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1

U-098: ISC BIND Deleted Domain Name Resolving Vulnerability | Department of  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

098: ISC BIND Deleted Domain Name Resolving Vulnerability 098: ISC BIND Deleted Domain Name Resolving Vulnerability U-098: ISC BIND Deleted Domain Name Resolving Vulnerability February 8, 2012 - 7:00am Addthis PROBLEM: A vulnerability has been reported in ISC BIND, which can be exploited by malicious people to bypass certain security restrictions. PLATFORM: ISC BIND 9.2.x ISC BIND 9.3.x ISC BIND 9.4.x ISC BIND 9.5.x ISC BIND 9.6.x ISC BIND 9.7.x ISC BIND 9.8.x ABSTRACT: The vulnerability is caused due to an error within the cache update policy. reference LINKS: Original Advisory Secunia Advisory SA47884 CVE-2012-1033 IMPACT ASSESSMENT: High Discussion: Researchers discovered a vulnerability affecting the large majority of popular DNS implementations which allows a malicious domain name to stay resolvable long after it has been removed from the upper level servers. The

2

U-183: ISC BIND DNS Resource Records Handling Vulnerability ...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

U-098: ISC BIND Deleted Domain Name Resolving Vulnerability U-038: BIND 9 Resolver crashes after logging an error in query.c T-617: BIND RPZ Processing Flaw Lets Remote Users...

3

V-079: ISC BIND AAAA Record Lookup Handling Assertion Failure...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Lets Remote Users Deny Service T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service U-183: ISC BIND DNS Resource Records Handling Vulnerability...

4

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Off-by-one Bug Lets Remote Users Deny Service U-260: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service U-183: ISC BIND DNS Resource Records Handling Vulnerability...

5

U-183: ISC BIND DNS Resource Records Handling Vulnerability | Department of  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

3: ISC BIND DNS Resource Records Handling Vulnerability 3: ISC BIND DNS Resource Records Handling Vulnerability U-183: ISC BIND DNS Resource Records Handling Vulnerability June 5, 2012 - 7:00am Addthis PROBLEM: A vulnerability has been reported in ISC BIND, which can be exploited by malicious people to disclose potentially sensitive information or cause a DoS (Denial of Service). PLATFORM: Version(s): ISC BIND 9.2.x ISC BIND 9.3.x ISC BIND 9.4.x ISC BIND 9.5.x ISC BIND 9.6.x ISC BIND 9.7.x ISC BIND 9.8.x ISC BIND 9.9.x ABSTRACT: This problem was uncovered while testing with experimental DNS record types. It is possible to add records to BIND with null (zero length) rdata fields. Reference List: Secunia Advisory 49338 CVE-2012-1667 Original Advisory IMPACT ASSESSMENT: High Discussion: Recursive servers may crash or disclose some portion of memory to the

6

U-039: ISC Update: BIND 9 Resolver crashes after logging an error in  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

9: ISC Update: BIND 9 Resolver crashes after logging an error 9: ISC Update: BIND 9 Resolver crashes after logging an error in query.c U-039: ISC Update: BIND 9 Resolver crashes after logging an error in query.c November 16, 2011 - 2:30pm Addthis PROBLEM: ISC Update: BIND 9 Resolver crashes after logging an error in query.c. PLATFORM: Versions of BIND, 9.4-ESV, 9.6-ESV, 9.7.x, 9.8.x ABSTRACT: A remote server can cause the target connected client to crash. Organizations across the Internet are reporting crashes interrupting service on BIND 9 nameservers performing recursive queries. Affected servers crash after logging an error in query.c with the following message: "INSIST(! dns_rdataset_isassociated(sigrdataset))" Multiple versions are reported as being affected, including all currently supported release versions of ISC BIND 9. ISC is actively investigating the root cause and

7

V-172: ISC BIND RUNTIME_CHECK Error Lets Remote Users Deny Service...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Addthis Related Articles U-038: BIND 9 Resolver crashes after logging an error in query.c U-039: ISC Update: BIND 9 Resolver crashes after logging an error in query.c T-662:...

8

V-007: McAfee Firewall Enterprise ISC BIND Record Handling Lockup  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

7: McAfee Firewall Enterprise ISC BIND Record Handling Lockup 7: McAfee Firewall Enterprise ISC BIND Record Handling Lockup Vulnerability V-007: McAfee Firewall Enterprise ISC BIND Record Handling Lockup Vulnerability October 22, 2012 - 6:00am Addthis PROBLEM: McAfee Firewall Enterprise ISC BIND Record Handling Lockup Vulnerability PLATFORM: Versions 8.2.x prior to 8.2.1P06, and 8.3.x prior to 8.3.0P02 REFERENCE LINKS: Secunia Advisory SA51050 CVE-2012-5166 McAfee Corporate Knowledge Base IMPACT ASSESSMENT: Medium DISCUSSION: The vulnerability is caused due to an error when handling queries for certain records and can be exploited to cause the named process to lockup. IMPACT: If specific combinations of RDATA are loaded into a nameserver, either via cache or an authoritative zone, a subsequent query for a related record

9

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service 1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability July 26, 2012 - 7:00am Addthis PROBLEM: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability PLATFORM: BIND 9.6-ESV-R1 through versions 9.6-ESV-R7-P1 BIND 9.7.1 through versions 9.7.6-P1 BIND 9.8.0 through versions 9.8.3-P1 BIND 9.9.0 through versions 9.9.1-P1 ABSTRACT: ISC BIND is prone to a denial-of-service vulnerability. reference LINKS: The Vendor's Advisory CVE-2012-3817 Bugtraq ID: 54658 SecurityTracker Alert ID: 1027296 IMPACT ASSESSMENT: High Discussion: When DNSSEC validation is enabled, does not properly initialize the failing-query cache, which allows remote attackers to cause a denial of

10

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service 1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability July 26, 2012 - 7:00am Addthis PROBLEM: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability PLATFORM: BIND 9.6-ESV-R1 through versions 9.6-ESV-R7-P1 BIND 9.7.1 through versions 9.7.6-P1 BIND 9.8.0 through versions 9.8.3-P1 BIND 9.9.0 through versions 9.9.1-P1 ABSTRACT: ISC BIND is prone to a denial-of-service vulnerability. reference LINKS: The Vendor's Advisory CVE-2012-3817 Bugtraq ID: 54658 SecurityTracker Alert ID: 1027296 IMPACT ASSESSMENT: High Discussion: When DNSSEC validation is enabled, does not properly initialize the failing-query cache, which allows remote attackers to cause a denial of

11

U-260: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service |  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

0: ISC BIND RDATA Processing Flaw Lets Remote Users Deny 0: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service U-260: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service September 14, 2012 - 6:00am Addthis PROBLEM: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service PLATFORM: Version(s): 9.0.x -> 9.6.x, 9.4-ESV->9.4-ESV-R5-P1, 9.6-ESV->9.6-ESV-R7-P2, 9.7.0->9.7.6-P2, 9.8.0->9.8.3-P2, 9.9.0->9.9.1-P2 ABSTRACT: A vulnerability was reported in ISC BIND. reference LINKS: The vendor's advisory SecurityTracker Alert ID: 1027529 Bugtraq ID: 55522 Red Hat Bugzilla - Bug 856754 CVE-2012-4244 IMPACT ASSESSMENT: High Discussion: A remote user can send a query for a record that has RDATA in excess of 65535 bytes to cause named to exit. This can be exploited against recursive servers by causing the server to query for records provided by an

12

T-662: ISC BIND Packet Processing Flaw Lets Remote Users Deny Service |  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

2: ISC BIND Packet Processing Flaw Lets Remote Users Deny 2: ISC BIND Packet Processing Flaw Lets Remote Users Deny Service T-662: ISC BIND Packet Processing Flaw Lets Remote Users Deny Service July 6, 2011 - 7:47am Addthis PROBLEM: A vulnerability was reported in ISC BIND. A remote user can cause denial of service conditions. PLATFORM: 9.6.3, 9.6-ESV-R4, 9.6-ESV-R4-P1, 9.6-ESV-R5b1 9.7.0, 9.7.0-P1, 9.7.0-P2, 9.7.1, 9.7.1-P1, 9.7.1-P2, 9.7.2, 9.7.2-P1, 9.7.2-P2, 9.7.2-P3, 9.7.3, 9.7.3-P1, 9.7.3-P2, 9.7.4b1 9.8.0, 9.8.0-P1, 9.8.0-P2, 9.8.0-P3, 9.8.1b1 ABSTRACT: A defect in the affected BIND 9 versions allows an attacker to remotely cause the "named" process to exit using a specially crafted packet. This defect affects both recursive and authoritative servers. The code location of the defect makes it impossible to protect BIND using ACLs configured

