aryl hydrocarbon receptor-dependent regulation of miR-196a expression controls lung fibroblast apoptosis but not proliferation

    SciTech Connect (OSTI)

    Hecht, Emelia; Zago, Michela; Sarill, Miles; Rico de Souza, Angela; Gomez, Alvin; Matthews, Jason; Hamid, Qutayba; Eidelman, David H.; Baglole, Carolyn J.

    2014-11-01

    The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor implicated in the regulation of apoptosis and proliferation. Although activation of the AhR by xenobiotics such as dioxin inhibits the cell cycle and control apoptosis, paradoxically, AhR expression also promotes cell proliferation and survival independent of exogenous ligands. The microRNA (miRNA) miR-196a has also emerged as a regulator of proliferation and apoptosis but a relationship between the AhR and miR-196a is not known. Therefore, we hypothesized that AhR-dependent regulation of endogenous miR-196a expression would promote cell survival and proliferation. Utilizing lung fibroblasts from AhR deficient (AhR{sup −/−}) and wild-type (AhR{sup +/+}) mice, we show that there is ligand-independent regulation of miRNA, including low miR-196a in AhR{sup −/−} cells. Validation by qRT-PCR revealed a significant decrease in basal expression of miR-196a in AhR{sup −/−} compared to AhR{sup +/+} cells. Exposure to AhR agonists benzo[a]pyrene (B[a]P) and FICZ as well as AhR antagonist CH-223191 decreased miR-196a expression in AhR{sup +/+} fibroblasts concomitant with decreased AhR protein levels. There was increased proliferation only in AhR{sup +/+} lung fibroblasts in response to serum, corresponding to a decrease in p27{sup KIP1} protein, a cyclin-dependent kinase inhibitor. Increasing the cellular levels of miR-196a had no effect on proliferation or expression of p27{sup KIP1} in AhR{sup −/−} fibroblasts but attenuated cigarette smoke-induced apoptosis. This study provides the first evidence that AhR expression is essential for the physiological regulation of cellular miRNA levels- including miR-196a. Future experiments designed to elucidate the functional relationship between the AhR and miR-196a may delineate additional novel ligand-independent roles for the AhR. - Highlights: • The AhR controls proliferation and apoptosis in lung cells. • The AhR regulates the

  1. Curcumin inhibits oral squamous cell carcinoma SCC-9 cells proliferation by regulating miR-9 expression

    SciTech Connect (OSTI)

    Xiao, Can; Wang, Lili; Zhu, Lifang; Zhang, Chenping; Zhou, Jianhua

    2014-11-28

    Highlights: • miR-9 expression level was significantly decreased in OSCC tissues. • Curcumin significantly inhibited SCC-9 cells proliferation. • miR-9 mediates the inhibition of SCC-9 proliferation by curcumin. • Curcumin suppresses Wnt/β-catenin signaling in SCC-9 cells. • miR-9 mediates the suppression of Wnt/β-catenin signaling by curcumin. - Abstract: Curcumin, a phytochemical derived from the rhizome of Curcuma longa, has shown anticancer effects against a variety of tumors. In the present study, we investigated the effects of curcumin on the miR-9 expression in oral squamous cell carcinoma (OSCC) and explored the potential relationships between miR-9 and Wnt/β-catenin pathway in curcumin-mediated OSCC inhibition in vitro. As the results shown, the expression levels of miR-9 were significantly lower in clinical OSCC specimens than those in the adjacent non-tumor tissues. Furthermore, our results indicated that curcumin inhibited OSCC cells (SCC-9 cells) proliferation through up-regulating miR-9 expression, and suppressing Wnt/β-catenin signaling by increasing the expression levels of the GSK-3β, phosphorylated GSK-3β and β-catenin, and decreasing the cyclin D1 level. Additionally, the up-regulation of miR-9 by curcumin in SCC-9 cells was significantly inhibited by delivering anti-miR-9 but not control oligonucleotides. Downregulation of miR-9 by anti-miR-9 not only attenuated the growth-suppressive effects of curcumin on SCC-9 cells, but also re-activated Wnt/β-catenin signaling that was inhibited by curcumin. Therefore, our findings would provide a new insight into the use of curcumin against OSCC in future.

  2. Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses

    SciTech Connect (OSTI)

    Schwessinger, Benjamin; Bahar, Ofir; Thomas, Nicolas; Holton, Nicolas; Nekrasov, Vladimir; Ruan, Deling; Canlas, Patrick E.; Daudi, Arsalan; Petzold, Christopher J.; Singan, Vasanth R.; Kuo, Rita; Chovatia, Mansi; Daum, Christopher; Heazlewood, Joshua L.; Zipfel, Cyril; Ronald, Pamela C.

    2015-03-30

    Plant plasma membrane localized pattern recognition receptors (PRRs) detect extracellular pathogen-associated molecules. PRRs such as Arabidopsis EFR and rice XA21 are taxonomically restricted and are absent from most plant genomes. Here we show that rice plants expressing EFR or the chimeric receptor EFR::XA21, containing the EFR ectodomain and the XA21 intracellular domain, sense both Escherichia coli- and Xanthomonas oryzae pv. oryzae (Xoo)-derived elf18 peptides at sub-nanomolar concentrations. Treatment of EFR and EFR::XA21 rice leaf tissue with elf18 leads to MAP kinase activation, reactive oxygen production and defense gene expression. Although expression of EFR does not lead to robust enhanced resistance to fully virulent Xoo isolates, it does lead to quantitatively enhanced resistance to weakly virulent Xoo isolates. EFR interacts with OsSERK2 and the XA21 binding protein 24 (XB24), two key components of the rice XA21-mediated immune response. Rice-EFR plants silenced for OsSERK2, or overexpressing rice XB24 are compromised in elf18-induced reactive oxygen production and defense gene expression indicating that these proteins are also important for EFR-mediated signaling in transgenic rice. Taken together, our results demonstrate the potential feasibility of enhancing disease resistance in rice and possibly other monocotyledonous crop species by expression of dicotyledonous PRRs. Our results also suggest that Arabidopsis EFR utilizes at least a subset of the known endogenous rice XA21 signaling components.

  3. Gender-specific reduction of hepatic Mrp2 expression by high-fat diet protects female mice from ANIT toxicity

    SciTech Connect (OSTI)

    Kong, Bo; Csanaky, Ivn L.; Aleksunes, Lauren M.; Patni, Meghan; Chen, Qi; Ma, Xiaochao; Jaeschke, Hartmut; Weir, Scott; Broward, Melinda; Klaassen, Curtis D.; University of Kansas Cancer Center, Kansas City, KS ; Guo, Grace L.

    2012-06-01

    Emerging evidence suggests that feeding a high-fat diet (HFD) to rodents affects the expression of genes involved in drug transport. However, gender-specific effects of HFD on drug transport are not known. The multidrug resistance-associated protein 2 (Mrp2, Abcc2) is a transporter highly expressed in the hepatocyte canalicular membrane and is important for biliary excretion of glutathione-conjugated chemicals. The current study showed that hepatic Mrp2 expression was reduced by HFD feeding only in female, but not male, C57BL/6J mice. In order to determine whether down-regulation of Mrp2 in female mice altered chemical disposition and toxicity, the biliary excretion and hepatotoxicity of the Mrp2 substrate, ?-naphthylisothiocyanate (ANIT), were assessed in male and female mice fed control diet or HFD for 4 weeks. ANIT-induced biliary injury is a commonly used model of experimental cholestasis and has been shown to be dependent upon Mrp2-mediated efflux of an ANIT glutathione conjugate that selectively injures biliary epithelial cells. Interestingly, HFD feeding significantly reduced early-phase biliary ANIT excretion in female mice and largely protected against ANIT-induced liver injury. In summary, the current study showed that, at least in mice, HFD feeding can differentially regulate Mrp2 expression and function and depending upon the chemical exposure may enhance or reduce susceptibility to toxicity. Taken together, these data provide a novel interaction between diet and gender in regulating hepatobiliary excretion and susceptibility to injury. -- Highlights: ? High-fat diet decreases hepatic Mrp2 expression only in female but not in male mice. ? HFD significantly reduces early-phase biliary ANIT excretion in female mice. ? HFD protects female mice against ANIT-induced liver injury.

  4. IL-33 inhibits RANKL-induced osteoclast formation through the regulation of Blimp-1 and IRF-8 expression

    SciTech Connect (OSTI)

    Kiyomiya, Hiroyasu; Ariyoshi, Wataru; Okinaga, Toshinori; Kaneuji, Takeshi; Mitsugi, Sho; Sakurai, Takuma; Habu, Manabu; Yoshioka, Izumi; Tominaga, Kazuhiro; and others

    2015-05-01

    Interleukin (IL)-33 is a recently discovered proinflammatory cytokine that belongs to the IL-1 family. Several studies have reported that IL-33 inhibits osteoclast differentiation. However, the mechanism of IL-33 regulation of osteoclastogenesis remains unclear. In the present study, we examined the effect of IL-33 on osteoclast formation in vitro. IL-33 suppressed osteoclast formation in both mouse bone marrow cells and monocyte/macrophage cell line RAW264.7 cells induced by receptor activator of NF-κB ligand (RANKL) and/or macrophage stimulating factor (M-CSF). IL-33 also inhibited the expression of RANKL-induced nuclear factor of activated T-cell cytoplasmic 1 (NFATc1), thereby decreasing the expression of osteoclastogenesis-related marker genes, including Cathepsin K, Osteoclast stimulatory transmembrane protein (Oc-stamp) and Tartrate-resistant acid phosphatase (Trap). Blockage of IL-33-ST2 binding suppressed the IL-33-mediated inhibition of NFATc1. RANKL-induced B-lymphocyte-induced maturation protein-1 (Blimp-1) expression was also suppressed by IL-33, which was followed by the stimulation of anti-osteoclastic genes such as interferon regulatory factor-8 (IRF-8). These results suggest that IL-33-ST2 interactions down-regulate both RANKL-induced NFATc1 activation and osteoclast differentiation via the regulation of Blimp-1 and IRF-8 expression. - Highlights: • IL-33 inhibits RANKL-induced osteoclast formation. • IL-33 has inhibitory effect on the RANKL-induced NFATc1 expression. • IL-33-induced NFATc1 suppression depends on the regulation of Blimp-1 and IRF-8.

  5. Tetraspanin 7 (TSPAN7) expression is upregulated in multiple myeloma patients and inhibits myeloma tumour development in vivo

    SciTech Connect (OSTI)

    Cheong, Chee Man; Chow, Annie W.S.; Fitter, Stephen; Hewett, Duncan R.; Martin, Sally K.; Williams, Sharon A.; To, L. Bik; and others

    2015-03-01

    Background: Increased expression of the tetraspanin TSPAN7 has been observed in a number of cancers; however, it is unclear how TSPAN7 plays a role in cancer progression. Methods: We investigated the expression of TSPAN7 in the haematological malignancy multiple myleoma (MM) and assessed the consequences of TSPAN7 expression in the adhesion, migration and growth of MM plasma cells (PC) in vitro and in bone marrow (BM) homing and tumour growth in vivo. Finally, we characterised the association of TSPAN7 with cell surface partner molecules in vitro. Results: TSPAN7 was found to be highly expressed at the RNA and protein level in CD138{sup +} MM PC from approximately 50% of MM patients. TSPAN7 overexpression in the murine myeloma cell line 5TGM1 significantly reduced tumour burden in 5TGM1/KaLwRij mice 4 weeks after intravenous adminstration of 5TGM1 cells. While TSPAN7 overexpression did not affect cell proliferation in vitro, TSPAN7 increased 5TGM1 cell adhesion to BM stromal cells and transendothelial migration. In addition, TSPAN7 was found to associate with the molecular chaperone calnexin on the cell surface. Conclusion: These results suggest that elevated TSPAN7 may be associated with better outcomes for up to 50% of MM patients. - Highlights: • TSPAN7 expression is upregulated in newly-diagnosed patients with active multiple myeloma. • Overexpression of TSPAN7 inhibits myeloma tumour development in vivo. • TSPAN7 interacts with calnexin at the plasma membrane in a myeloma cell line.

  6. Preferential cytotoxicity of bortezomib toward highly malignant human liposarcoma cells via suppression of MDR1 expression and function

    SciTech Connect (OSTI)

    Hu, Yamei; Wang, Lingxian; Wang, Lu; Wu, Xuefeng; Wu, Xudong; Gu, Yanhong; Shu, Yongqian; Sun, Yang; Shen, Yan; Xu, Qiang

    2015-02-15

    Liposarcoma is the most common soft tissue sarcoma with a high risk of relapse. Few therapeutic options are available for the aggressive local or metastatic disease. Here, we report that the clinically used proteasome inhibitor bortezomib exhibits significantly stronger cytotoxicity toward highly malignant human liposarcoma SW872-S cells compared with its parental SW872 cells, which is accompanied by enhanced activation of apoptotic signaling both in vitro and in vivo. Treatment of cells with Jun-N-terminal kinase (JNK) inhibitor SP60015 or the translation inhibitor cycloheximide ameliorated this enhanced apoptosis. Bortezomib inhibited MDR1 expression and function more effectively in SW872-S cells than in SW872 cells, indicating that the increased cytotoxicity relies on the degree of proteasome inhibition. Furthermore, the pharmacological or genetic inhibition of sarco/endoplasmic reticulum calcium-ATPase (SERCA) 2, which is highly expressed in SW872-S cells, resulted in partial reversal of cell growth inhibition and increase of MDR1 expression in bortezomib-treated SW872-S cells. These results show that bortezomib exhibits preferential cytotoxicity toward SW872-S cells possibly via highly expressed SERCA2-associated MDR1 suppression and suggest that bortezomib may serve as a potent agent for treating advanced liposarcoma. - Highlights: • We compare the cytotoxicity of different drugs between SW872-S and SW872 cells. • Highly malignant liposarcoma cells SW872-S show hypersensitivity to bortezomib. • Apoptotic signaling is robustly enhanced in bortezomib-treated SW872-S cells. • Bortezomib has strong suppression on MDR1 expression and function in SW872-S cells. • Inhibition of SERCA2 protects SW872-S cells from bortezomib.

  7. Th Cell Gene Expression and Function in Response to Low Dose and Acute Radiation

    SciTech Connect (OSTI)

    Daila S. Gridley, PhD

    2012-03-30

    FINAL TECHNICAL REPORT Supported by the Low Dose Radiation Research Program, Office of Science U.S. Department of Energy Grant No. DE-FG02-07ER64345 Project ID: 0012965 Award Register#: ER64345 Project Manager: Noelle F. Metting, Sc.D. Phone: 301-903-8309 Division SC-23.2 noelle.metting@science.doe.gov Submitted March 2012 To: https://www.osti.gov/elink/241.3.jsp Title: Th Cell Gene Expression and Function in Response to Low Dose and Acute Radiation PI: Daila S. Gridley, Ph.D. Human low dose radiation data have been derived primarily from studies of space and airline flight personnel, nuclear plant workers and others exposed occupationally, as well as victims in the vicinity of atomic bomb explosions. The findings remain inconclusive due to population inconsistencies and complex interactions among total dose, dose rate, radiation quality and age at exposure. Thus, safe limits for low dose occupational irradiation are currently based on data obtained with doses far exceeding the levels expected for the general population and health risks have been largely extrapolated using the linear-nonthreshold dose-response model. The overall working hypothesis of the present study is that priming with low dose, low-linear energy transfer (LET) radiation can ameliorate the response to acute high-dose radiation exposure. We also propose that the efficacy of low-dose induced protection will be dependent upon the form and regimen of the high-dose exposure: photons versus protons versus simulated solar particle event protons (sSPE). The emphasis has been on gene expression and function of CD4+ T helper (Th) lymphocytes harvested from spleens of whole-body irradiated C57BL/6 mice, a strain that provides the genetic background for many genetically engineered strains. Evaluations of the responses of other selected cells, tissues such as skin, and organs such as lung, liver and brain were also initiated (partially funded by other sources). The long-term goal is to provide information

  8. Myocardial regeneration in adriamycin cardiomyopathy by nuclear expression of GLP1 using ultrasound targeted microbubble destruction

    SciTech Connect (OSTI)

    Chen, Shuyuan; Chen, Jiaxi; Huang, Pintong; Meng, Xing-Li; Clayton, Sandra; Shen, Jin-Song; Grayburn, Paul A.

    2015-03-20

    Recently GLP-1 was found to have cardioprotective effects independent of those attributable to tight glycemic control. Methods and results: We employed ultrasound targeted microbubble destruction (UTMD) to deliver piggybac transposon plasmids encoding the GLP-1 gene with a nuclear localizing signal to rat hearts with adriamycin cardiomyopathy. After a single UTMD treatment, overexpression of transgenic GLP-1 was found in nuclei of rat heart cells with evidence that transfected cardiac cells had undergone proliferation. UTMD-GLP-1 gene therapy restored LV mass, fractional shortening index, and LV posterior wall diameter to nearly normal. Nuclear overexpression of GLP-1 by inducing phosphorylation of FoxO1-S256 and translocation of FoxO1 from the nucleus to the cytoplasm significantly inactivated FoxO1 and activated the expression of cyclin D1 in nuclei of cardiac muscle cells. Reversal of adriamycin cardiomyopathy appeared to be mediated by dedifferentiation and proliferation of nuclear FoxO1-positive cardiac muscle cells with evidence of embryonic stem cell markers (OCT4, Nanog, SOX2 and c-kit), cardiac early differentiation markers (NKX2.5 and ISL-1) and cellular proliferation markers (BrdU and PHH3) after UTMD with GLP-1 gene therapy. Conclusions: Intranuclear myocardial delivery of the GLP-1gene can reverse established adriamycin cardiomyopathy by stimulating myocardial regeneration. - Highlights: • The activation of nuclear FoxO1 in cardiac muscle cells associated with adriamycin cardiomyopathy. • Myocardial nuclear GLP-1 stimulates myocardial regeneration and reverses adriamycin cardiomyopathy. • The process of myocardial regeneration associated with dedifferentiation and proliferation.

  9. Concentration-dependent gene expression responses to flusilazole in embryonic stem cell differentiation cultures

    SciTech Connect (OSTI)

    Dartel, Dorien A.M. van; Pennings, Jeroen L.A.; Fonteyne, Liset J.J. de la; Brauers, Karen J.J.; Claessen, Sandra; Delft, Joost H. van; Kleinjans, Jos C.S.; Piersma, Aldert H.

    2011-03-01

    The murine embryonic stem cell test (EST) is designed to evaluate developmental toxicity based on compound-induced inhibition of embryonic stem cell (ESC) differentiation into cardiomyocytes. The addition of transcriptomic evaluation within the EST may result in enhanced predictability and improved characterization of the applicability domain, therefore improving usage of the EST for regulatory testing strategies. Transcriptomic analyses assessing factors critical for risk assessment (i.e. dose) are needed to determine the value of transcriptomic evaluation in the EST. Here, using the developmentally toxic compound, flusilazole, we investigated the effect of compound concentration on gene expression regulation and toxicity prediction in ESC differentiation cultures. Cultures were exposed for 24 h to multiple concentrations of flusilazole (0.54-54 {mu}M) and RNA was isolated. In addition, we sampled control cultures 0, 24, and 48 h to evaluate the transcriptomic status of the cultures across differentiation. Transcriptomic profiling identified a higher sensitivity of development-related processes as compared to cell division-related processes in flusilazole-exposed differentiation cultures. Furthermore, the sterol synthesis-related mode of action of flusilazole toxicity was detected. Principal component analysis using gene sets related to normal ESC differentiation was used to describe the dynamics of ESC differentiation, defined as the 'differentiation track'. The concentration-dependent effects on development were reflected in the significance of deviation of flusilazole-exposed cultures from this transcriptomic-based differentiation track. Thus, the detection of developmental toxicity in EST using transcriptomics was shown to be compound concentration-dependent. This study provides further insight into the possible application of transcriptomics in the EST as an improved alternative model system for developmental toxicity testing.

  10. Gestational exposure to diethylstilbestrol alters cardiac structure/function, protein expression and DNA methylation in adult male mice progeny

    SciTech Connect (OSTI)

    Haddad, Rami, E-mail: rami.haddad@mail.mcgill.ca [Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 chemin Cote Ste Catherine, Montral, Qubec, Canada H3T 1E2 (Canada) [Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 chemin Cote Ste Catherine, Montral, Qubec, Canada H3T 1E2 (Canada); Division of Experimental Medicine, Department of Medicine, McGill University, 850 Sherbrooke Street, Montral, Qubec, Canada H3A 1A2 (Canada); Kasneci, Amanda, E-mail: amanda.kasneci@mail.mcgill.ca [Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 chemin Cote Ste Catherine, Montral, Qubec, Canada H3T 1E2 (Canada)] [Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 chemin Cote Ste Catherine, Montral, Qubec, Canada H3T 1E2 (Canada); Mepham, Kathryn, E-mail: katherine.mepham@mail.mcgill.ca [Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 chemin Cote Ste Catherine, Montral, Qubec, Canada H3T 1E2 (Canada) [Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 chemin Cote Ste Catherine, Montral, Qubec, Canada H3T 1E2 (Canada); Division of Experimental Medicine, Department of Medicine, McGill University, 850 Sherbrooke Street, Montral, Qubec, Canada H3A 1A2 (Canada); Sebag, Igal A., E-mail: igal.sebag@mcgill.ca [Division of Cardiology, Jewish General Hospital, 3755 chemin Cote Ste Catherine, Montral, Qubec, Canada H3T 1E2 (Canada); and others

    2013-01-01

    Pregnant women, and thus their fetuses, are exposed to many endocrine disruptor compounds (EDCs). Fetal cardiomyocytes express sex hormone receptors making them potentially susceptible to re-programming by estrogenizing EDCs. Diethylstilbestrol (DES) is a proto-typical, non-steroidal estrogen. We hypothesized that changes in adult cardiac structure/function after gestational exposure to the test compound DES would be a proof in principle for the possibility of estrogenizing environmental EDCs to also alter the fetal heart. Vehicle (peanut oil) or DES (0.1, 1.0 and 10.0 ?g/kg/da.) was orally delivered to pregnant C57bl/6n dams on gestation days 11.514.5. At 3 months, male progeny were left sedentary or were swim trained for 4 weeks. Echocardiography of isoflurane anesthetized mice revealed similar cardiac structure/function in all sedentary mice, but evidence of systolic dysfunction and increased diastolic relaxation after swim training at higher DES doses. The calcium homeostasis proteins, SERCA2a, phospholamban, phospho-serine 16 phospholamban and calsequestrin 2, are important for cardiac contraction and relaxation. Immunoblot analyses of ventricle homogenates showed increased expression of SERCA2a and calsequestrin 2 in DES mice and greater molecular remodeling of these proteins and phospho-serine 16 phospholamban in swim trained DES mice. DES increased cardiac DNA methyltransferase 3a expression and DNA methylation in the CpG island within the calsequestrin 2 promoter in heart. Thus, gestational DES epigenetically altered ventricular DNA, altered cardiac function and expression, and reduced the ability of adult progeny to cardiac remodel when physically challenged. We conclude that gestational exposure to estrogenizing EDCs may impact cardiac structure/function in adult males. -- Highlights: ? Gestational DES changes cardiac SERCA2a and CASQ2 expression. ? Echocardiography identified systolic dysfunction and increased diastolic relaxation. ? DES increased DNMT

  11. A constitutive expression system for glycosyl hydrolase family 7 cellobiohydrolases in Hypocrea jecorina

    SciTech Connect (OSTI)

    Linger, Jeffrey G.; Taylor, II, Larry E.; Baker, John O.; Vander Wall, Todd; Hobdey, Sarah E.; Podkaminer, Kara; Himmel, Michael E.; Decker, Stephen R.

    2015-03-18

    One of the primary industrial-scale cellulase producers is the ascomycete fungus, Hypocrea jecorina, which produces and secretes large quantities of diverse cellulolytic enzymes. Perhaps the single most important biomass degrading enzyme is cellobiohydrolase I (cbh1or Cel7A) due to its enzymatic proficiency in cellulose depolymerization. However, production of Cel7A with native-like properties from heterologous expression systems has proven difficult. In this study, we develop a protein expression system in H. jecorina (Trichoderma reesei) useful for production and secretion of heterologous cellobiohydrolases from glycosyl hydrolase family 7. Building upon previous work in heterologous protein expression in filamentous fungi, we have integrated a native constitutive enolase promoter with the native cbh1 signal sequence. The results are the following: The constitutive eno promoter driving the expression of Cel7A allows growth on glucose and results in repression of the native cellulase system, severely reducing background endo- and other cellulase activity and greatly simplifying purification of the recombinant protein. Coupling this system to a Δcbh1 strain of H. jecorina ensures that only the recombinant Cel7A protein is produced. Two distinct transformant colony morphologies were observed and correlated with high and null protein production. Production levels in ‘fast’ transformants are roughly equivalent to those in the native QM6a strain of H. jecorina, typically in the range of 10 to 30 mg/L when grown in continuous stirred-tank fermenters. ‘Slow’ transformants showed no evidence of Cel7A production. Specific activity of the purified recombinant Cel7A protein is equivalent to that of native protein when assayed on pretreated corn stover, as is the thermal stability and glycosylation level. Purified Cel7A produced from growth on glucose demonstrated remarkably consistent specific activity. Purified Cel7A from the same strain grown on lactose

  12. Development of an equivalent diameter expression for vertical U-tubes used in ground-coupled heat pumps

    SciTech Connect (OSTI)

    Gu, Y.; O`Neal, D.L.

    1998-12-31

    An expression for the equivalent diameter was developed for the heat transfer of a vertical U-tube heat exchanger used in applications of ground-coupled heat pumps. The expression was derived using the assumptions of steady-state heat transfer and concentricity of one leg and the borehole. Potential errors in applying the results to a transient start-up problem are also quantified and discussed in this paper, using transient cylindrical heat source solutions available in the literature. A conformal mapping technique was used to develop a solution to examine the errors in evaluating the external thermal resistance with a concentricity assumption. The principle of superposition of multiple heat sources was applied in the present work. The results show that the equivalent diameter depends on the tube diameter and the leg spacing. The ratio of the calculated equivalent diameter to the tube diameter can be two or greater.

  13. o-p?-DDT-mediated uterotrophy and gene expression in immature C57BL/6 mice and SpragueDawley rats

    SciTech Connect (OSTI)

    Kwekel, Joshua C.; Forgacs, Agnes L.; Williams, Kurt J.; Zacharewski, Timothy R.