13

V-172: ISC BIND RUNTIME_CHECK Error Lets Remote Users Deny Service Against Recursive Resolvers  

Energy.gov (U.S. Department of Energy (DOE))

A defect exists which allows an attacker to crash a BIND 9 recursive resolver with a RUNTIME_CHECK error in resolver.c

14

U-224: ISC DHCP Multiple Denial of Service Vulnerabilities | Department of  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

4: ISC DHCP Multiple Denial of Service Vulnerabilities 4: ISC DHCP Multiple Denial of Service Vulnerabilities U-224: ISC DHCP Multiple Denial of Service Vulnerabilities July 31, 2012 - 7:00am Addthis PROBLEM: ISC DHCP Multiple Denial of Service Vulnerabilities PLATFORM: ISC DHCP before versions DHCP 4.1-ESV-R6 or DHCP 4.2.4-P1 ABSTRACT: ISC DHCP is prone to multiple denial-of-service vulnerabilities. reference LINKS: BIND and DHCP Security Updates Released Bugtraq ID: 54665 Secunia Advisory SA50018 CVE-2012-3571 CVE-2012-3570 CVE-2012-3954 IMPACT ASSESSMENT: Medium Discussion: Multiple vulnerabilities have been reported in ISC DHCP, which can be exploited by malicious people to cause a DoS (Denial of Service). 1) An error when handling client identifiers can be exploited to trigger an endless loop and prevent the server from processing further client requests

15

Institute for Sustainable Communities (ISC) | Open Energy Information  

Open Energy Info (EERE)

Communities (ISC) Jump to: navigation, search Logo: Institute for Sustainable Communities (ISC) Name Institute for Sustainable Communities (ISC) Address 535 Stone Cutters Way...

16

ISC-Reducing Congestion through Smart Parking Management | Open Energy  

Open Energy Info (EERE)

ISC-Reducing Congestion through Smart Parking Management ISC-Reducing Congestion through Smart Parking Management Jump to: navigation, search Tool Summary LAUNCH TOOL Name: ISC-Reducing Congestion through Smart Parking Management Agency/Company /Organization: Institute for Sustainable Communities (ISC) Sector: Climate, Energy Focus Area: Transportation Resource Type: Case studies/examples, Lessons learned/best practices Website: www.iscvt.org/resources/documents/san_francisco_sfpark.pdf Locality: San Francisco, California Cost: Free Language: English ISC-Reducing Congestion through Smart Parking Management Screenshot References: Reducing Congestion through Smart Parking Management[1] "The transit study concluded that congestion is a primary factor reducing the reliability and speed of onroad transit, which in turn is exacerbated

17

Integrated Support Center (ISC) Homepage | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Home Home Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Integrated Support Center The Office of Science Integrated Support Center proudly facilitates work across the ten Office of Science laboratories and site offices. Caption: The Hall D tagger area of the Continuous Electron Beam Accelerator Facility at Thomas Jefferson Laboratory. Hall D tagger area 1 of 2 Print Text Size: A A A RSS Feeds FeedbackShare Page The Office of Science's (SC) Integrated Support Center (ISC) provides

18

V-007: McAfee Firewall Enterprise ISC BIND Record Handling Lockup...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

are loaded into a nameserver, either via cache or an authoritative zone, a subsequent query for a related record will cause named to lock up. SOLUTION: Update to version 8.2.1P06...

19

T-617: BIND RPZ Processing Flaw Lets Remote Users Deny Service | Department  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

7: BIND RPZ Processing Flaw Lets Remote Users Deny Service 7: BIND RPZ Processing Flaw Lets Remote Users Deny Service T-617: BIND RPZ Processing Flaw Lets Remote Users Deny Service May 6, 2011 - 7:00am Addthis PROBLEM: A vulnerability has been reported in BIND, which can be exploited by malicious people to cause a DoS (Denial of Service). PLATFORM: ISC BIND version 9.8.0. ABSTRACT: When a name server is configured with a response policy zone (RPZ), queries for type RRSIG can trigger a server crash. REFERENCE LINKS: ISC Advisory: CVE-2011-1907 Secunia Advisory: SA44416 Vulnerability Report: ISC BIND CVE-2011-1907 SecurityTracker Alert ID: 1025503 IMPACT ASSESSMENT: High Discussion: This advisory only affects BIND users who are using the RPZ feature configured for RRset replacement. BIND 9.8.0 introduced Response Policy Zones (RPZ), a mechanism for modifying DNS responses returned by a

20

Microsoft Word - ORO ISC Functional Analysis and Inventory 3-6-07 FINAL.doc  

NLE Websites -- All DOE Office Websites (Extended Search)

Table of Contents Page Introduction 1 Mission 1 Distinctive Characteristics 2 Assumptions 3 Staffing and Trends 4 Critical Skills Inventory 6 Significant Successes 7 Strategic Goals and Objectives 9 Conclusions 10 Appendix A: Functional Descriptions 11 Appendix B: SC ISC Staffing Levels by Occupational Groupings 16 Appendix C: Organizational Metrics 21 F U N C T I O N A L A N A L Y S I S A N D I N V E N T O R Y Introduction The Manager, Oak Ridge Office (ORO), has requested this Functional Analysis and Inventory to identify and present quantifiable performance metrics for various matrix support activities performed by ORO. This analysis will be used to describe the ORO operating model as a component of the Office of Science (SC) Integrated

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Intrinsic Radiation Source Generation with the ISC Package: Data Comparisons and Benchmarking  

Science Conference Proceedings (OSTI)

The characterization of radioactive emissions from unstable isotopes (intrinsic radiation) is necessary for shielding and radiological-dose calculations from radioactive materials. While most radiation transport codes, e.g., MCNP [X-5 Monte Carlo Team, 2003], provide the capability to input user prescribed source definitions, such as radioactive emissions, they do not provide the capability to calculate the correct radioactive-source definition given the material compositions. Special modifications to MCNP have been developed in the past to allow the user to specify an intrinsic source, but these modification have not been implemented into the primary source base [Estes et al., 1988]. To facilitate the description of the intrinsic radiation source from a material with a specific composition, the Intrinsic Source Constructor library (LIBISC) and MCNP Intrinsic Source Constructor (MISC) utility have been written. The combination of LIBISC and MISC will be herein referred to as the ISC package. LIBISC is a statically linkable C++ library that provides the necessary functionality to construct the intrinsic-radiation source generated by a material. Furthermore, LIBISC provides the ability use different particle-emission databases, radioactive-decay databases, and natural-abundance databases allowing the user flexibility in the specification of the source, if one database is preferred over others. LIBISC also provides functionality for aging materials and producing a thick-target bremsstrahlung photon source approximation from the electron emissions. The MISC utility links to LIBISC and facilitates the description of intrinsic-radiation sources into a format directly usable with the MCNP transport code. Through a series of input keywords and arguments the MISC user can specify the material, age the material if desired, and produce a source description of the radioactive emissions from the material in an MCNP readable format. Further details of using the MISC utility can be obtained from the user guide [Solomon, 2012]. The remainder of this report presents a discussion of the databases available to LIBISC and MISC, a discussion of the models employed by LIBISC, a comparison of the thick-target bremsstrahlung model employed, a benchmark comparison to plutonium and depleted-uranium spheres, and a comparison of the available particle-emission databases.

Solomon, Clell J. Jr. [Los Alamos National Laboratory

2012-04-26T23:59:59.000Z

22

REVIEW OF FAST FLUX TEST FACILITY (FFTF) FUEL EXPERIMENTS FOR STORAGE IN INTERIM STORAGE CASKS (ISC)  

SciTech Connect

Appendix H, Section H.3.3.10.11 of the Final Safety Analysis Report (FSAR), provides the limits to be observed for fueled components authorized for storage in the Fast Flux Test Facility (FFTF) spent fuel storage system. Currently, the authorization basis allows standard driver fuel assemblies (DFA), as described in the FSAR Chapter 17, Section 17.5.3.1, to be stored provided decay power per assembly is {le} 250 watts, post-irradiation time is four years minimum, average assembly burn-up is 150,000 MWD/MTHM maximum and the pre-irradiation enrichment is 29.3% maximum (per H.3.3.10.11). In addition, driver evaluation (DE), core characterizer assemblies (CCA), and run-to-cladding-breach (RTCB) assemblies are included based on their similarities to a standard DFA. Ident-69 pin containers with fuel pins from these DFAs can also be stored. Section H.3.3.10.11 states that fuel types outside the specification criteria above will be addressed on a case-by-case basis. There are many different types of fuel and blanket experiments that were irradiated in the FFTF which now require offload to the spent fuel storage system. Two reviews were completed for a portion of these special type fuel components to determine if placement into the Core Component Container (CCC)/Interim Storage Cask (ISC) would require any special considerations or changes to the authorization basis. Project mission priorities coupled with availability of resources and analysts prevented these evaluations from being completed as a single effort. Areas of review have included radiological accident release consequences, radiological shielding adequacy, criticality safety, thermal limits, confinement, and stress. The results of these reviews are available in WHC-SD-FF-RPT-005, Rev. 0 and 1, ''Review of FFTF Fuel Experiments for Storage at ISA'', (Reference I), which subsequently allowed a large portion of these components to be included in the authorization basis (Table H.3.3-21). The report also identified additional components and actions in Section 3.0 and Table 3 that require further evaluation. The purpose of this report is to evaluate another portion of the remaining inventory (i.e., delayed neutron signal fuel, blanket assemblies, highly enriched assemblies, newly loaded Ident-69 pin containers, and returned fuel) to ensure it can be safely off loaded to the FFTF spent fuel storage system.