    2013-12-15

    1,1,1-Trichloro-2,2-bis(2-chlorophenyl-4-chlorophenyl)ethane (o,p?-DDT) is an organochlorine pesticide and endocrine disruptor known to activate the estrogen receptor. Comprehensive ligand- and species-comparative dose- and time-dependent studies were conducted to systematically assess the uterine physiological, morphological and gene expression responses elicited by o,p?-DDT and ethynyl estradiol (EE) in immature ovariectomized C57BL/6 mice and SpragueDawley rats. Custom cDNA microarrays were used to identify conserved and divergent differential gene expression responses. A total of 1256 genes were differentially expressed by both ligands in both species, 559 of which exhibited similar temporal expression profiles suggesting that o,p?-DDT elicits estrogenic effects at high doses when compared to EE. However, 51 genes exhibited species-specific uterine expression elicited by o,p?-DDT. For example, carbonic anhydrase 2 exhibited species- and ligand-divergent expression as confirmed by quantitative real-time PCR. The identification of comparable temporal phenotypic responses linked to gene expression demonstrates that systematic comparative gene expression assessments are valuable for elucidating conserved and divergent estrogen signaling mechanisms in rodent uterotrophy. - Highlights: o,p?-DDT and enthynyl estradiol (EE) both elicit uterotrophy in mice and rats. o,p?-DDT and EE have different kinetics in uterine wet weight induction. o,p?-DDT elicited stromal hypertrophy in rats but myometrial hypertrophy in mice. 1256 genes were differentially expressed by both ligands in both species. Only 51 genes had species-specific uterine expression.

  14. Autoantibodies in dilated cardiomyopathy induce vascular endothelial growth factor expression in cardiomyocytes

    SciTech Connect (OSTI)

    Saygili, Erol; Noor-Ebad, Fawad; Schröder, Jörg W.; Mischke, Karl; Saygili, Esra; Rackauskas, Gediminas; Marx, Nikolaus; Kelm, Malte; Rana, Obaida R.

    2015-09-11

    Background: Autoantibodies have been identified as major predisposing factors for dilated cardiomyopathy (DCM). Patients with DCM show elevated serum levels of vascular endothelial growth factor (VEGF) whose source is unknown. Besides its well-investigated effects on angiogenesis, evidence is present that VEGF signaling is additionally involved in fibroblast proliferation and cardiomyocyte hypertrophy, hence in cardiac remodeling. Whether autoimmune effects in DCM impact cardiac VEGF signaling needs to be elucidated. Methods: Five DCM patients were treated by the immunoadsorption (IA) therapy on five consecutive days. The eluents from the IA columns were collected and prepared for cell culture. Cardiomyocytes from neonatal rats (NRCM) were incubated with increasing DCM-immunoglobulin-G (IgG) concentrations for 48 h. Polyclonal IgG (Venimmun N), which was used to restore IgG plasma levels in DCM patients after the IA therapy was additionally used for control cell culture purposes. Results: Elevated serum levels of VEGF decreased significantly after IA (Serum VEGF (ng/ml); DCM pre-IA: 45 ± 9.1 vs. DCM post–IA: 29 ± 6.7; P < 0.05). In cell culture, pretreatment of NRCM by DCM-IgG induced VEGF expression in a time and dose dependent manner. Biologically active VEGF that was secreted by NRCM significantly increased BNP mRNA levels in control cardiomyocytes and induced cell-proliferation of cultured cardiac fibroblast (Fibroblast proliferation; NRCM medium/HC-IgG: 1 ± 0.0 vs. NRCM medium/DCM-IgG 100 ng/ml: 5.6 ± 0.9; P < 0.05). Conclusion: The present study extends the knowledge about the possible link between autoimmune signaling in DCM and VEGF induction. Whether this observation plays a considerable role in cardiac remodeling during DCM development needs to be further elucidated. - Highlights: • Mechanisms of remodeling in dilated cardiomyopathy (DCM) are not fully understood. • Autoantibodies have been identified as major predisposing factors

  15. Aluminium induced oxidative stress results in decreased mitochondrial biogenesis via modulation of PGC-1? expression

    SciTech Connect (OSTI)

    Sharma, Deep Raj; Sunkaria, Aditya; Wani, Willayat Yousuf; Sharma, Reeta Kumari; Kandimalla, Ramesh J.L.; Bal, Amanjit; Gill, Kiran Dip

    2013-12-01

    The present investigation was carried out to elucidate a possible molecular mechanism related to the effects of aluminium-induced oxidative stress on various mitochondrial respiratory complex subunits with special emphasis on the role of Peroxisome proliferator activated receptor gamma co-activator 1? (PGC-1?) and its downstream targets i.e. Nuclear respiratory factor-1(NRF-1), Nuclear respiratory factor-2(NRF-2) and Mitochondrial transcription factor A (Tfam) in mitochondrial biogenesis. Aluminium lactate (10 mg/kg b.wt./day) was administered intragastrically to rats for 12 weeks. After 12 weeks of exposure, we found an increase in ROS levels, mitochondrial DNA oxidation and decrease in citrate synthase activity in the Hippocampus (HC) and Corpus striatum (CS) regions of rat brain. On the other hand, there was a decrease in the mRNA levels of the mitochondrial encoded subunitsNADH dehydrogenase (ND) subunits i.e. ND1, ND2, ND3, Cytochrome b (Cytb), Cytochrome oxidase (COX) subunits i.e. COX1, COX3, ATP synthase (ATPase) subunit 6 along with reduced expression of nuclear encoded subunits COX4, COX5A, COX5B of Electron transport chain (ETC). Besides, a decrease in mitochondrial DNA copy number and mitochondrial content in both regions of rat brain was observed. The PGC-1? was down-regulated in aluminium treated rats along with NRF-1, NRF-2 and Tfam, which act downstream from PGC-1? in aluminium treated rats. Electron microscopy results revealed a significant increase in the mitochondrial swelling, loss of cristae, chromatin condensation and decreases in mitochondrial number in case of aluminium treated rats as compared to control. So, PGC-1? seems to be a potent target for aluminium neurotoxicity, which makes it an almost ideal target to control or limit the damage that has been associated with the defective mitochondrial function seen in neurodegenerative diseases. - Highlights: Aluminium decreases the mRNA levels of mitochondrial and nuclear encoded subunits

  16. Over-expression of a putative oxidoreductase (UcpA) for increasing furfural or 5-hydroxymethylfurfural tolerance

    DOE Patents [OSTI]

    Wang, Xuan; Miller, Elliot N.; Yomano, Lorraine P.; Shanmugam, Keelnatham T.; Ingram, Lonnie O'Neal

    2016-05-24

    The subject invention pertains to overexpression of a putative oxidoreductase (ucpA) for increasing furfural tolerance in genetically modified microorganisms. Genetically modified microorganisms capable of overexpressing UcpA are also provided. Increased expression of ucpA was shown to increase furfural tolerance by 50%, and to permit the fermentation of sugars to products in the presence of 15 mM furfural.

  17. Protein expression and isotopic enrichment based on induction of the Entner-Doudoroff pathway in Escherichia coli

    SciTech Connect (OSTI)

    Refaeli, Bosmat; Goldbourt, Amir

    2012-10-12

    Highlights: Black-Right-Pointing-Pointer The Entner-Doudoroff pathway is induced during protein expression in E. coli. Black-Right-Pointing-Pointer 1-{sup 13}C-gluconate and {sup 15}NH{sub 4}Cl provide a carbonyl-amide protein backbone labeling scheme. Black-Right-Pointing-Pointer The enrichment pattern is determined by nuclear magnetic resonance. -- Abstract: The Entner-Doudoroff pathway is known to exist in many organisms including bacteria, archea and eukarya. Although the common route for carbon catabolism in Escherichia coli is the Embden-Meyerhof-Parnas pathway, it was shown that gluconate catabolism in E. coli occurs via the Entner-Doudoroff pathway. We demonstrate here that by supplying BL21(DE3) competent E.coli cells with gluconate in a minimal growth medium, protein expression can be induced. Nuclear magnetic resonance data of over-expressed ubiquitin show that by using [1-{sup 13}C]-gluconate as the only carbon source, and {sup 15}N-enriched ammonium chloride, sparse isotopic enrichment in the form of a spin-pair carbonyl-amide backbone enrichment is obtained. The specific amino acid labeling pattern is analyzed and is shown to be compatible with Entner-Doudoroff metabolism. Isotopic enrichment serves as a key factor in the biophysical characterization of proteins by various methods including nuclear magnetic resonance, mass spectrometry, infrared spectroscopy and more. Therefore, the method presented here can be applied to study proteins by obtaining sparse enrichment schemes that are not based on the regular glycolytic pathway, or to study the Entner-Doudoroff metabolism during protein expression.

  18. Project Results: Evaluating FedEx Express Hybrid-Electric Delivery Trucks (Fact Sheet), Vehicle Technologies Program (VTP)

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Renewable Energy Laboratory's (NREL's) Fleet Test and Evaluation Team evaluated the 12-month, in-service performance of three Class 4 gasoline hybrid-electric delivery trucks and three comparable conventional diesel trucks operated by FedEx Express in Southern California. In addition, the tailpipe emissions and fuel economy of one of the gasoline hybrid-electric vehicles (gHEVs) and one diesel truck were tested on a chassis dynamometer. The gHEVs were equipped with a parallel hybrid system

  19. Project Results: Evaluating FedEx Express Hybrid-Electric Delivery Trucks (Fact Sheet), Vehicle Technologies Program (VTP)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Renewable Energy Laboratory's (NREL's) Fleet Test and Evaluation Team evaluated the 12-month, in-service performance of three Class 4 gasoline hybrid-electric delivery trucks and three comparable conventional diesel trucks operated by FedEx Express in Southern California. In addition, the tailpipe emissions and fuel economy of one of the gasoline hybrid-electric vehicles (gHEVs) and one diesel truck were tested on a chassis dynamometer. The gHEVs were equipped with a parallel hybrid system

  20. Development of a reverse genetics system to generate a recombinant Ebola virus Makona expressing a green fluorescent protein

    SciTech Connect (OSTI)

    Albariño, César G. Wiggleton Guerrero, Lisa; Lo, Michael K.; Nichol, Stuart T.; Towner, Jonathan S.

    2015-10-15

    Previous studies have demonstrated the potential application of reverse genetics technology in studying a broad range of aspects of viral biology, including gene regulation, protein function, cell entry, and pathogenesis. Here, we describe a highly efficient reverse genetics system used to generate recombinant Ebola virus (EBOV) based on a recent isolate from a human patient infected during the 2014–2015 outbreak in Western Africa. We also rescued a recombinant EBOV expressing a fluorescent reporter protein from a cleaved VP40 protein fusion. Using this virus and an inexpensive method to quantitate the expression of the foreign gene, we demonstrate its potential usefulness as a tool for screening antiviral compounds and measuring neutralizing antibodies. - Highlights: • Recombinant Ebola virus (EBOV) derived from Makona variant was rescued. • New protocol for viral rescue allows 100% efficiency. • Modified EBOV expresses a green fluorescent protein from a VP40-fused protein. • Modified EBOV was tested as tool to screen antiviral compounds and measure neutralizing antibodies.

  1. Identification of candidate genes in Populus cell wall biosynthesis using text-mining, co-expression network and comparative genomics

    SciTech Connect (OSTI)

    Yang, Xiaohan; Ye, Chuyu; Bisaria, Anjali; Tuskan, Gerald A; Kalluri, Udaya C

    2011-01-01

    Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of ethanol from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidences supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. The 694 Arabidopsis genes were computationally divided into 22 clusters. Queries of the Populus genome using the Arabidopsis genes revealed 817 Populus orthologs. Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional genomics in relation to cell wall biosynthesis.

  2. Cloning and expression of soluble truncated variants of Borrelia OspA, OspB and Vmp7

    DOE Patents [OSTI]

    Dunn, J.J.; Barbour, A.G.

    1996-11-05

    A method is provided for preparing soluble recombinant variations of Borrelia lipoproteins such as Borrelia burgdorferi outer surface protein A (OspA) and outer surface protein B (OspB), and B. hermsii variable major protein 7 (Vmp7). The method includes synthesizing a set of oligonucleotide primers, amplifying the template DNA utilizing the PCR, purifying the amplification products, cloning the amplification products into a suitable expression vector, transforming a suitable host utilizing the cloned expression vector, cultivating the transformed host for protein production and subsequently isolating and purifying the resulting protein. Also provided are soluble, recombinant variations of Borrelia burgdorferi outer surface protein A (OspA), outer surface protein B (OspB), and B. hermsii variable major protein 7 (Vmp7). The expression vectors harboring DNA encoding the recombinant variations, pET9-OspA, pET9-OspB and pET9-Vmp7, as well as the E. coli host BL21(DE3)/pLysS transformed with each of these vectors, are also disclosed. 38 figs.

  3. Assessment of ERCC1 and XPF Protein Expression Using Quantitative Immunohistochemistry in Nasopharyngeal Carcinoma Patients Undergoing Curative Intent Treatment

    SciTech Connect (OSTI)

    Jagdis, Amanda; Phan, Tien; Faculty of Medicine, University of Calgary, Calgary, Alberta ; Klimowicz, Alexander C.; Faculty of Medicine, University of Calgary, Calgary, Alberta ; Laskin, Janessa J.; Faculty of Medicine, University of British Columbia, Vancouver, British Columbia ; Lau, Harold Y.; Faculty of Medicine, University of Calgary, Calgary, Alberta ; Petrillo, Stephanie K.; Siever, Jodi E.; Thomson, Thomas A.; Faculty of Medicine, University of British Columbia, Vancouver, British Columbia ; Magliocco, Anthony M.; Faculty of Medicine, University of Calgary, Calgary, Alberta ; Hao, Desire; Faculty of Medicine, University of Calgary, Calgary, Alberta

    2013-04-01

    Purpose: We sought to evaluate the prognostic/predictive value of ERCC1 and XPF in patients with nonmetastatic nasopharyngeal carcinoma (NPC) treated with curative intent. Methods and Materials: ERCC1 and XPF protein expression was evaluated by immunofluorescence combined with automated quantitative analysis (AQUA) using the FL297 and 3F2 antibodies, respectively. ERCC1 and XPF protein expression levels were correlated with clinical outcomes. Results: Patient characteristics were as follows: mean age 52 years (range, 18-85 years), 67% male, 72% Karnofsky performance status (KPS) ?90%, World Health Organization (WHO) type 1/2/3 = 12%/28%/60%, stage III/IV 65%. With a median follow-up time of 50 months (range, 2.9 to 120 months), the 5-year overall survival (OS) was 70.8%. Median standardized nuclear AQUA scores were used as cutpoints for ERCC1 (n=138) and XPF (n=130) protein expression. Agreement between dichotomized ERCC1 and XPF scores was high at 79.4% (kappa = 0.587, P<.001). Neither biomarker predicted locoregional recurrence, DFS, or OS after adjustment for age and KPS, irrespective of stratification by stage, WHO type, or treatment. Conclusions: Neither ERCC1 nor XPF, analyzed by quantitative immunohistochemistry using the FL297 and 3F2 antibodies, was prognostic or predictive in this cohort of NPC patients.

  4. Expression of acetate permease-like (apl) genes in subsurface communities of Geobacter species under fluctuating acetate concentrations

    SciTech Connect (OSTI)

    Elifantz, H.; N'Guessan, L.A.; Mouser, P.J.; Williams, K H.; Wilkins, M J.; Risso, C.; Holmes, D.E.; Long, P.E.; Lovley, D.R.

    2010-03-01

    The addition of acetate to uranium-contaminated aquifers in order to stimulate the growth and activity of Geobacter species that reduce uranium is a promising in situ bioremediation option. Optimizing this bioremediation strategy requires that sufficient acetate be added to promote Geobacter species growth. We hypothesized that under acetate-limiting conditions, subsurface Geobacter species would increase the expression of either putative acetate symporters genes (aplI and aplII). Acetate was added to a uranium-contaminated aquifer (Rifle, CO) in two continuous amendments separated by 5 days of groundwater flush to create changing acetate concentrations. While the expression of aplI in monitoring well D04 (high acetate) weakly correlated with the acetate concentration over time, the transcript levels for this gene were relatively constant in well D08 (low acetate). At the lowest acetate concentrations during the groundwater flush, the transcript levels of aplII were the highest. The expression of aplII decreased 2-10-fold upon acetate reintroduction. However, the overall instability of acetate concentrations throughout the experiment could not support a robust conclusion regarding the role of apl genes in response to acetate limitation under field conditions, in contrast to previous chemostat studies, suggesting that the function of a microbial community cannot be inferred based on lab experiments alone.

  5. Cloning and expression of soluble truncated variants of Borrelia OspA, OspB and Vmp7

    DOE Patents [OSTI]

    Dunn, John J.; Barbour, Alan G.

    1996-11-05

    A method is provided herein for preparing soluble recombinant variations of Borrelia lipoproteins such as Borrelia burgdorferi outer surface protein A (OspA) and outer surface protein B (OspB), and B. hermsii variable major protein 7 (Vmp7). The method includes synthesizing a set of oligonucleotide primers, amplifying the template DNA utilizing the PCR, purifying the amplification products, cloning the amplification products into a suitable expression vector, transforming a suitable host utilizing the cloned expression vector, cultivating the transformed host for protein production and subsequently isolating and purifying the resulting protein. Also provided are soluble, recombinant variations of Borrelia burgdorferi outer surface protein A (OspA), outer surface protein B (OspB), and B. hermsii variable major protein 7 (Vmp7). The expression vectors harboring DNA encoding the recombinant variations, pET9-OspA, pET9-OspB and pET9-Vmp7, as well as the E. coli host BL21(DE3)/pLysS transformed with each of these vectors, are also disclosed.

  6. Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    He, Fei; Maslov, Sergei; Yoo, Shinjae; Wang, Daifeng; Kumari, Sunita; Gerstein, Mark; Ware, Doreen

    2016-03-25

    Here, transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metadata or differences in annotation styles by different labs. In this study, we carefully selected and integrated 6,057 Arabidopsis microarray expression samples from 304 experiments deposited to NCBI GEO. Metadata such as tissue type, growth condition, and developmental stage were manually curated for each sample. We then studied global expression landscape of the integrated dataset andmore » found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome compared to aerial tissues, but the transcriptome of cultured root is more similar to those of aerial tissues as the former samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating re-use of plant transcriptome data. As a proof of principle we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified accuracy of our predictions with samples’ metadata provided by authors.« less

  7. Estrogen induced concentration dependent differential gene expression in human breast cancer (MCF7) cells: Role of transcription factors

    SciTech Connect (OSTI)

    Chandrasekharan, Sabarinath; Kandasamy, Krishna Kumar; Dayalan, Pavithra; Ramamurthy, Viraragavan

    2013-08-02

    Highlights: Estradiol (E2) at low dose induced cell proliferation in breast cancer cells. E2 at high concentration induced cell stress in breast cancer cells. Estrogen receptor physically interacts only with a few transcription factors. Differential expression of genes with Oct-1 binding sites increased under stress. Transcription factor binding sites showed distinct spatial distribution on genes. -- Abstract: Background: Breast cancer cells respond to estrogen in a concentration dependent fashion, resulting in proliferation or apoptosis. The mechanism of this concentration dependent differential outcome is not well understood yet. Methodology: Meta-analysis of the expression data of MCF7 cells treated with low (1 nM) or high (100 nM) dose of estradiol (E2) was performed. We identified genes differentially expressed at the low or the high dose, and examined the nature of regulatory elements in the vicinity of these genes. Specifically, we looked for the difference in the presence, abundance and spatial distribution of binding sites for estrogen receptor (ER) and selected transcription factors (TFs) in the genomic region up to 25 kb upstream and downstream from the transcription start site (TSS) of these genes. Results: It was observed that at high dose E2 induced the expression of stress responsive genes, while at low dose, genes involved in cell cycle were induced. We found that the occurrence of transcription factor binding regions (TFBRs) for certain factors such as Sp1 and SREBP1 were higher on regulatory regions of genes expressed at low dose. At high concentration of E2, genes with a higher frequency of Oct-1 binding regions were predominantly involved. In addition, there were differences in the spatial distribution pattern of the TFBRs in the genomic regions among the two sets of genes. Discussion: E2 induced predominantly proliferative/metabolic response at low concentrations; but at high concentration, stressrescue responses were induced. At high E2

  8. Transforming growth factor β-activated kinase 1 negatively regulates interleukin-1α-induced stromal-derived factor-1 expression in vascular smooth muscle cells

    SciTech Connect (OSTI)

    Yang, Bin; Li, Wei; Zheng, Qichang; Qin, Tao; Wang, Kun; Li, Jinjin; Guo, Bing; Yu, Qihong; Wu, Yuzhe; Gao, Yang; Cheng, Xiang; Hu, Shaobo; Kumar, Stanley Naveen; Liu, Sanguang; Song, Zifang

    2015-07-17

    Stromal-derived Factor-1 (SDF-1) derived from vascular smooth muscle cells (VSMCs) contributes to vascular repair and remodeling in various vascular diseases. In this study, the mechanism underlying regulation of SDF-1 expression by interleukin-1α (IL-1α) was investigated in primary rat VSMCs. We found IL-1α promotes SDF-1 expression by up-regulating CCAAT-enhancer-binding protein β (C/EBPβ) in an IκB kinase β (IKKβ) signaling-dependent manner. Moreover, IL-1α-induced expression of C/EBPβ and SDF-1 was significantly potentiated by knockdown of transforming growth factor β-activated kinase 1 (TAK1), an upstream activator of IKKβ signaling. In addition, we also demonstrated that TAK1/p38 mitogen-activated protein kinase (p38 MAPK) signaling exerted negative effect on IL-1α-induced expression of C/EBPβ and SDF-1 through counteracting ROS-dependent up-regulation of nuclear factor erythroid 2-related factor 2 (NRF2). In conclusion, TAK1 acts as an important regulator of IL-1α-induced SDF-1 expression in VSMCs, and modulating activity of TAK1 may serve as a potential strategy for modulating vascular repair and remodeling. - Highlights: • IL-1α induces IKKβ signaling-dependent SDF-1 expression by up-regulating C/EBPβ. • Activation of TAK1 by IL-1α negatively regulates C/EBPβ-dependent SDF-1 expression. • IL-1α-induced TAK1/p38 MAPK signaling counteracts ROS-dependent SDF-1 expression. • TAK1 counteracts IL-1α-induced SDF-1 expression by attenuating NRF2 up-regulation.

  9. Urine acidification has no effect on peroxisome proliferator-activated receptor (PPAR) signaling or epidermal growth factor (EGF) expression in rat urinary bladder urothelium

    SciTech Connect (OSTI)

    Achanzar, William E. Moyer, Carolyn F.; Marthaler, Laura T.; Gullo, Russell; Chen, Shen-Jue; French, Michele H.; Watson, Linda M.; Rhodes, James W.; Kozlosky, John C.; White, Melvin R.; Foster, William R.; Burgun, James J.; Car, Bruce D.; Cosma, Gregory N.; Dominick, Mark A.

    2007-09-15

    We previously reported prevention of urolithiasis and associated rat urinary bladder tumors by urine acidification (via diet acidification) in male rats treated with the dual peroxisome proliferator-activated receptor (PPAR){alpha}/{gamma} agonist muraglitazar. Because urine acidification could potentially alter PPAR signaling and/or cellular proliferation in urothelium, we evaluated urothelial cell PPAR{alpha}, PPAR{delta}, PPAR{gamma}, and epidermal growth factor receptor (EGFR) expression, PPAR signaling, and urothelial cell proliferation in rats fed either a normal or an acidified diet for 5, 18, or 33 days. A subset of rats in the 18-day study also received 63 mg/kg of the PPAR{gamma} agonist pioglitazone daily for the final 3 days to directly assess the effects of diet acidification on responsiveness to PPAR{gamma} agonism. Urothelial cell PPAR{alpha} and {gamma} expression and signaling were evaluated in the 18- and 33-day studies by immunohistochemical assessment of PPAR protein (33-day study only) and quantitative real-time polymerase chain reaction (qRT-PCR) measurement of PPAR-regulated gene expression. In the 5-day study, EGFR expression and phosphorylation status were evaluated by immunohistochemical staining and egfr and akt2 mRNA levels were assessed by qRT-PCR. Diet acidification did not alter PPAR{alpha}, {delta}, or {gamma} mRNA or protein expression, PPAR{alpha}- or {gamma}-regulated gene expression, total or phosphorylated EGFR protein, egfr or akt2 gene expression, or proliferation in urothelium. Moreover, diet acidification had no effect on pioglitazone-induced changes in urothelial PPAR{gamma}-regulated gene expression. These results support the contention that urine acidification does not prevent PPAR{gamma} agonist-induced bladder tumors by altering PPAR{alpha}, {gamma}, or EGFR expression or PPAR signaling in rat bladder urothelium.

  10. Transplacental exposure to inorganic arsenic at a hepatocarcinogenic dose induces fetal gene expression changes in mice indicative of aberrant estrogen signaling and disrupted steroid metabolism

    SciTech Connect (OSTI)

    Liu Jie . E-mail: Liu6@niehs.nih.gov; Xie Yaxiong; Cooper, Ryan; Ducharme, Danica M.K.; Tennant, Raymond; Diwan, Bhalchandra A.; Waalkes, Michael P.

    2007-05-01

    Exposure to inorganic arsenic in utero in C3H mice produces hepatocellular carcinoma in male offspring when they reach adulthood. To help define the molecular events associated with the fetal onset of arsenic hepatocarcinogenesis, pregnant C3H mice were given drinking water containing 0 (control) or 85 ppm arsenic from day 8 to 18 of gestation. At the end of the arsenic exposure period, male fetal livers were removed and RNA isolated for microarray analysis using 22K oligo chips. Arsenic exposure in utero produced significant (p < 0.001) alterations in expression of 187 genes, with approximately 25% of aberrantly expressed genes related to either estrogen signaling or steroid metabolism. Real-time RT-PCR on selected genes confirmed these changes. Various genes controlled by estrogen, including X-inactive-specific transcript, anterior gradient-2, trefoil factor-1, CRP-ductin, ghrelin, and small proline-rich protein-2A, were dramatically over-expressed. Estrogen-regulated genes including cytokeratin 1-19 and Cyp2a4 were over-expressed, although Cyp3a25 was suppressed. Several genes involved with steroid metabolism also showed remarkable expression changes, including increased expression of 17{beta}-hydroxysteroid dehydrogenase-7 (HSD17{beta}7; involved in estradiol production) and decreased expression of HSD17{beta}5 (involved in testosterone production). The expression of key genes important in methionine metabolism, such as methionine adenosyltransferase-1a, betaine-homocysteine methyltransferase and thioether S-methyltransferase, were suppressed. Thus, exposure of mouse fetus to inorganic arsenic during a critical period in development significantly alters the expression of various genes encoding estrogen signaling and steroid or methionine metabolism. These alterations could disrupt genetic programming at the very early life stage, which could impact tumor formation much later in adulthood.