CHASTAIN, S.A.

2005-10-24T23:59:59.000Z

23

U-038: BIND 9 Resolver crashes after logging an error in query.c |  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

8: BIND 9 Resolver crashes after logging an error in query.c 8: BIND 9 Resolver crashes after logging an error in query.c U-038: BIND 9 Resolver crashes after logging an error in query.c November 16, 2011 - 8:37am Addthis PROBLEM: BIND 9 Resolver crashes after logging an error in query.c. PLATFORM: Multiple version of BIND 9. Specific versions under investigation ABSTRACT: A remote server can cause the target connected client to crash. Organizations across the Internet are reporting crashes interrupting service on BIND 9 nameservers performing recursive queries. Affected servers crash after logging an error in query.c with the following message: "INSIST(! dns_rdataset_isassociated(sigrdataset))" Multiple versions are reported as being affected, including all currently supported release versions of ISC BIND 9. ISC is actively investigating the root cause and

24

V-204: A specially crafted query can cause BIND to terminate abnormally |  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

V-204: A specially crafted query can cause BIND to terminate V-204: A specially crafted query can cause BIND to terminate abnormally V-204: A specially crafted query can cause BIND to terminate abnormally July 27, 2013 - 4:35am Addthis PROBLEM: A specially crafted query that includes malformed rdata can cause named to terminate with an assertion failure while rejecting the malformed query. PLATFORM: BIND 9.7 ABSTRACT: A specially crafted query sent to a BIND nameserver can cause it to crash (terminate abnormally). REFERENCE LINKS: ISC Knowledge Base CVE-2013-4854 IMPACT ASSESSMENT: High DISCUSSION: BIND is an implementation of the Domain Name System (DNS) protocols. Authoritative and recursive servers are equally vulnerable. Intentional exploitation of this condition can cause a denial of service in all nameservers running affected versions of BIND 9. Access Control Lists do

25

Inhibition of selectin binding  

DOE Patents (OSTI)

This invention provides a system for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, this system can be used to palliate certain inflammatory and immunological conditions.

Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Carolyn (Albany, CA)

1999-10-05T23:59:59.000Z

26

Inhibition of selectin binding  

DOE Patents (OSTI)

This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Caroline (Albany, CA)

1999-01-01T23:59:59.000Z

27

Inhibition of selectin binding  

DOE Patents (OSTI)

This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Caroline (Albany, CA)

2001-10-09T23:59:59.000Z

28

Radon Binding to Water-Soluble Cryptophane  

Science Conference Proceedings (OSTI)

Radon Binding to Water-Soluble Cryptophane. Summary: Collaboration on investigating the thermodynamics of radon binding ...

2012-06-27T23:59:59.000Z

29

Cellulose binding domain proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc (Davis, CA); Doi, Roy (Davis, CA)

1998-01-01T23:59:59.000Z

30

Page not found | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

to it, such as buildings, fences, and roads. http:energy.govlmarticleslm-fims-database Article V-079: ISC BIND AAAA Record Lookup Handling Assertion Failure...

31

How Dynein Binds to Microtubules  

NLE Websites -- All DOE Office Websites (Extended Search)

with binding. Confirmation was provided by docking the crystal structure into an electron-density map of a dynein stalk bound to microtubules that was obtained by...

32

Cellulose binding domain fusion proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1998-01-01T23:59:59.000Z

33

Cellulose binding domain fusion proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

Shoseyov, O.; Yosef, K.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1998-02-17T23:59:59.000Z

34

Bindings  

E-Print Network (OSTI)

With Debian or Ubuntu the installation is very simple apt-get install python Versions Several versions of Python are available 2.4, 2.5 and 2.6. ? python-V gives the version of Python that will be used % python-V Python 2.5.4Outline

Francois Faure

2009-01-01T23:59:59.000Z

35

Erythropoietin binding protein from mammalian serum  

DOE Patents (OSTI)

Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described.

Clemons, Gisela K. (Berkeley, CA)

1997-01-01T23:59:59.000Z

36

Erythropoietin binding protein from mammalian serum  

DOE Patents (OSTI)

Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described. 11 figs.

Clemons, G.K.

1997-04-29T23:59:59.000Z

37

Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein-Ligand Binding Affinities  

E-Print Network (OSTI)

Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein-Ligand Binding Jersey 08854 Received June 2, 2010 Abstract: The binding energy distribution analysis method (BEDAM of the probability distribution of the binding energy obtained in the canonical ensemble in which the ligand

38

Synthetic heparin-binding factor analogs  

DOE Patents (OSTI)

The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain, and preferably two peptide chains branched from a dipeptide branch moiety composed of two trifunctional amino acid residues, which peptide chain or chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a linker, which may be a hydrophobic linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

Pena, Louis A. (Poquott, NY); Zamora, Paul O. (Gaithersburg, MD); Lin, Xinhua (Plainview, NY); Glass, John D. (Shoreham, NY)

2010-04-20T23:59:59.000Z

39

Identifying binding sites in sequential genomic data  

Science Conference Proceedings (OSTI)

The identification of cis-regulatory binding sites in DNA is a difficult problem in computational biology. To obtain a full understanding of the complex machinery embodied in genetic regulatory networks it is necessary to know both the identity of the ... Keywords: computational biology, imbalanced data, sampling, support vector machine, transcription factor binding sites

Mark Robinson; Cristina Gonzlez Castellano; Rod Adams; Neil Davey; Yi Sun

2007-09-01T23:59:59.000Z

40

Complexity measures for binding-blocking automata  

Science Conference Proceedings (OSTI)

We define three complexity measures for binding-blocking automata (BBA) namely, blocking number, blocking instant and blocking quotient. We also study some hierarchical structures of BBA arising out of it. Keywords: binding-blocking automata, complexity measures, peptide-antibody interaction

M. Sakthi Balan

2008-04-01T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

A Tcl Binding to Motif  

E-Print Network (OSTI)

Tcl is a type--free interpreted language intended for use as an embedded command language for applications. Motif is the standard GUI for the XWindow System, but this has a complex C--based API. This paper discusses a binding of tcl to Motif which allows for a simpler API. 1. Introduction The XWindow System is now accepted as the standard windowing systems for Unix graphics workstations and terminals [1]. It provides a low--level set of tools to build applications. Most applications now are built using a higher--level toolkit which typically supplies objects usually known as widgets. There are a number of such toolkits, but the one that has achieved the major success is the Motif toolkit [] based on the Xt Intrinsics [8]. Motif has defined a look--and--feel that is copied to a greater or lesser extent by other toolkits, and forms a component of specifications such as COSE. The specification for Motif [7] basically assumes a C--like language, and the only implementation of that specif...

Jan Newmarch

1994-01-01T23:59:59.000Z

42

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

DOE Patents (OSTI)

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.