  11. Compound-specific effects of diverse neurodevelopmental toxicants on global gene expression in the neural embryonic stem cell test (ESTn)

    SciTech Connect (OSTI)

    Theunissen, P.T.; Robinson, J.F.; Department of Toxicogenomics, Maastricht University, Maastricht; Netherlands Toxicogenomics Centre, Maastricht ; Pennings, J.L.A.; Netherlands Toxicogenomics Centre, Maastricht ; Herwijnen, M.H. van; Kleinjans, J.C.S.; Netherlands Toxicogenomics Centre, Maastricht ; Piersma, A.H.; Netherlands Toxicogenomics Centre, Maastricht; Institute for Risk Assessment Sciences, Faculty of Veterinary Sciences, Utrecht University, Utrecht

    2012-08-01

    Alternative assays for developmental toxicity testing are needed to reduce animal use in regulatory toxicology. The in vitro murine neural embryonic stem cell test (ESTn) was designed as an alternative for neurodevelopmental toxicity testing. The integration of toxicogenomic-based approaches may further increase predictivity as well as provide insight into underlying mechanisms of developmental toxicity. In the present study, we investigated concentration-dependent effects of six mechanistically diverse compounds, acetaldehyde (ACE), carbamazepine (CBZ), flusilazole (FLU), monoethylhexyl phthalate (MEHP), penicillin G (PENG) and phenytoin (PHE), on the transcriptome and neural differentiation in the ESTn. All compounds with the exception of PENG altered ESTn morphology (cytotoxicity and neural differentiation) in a concentration-dependent manner. Compound induced gene expression changes and corresponding enriched gene ontology biological processes (GO–BP) were identified after 24 h exposure at equipotent differentiation-inhibiting concentrations of the compounds. Both compound-specific and common gene expression changes were observed between subsets of tested compounds, in terms of significance, magnitude of regulation and functionality. For example, ACE, CBZ and FLU induced robust changes in number of significantly altered genes (≥ 687 genes) as well as a variety of GO–BP, as compared to MEHP, PHE and PENG (≤ 55 genes with no significant changes in GO–BP observed). Genes associated with developmentally related processes (embryonic morphogenesis, neuron differentiation, and Wnt signaling) showed diverse regulation after exposure to ACE, CBZ and FLU. In addition, gene expression and GO–BP enrichment showed concentration dependence, allowing discrimination of non-toxic versus toxic concentrations on the basis of transcriptomics. This information may be used to define adaptive versus toxic responses at the transcriptome level.

  12. Polychlorinated biphenyl-induced VCAM-1 expression is attenuated in aortic endothelial cells isolated from caveolin-1 deficient mice

    SciTech Connect (OSTI)

    Han, Sung Gu; Eum, Sung Yong; Toborek, Michal; Smart, Eric; Hennig, Bernhard

    2010-07-15

    Exposure to environmental contaminants, such as polychlorinated biphenyls (PCBs), is a risk factor for the development of cardiovascular diseases such as atherosclerosis. Vascular cell adhesion molecule-1 (VCAM-1) is a critical mediator for adhesion and uptake of monocytes across the endothelium in the early stages of atherosclerosis development. The upregulation of VCAM-1 by PCBs may be dependent on functional membrane domains called caveolae. Caveolae are particularly abundant in endothelial cell membranes and involved in trafficking and signal transduction. The objective of this study was to investigate the role of caveolae in PCB-induced endothelial cell dysfunction. Primary mouse aortic endothelial cells (MAECs) isolated from caveolin-1-deficient mice and background C57BL/6 mice were treated with coplanar PCBs, such as PCB77 and PCB126. In addition, siRNA gene silencing technique was used to knockdown caveolin-1 in porcine vascular endothelial cells. In MAECs with functional caveolae, VCAM-1 protein levels were increased after exposure to both coplanar PCBs, whereas expression levels of VCAM-1 were not significantly altered in cells deficient of caveolin-1. Furthermore, PCB-induced monocyte adhesion was attenuated in caveolin-1-deficient MAECs. Similarly, siRNA silencing of caveolin-1 in porcine endothelial cells confirmed the caveolin-1-dependent VCAM-1 expression. Treatment of cells with PCB77 and PCB126 resulted in phosphorylation of extracellular signal-regulated kinase-1/2 (ERK1/2), and pharmacological inhibition of ERK1/2 diminished the observed PCB-induced increase in monocyte adhesion. These findings suggest that coplanar PCBs induce adhesion molecule expression, such as VCAM-1, in endothelial cells, and that this response is regulated by caveolin-1 and functional caveolae. Our data demonstrate a critical role of functional caveolae in the activation and dysfunction of endothelial cells by coplanar PCBs.

  13. Multi-walled carbon nanotube-induced gene expression in the mouse lung: Association with lung pathology

    SciTech Connect (OSTI)

    Pacurari, M.; Qian, Y.; Porter, D.W.; Wolfarth, M.; Wan, Y.; Luo, D.; Ding, M.; Castranova, V.; Guo, N.L.

    2011-08-15

    Due to the fibrous shape and durability of multi-walled carbon nanotubes (MWCNT), concerns regarding their potential for producing environmental and human health risks, including carcinogenesis, have been raised. This study sought to investigate how previously identified lung cancer prognostic biomarkers and the related cancer signaling pathways are affected in the mouse lung following pharyngeal aspiration of well-dispersed MWCNT. A total of 63 identified lung cancer prognostic biomarker genes and major signaling biomarker genes were analyzed in mouse lungs (n = 80) exposed to 0, 10, 20, 40, or 80 {mu}g of MWCNT by pharyngeal aspiration at 7 and 56 days post-exposure using quantitative PCR assays. At 7 and 56 days post-exposure, a set of 7 genes and a set of 11 genes, respectively, showed differential expression in the lungs of mice exposed to MWCNT vs. the control group. Additionally, these significant genes could separate the control group from the treated group over the time series in a hierarchical gene clustering analysis. Furthermore, 4 genes from these two sets of significant genes, coiled-coil domain containing-99 (Ccdc99), muscle segment homeobox gene-2 (Msx2), nitric oxide synthase-2 (Nos2), and wingless-type inhibitory factor-1 (Wif1), showed significant mRNA expression perturbations at both time points. It was also found that the expression changes of these 4 overlapping genes at 7 days post-exposure were attenuated at 56 days post-exposure. Ingenuity Pathway Analysis (IPA) found that several carcinogenic-related signaling pathways and carcinogenesis itself were associated with both the 7 and 11 gene signatures. Taken together, this study identifies that MWCNT exposure affects a subset of lung cancer biomarkers in mouse lungs. - Research Highlights: > Multi-Walled Carbon Nanotubes affect lung cancer biomarkers in mouse lungs. > The results suggest potentially harmful effects of MWCNT exposure on human lungs. > The results could potentially be used for

  14. Differential gene expression profiling of mouse skin after sulfur mustard exposure: Extended time response and inhibitor effect

    SciTech Connect (OSTI)

    Gerecke, Donald R. Chen Minjun; Isukapalli, Sastry S.; Gordon, Marion K.; Chang, Y.-C.; Tong Weida; Androulakis, Ioannis P.; Georgopoulos, Panos G.

    2009-01-15

    Sulfur mustard (HD, SM), is a chemical warfare agent that within hours causes extensive blistering at the dermal-epidermal junction of skin. To better understand the progression of SM-induced blistering, gene expression profiling for mouse skin was performed after a single high dose of SM exposure. Punch biopsies of mouse ears were collected at both early and late time periods following SM exposure (previous studies only considered early time periods). The biopsies were examined for pathological disturbances and the samples further assayed for gene expression profiling using the Affymetrix microarray analysis system. Principal component analysis and hierarchical cluster analysis of the differently expressed genes, performed with ArrayTrack showed clear separation of the various groups. Pathway analysis employing the KEGG library and Ingenuity Pathway Analysis (IPA) indicated that cytokine-cytokine receptor interaction, cell adhesion molecules (CAMs), and hematopoietic cell lineage are common pathways affected at different time points. Gene ontology analysis identified the most significantly altered biological processes as the immune response, inflammatory response, and chemotaxis; these findings are consistent with other reported results for shorter time periods. Selected genes were chosen for RT-PCR verification and showed correlations in the general trends for the microarrays. Interleukin 1 beta was checked for biological analysis to confirm the presence of protein correlated to the corresponding microarray data. The impact of a matrix metalloproteinase inhibitor, MMP-2/MMP-9 inhibitor I, against SM exposure was assessed. These results can help in understanding the molecular mechanism of SM-induced blistering, as well as to test the efficacy of different inhibitors.

  15. Activation of nuclear receptor NR5A2 increases Glut4 expression and glucose metabolism in muscle cells

    SciTech Connect (OSTI)

    Bolado-Carrancio, A.; Riancho, J.A.; Sainz, J.; Rodrguez-Rey, J.C.

    2014-04-04

    Highlights: NR5A2 expression in C2C12 is associated with myotube differentiation. DLPC induces an increase in GLUT4 levels and glucose uptake in C2C12 myotubes. In high glucose conditions the activation of NR5A2 inhibits fatty acids oxidation. - Abstract: NR5A2 is a nuclear receptor which regulates the expression of genes involved in cholesterol metabolism, pluripotency maintenance and cell differentiation. It has been recently shown that DLPC, a NR5A2 ligand, prevents liver steatosis and improves insulin sensitivity in mouse models of insulin resistance, an effect that has been associated with changes in glucose and fatty acids metabolism in liver. Because skeletal muscle is a major tissue in clearing glucose from blood, we studied the effect of the activation of NR5A2 on muscle metabolism by using cultures of C2C12, a mouse-derived cell line widely used as a model of skeletal muscle. Treatment of C2C12 with DLPC resulted in increased levels of expression of GLUT4 and also of several genes related to glycolysis and glycogen metabolism. These changes were accompanied by an increased glucose uptake. In addition, the activation of NR5A2 produced a reduction in the oxidation of fatty acids, an effect which disappeared in low-glucose conditions. Our results suggest that NR5A2, mostly by enhancing glucose uptake, switches muscle cells into a state of glucose preference. The increased use of glucose by muscle might constitute another mechanism by which NR5A2 improves blood glucose levels and restores insulin sensitivity.

  16. Ortho-aminoazotoluene activates mouse constitutive androstane receptor (mCAR) and increases expression of mCAR target genes

    SciTech Connect (OSTI)

    Smetanina, Mariya A.; Pakharukova, Mariya Y.; Kurinna, Svitlana M.; Dong, Bingning; Hernandez, Juan P.; Moore, David D.; Merkulova, Tatyana I.

    2011-08-15

    2'-3-dimethyl-4-aminoazobenzene (ortho-aminoazotoluene, OAT) is an azo dye and a rodent carcinogen that has been evaluated by the International Agency for Research on Cancer (IARC) as a possible (class 2B) human carcinogen. Its mechanism of action remains unclear. We examined the role of the xenobiotic receptor Constitutive Androstane Receptor (CAR, NR1I3) as a mediator of the effects of OAT. We found that OAT increases mouse CAR (mCAR) transactivation in a dose-dependent manner. This effect is specific because another closely related azo dye, 3'-methyl-4-dimethyl-aminoazobenzene (3'MeDAB), did not activate mCAR. Real-time Q-PCR analysis in wild-type C57BL/6 mice revealed that OAT induces the hepatic mRNA expression of the following CAR target genes: Cyp2b10, Cyp2c29, Cyp3a11, Ugt1a1, Mrp4, Mrp2 and c-Myc. CAR-null (Car{sup -/-}) mice showed no increased expression of these genes following OAT treatment, demonstrating that CAR is required for their OAT dependent induction. The OAT-induced CAR-dependent increase of Cyp2b10 and c-Myc expression was confirmed by Western blotting. Immunohistochemistry analysis of wild-type and Car{sup -/-} livers showed that OAT did not acutely induce hepatocyte proliferation, but at much later time points showed an unexpected CAR-dependent proliferative response. These studies demonstrate that mCAR is an OAT xenosensor, and indicate that at least some of the biological effects of this compound are mediated by this nuclear receptor. - Highlights: > The azo dye and mouse carcinogen OAT is a very effective mCAR activator. > OAT increases mCAR transactivation in a dose-dependent manner. > OAT CAR-dependently increases the expression of a specific subset of CAR target genes. > OAT induces an unexpectedly deferred, but CAR-dependent hepatocyte proliferation.

  17. Functional Toll-like receptor 4 expressed in lactotrophs mediates LPS-induced proliferation in experimental pituitary hyperplasia

    SciTech Connect (OSTI)

    Sabatino, Mara Eugenia; Sosa, Liliana del Valle; Petiti, Juan Pablo; Mukdsi, Jorge Humberto; Mascanfroni, Ivn Daro; Pellizas, Claudia Gabriela; Gutirrez, Silvina; Torres, Alicia Ins; De Paul, Ana Luca

    2013-11-15

    Toll like receptor 4 (TLR4) has been characterized for its ability to recognize bacterial endotoxin lipopolysaccharide (LPS). Considering that infections or inflammatory processes might contribute to the progression of pituitary tumors, we analyzed the TLR4 functional role by evaluating the LPS effect on lactotroph proliferation in primary cultures from experimental pituitary tumors, and examined the involvement of PI3K-Akt and NF-?B activation in this effect. In addition, the role of 17?-estradiol as a possible modulator of LPS-induced PRL cell proliferation was further investigated. In estrogen-induced hyperplasic pituitaries, LPS triggered lactotroph cell proliferation. However, endotoxin failed to increase the number of lactotrophs taking up BrdU in normal pituitaries. Moreover, incubation with anti-TLR4 antibody significantly reduced LPS-induced lactotroph proliferation, suggesting a functional role of this receptor. As a sign of TLR4 activation, an LPS challenge increased IL-6 release in normal and tumoral cells. By flow cytometry, TLR4 baseline expression was revealed at the plasma membrane of tumoral lactotrophs, without changes noted in the percentage of double PRL/TLR4 positive cells after LPS stimulus. Increases in TLR4 intracellular expression were detected as well as rises in CD14, p-Akt and NF-?B after an LPS challenge, as assessed by western blotting. The TLR4/PRL and PRL/NF-?B co-localization was also corroborated by immunofluorescence and the involvement of PI3K/Akt signaling in lactotroph proliferation and IL-6 release was revealed through the PI3K inhibitor Ly-294002. In addition, 17?-estradiol attenuated the LPS-evoked increase in tumoral lactotroph proliferation and IL-6 release. Collectively these results demonstrate the presence of functional TLR4 in lactotrophs from estrogen-induced hyperplasic pituitaries, which responded to the proliferative stimulation and IL-6 release induced by LPS through TLR4/CD14, with a contribution of the PI3K

  18. Clock-controlled output gene Dbp is a regulator of Arnt/Hif-1β gene expression in pancreatic islet β-cells

    SciTech Connect (OSTI)

    Nakabayashi, Hiroko; Ohta, Yasuharu Yamamoto, Masayoshi; Susuki, Yosuke; Taguchi, Akihiko; Tanabe, Katsuya; Kondo, Manabu; Hatanaka, Masayuki; Nagao, Yuko; Tanizawa, Yukio

    2013-05-03

    Highlights: •Arnt mRNA expressed in a circadian manner in mouse pancreatic islets. •Expressions of Dbp and Arnt damped in the islets of a diabetic model mouse. •DBP and E4BP4 regulate Arnt promoter activity by direct binding. •Arnt may have a role in connecting circadian rhythm and metabolism. -- Abstract: Aryl hydrocarbon receptor nuclear translocator (ARNT)/hypoxia inducible factor-1β (HIF-1β) has emerged as a potential determinant of pancreatic β-cell dysfunction and type 2 diabetes in humans. An 82% reduction in Arnt expression was observed in islets from type 2 diabetic donors as compared to non-diabetic donors. However, few regulators of Arnt expression have been identified. Meanwhile, disruption of the clock components CLOCK and BMAL1 is known to result in hypoinsulinemia and diabetes, but the molecular details remain unclear. In this study, we identified a novel molecular connection between Arnt and two clock-controlled output genes, albumin D-element binding protein (Dbp) and E4 binding protein 4 (E4bp4). By conducting gene expression studies using the islets of Wfs1{sup −/−} A{sup y}/a mice that develop severe diabetes due to β-cell apoptosis, we demonstrated clock-related gene expressions to be altered in the diabetic mice. Dbp mRNA decreased by 50%, E4bp4 mRNA increased by 50%, and Arnt mRNA decreased by 30% at Zeitgever Time (ZT) 12. Mouse pancreatic islets exhibited oscillations of clock gene expressions. E4BP4, a D-box negative regulator, oscillated anti-phase to DBP, a D-box positive regulator. We also found low-amplitude circadian expression of Arnt mRNA, which peaked at ZT4. Over-expression of DBP raised both mRNA and protein levels of ARNT in HEK293 and MIN6 cell lines. Arnt promoter-driven luciferase reporter assay in MIN6 cells revealed that DBP increased Arnt promoter activity by 2.5-fold and that E4BP4 competitively inhibited its activation. In addition, on ChIP assay, DBP and E4BP4 directly bound to D-box elements within the

  19. Caffeic acid phenethyl ester inhibits 3-MC-induced CYP1A1 expression through induction of hypoxia-inducible factor-1α

    SciTech Connect (OSTI)

    Kim, Hyung Gyun; Han, Eun Hee; Im, Ji Hye; Lee, Eun Ji; Jin, Sun Woo; Jeong, Hye Gwang

    2015-09-25

    Caffeic acid phenethyl ester (CAPE), a natural component of propolis, is reported to have anticarcinogenic properties, although its precise chemopreventive mechanism remains unclear. In this study, we examined the effects of CAPE on 3-methylcholanthrene (3-MC)-induced CYP1A1 expression and activities. CAPE reduced the formation of the benzo[a]pyrene-DNA adduct. Moreover, CAPE inhibited 3-MC-induced CYP1A1 activity, mRNA expression, protein level, and promoter activity. CAPE treatment also decreased 3-MC-inducible xenobiotic-response element (XRE)-linked luciferase, aryl hydrocarbons receptor (AhR) transactivation and nuclear localization. CAPE induced hypoxia inducible factor-1α (HIF-1α) protein level and HIF-1α responsible element (HRE) transcriptional activity. CAPE-mediated HIF-1α reduced 3-MC-inducible CYP1A1 protein expression. Taken together, CAPE decreases 3-MC-mediated CYP1A1 expression, and this inhibitory response is associated with inhibition of AhR and HIF-1α induction. - Highlights: • CAPE reduced the formation of the benzo[a]pyrene-DNA adduct. • CAPE inhibited 3-MC-induced CYP1A1 expression. • CAPE induced HIF-1α induction. • CAPE-mediated HIF-1α reduced 3-MC-inducible CYP1A1 expression.

  20. The Fe-type nitrile hydratase from Comamonas testosteroni Ni1 does not require an activator accessory protein for expression in Escherichia coli

    SciTech Connect (OSTI)

    Kuhn, Misty L.; Martinez, Salette; Gumataotao, Natalie; Bornscheuer, Uwe; Liu, Dali; Holz, Richard C.

    2012-10-10

    We report herein the functional expression of an Fe-type nitrile hydratase (NHase) without the co-expression of an activator protein or the Escherichia coli chaperone proteins GroES/EL. Soluble protein was obtained when the {alpha}- and {beta}-subunit genes of the Fe-type NHase Comamonas testosteroni Ni1 (CtNHase) were synthesized with optimized E. coli codon usage and co-expressed. As a control, the Fe-type NHase from Rhodococcus equi TG328-2 (ReNHase) was expressed with (ReNHase{sup +Act}) and without (ReNHase{sup -Act}) its activator protein, establishing that expression of a fully functional, metallated ReNHase enzyme requires the co-expression of its activator protein, similar to all other Fe-type NHase enzymes reported to date, whereas the CtNHase does not. The X-ray crystal structure of CtNHase was determined to 2.4 {angstrom} resolution revealing an {alpha}{beta} heterodimer, similar to other Fe-type NHase enzymes, except for two important differences. First, two His residues reside in the CtNHase active site that are not observed in other Fe-type NHase enzymes and second, the active site Fe(III) ion resides at the bottom of a wide solvent exposed channel. The solvent exposed active site, along with the two active site histidine residues, are hypothesized to play a role in iron incorporation in the absence of an activator protein.

  1. Urotensin II increases foam cell formation by repressing ABCA1 expression through the ERK/NF-κB pathway in THP-1 macrophages

    SciTech Connect (OSTI)

    Wang, Yan; Wu, Jian-Feng; Tang, Yan-Yan; Zhang, Min; Li, Yuan; Chen, Kong; Zeng, Meng-Ya; Yao, Feng; Xie, Wei; Zheng, Xi-Long; Zeng, Gao-Feng; Tang, Chao-Ke

    2014-10-03

    Highlights: • U II reduces cholesterol efflux in THP-1 macrophages. • U II decreases the expression of ABCA1. • Inhibition of the ERK/NF-κB pathway reduces U II effects on ABCA1 expression and cholesterol efflux. - Abstract: Objective: Foam cell formation in the arterial wall plays a key role in the development of atherosclerosis. Recent studies showed that Urotensin II (U II) is involved in the pathogenesis of atherosclerosis. Here we examined the effects of human U II on ATP-binding cassette transporter A1 (ABCA1) expression and the underlying mechanism in THP-1 macrophages. Methods and results: Cultured THP-1 macrophages were treated with U II, followed by measuring the intracellular lipid contents, cholesterol efflux and ABCA1 levels. The results showed that U II dramatically decreased ABCA1 levels and impaired cholesterol efflux. However, the effects of U II on ABCA1 protein expression and cellular cholesterol efflux were partially reversed by inhibition of extracellular signal regulated kinase 1/2 (ERK1/2) and nuclear factor kappa B (NF-κB) activity, suggesting the potential roles of ERK1/2 and NF-κB in ABCA1 expression, respectively. Conclusion: Our current data indicate that U II may have promoting effects on the progression of atherosclerosis, likely through suppressing ABCA1 expression via activation of the ERK/NF-κB pathway and reducing cholesterol efflux to promote macrophage foam cell formation.

  2. Expression, purification and preliminary X-ray characterization of dl-2-haloacid dehalogenase from Methylobacterium sp. CPA1

    SciTech Connect (OSTI)

    Omi, Rie; Jitsumori, Keiji; Yamauchi, Takahiro; Ichiyama, Susumu; Kurihara, Tatsuo; Esaki, Nobuyoshi; Kamiya, Nobuo; Hirotsu, Ken Miyahara, Ikuko

    2007-07-01

    A recombinant form of dl-2-haloacid dehalogenase from Methylobacterium sp. CPA1 has been expressed in E. coli, purified and crystallized. The crystal belongs to space group P6{sub 3}. Diffraction data have been collected to 1.75 Å resolution. dl-2-Haloacid dehalogenase from Methylobacterium sp. CPA1 (dl-DEX Mb) is a unique enzyme that catalyzes the dehalogenation reaction without the formation of an ester intermediate. A recombinant form of dl-DEX Mb has been expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystal belongs to the hexagonal space group P6{sub 3}, with unit-cell parameters a = b = 186.2, c = 114.4 Å. The crystals are likely to contain between four and eight monomers in the asymmetric unit, with a V{sub M} value of 4.20–2.10 Å{sup 3} Da{sup −1}. A self-rotation function revealed peaks on the χ = 180° section. X-ray data have been collected to 1.75 Å resolution.

  3. Molecular cloning of amphioxus uncoupling protein and assessment of its uncoupling activity using a yeast heterologous expression system

    SciTech Connect (OSTI)

    Chen, Kun; Sun, Guoxun; Lv, Zhiyuan; Wang, Chen; Jiang, Xueyuan; Li, Donghai; Zhang, Chenyu

    2010-10-01

    Research highlights: {yields} Invertebrates, for example amphioxus, do express uncoupling proteins. {yields} Both the sequence and the uncoupling activity of amphioxus UCP resemble UCP2. {yields} UCP1 is the only UCP that can form dimer on yeast mitochondria. -- Abstract: The present study describes the molecular cloning of a novel cDNA fragment from amphioxus (Branchiostoma belcheri) encoding a 343-amino acid protein that is highly homologous to human uncoupling proteins (UCP), this protein is therefore named amphioxus UCP. This amphioxus UCP shares more homology with and is phylogenetically more related to mammalian UCP2 as compared with UCP1. To further assess the functional similarity of amphioxus UCP to mammalian UCP1 and -2, the amphioxus UCP, rat UCP1, and human UCP2 were separately expressed in Saccharomyces cerevisiae, and the recombinant yeast mitochondria were isolated and assayed for the state 4 respiration rate and proton leak, using pYES2 empty vector as the control. UCP1 increased the state 4 respiration rate by 2.8-fold, and the uncoupling activity was strongly inhibited by GDP, while UCP2 and amphioxus UCP only increased the state 4 respiration rate by 1.5-fold and 1.7-fold in a GDP-insensitive manner, moreover, the proton leak kinetics of amphioxus UCP was very similar to UCP2, but much different from UCP1. In conclusion, the amphioxus UCP has a mild, unregulated uncoupling activity in the yeast system, which resembles mammalian UCP2, but not UCP1.

  4. Kinase Expression and Chromosomal Rearrangements in Papillary Thyroid Cancer Tissues: Investigations at the Molecular and Microscopic Levels

    SciTech Connect (OSTI)

    Weier, Heinz-Ulrich; Kwan, Johnson; Lu, Chun-Mei; Ito, Yuko; Wang, Mei; Baumgartner, Adolf; Hayward, Simon W.; Weier, Jingly F.; Zitzelsberger, Horst F.

    2009-07-07

    Structural chromosome aberrations are known hallmarks of many solid tumors. In the papillary form of thyroid cancer (PTC), for example, activation of the receptor tyrosine kinase (RTK) genes, ret or the neurotrophic tyrosine kinase receptor type I (NTRK1) by intra- or interchromosomal rearrangements have been suggested as a cause of the disease. The 1986 accident at the nuclear power plant in Chernobyl, USSR, led to the uncontrolled release of high levels of radioisotopes. Ten years later, the incidence of childhood papillary thyroid cancer (chPTC) near Chernobyl had risen by two orders of magnitude. Tumors removed from some of these patients showed aberrant expression of the ret RTK gene due to a ret/PTC1 or ret/PTC3 rearrangement involving chromosome 10. However, many cultured chPTC cells show a normal G-banded karyotype and no ret rearrangement. We hypothesize that the 'ret-negative' tumors inappropriately express a different oncogene or have lost function of a tumor suppressor as a result of chromosomal rearrangements, and decided to apply molecular and cytogenetic methods to search for potentially oncogenic chromosomal rearrangements in Chernobyl chPTC cases. Knowledge of the kind of genetic alterations may facilitate the early detection and staging of chPTC as well as provide guidance for therapeutic intervention.

  5. Developing and bounding ice particle mass- and area-dimension expressions for use in atmospheric models and remote sensing

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Erfani, Ehsan; Mitchell, David L.