Mayfield, Stephen (Cardiff, CA)

2000-01-01T23:59:59.000Z

43

An InterdIscIplInAry MIt study InterIM report  

E-Print Network (OSTI)

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253 B.2.1 Cartesian . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253 B.2

Wurtman, Richard

44

Using ISC & GIS to predict sulfur deposition from coal-fired power plants  

E-Print Network (OSTI)

The goal of this research project was to determine if atmospheric sources have the potential of contributing significantly to the sulfur content of grazed forage. Sulfur deposition resulting from sulfur dioxide emissions from coal- fired power plants was predicted utilizing the Industrial Source Complex Long-Term (ISCLT2) Model for the areas ofa interest in East Texas. GRASS, a geographical information system (GIS), was used to pull together all predicted values from ISCLT2 and present them in the form of predicted sulfur deposition maps with different ranges of deposition. Two field trips to NE Texas were taken to obtain data on soil and forage sulfur content. GRASS was used extensively in the planning process before each trip and the global positioning system was also used extensively during the trip to locate sampling sites and to obtain the geographical location of each site. The methodology developed predicts that 11 to 21 kg sulfur/ha per year can be deposited as far as 100 to 160 km from the source. Data from both field trips do not show a statistical significant relation between predicted sulfur deposition and either soil or forage sulfur content. However, the data do show that there is a trend of increasing soil and forage sulfur content as predicted sulfur deposition increases.

Lopez, Jose Ignacio

1993-01-01T23:59:59.000Z

45

ISC Conventional Reading Rooms | U.S. DOE Office of Science ...  

Office of Science (SC) Website

you can visit that location or call, 865-241-4780, via fax at 865-574-3521, toll free at 800-382-6938, option 6; or via e-mail at DOEIC@oro.doe.gov. General Disclaimer This...

46

JC3 Bulletin Archive | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

on the target user's system. A remote user can conduct cross-site scripting attacks. A remote user can obtain potentially sensitive information. June 5, 2012 U-183: ISC BIND DNS...

47

Exciton binding energy in semiconductor quantum dots  

Science Conference Proceedings (OSTI)

In the adiabatic approximation in the context of the modified effective mass approach, in which the reduced exciton effective mass {mu} = {mu}(a) is a function of the radius a of the semiconductor quantum dot, an expression for the exciton binding energy E{sub ex}(a) in the quantum dot is derived. It is found that, in the CdSe and CdS quantum dots with the radii a comparable to the Bohr exciton radii a{sub ex}, the exciton binding energy E{sub ex}(a) is substantially (respectively, 7.4 and 4.5 times) higher than the exciton binding energy in the CdSe and CdS single crystals.

Pokutnii, S. I., E-mail: Pokutnyi_Sergey@inbox.ru [National Academy of Sciences of Ukraine, G.V. Kurdjumov Institute for Metal Physics (Ukraine)

2010-04-15T23:59:59.000Z

48

Binding energies of hypernuclei and hypernuclear interactions  

SciTech Connect

In part 1 the effect of nuclear core dynamics on the binding energies of {Lambda} hypernuclei is discussed in the framework of variational correlated wave functions. In particular, the authors discuss a new rearrangement energy contribution and its effect on the core polarization. In part 2 they consider the interpretation of the {Lambda} single-particle energy in terms of basic {Lambda}-nuclear interactions using a local density approximation based on a Fermi hypernetted chain calculation of the A binding to nuclear matter. To account for the data strongly repulsive 3-body {Lambda}NN forces are required. Also in this framework they discuss core polarization for medium and heavier hypernuclei.

Bodmer, A.R. [Argonne National Lab., IL (United States)]|[Univ. of Illinois, Chicago, IL (United States). Dept. of Physics; Murali, S.; Usmani, Q.N. [Jamia Millia Islamia, New Delhi (India). Dept. of Physics

1996-05-01T23:59:59.000Z

49

Hydrogen Bonding Penalty upon Ligand Binding  

E-Print Network (OSTI)

Ligand binding involves breakage of hydrogen bonds with water molecules and formation of new hydrogen bonds between protein and ligand. In this work, the change of hydrogen bonding energy in the binding process, namely hydrogen bonding penalty, is evaluated with a new method. The hydrogen bonding penalty can not only be used to filter unrealistic poses in docking, but also improve the accuracy of binding energy calculation. A new model integrated with hydrogen bonding penalty for free energy calculation gives a root mean square error of 0.7 kcal/mol on 74 inhibitors in the training set and of 1.1 kcal/mol on 64 inhibitors in the test set. Moreover, an application of hydrogen bonding penalty into a high throughput docking campaign for EphB4 inhibitors is presented, and remarkably, three novel scaffolds are discovered out of seven tested. The binding affinity and ligand efficiency of the most potent compound is about 300 nM and 0.35 kcal/mol per non-hydrogen atom, respectively.

Hongtao Zhao; Danzhi Huang

2011-01-01T23:59:59.000Z

50

Nucleic acids encoding a cellulose binding domain  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 15 figs.

Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1996-03-05T23:59:59.000Z

51

Nucleic acids encoding a cellulose binding domain  

SciTech Connect

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1996-01-01T23:59:59.000Z

52

U-101: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

to a use-after-free error in the "nsXBLDocumentInfo::ReadPrototypeBindings()" method when handling XBL bindings in a hash table and can be exploited to cause a cycle collector to...

53

Gene encoding herbicide safener binding protein  

DOE Patents (OSTI)

The cDNA encoding safener binding protein (SafBP), also referred to as SBP1, is set forth in FIG. 5 and SEQ ID No. 1. The deduced amino acid sequence is provided in FIG. 5 and SEQ ID No. 2. Methods of making and using SBP1 and SafBP to alter a plant's sensitivity to certain herbicides or a plant's responsiveness to certain safeners are also provided, as well as expression vectors, transgenic plants or other organisms transfected with said vectors and seeds from said plants.

Walton, Jonathan D. (East Lansing, MI); Scott-Craig, John S. (East Lansing, MI)

1999-01-01T23:59:59.000Z

54

Reflection-Based Python-C++ Bindings  

Science Conference Proceedings (OSTI)

Python is a flexible, powerful, high-level language with excellent interactive and introspective capabilities and a very clean syntax. As such, it can be a very effective tool for driving physics analysis. Python is designed to be extensible in low-level C-like languages, and its use as a scientific steering language has become quite widespread. To this end, existing and custom-written C or C++ libraries are bound to the Python environment as so-called extension modules. A number of tools for easing the process of creating such bindings exist, such as SWIG and Boost. Python. Yet, the process still requires a considerable amount of effort and expertise. The C++ language has few built-in introspective capabilities, but tools such as LCGDict and CINT add this by providing so-called dictionaries: libraries that contain information about the names, entry points, argument types, etc. of other libraries. The reflection information from these dictionaries can be used for the creation of bindings and so the process can be fully automated, as dictionaries are already provided for many end-user libraries for other purposes, such as object persistency. PyLCGDict is a Python extension module that uses LCG dictionaries, as PyROOT uses CINT reflection information, to allow /cwPython users to access C++ libraries with essentially no preparation on the users' behalf. In addition, and in a similar way, PyROOT gives ROOT users access to Python libraries.

Generowicz, Jacek; Lavrijsen, Wim T.L.P.; Marino, Massimo; Mato, Pere

2004-10-14T23:59:59.000Z

55

Functionalized Polymers For Binding To Solutes In Aqueous Solutions  

NLE Websites -- All DOE Office Websites (Extended Search)

Functionalized Polymers For Binding To Solutes In Aqueous Solutions Functionalized Polymers For Binding To Solutes In Aqueous Solutions Functionalized Polymers For Binding To Solutes In Aqueous Solutions A functionalized polymer for binding a dissolved molecule in an aqueous solution is presented. Available for thumbnail of Feynman Center (505) 665-9090 Email Functionalized Polymers For Binding To Solutes In Aqueous Solutions A functionalized polymer for binding a dissolved molecule in an aqueous solution is presented. The polymer has a backbone polymer to which one or more functional groups are covalently linked. The backbone polymer can be such polymers as polyethylenimine, polyvinylamine, polyallylamine, and polypropylamine. These polymers are generally water-soluble, but can be insoluble when cross-linked. The functional group can be for example diol

56

Hardware device to physical structure binding and authentication  

Science Conference Proceedings (OSTI)

Detection and deterrence of device tampering and subversion may be achieved by including a cryptographic fingerprint unit within a hardware device for authenticating a binding of the hardware device and a physical structure. The cryptographic fingerprint unit includes an internal physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generate an internal PUF value. Binding logic is coupled to receive the internal PUF value, as well as an external PUF value associated with the physical structure, and generates a binding PUF value, which represents the binding of the hardware device and the physical structure. The cryptographic fingerprint unit also includes a cryptographic unit that uses the binding PUF value to allow a challenger to authenticate the binding.

Hamlet, Jason R.; Stein, David J.; Bauer, Todd M.