    2016-04-07

    Here, ice particle mass- and projected area-dimension (m-D and A-D) power laws are commonly used in the treatment of ice cloud microphysical and optical properties and the remote sensing of ice cloud properties. Although there has long been evidence that a single m-D or A-D power law is often not valid over all ice particle sizes, few studies have addressed this fact. This study develops self-consistent m-D and A-D expressions that are not power laws but can easily be reduced to power laws for the ice particle size (maximum dimension or D) range of interest, and they are valid overmore » a much larger D range than power laws. This was done by combining ground measurements of individual ice particle m and D formed at temperature T < –20 °C during a cloud seeding field campaign with 2-D stereo (2D-S) and cloud particle imager (CPI) probe measurements of D and A, and estimates of m, in synoptic and anvil ice clouds at similar temperatures. The resulting m-D and A-D expressions are functions of temperature and cloud type (synoptic vs. anvil), and are in good agreement with m-D power laws developed from recent field studies considering the same temperature range (–60 °C < T < –20 °C).« less

  6. Transcriptome sequencing and differential gene expression analysis in Viola yedoensis Makino (Fam. Violaceae) responsive to cadmium (Cd) pollution

    SciTech Connect (OSTI)

    Gao, Jian; Luo, Mao; Zhu, Ye; He, Ying; Wang, Qin; Zhang, Chun

    2015-03-27

    Viola yedoensis Makino is an important Chinese traditional medicine plant adapted to cadmium (Cd) pollution regions. Illumina sequencing technology was used to sequence the transcriptome of V. yedoensis Makino. We sequenced Cd-treated (VIYCd) and untreated (VIYCK) samples of V. yedoensis, and obtained 100,410,834 and 83,587,676 high quality reads, respectively. After de novo assembly and quantitative assessment, 109,800 unigenes were finally generated with an average length of 661 bp. We then obtained functional annotations by aligning unigenes with public protein databases including NR, NT, SwissProt, KEGG and COG. In addition, 892 differentially expressed genes (DEGs) were investigated between the two libraries of untreated (VIYCK) and Cd-treated (VIYCd) plants. Moreover, 15 randomly selected DEGs were further validated with qRT-PCR and the results were highly accordant with the Solexa analysis. This study firstly generated a successful global analysis of the V. yedoensis transcriptome and it will provide for further studies on gene expression, genomics, and functional genomics in Violaceae. - Highlights: • A de novo assembly generated 109,800 unigenes and 5,4479 of them were annotated. • 31,285 could be classified into 26 COG categories. • 263 biosynthesis pathways were predicted and classified into five categories. • 892 DEGs were detected and 15 of them were validated by qRT-PCR.

  7. Farnesoid X receptor up-regulates expression of Lipid transfer inhibitor protein in liver cells and mice

    SciTech Connect (OSTI)

    Li, Liangpeng; Liu, Hong; Peng, Jiahe; Wang, Yongchao; Zhang, Yan; Dong, Jinyu; Liu, Xiaohua; Guo, Dongmei; Jiang, Yu

    2013-11-29

    Highlights: •FXR up-regulates apoF. •It binds to ER1 element. •It activates apoF gene promoter. -- Abstract: Apolipoprotein F is a component protein mainly secreted by liver and resides on several lipoprotein classes. It can inhibit lipids transfer between different lipoproteins. FXR is a member of the nuclear receptor superfamily which is also highly expressed in the liver. It modulates bile acids synthesis and lipids metabolism by transcriptional regulation. We aimed to determine whether apoF can be regulated by FXR. The FXR agonist Chenodeoxycholic acid (CDCA) and GW4064 both can activate the expression of apoF in liver cell lines and in C57/BL6 mouse liver. This is dependent on the binding of FXR to the FXR element ER1 (−2904 to −2892 bp) in the apoF gene promoter. Taken together, we have identified apoF as likely another target gene of FXR.

  8. The systemic delivery of an oncolytic adenovirus expressing decorin inhibits bone metastasis in a mouse model of human prostate cancer

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Xu, Weidong; Neill, Thomas; Yang, Yuefeng; Hu, Zebin; Cleveland, Elyse; Wu, Ying; Hutten, Ryan; Xiao, Xianghui; Stock, Stuart R.; Shevrin, Daniel; et al

    2014-12-11

    In an effort to develop a new therapy for prostate cancer bone metastases, we have created Ad.dcn, a recombinant oncolytic adenovirus carrying the human decorin gene. Infection of PC-3 and DU-145, the human prostate tumor cells, with Ad.dcn or a non-replicating adenovirus Ad(E1-).dcn resulted in decorin expression; Ad.dcn produced high viral titers and cytotoxicity in human prostate tumor cells. Adenoviral-mediated decorin expression inhibited Met, the Wnt/β- catenin signaling axis, vascular endothelial growth factor A, reduced mitochondrial DNA levels, and inhibited tumor cell migration. To examine the anti-tumor response of Ad.dcn, PC-3-luc cells were inoculated in the left heart ventricle tomore » establish bone metastases in nude mice. Ad.dcn, in conjunction with control replicating and non-replicating vectors were injected via tail vein. The real-time monitoring of mice, once a week, by bioluminescence imaging and X-ray radiography showed that Ad.dcn produced significant inhibition of skeletal metastases. Analyses of the mice at the terminal time point indicated a significant reduction in the tumor burden, osteoclast number, serum TRACP 5b levels, osteocalcin levels, hypercalcemia, inhibition of cancer cachexia, and an increase in the animal survival. Finally, based on these studies, we believe that Ad.dcn can be developed as a potential new therapy for prostate cancer bone metastasis.« less

  9. BdCESA7, BdCESA8, and BdPMT utility promoter constructs for targeted expression to secondary cell-wall-forming cells of grasses

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Petrik, Deborah L.; Cass, Cynthia L.; Padmakshan, Dharshana; Foster, Cliff E.; Vogel, John P.; Karlen, Steven D.; Ralph, John; Sedbrook, John C.

    2016-02-04

    Utility vectors with promoters that confer desired spatial and temporal expression patterns are useful tools for studying gene and cellular function and for industrial applications. To target the expression of DNA sequences of interest to cells forming plant secondary cell walls, which generate most of the vegetative biomass, upstream regulatory sequences of the Brachypodium distachyon lignin biosynthetic gene BdPMT and the cellulose synthase genes BdCESA7 and BdCESA8 were isolated and cloned into binary vectors designed for Agrobacterium-mediated transformation of monocots. Expression patterns were assessed using the β-glucuronidase gene GUSPlus and X-glucuronide staining. All three promoters showed strong expression levels inmore » stem tissue at the base of internodes where cell wall deposition is most active, in both vascular bundle xylem vessels and tracheids, and in interfascicular tissues, with expression less pronounced in developmentally older tissues. In leaves, BdCESA7 and BdCESA8 promoter-driven expression was strongest in leaf veins, leaf margins, and trichomes; relatively weaker and patchy expression was observed in the epidermis. BdPMT promoter-driven expression was similar to the BdCESA promoters expression patterns, including strong expression in trichomes. The intensity and extent of GUS staining varied considerably between transgenic lines, suggesting that positional effects influenced promoter activity. Introducing the BdPMT and BdCESA8 Open Reading Frames into BdPMT and BdCESA8 utility promoter binary vectors, respectively, and transforming those constructs into Brachypodium pmt and cesa8 loss-of-function mutants resulted in rescue of the corresponding mutant phenotypes. This work therefore validates the functionality of these utility promoter binary vectors for use in Brachypodium and likely other grass species. Lastly, the identification, in Bdcesa8-1 T-DNA mutant stems, of an 80% reduction in crystalline cellulose levels confirms that the

  10. Sex-specific patterns and deregulation of endocrine pathways in the gene expression profiles of Bangladeshi adults exposed to arsenic contaminated drinking water

    SciTech Connect (OSTI)

    Muñoz, Alexandra; Chervona, Yana; Hall, Megan; Kluz, Thomas; Gamble, Mary V.; Costa, Max

    2015-05-01

    Arsenic contamination of drinking water occurs globally and is associated with numerous diseases including skin, lung and bladder cancers, and cardiovascular disease. Recent research indicates that arsenic may be an endocrine disruptor. This study was conducted to evaluate the nature of gene expression changes among males and females exposed to arsenic contaminated water in Bangladesh at high and low doses. Twenty-nine (55% male) Bangladeshi adults with water arsenic exposure ranging from 50 to 1000 μg/L were selected from the Folic Acid Creatinine Trial. RNA was extracted from peripheral blood mononuclear cells for gene expression profiling using Affymetrix 1.0 ST arrays. Differentially expressed genes were assessed between high and low exposure groups for males and females separately and findings were validated using quantitative real-time PCR. There were 534 and 645 differentially expressed genes (p < 0.05) in the peripheral blood mononuclear cells of males and females, respectively, when high and low water arsenic exposure groups were compared. Only 43 genes overlapped between the two sexes, with 29 changing in opposite directions. Despite the difference in gene sets both males and females exhibited common biological changes including deregulation of 17β-hydroxysteroid dehydrogenase enzymes, deregulation of genes downstream of Sp1 (specificity protein 1) transcription factor, and prediction of estrogen receptor alpha as a key hub in cardiovascular networks. Arsenic-exposed adults exhibit sex-specific gene expression profiles that implicate involvement of the endocrine system. Due to arsenic's possible role as an endocrine disruptor, exposure thresholds for arsenic may require different parameters for males and females. - Highlights: • Males and females exhibit unique gene expression changes in response to arsenic. • Only 23 genes are common among the differentially expressed genes for the sexes. • Male and female gene lists exhibit common biological

  11. Expression of REST4 in human gliomas in vivo and influence of pioglitazone on REST in vitro

    SciTech Connect (OSTI)

    Ren, Huan; Gao, Zhangfeng; Wu, Nayiyuan; Zeng, Liu; Tang, Xinyue; Chen, Xiaoping; Liu, Zhaoqian; Zhang, Wei; Wang, Liansheng; Li, Zhi

    2015-08-07

    The repressor element-1 (RE1) silencing transcription factor/neuron-restrictive silencer factor (REST/NRSF) has an irreplaceable role during the differentiation of neurons. REST has multiple splice variants which link to various types of cancer. Previous work had highlighted the role of REST in glioma, where the expression of REST is enhanced. But whether alternative splicing of REST is expressed in glioma has not been described. Here, we show that a specific isoform REST4 is expressed in glioma specimens, and will influence the mRNA level of REST in vivo. Peroxisome proliferator-activated receptor-γ (PPARγ) agonists have a role of antineoplastic in various tumor cells, which including glioma cells. Moreover, study indicated that PPARγ agonist pioglitazone can promote alternative splicing of REST pre-mRNA. In this study, we selected pioglitazone as a tool drug to explore whether the role of pioglitazone in anti-glioma is mediated by regulating REST expression or promoting alternative splicing of REST in glioma cells. Results show that pioglitazone can inhibit proliferation and induce apoptosis of glioma cell in vitro, which may be mediated by down-regulating REST mRNA level but not by inducing alternative splicing of REST pre-mRNA. Our study firstly reports the expression of REST4 in glioma tissue samples. And we recommend that pioglitazone, which can reduce the expression level of REST, represents a promising drug for therapy of glioma. - Highlights: • A specific isoform REST4 is expressed in glioma specimens in vivo. • REST4 will influence the mRNA level of REST in vivo. • Pioglitazone can inhibit proliferation and induce apoptosis of glioma cells. • The role of pioglitazone in anti-glioma may be mediated by down-regulating REST.

  12. The expression level of HJURP has an independent prognostic impact and predicts the sensitivity to radiotherapy in breast cancer

    SciTech Connect (OSTI)

    Hu, Zhi; Huang, Ge; Sadanandam, Anguraj; Gu, Shenda; Lenburg, Marc E; Pai, Melody; Bayani, Nora; Blakely, Eleanor A; Gray, Joe W; Mao, Jian-Hua

    2010-06-25

    Introduction: HJURP (Holliday Junction Recognition Protein) is a newly discovered gene reported to function at centromeres and to interact with CENPA. However its role in tumor development remains largely unknown. The goal of this study was to investigate the clinical significance of HJURP in breast cancer and its correlation with radiotherapeutic outcome. Methods: We measured HJURP expression level in human breast cancer cell lines and primary breast cancers by Western blot and/or by Affymetrix Microarray; and determined its associations with clinical variables using standard statistical methods. Validation was performed with the use of published microarray data. We assessed cell growth and apoptosis of breast cancer cells after radiation using high-content image analysis. Results: HJURP was expressed at higher level in breast cancer than in normal breast tissue. HJURP mRNA levels were significantly associated with estrogen receptor (ER), progesterone receptor (PR), Scarff-Bloom-Richardson (SBR) grade, age and Ki67 proliferation indices, but not with pathologic stage, ERBB2, tumor size, or lymph node status. Higher HJURP mRNA levels significantly decreased disease-free and overall survival. HJURP mRNA levels predicted the prognosis better than Ki67 proliferation indices. In a multivariate Cox proportional-hazard regression, including clinical variables as covariates, HJURP mRNA levels remained an independent prognostic factor for disease-free and overall survival. In addition HJURP mRNA levels were an independent prognostic factor over molecular subtypes (normal like, luminal, Erbb2 and basal). Poor clinical outcomes among patients with high HJURP expression werevalidated in five additional breast cancer cohorts. Furthermore, the patients with high HJURP levels were much more sensitive to radiotherapy. In vitro studies in breast cancer cell lines showed that cells with high HJURP levels were more sensitive to radiation treatment and had a higher rate of apoptosis

  13. In vivo corrosion, tumor outcome, and microarray gene expression for two types of muscle-implanted tungsten alloys

    SciTech Connect (OSTI)

    Schuster, B.E.; Roszell, L.E.; Murr, L.E.; Ramirez, D.A.; Demaree, J.D.; Klotz, B.R.; Rosencrance, A.B.; Dennis, W.E.; Bao, W.; Perkins, E.J.; Dillman, J.F.; Bannon, D.I.

    2012-11-15

    Tungsten alloys are composed of tungsten microparticles embedded in a solid matrix of transition metals such as nickel, cobalt, or iron. To understand the toxicology of these alloys, male F344 rats were intramuscularly implanted with pellets of tungsten/nickel/cobalt, tungsten/nickel/iron, or pure tungsten, with tantalum pellets as a negative control. Between 6 and 12 months, aggressive rhabdomyosarcomas formed around tungsten/nickel/cobalt pellets, while those of tungsten/nickel/iron or pure tungsten did not cause cancers. Electron microscopy showed a progressive corrosion of the matrix phase of tungsten/nickel/cobalt pellets over 6 months, accompanied by high urinary concentrations of nickel and cobalt. In contrast, non-carcinogenic tungsten/nickel/iron pellets were minimally corroded and urinary metals were low; these pellets having developed a surface oxide layer in vivo that may have restricted the mobilization of carcinogenic nickel. Microarray analysis of tumors revealed large changes in gene expression compared with normal muscle, with biological processes involving the cell cycle significantly up‐regulated and those involved with muscle development and differentiation significantly down‐regulated. Top KEGG pathways disrupted were adherens junction, p53 signaling, and the cell cycle. Chromosomal enrichment analysis of genes showed a highly significant impact at cytoband 7q22 (chromosome 7) which included mouse double minute (MDM2) and cyclin‐dependant kinase (CDK4) as well as other genes associated with human sarcomas. In conclusion, the tumorigenic potential of implanted tungsten alloys is related to mobilization of carcinogenic metals nickel and cobalt from corroding pellets, while gene expression changes in the consequent tumors are similar to radiation induced animal sarcomas as well as sporadic human sarcomas. -- Highlights: ► Tungsten/nickel/cobalt, tungsten/nickel/iron, and pure tungsten were studied. ► Male Fischer rats implanted with

  14. Over-expression of human endosulfatase-1 exacerbates cadmium-induced injury to transformed human lung cells in vitro

    SciTech Connect (OSTI)

    Zhang, Huiying; Department of Environmental and Molecular Toxicology, College of Agriculture and Life Sciences, NC State University, Raleigh, NC 27695 ; Newman, Donna R.; Bonner, James C.; Sannes, Philip L.

    2012-11-15

    Environmental exposure to cadmium is known to cause damage to alveolar epithelial cells of the lung, impair their capacity to repair, and result in permanent structural alterations. Cell surface heparan sulfate proteoglycans (HSPGs) can modulate cell responses to injury through their interactions with soluble effector molecules. These interactions are often sulfate specific, and the removal of sulfate groups from HS side chains could be expected to influence cellular injury, such as that caused by exposure to cadmium. The goal of this study was to define the role 6-O-sulfate plays in cellular responses to cadmium exposure in two pulmonary epithelial cancer cell lines (H292 and A549) and in normal human primary alveolar type II (hAT2) cells. Sulfate levels were modified by transduced transient over-expression of 6-O-endosulfatase (HSulf-1), a membrane-bound enzyme which specifically removes 6-O-sulfate groups from HSPG side chains. Results showed that cadmium decreased cell viability and activated apoptosis pathways at low concentrations in hAT2 cells but not in the cancer cells. HSulf-1 over-expression, on the contrary, decreased cell viability and activated apoptosis pathways in H292 and A549 cells but not in hAT2 cells. When combined with cadmium, HSulf-1 over-expression further decreased cell viability and exacerbated the activation of apoptosis pathways in the transformed cells but did not add to the toxicity in hAT2 cells. The finding that HSulf-1 sensitizes these cancer cells and intensifies the injury induced by cadmium suggests that 6-O-sulfate groups on HSPGs may play important roles in protection against certain environmental toxicants, such as heavy metals. -- Highlights: ? Primary human lung alveolar type 2 (hAT2) cells and H292 and A549 cells were used. ? Cadmium induced apoptosis in hAT2 cells but not in H292 or A549 cells. ? HSulf-1exacerbates apoptosis induced by cadmium in H292 and A549 but not hAT2 cells.

  15. Gene expression responses of HeLa cells to chemical species generated by an atmospheric plasma flow

    SciTech Connect (OSTI)

    Yokoyama, Mayo; Johkura, Kohei; Sato, Takehiko

    2014-08-08

    Highlights: • Response of HeLa cells to a plasma-irradiated medium was revealed by DNA microarray. • Gene expression pattern was basically different from that in a H{sub 2}O{sub 2}-added medium. • Prominently up-/down-regulated genes were partly shared by the two media. • Gene ontology analysis showed both similar and different responses in the two media. • Candidate genes involved in response to ROS were detected in each medium. - Abstract: Plasma irradiation generates many factors able to affect the cellular condition, and this feature has been studied for its application in the field of medicine. We previously reported that hydrogen peroxide (H{sub 2}O{sub 2}) was the major cause of HeLa cell death among the chemical species generated by high level irradiation of a culture medium by atmospheric plasma. To assess the effect of plasma-induced factors on the response of live cells, HeLa cells were exposed to a medium irradiated by a non-lethal plasma flow level, and their gene expression was broadly analyzed by DNA microarray in comparison with that in a corresponding concentration of 51 μM H{sub 2}O{sub 2}. As a result, though the cell viability was sufficiently maintained at more than 90% in both cases, the plasma-medium had a greater impact on it than the H{sub 2}O{sub 2}-medium. Hierarchical clustering analysis revealed fundamentally different cellular responses between these two media. A larger population of genes was upregulated in the plasma-medium, whereas genes were downregulated in the H{sub 2}O{sub 2}-medium. However, a part of the genes that showed prominent differential expression was shared by them, including an immediate early gene ID2. In gene ontology analysis of upregulated genes, the plasma-medium showed more diverse ontologies than the H{sub 2}O{sub 2}-medium, whereas ontologies such as “response to stimulus” were common, and several genes corresponded to “response to reactive oxygen species.” Genes of AP-1 proteins, e.g., JUN

  16. Enhancing digestibility and ethanol yield of Populus wood via expression of an engineered monolignol 4-O-methyltransferase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Cai, Yuanheng; Zhang, Kewei; Kim, Hoon; Hou, Guichuan; Zhang, Xuebin; Yang, Huijun; Feng, Huan; Miller, Lisa; Ralph, John; Liu, Chang -Jun

    2016-06-28

    Producing cellulosic biofuels and bio-based chemicals from woody biomass is impeded by the presence of lignin polymer in the plant cell wall. Manipulating the monolignol biosynthetic pathway offers a promising approach to improved processability, but often impairs plant growth and development. Here, we show that expressing an engineered 4-O-methyltransferase that chemically modifies the phenolic moiety of lignin monomeric precursors, thus preventing their incorporation into the lignin polymer, substantially alters hybrid aspens’ lignin content and structure. Woody biomass derived from the transgenic aspens shows a 62% increase in the release of simple sugars and up to a 49% increase in themore » yield of ethanol when the woody biomass is subjected to enzymatic digestion and yeast-mediated fermentation. Furthermore, the cell wall structural changes do not affect growth and biomass production of the trees. Our study provides a useful strategy for tailoring woody biomass for bio-based applications.« less

  17. The effects of 5-fluorouracil and doxorubicin on expression of human immunodeficiency virus type 1 long terminal repeat

    SciTech Connect (OSTI)

    Panozzo, J.; Akan, E.; Griffiths, T.D.; Woloschak, G.E.

    1996-03-01

    Previous work by many groups has documented induction of the HIV-LTR following exposure of cells to ultraviolet light and other DNA damaging agents. Our experiments set out to determine the relative activation or repression of the HIV-LTR in response to two classes of chemotherapeutic agents: Doxorubicin is a DNA-damage inducing agent, and 5-fluorouracil has an antimetabolic mode of action. Using HeLa cells stably transfected with a construct in which HIV-LTR drives expression of the chloramphenicol acetyl transferase reporter gene, we demonstrated an up to 10-fold induction following doxorubicin treatment in 24 h post-treatment. This induction was repressed by treatment with salicylic acid, suggesting a role for prostaglandin/cyclo-oxygenase pathways and/or NFKB in the inductive response. Induction by 5-fluorouracil, in contrast, was more modest (two-fold at most) though it was consistently elevated over controls.

  18. Ran GTPase protein promotes human pancreatic cancer proliferation by deregulating the expression of Survivin and cell cycle proteins

    SciTech Connect (OSTI)

    Deng, Lin; Lu, Yuanyuan; Zhao, Xiaodi; Sun, Yi; Shi, Yongquan; Fan, Hongwei; Liu, Changhao; Zhou, Jinfeng; Nie, Yongzhan; Wu, Kaichun; Fan, Daiming; Guo, Xuegang

    2013-10-18

    Highlights: •Overexpression of Ran in pancreatic cancer was correlated with histological grade. •Downregulation of Ran could induce cell apoptosis and inhibit cell proliferation. •The effects were mediated by cell cycle proteins, Survivin and cleaved Caspase-3. -- Abstract: Ran, a member of the Ras GTPase family, has important roles in nucleocytoplasmic transport. Herein, we detected Ran expression in pancreatic cancer and explored its potential role on tumour progression. Overexpressed Ran in pancreatic cancer tissues was found highly correlated with the histological grade. Downregulation of Ran led to significant suppression of cell proliferation, cell cycle arrest at the G1/S phase and induction of apoptosis. In vivo studies also validated that result. Further studies revealed that those effects were at least partly mediated by the downregulation of Cyclin A, Cyclin D1, Cyclin E, CDK2, CDK4, phospho-Rb and Survivin proteins and up regulation of cleaved Caspase-3.

  19. Determination of gene expression patterns using high-throughput RNA in situ hybridizaion to whole-mount Drosophila embryos

    SciTech Connect (OSTI)

    Weiszmann, R.; Hammonds, A.S.; Celniker, S.E.

    2009-04-09

    We describe a high-throughput protocol for RNA in situ hybridization (ISH) to Drosophila embryos in a 96-well format. cDNA or genomic DNA templates are amplified by PCR and then digoxigenin-labeled ribonucleotides are incorporated into antisense RNA probes by in vitro transcription. The quality of each probe is evaluated before ISH using a RNA probe quantification (dot blot) assay. RNA probes are hybridized to fixed, mixed-staged Drosophila embryos in 96-well plates. The resulting stained embryos can be examined and photographed immediately or stored at 4oC for later analysis. Starting with fixed, staged embryos, the protocol takes 6 d from probe template production through hybridization. Preparation of fixed embryos requires a minimum of 2 weeks to collect embryos representing all stages. The method has been used to determine the expression patterns of over 6,000 genes throughout embryogenesis.

  20. MicroRNA-101 mediates the suppressive effect of laminar shear stress on mTOR expression in vascular endothelial cells

    SciTech Connect (OSTI)

    Chen, Kui; Fan, Wendong; Wang, Xing; Ke, Xiao [Division of Cardiology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080 (China)] [Division of Cardiology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080 (China); Wu, Guifu, E-mail: eecpchina@yahoo.com.cn [Key Laboratory on Assisted Circulation, Ministry of Health, Guangzhou 510080 (China)] [Key Laboratory on Assisted Circulation, Ministry of Health, Guangzhou 510080 (China); Hu, Chengheng, E-mail: huchenghengpci@yahoo.com.cn [Division of Cardiology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080 (China)] [Division of Cardiology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080 (China)

    2012-10-12

    Highlights: Black-Right-Pointing-Pointer Laminar shear stress upregulates miR-101 expression in vascular endothelial cells. Black-Right-Pointing-Pointer miR-101 represses mTOR expression through a specific 3 Prime UTR binding site. Black-Right-Pointing-Pointer Overexpression of miR-101 inhibits G1/S transition and endothelial cell proliferation. Black-Right-Pointing-Pointer Blockade of miR-101 attenuates the suppressive effect of laminar flow on mTOR expression. -- Abstract: Shear stress associated with blood flow plays an important role in regulating gene expression and cell function in endothelial cells (ECs). MicroRNAs (miRNAs) are highly conserved, small non-coding RNAs that negatively regulate the expression of target genes by binding to the mRNA 3 Prime -untranslated region (3 Prime UTR) at the posttranscriptional level involved in diverse cellular processes. This study demonstrates that microRNA-101 in response to laminar shear stress (LSS) is involved in the flow regulation of gene expression in ECs. qRT-PCR analysis showed that miR-101 expression was significantly upregulated in human umbilical vein endothelial cells (HUVECs) exposed to 12 dyn/cm{sup 2} laminar shear stress for 12 h. We found that transfection of miR-101 significantly decreased the luciferase activity of plasmid reporter containing the 3 Prime UTR of mammalian target of rapamycin (mTOR) gene. Western analysis revealed that the protein level of mTOR was significantly reduced in ECs transfected with miR-101. Furthermore, miR-101 overexpression induced cell cycle arrest at the G1/S transition and suppressed endothelial cell proliferation. Finally, transfection of miR-101 inhibitors attenuated the suppressive effects of LSS on mTOR expression, which identified the efficacy of loss-of-function of miR-101 in laminar flow-treated ECs. In conclusion, we have demonstrated that upregulation of miR-101 in response to LSS contributes to the suppressive effects of LSS on mTOR expression and EC