2013-08-20T23:59:59.000Z

57

Method and apparatus for detecting chemical binding  

DOE Patents (OSTI)

The method for screening binding between a target binder and potential pharmaceutical chemicals involves sending a solution (preferably an aqueous solution) of the target binder through a conduit to a size exclusion filter, the target binder being too large to pass through the size exclusion filter, and then sending a solution of one or more potential pharmaceutical chemicals (preferably an aqueous solution) through the same conduit to the size exclusion filter after target binder has collected on the filter. The potential pharmaceutical chemicals are small enough to pass through the filter. Afterwards, x-rays are sent from an x-ray source to the size exclusion filter, and if the potential pharmaceutical chemicals form a complex with the target binder, the complex produces an x-ray fluorescence signal having an intensity that indicates that a complex has formed.

Warner, Benjamin P. (Los Alamos, NM); Havrilla, George J. (Los Alamos, NM); Miller, Thomasin C. (Los Alamos, NM); Wells, Cyndi A. (Los Alamos, NM)

2007-07-10T23:59:59.000Z

58

Sequestering Uranium from Seawater: Binding Strength and Modes...  

NLE Websites -- All DOE Office Websites (Extended Search)

YouTube: AdvancedLightSource Home Science Highlights Journal Covers Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl Complexes with Glutarimidedioxime...

59

Comprehensive investigation of the non-covalent binding of MRI ...  

Science Conference Proceedings (OSTI)

of MRI contrast agents with human serum albumin. Virginie ... binding between human serum albumin (HSA) and MRI contrast .... The relative error on the T1...

60

A-84: Tight Binding Understanding of Carbon Defects in Steel  

Science Conference Proceedings (OSTI)

Thus, a coherent transferable tight-binding (TB) parameterization was developed for Fe-C by ... A-54: Used Foundry Sand Reclamation in New Vibratory Unit.

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

Enumeration Algorithm for Determination of Binding Constants in Capillary Electrophoresis  

E-Print Network (OSTI)

result in the new migration time. Because the true binding constant and complex mobility values have. With the enumeration algorithm, all possible combinations of the binding constant and the complex mobility in certain and the mobility of the complex formed between the interacting pair, to form a 2-D curve. When the experimental

Chen, David D.Y.

62

BPA FINAL Binding Arbitration policy | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

BPA FINAL Binding Arbitration policy BPA FINAL Binding Arbitration policy BPA FINAL Binding Arbitration policy Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited

63

Babel Fortran 2003 Binding for Structured Data Types  

SciTech Connect

Babel is a tool aimed at the high-performance computing community that addresses the need for mixing programming languages (Java, Python, C, C++, Fortran 90, FORTRAN 77) in order to leverage the specific benefits of those languages. Scientific codes often rely on structured data types (structs, derived data types) to encapsulate data, and Babel has been lacking in this type of support until recently. We present a new language binding that focuses on their interoperability of C/C++ with Fortran 2003. The new binding builds on the existing Fortran 90 infrastructure by using the iso-c-binding module defined in the Fortran 2003 standard as the basis for C/C++ interoperability. We present the technical approach for the new binding and discuss our initial experiences in applying the binding in FACETS (Framework Application for Core-Edge Transport Simulations) to integrate C++ with legacy Fortran codes.

Muszala, S; Epperly, T; Wang, N

2008-05-02T23:59:59.000Z

64

Angiotensin II receptor binding sites in brain microvessels  

SciTech Connect

The authors assessed the specific binding of /sup 125/I-labeled angiotensin II (/sup 125/I-Ang II) to particulate fractions of the cerebral cortex and cerebellum and to microvessels obtained by bulk isolation from these two brain regions in the dog. /sup 125/I-Ang II binds to cerebral and cerebellar microvessels in a specific, saturable, and reversible manner and with high affinity (dissociation constant about 1 nM). Maximal binding of /sup 125/I-Ang II to brain microvessels was about 2-fold higher than the maximal binding to particulate fractions of the cerebellum and more than 15-fold higher than that of the cerebral cortex. Furthermore, finding that analogues of Ang II displace specific /sup 125/I-Ang II binding to brain microvessels in a rank order that correlates with their pharmacological activities confers biological relevance on the ligand-binding studies. These results strongly suggest that specific Ang II receptor binding sites are present in brain microvessels. Such Ang II receptors may have an important role in regulating the microcirculation of the brain.

Speth, R.C.; Harik, S.I.

1985-09-01T23:59:59.000Z

65

Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes  

DOE Green Energy (OSTI)

Cellulases hydrolyze {beta}-1,4 glycosidic linkages in cellulose, which are among the most prevalent and stable bonds in Nature. Cellulases comprise many glycoside hydrolase families and exist as processive or nonprocessive enzymes. Product inhibition negatively impacts cellulase action, but experimental measurements of product-binding constants vary significantly, and there is little consensus on the importance of this phenomenon. To provide molecular level insights into cellulase product inhibition, we examine the impact of product binding on processive and nonprocessive cellulases by calculating the binding free energy of cellobiose to the product sites of catalytic domains of processive and nonprocessive enzymes from glycoside hydrolase families 6 and 7. The results suggest that cellobiose binds to processive cellulases much more strongly than nonprocessive cellulases. We also predict that the presence of a cellodextrin bound in the reactant site of the catalytic domain, which is present during enzymatic catalysis, has no effect on product binding in nonprocessive cellulases, whereas it significantly increases product binding to processive cellulases. This difference in product binding correlates with hydrogen bonding between the substrate-side ligand and the cellobiose product in processive cellulase tunnels and the additional stabilization from the longer tunnel-forming loops. The hydrogen bonds between the substrate- and product-side ligands are disrupted by water in nonprocessive cellulase clefts, and the lack of long tunnel-forming loops results in lower affinity of the product ligand. These findings provide new insights into the large discrepancies reported for binding constants for cellulases and suggest that product inhibition will vary significantly based on the amount of productive binding for processive cellulases on cellulose.

Bu, L.; Nimlos, M. R.; Shirts, M. R.; Stahlberg, J.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T.

2012-07-13T23:59:59.000Z

66

Binding Parameters of Alkaloids Berberine and Sanguinarine with DNA  

E-Print Network (OSTI)

We study the interaction of berberine and sanguinarine (plant alkaloids) with DNA in aqueous solutions, by using optical spectroscopy methods (absorption and fluorescence). The dependencies of alkaloid spectral characteristics on the concentration ratio N/c between the DNA base pairs and alkaloid molecules in the solutions are considered, and the manifestations of the alkaloid-DNA binding are revealed. The character of binding is found to depend on N/c. The parameters of the binding of berberine and sanguinarine with DNA are determined, by using the modified Scatchard and McGhee-von Hippel equations

Gumenyuk, V G; Kutovyy, S Yu; Yashchuk, V M; Zaika, L A

2012-01-01T23:59:59.000Z

67

Binding Preferences, Surface Attachment, Diffusivity, and Orientation of a Family 1 Carbohydrate-Binding Module on Cellulose  

DOE Green Energy (OSTI)

Cellulase enzymes often contain carbohydrate-binding modules (CBMs) for binding to cellulose. The mechanisms by which CBMs recognize specific surfaces of cellulose and aid in deconstruction are essential to understand cellulase action. The Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase, Cel7A, is known to selectively bind to hydrophobic surfaces of native cellulose. It is most commonly suggested that three aromatic residues identify the planar binding face of this CBM, but several recent studies have challenged this hypothesis. Here, we use molecular simulation to study the CBM binding orientation and affinity on hydrophilic and hydrophobic cellulose surfaces. Roughly 43 {mu}s of molecular dynamics simulations were conducted, which enables statistically significant observations. We quantify the fractions of the CBMs that detach from crystal surfaces or diffuse to other surfaces, the diffusivity along the hydrophobic surface, and the overall orientation of the CBM on both hydrophobic and hydrophilic faces. The simulations demonstrate that there is a thermodynamic driving force for the Cel7A CBM to bind preferentially to the hydrophobic surface of cellulose relative to hydrophilic surfaces. In addition, the simulations demonstrate that the CBM can diffuse from hydrophilic surfaces to the hydrophobic surface, whereas the reverse transition is not observed. Lastly, our simulations suggest that the flat faces of Family 1 CBMs are the preferred binding surfaces. These results enhance our understanding of how Family 1 CBMs interact with and recognize specific cellulose surfaces and provide insights into the initial events of cellulase adsorption and diffusion on cellulose.

Nimlos, M. R.; Beckham, G. T.; Matthews, J. F.; Bu, L.; Himmel, M. E.; Crowley, M. F.

2012-06-08T23:59:59.000Z

68

A Fortran binding for the GNU scientific library  

Science Conference Proceedings (OSTI)

The GNU scientific library is a collection of numerical routines for scientific computing. This article discusses some aspects of the design of a fully standard-conforming Fortran binding for GSL via incremental usage of Fortran 2003 features, in particular ...

Reinhold Bader

2007-08-01T23:59:59.000Z

69

Bayesian unsupervised learning of DNA regulatory binding regions  

Science Conference Proceedings (OSTI)

Identification of regulatory binding motifs, that is, short specific words, within DNA sequences is a commonly occurring problem in computational bioinformatics. A wide variety of probabilistic approaches have been proposed in the literature to either ...

Jukka Corander; Magnus Ekdahl; Timo Koski

2009-01-01T23:59:59.000Z

70

Assessing phylogenetic motif models for predicting transcription factor binding sites  

Science Conference Proceedings (OSTI)

Motivation: A variety of algorithms have been developed to predict transcription factor binding sites (TFBSs) within the genome by exploiting the evolutionary information implicit in multiple alignments of the genomes of related species. One such ...

John Hawkins; Charles Grant; William Stafford Noble; Timothy L. Bailey

2009-06-01T23:59:59.000Z

71

Reversible and irreversible binding of nanoparticles to polymeric surfaces  

Science Conference Proceedings (OSTI)

Reversible and irreversible binding of CdSe-nanoparticles and nanorods to polymeric surfaces via a strong, multiple hydrogen bond (= Hamilton-receptor/barbituric acid) is described. Based on ROMP-copolymers, the supramolecular interaction on a thin polymer ...

Wolfgang H. Binder; Marina Lomoschitz; Robert Sachsenhofer; Gernot Friedbacher

2009-01-01T23:59:59.000Z

72

MONKEY: Identifying conserved transcription-factor binding sitesin multiple alignments using a binding site-specific evolutionarymodel  

SciTech Connect

We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

Moses, Alan M.; Chiang, Derek Y.; Pollard, Daniel A.; Iyer, VenkyN.; Eisen, Michael B.

2004-10-28T23:59:59.000Z

73

MANAGING TIGHT BINDING RECEPTORS FOR NEW SPEARATIONS TECHNOLOGIES  

DOE Green Energy (OSTI)

Much of the earth's pollution involves compounds of the metallic elements, including actinides, strontium, cesium, technetium, and RCRA metals. Metal ions bind to molecules called ligands, which are the molecular tools that can manipulate the metal ions under most conditions. This DOE-EMSP sponsored program strives (1) to provide the foundations for using the most powerful ligands in transformational separations technologies and (2) to produce seminal examples of their applications to separations appropriate to the DOE EM mission. These ultra tight-binding ligands can capture metal ions in the most competitive of circumstances (from mineralized sites, lesser ligands, and even extremely dilute solutions), but they react so slowly that they are useless in traditional separations methodologies. Two attacks on this problem are underway. The first accommodates to the challenging molecular lethargy by developing a seminal slow separations methodology termed the soil poultice. The second designs ligands that are only tight-binding while wrapped around the targeted metal ion, but can be put in place by switch-binding and removed by switch-release. We envision a kind of molecular switching process to accelerate the union between metal ion and tight-binding ligand. Molecular switching processes are suggested for overcoming the slow natural equilibration rate with which ultra tight-binding ligands combine with metal ions. Ligands that bind relatively weakly combine with metal ions rapidly, so the trick is to convert a ligand from a weak, rapidly binding species to a powerful, slow releasing ligand--during the binding of the ligand to the metal ion. Such switch-binding ligands must react with themselves, and the reaction must take place under the influence of the metal ion. For example, our generation 1 ligands showed that a well-designed linear ligand with ends that readily combine, forms a cyclic molecule when it wraps around a metal ion. Our generation 2 ligands are even more interesting. They convert from rings to structures that wrap around a metal ion to form a cage. These ligands are called cryptands. Switch release is accomplished by photolytic cleavage of a bond to convert a cyclic ligand into a linear ligand or to break similar bonds in a cryptate. Our studies have demonstrated switch binding and switch release with cryptates of calcium. These remarkable cyclic ligands and cage-like ligands are indeed tight-binding and may, in principle, be incorporated in various separations methodologies, including the soil poultice. The soil poultice mimics the way in which microbes secrete extremely powerful ligands into the soil in order to harvest iron. The cellular membrane of the microbe recognizes the iron/ligand complex and admits it into the cell. The soil poultice uses molecularly imprinted polymers (MIPs) to play the role of the cellular membrane. Imprinting involves creation of the polymer in the presence of the metal/ligand complex. In principle, a well design ligand/MIP combination can be highly selective toward almost any targeted metal ion. The principles for that design are the focus of these investigations. An imprinting molecule can interact with the polymer through any, some, or all of the so-called supramolecular modes; e.g., hydrogen bonding, electrostatic charge, minor ligand bonding, Pi-Pi stacking, and hydrophobic and van der Waals interactions. Historically these modes of binding have given MIPs only small re-binding capacities and very limited selectivities. This program has shown that each mode of interaction can be made more powerful than previously suspected and that combinations of different supramolecular interaction modes can produce remarkable synergisms. The results of this systematic study provide a firm foundation for tailoring molecular imprinted polymers for reclamation of specific metal ion, including those important to the DOE EM mission.

DARYLE H BUSCH RICHARD S GIVENS

2004-12-10T23:59:59.000Z

74

Page not found | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

81 - 25790 of 28,904 results. 81 - 25790 of 28,904 results. Article V-079: ISC BIND AAAA Record Lookup Handling Assertion Failure Vulnerability ISC has learned of the potential for an error condition to occur in BIND 9 http://energy.gov/cio/articles/v-079-isc-bind-aaaa-record-lookup-handling-assertion-failure-vulnerability Article EM Helps Military Families in Need LAS VEGAS - Six families from Nellis Air Force Base in Las Vegas recently received nearly $4,000 in donations - funds that helped provide a welcome relief during the holidays. http://energy.gov/em/articles/em-helps-military-families-need Download CX-009224: Categorical Exclusion Determination Project L-718, Electrical Utilities Transformer Management Support Facility CX(s) Applied: B1.15 Date: 09/04/2012 Location(s): Washington

75

An angiogenin-binding protein from endothelial cells  

SciTech Connect

A 42-kDa bovine protein that binds bovine angiogenin (angiogenin binding protein (AngBP)) has been identified as a dissociable cell-surface component of calf pulmonary artery endothelial cells and a transformed bovine endothelial cell line, GM7373. {sup 125}I-Ang can be crosslinked efficiently to AngBP by a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)carbo-diimide. Bovine ribonuclease A competes with the binding of {sup 125}I-Ang to AngBP, but lysozyme does not. Direct binding to AngBP of {sup 125}I-labeled bovine ribonuclease A is, however, much weaker than that of {sup 125}I-Ang. Two enzymatically active derivatives of angiogenin cleaved at residues 60-61 and 67-68, respectively, fail to induce angiogenesis and also bind to AngBP only weakly. AngBP has been isolated by treatment of cells with heparan sulfate, affinity chromatography on angiogenin-Sepharose of the material dissociated from the cell surface, and gel filtration HPLC. The results suggest that AngBP has the characteristics of a receptor that may likely function in angiogenesis.

Hu, Guofu; Chang, Sooik; Riordan, J.F.; Vallee, B.L. (Harvard Medical School, Boston, MA (United States))

1991-03-15T23:59:59.000Z

76

Anchored Clathrate Waters Bind Antifreeze Proteins to Ice  

DOE Green Energy (OSTI)

The mechanism by which antifreeze proteins (AFPs) irreversibly bind to ice has not yet been resolved. The ice-binding site of an AFP is relatively hydrophobic, but also contains many potential hydrogen bond donors/acceptors. The extent to which hydrogen bonding and the hydrophobic effect contribute to ice binding has been debated for over 30 years. Here we have elucidated the ice-binding mechanism through solving the first crystal structure of an Antarctic bacterial AFP. This 34-kDa domain, the largest AFP structure determined to date, folds as a Ca{sup 2+}-bound parallel beta-helix with an extensive array of ice-like surface waters that are anchored via hydrogen bonds directly to the polypeptide backbone and adjacent side chains. These bound waters make an excellent three-dimensional match to both the primary prism and basal planes of ice and in effect provide an extensive X-ray crystallographic picture of the AFP{vert_ellipsis}ice interaction. This unobstructed view, free from crystal-packing artefacts, shows the contributions of both the hydrophobic effect and hydrogen bonding during AFP adsorption to ice. We term this mode of binding the 'anchored clathrate' mechanism of AFP action.

C Garnham; R Campbell; P Davies

2011-12-31T23:59:59.000Z

77

Acid Gas Capture Using CO2-Binding Organic Liquids  

SciTech Connect

Current chemical CO2 scrubbing technology is primarily aqueous alkanolamine based. These systems rapidly bind CO2 (forming water-soluble carbamate and bicarbonate salts) however, the process has serious disadvantages. The concentration of monoethanolamine rarely exceeds 30 wt % due to the corrosive nature of the solution, and this reduces the maximum CO2 volumetric (?108 g/L) and gravimetric capacity (?7 wt%) of the CO2 scrubber. The ?30 wt % loading of ethanolamine also means that a large excess of water must be pumped and heated during CO2 capture and release, and this greatly increases the energy requirements especially considering the high specific heat of water (4 j/g-1K-1). Our approach is to switch to organic systems that chemically bind CO2 as liquid alkylcarbonate salts. Our CO2-binding organic liquids have higher CO2 solubility, lower specific heats, potential for less corrosion and lower binding energies for CO2 than aqueous systems. CO2BOLs also reversibly bind and release mixed sulfur oxides. Furthermore the CO2BOL system can be direct solvent replacements for any solvent based CO2 capture systems because they are commercially available reagents and because they are fluids they would not require extensive process re-engineering.

Heldebrant, David J.; Koech, Phillip K.; Rainbolt, James E.; Zheng, Feng

2010-11-10T23:59:59.000Z

78

BPA GUIDANCE ON THE USE OF BINDING ARBITRATION  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

BONNEVILLE POWER ADMINISTRATION'S BONNEVILLE POWER ADMINISTRATION'S GUIDANCE ON THE USE OF BINDING ARBITRATION FOR BPA CONTRACTS Introduction Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited discovery, a

79

BPA GUIDANCE ON THE USE OF BINDING ARBITRATION  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

BONNEVILLE POWER ADMINISTRATION'S BONNEVILLE POWER ADMINISTRATION'S GUIDANCE ON THE USE OF BINDING ARBITRATION FOR BPA CONTRACTS Introduction Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited discovery, a

80

Decreased angiotensin II binding affinity and binding capacity in the anterior pituitary gland of adult spontaneously hypertensive rats  

SciTech Connect

Angiotensin II (ANG) binding sites were quantified in single pituitary glands from 4-week-old and 14-week-old male spontaneously hypertensive rats (SHR) and age-matched male normotensive Wistar-Kyoto (WKY) control rats after incubation with /sup 125/I-(Sar/sup 1/)-ANG, autoradiography with computerized densitometry, and comparison to /sup 125/I-standards. The maximum binding capacity (B/sub max/) decreased while the dissociation constant (K/sub d/) for ANG increased in 14-week-old SHR when compared to age-matched WKY control rats. Conversely, no difference between rat strains was found in 4-week-old animals. Our results suggest that pituitary ANG binding sites may play a role in the pathophysiology of established genetic hypertension.

Gutkind, J.S.; Castren, E.; Saavedra, J.M.

1988-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

Methods of detection using a cellulose binding domain fusion product  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Shimshon, IL); Shpiegl, Itai (North Gallilea, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1999-01-01T23:59:59.000Z

82

Scheduling and resource binding algorithm considering timing variation  

Science Conference Proceedings (OSTI)

The timing closure problem (e.g., meeting timing/ clock period constraint) is one of the most important problems in the design automation. However, the rapid increase of the impact of the process variation on circuit timing makes the problem much more ... Keywords: binding, high-level synthesis, scheduling, timing analysis, timing variation

Jongyoon Jung; Taewhan Kim

2011-02-01T23:59:59.000Z

83

DNA-Binding Mechanism in Prokaryotic Partition Complex Formation  

NLE Websites -- All DOE Office Websites (Extended Search)

DNA-Binding Mechanism in DNA-Binding Mechanism in Prokaryotic Partition Complex Formation DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print Wednesday, 29 March 2006 00:00 The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of prokaryotic partition is the Escherichia coli P1 plasmid par system, which consists of a centromere site (parS) on the plasmid DNA and two proteins, ParA and ParB. The initial formation of the so-called partition complex between ParB and the centromere is a critical step in partition. To understand the DNA-binding mechanism utilized by ParB, Schumacher and Funnell determined crystal structures of the C-terminal region of ParB, known as ParB(142-333), bound to centromere sites.

84

Workshop on gate valve pressure locking and thermal binding  

SciTech Connect

The purpose of the Workshop on Gate Valve Pressure Locking and Thermal Binding was to discuss pressure locking and thermal binding issues that could lead to inoperable gate valves in both boiling water and pressurized water reactors. The goal was to foster exchange of information to develop the technical bases to understand the phenomena, identify the components that are susceptible, discuss actual events, discuss the safety significance, and illustrate known corrective actions that can prevent or limit the occurrence of pressure locking or thermal binding. The presentations were structured to cover U.S. Nuclear Regulatory Commission staff evaluation of operating experience and planned regulatory activity; industry discussions of specific events, including foreign experience, and efforts to determine causes and alleviate the affects; and valve vendor experience and recommended corrective action. The discussions indicated that identifying valves susceptible to pressure locking and thermal binding was a complex process involving knowledge of components, systems, and plant operations. The corrective action options are varied and straightforward.

Brown, E.J.

1995-07-01T23:59:59.000Z

85

Inhibition Of Call-Cell Binding By Kipid Assemblies  

DOE Patents (OSTI)

This invention relates generally to the field of therapeutic compounds designed to interfere between the binding of ligands and their receptors on cell surface. More specifically, it provides products and methods for inhibiting cell migration and activation using lipid assemblies with surface recognition elements that are specific for the receptors involved in cell migration and activation.

Nagy, Jon O. (Rodeo, CA), Bargatze, Robert F. (Bozeman, MT)

2003-12-16T23:59:59.000Z

86

Automatic Generation of Tcl Bindings for C and C++ Libraries  

E-Print Network (OSTI)

Automatic Generation of Tcl Bindings for C and C++ Libraries Wolfgang Heidrich Computer Graphics@informatik.uni-erlangen.de Abstract In the past few years Tcl has found widespread in- terest as a extensible scripting language. Numerous Tcl interfaces for a variety of C libraries have been created. While most of these language

Heidrich, Wolfgang

87

Automatic Generation of Tcl Bindings for C and C++ Libraries  

E-Print Network (OSTI)

In the past few years Tcl has found widespread interest as a extensible scripting language. Numerous Tcl interfaces for a variety of C libraries have been created. While most of these language bindings have been created by hand, others have made use of dedicated code generators designed for the specific library. In this paper we present a tool for the automatic generation of Tcl language bindings for arbitrary C libraries. Moreover, the mapping of C++ class hierarchies to [incr Tcl] classes will be described. 1 Introduction 1.1 Prior Work One of the reasons for the recent success of Tcl is its powerful API to C and C++, which allows the extension of the core language with commands implemented as C functions. This facility has been used to create a variety of language bindings for C libraries, ranging from different 3D graphics libraries (iris gl, OpenGL, vogle, sipp) to several X widget sets, for example Wafe and tclMotif. While most of this work has been done manually, other bind...

Wolfgang Heidrich; Philipp Slusallek

1995-01-01T23:59:59.000Z

88

Inhibition of cell-cell binding by lipid assemblies  

DOE Patents (OSTI)

This invention relates generally to the field of therapeutic compounds designed to interfere between the binding of ligands and their receptors on cell surface. More specifically, it provides products and methods for inhibiting cell migration and activation using lipid assemblies with surface recognition elements that are specific for the receptors involved in cell migration and activation.

Nagy, Jon O. (Rodeo, CA); Bargatze, Robert F. (Bozeman, MT)

2001-05-22T23:59:59.000Z

89

AAAS Office of Opportunities in Science The Double Bind  

E-Print Network (OSTI)

of scientists regardless of race, ethnicity or gender. Conserving of their time and energies, they tackled. Science careers in the context of gender and race or ethnic bias have been a major part of our lives of biases related to both their race or ethnicity and gender, constituting a double bind. Programs

Ortiz, Christine

90

A Unitary Anesthetic Binding Site at High Resolution  

DOE Green Energy (OSTI)

Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABA{sub A} receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA{sub A} receptor, it will be necessary to use more tractable surrogates to probe the molecular details of anesthetic recognition. We have previously shown that recognition of inhalational general anesthetics by the model protein apoferritin closely mirrors recognition by more complex and clinically relevant protein targets; here we show that apoferritin also binds propofol and related GABAergic anesthetics, and that the same binding site mediates recognition of both inhalational and injectable anesthetics. Apoferritin binding affinities for a series of propofol analogs were found to be strongly correlated with the ability to potentiate GABA responses at GABA{sub A} receptors, validating this model system for injectable anesthetics. High resolution x-ray crystal structures reveal that, despite the presence of hydrogen bond donors and acceptors, anesthetic recognition is mediated largely by van der Waals forces and the hydrophobic effect. Molecular dynamics simulations indicate that the ligands undergo considerable fluctuations about their equilibrium positions. Finally, apoferritin displays both structural and dynamic responses to anesthetic binding, which may mimic changes elicited by anesthetics in physiologic targets like ion channels.

Vedula, L. Sangeetha; Brannigan, Grace; Economou, Nicoleta J.; Xi, Jin; Hall, Michael A.; Liu, Renyu; Rossi, Matthew J.; Dailey, William P.; Grasty, Kimberly C.; Klein, Michael L.; Eckenhoff, Roderic G.; Loll, Patrick J.; (Drexel-MED); (UPENN)

2009-10-21T23:59:59.000Z

91

A Unitary Anesthetic Binding Site at High Resolution  

DOE Green Energy (OSTI)

Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABA{sub A} receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA{sub A} receptor, it will be necessary to use more tractable surrogates to probe the molecular details of anesthetic recognition. We have previously shown that recognition of inhalational general anesthetics by the model protein apoferritin closely mirrors recognition by more complex and clinically relevant protein targets; here we show that apoferritin also binds propofol and related GABAergic anesthetics, and that the same binding site mediates recognition of both inhalational and injectable anesthetics. Apoferritin binding affinities for a series of propofol analogs were found to be strongly correlated with the ability to potentiate GABA responses at GABA{sub A} receptors, validating this model system for injectable anesthetics. High resolution x-ray crystal structures reveal that, despite the presence of hydrogen bond donors and acceptors, anesthetic recognition is mediated largely by van der Waals forces and the hydrophobic effect. Molecular dynamics simulations indicate that the ligands undergo considerable fluctuations about their equilibrium positions. Finally, apoferritin displays both structural and dynamic responses to anesthetic binding, which may mimic changes elicited by anesthetics in physiologic targets like ion channels.

L Vedula; G Brannigan; N Economou; J Xi; M Hall; R Liu; M Rossi; W Dailey; K Grasty; et. al.

2011-12-31T23:59:59.000Z

92

Methods of use of cellulose binding domain proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1997-09-23T23:59:59.000Z

93

Methods of detection using a cellulose binding domain fusion product  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 34 figs.

Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1999-01-05T23:59:59.000Z

94

PHYS 551 Lecture #27 Title: TightBinding  

E-Print Network (OSTI)

PHYS 551 Lecture #27 Title: Tight­Binding Now that we have shown that /( ~ k; ~r) = \\Gamma P ~ R e i ~ k \\Delta ~ R OE A (~r \\Gamma ~ R) satisfies the Bloch condition, all that remains is to grind the calculation explicitly. First, the wave­function /( ~ k; ~r) must be normalized. Thus Z / \\Lambda / dV = 1 = j

Winokur, Michael

95

Methods of use of cellulose binding domain proteins  

SciTech Connect

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1997-01-01T23:59:59.000Z

96

Nuclear deformation effect on the binding energies in heavy ions  

E-Print Network (OSTI)

Nuclear deformation effects on the binding energies in heavy ions are investigated. Approximate formulas for the nuclear-size correction and the isotope shift for deformed nuclei are derived. Combined with direct numerical evaluations, these formulas are employed to reanalyse experimental data on the nuclear-charge-distribution parameters in $^{238}\\textrm{U}$ and to revise the nuclear-size corrections to the binding energies in H- and Li-like $^{238}\\textrm{U}$. As a result, the theoretical uncertainties for the ground-state Lamb shift in $^{238}\\textrm{U}^{91+}$ and for the $2p_{1/2}-2s$ transition energy in $^{238}\\textrm{U}^{89+}$ are significantly reduced. The isotope shift of the $2p_{j}-2s$ transition energies for $^{142}\\textrm{Nd}^{57+}$ and $^{150}\\textrm{Nd}^{57+}$ is also evaluated including nuclear size and nuclear recoil effects within a full QED treatment.

Kozhedub, Y S; Shabaev, V M; Tupitsyn, I I; Brandau, C; Kozhuharov, C; Plunien, G; Sthlker, T

2007-01-01T23:59:59.000Z

97

Nuclear binding energies from a BPS Skyrme model  

E-Print Network (OSTI)

Recently, within the space of generalized Skyrme models, a BPS submodel was identified which reproduces some bulk properties of nuclear matter already on a classical level and, as such, constitutes a promising field theory candidate for the detailed and reliable description of nuclei and hadrons. Here we extend and further develop these investigations by applying the model to the calculation of nuclear binding energies. Concretely, we calculate these binding energies by including the classical soliton energies, the excitation energies from the collective coordinate quantization of spin and isospin, the electrostatic Coulomb energies and a small explicit isospin symmetry breaking, which accounts for the mass difference between proton and neutron. The integrability properties of the BPS Skyrme model allow, in fact, for an analytical calculation of all contributions, which may then be compared with the semi-empirical mass formula. We find that for heavier nuclei, where the model is expected to be more accurate o...

Adam, C; Sanchez-Guillen, J; Wereszczynski, A

2013-01-01T23:59:59.000Z

98

Reversible Acid Gas Capture Using CO2-Binding Organic Liquids  

SciTech Connect

Acid gas scrubbing technology is predominantly aqueous alkanolamine based. Of the acid gases, CO2, H2S and SO2 have been shown to be reversible, however there are serious disadvantages with corrosion and high regeneration costs. The primary scrubbing system composed of monoethanolamine is limited to 30% by weight because of the highly corrosive solution. This gravimetric limitation limits the CO2 volumetric (?108 g/L) and gravimetric capacity (?7 wt%) of the system. Furthermore the scrubbing system has a large energy penalty from pumping and heating the excess water required to dissolve the MEA bicarbonate salt. Considering the high specific heat of water (4 j/g-1K-1), low capacities and the high corrosion we set out to design a fully organic solvent that can chemically bind all acid gases i.e. CO2 as reversible alkylcarbonate ionic liquids or analogues thereof. Having a liquid acid gas carrier improves process economics because there is no need for excess solvent to pump and to heat. We have demonstrated illustrated in Figure 1, that CO2-binding organic liquids (CO2BOLs) have a high CO2 solubility paired with a much lower specific heat (<1.5 J/g-1K-1) than aqueous systems. CO2BOLs are a subsection of a larger class of materials known as Binding Organic Liquids (BOLs). Our BOLs have been shown to reversibly bind and release COS, CS2, and SO2, which we denote COSBOLS, CS2BOLs and SO2BOLs. Our BOLs are highly tunable and can be designed for post or pre-combustion gas capture. The design and testing of the next generation zwitterionic CO2BOLs and SO2BOLs are presented.

Heldebrant, David J.; Koech, Phillip K.; Yonker, Clement R.; Rainbolt, James E.; Zheng, Feng

2010-08-31T23:59:59.000Z

99

A hypothesis driven approach to condition specific transcription factor binding site characterization in S.c.  

Science Conference Proceedings (OSTI)

We demonstrate a computational process by which transcription factor binding sites can be elucidated using genome-wide expression and binding profiles. The profiles direct us to the intergenic locations likely to contain the promoter regions for a given ...

Rhonda Harrison; Charles DeLisi

2002-03-01T23:59:59.000Z

100

High-resolution DNA-binding specificity analysis of yeast transcription factors  

E-Print Network (OSTI)

Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of ...

Zhu, Cong

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

8: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote...

102

Transferable tight-binding parameters: An application to Ni and Ni-Al alloys  

Science Conference Proceedings (OSTI)

Two approaches for obtaining tight-binding parameters for metallic alloys are compared and contrasted with special regard for the application to large scale simulations such as may occur in tight-binding molecular dynamics studies.

Sluiter, M.H.F.; Singh, P.P.

1993-07-01T23:59:59.000Z

103

Thermodynamics and Kinetics of Carbon Dioxide Binding to Two Stereoisomers  

NLE Websites -- All DOE Office Websites (Extended Search)

Binding to Stereoisomers of a Cobalt(I) Macrocycle Binding to Stereoisomers of a Cobalt(I) Macrocycle Carol Creutz, Harold A. Schwarz, James F. Wishart, Etsuko Fujita and Norman Sutin J. Am. Chem. Soc. 113, 3361-3371 (1991) Abstract: The thermodynamics and kinetics of binding of CO2, CO, and H+ to N-racemic and N-meso stereoisomers of the cobalt(I) macrocycle CoL+ (L=5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-diene) have been determined in aqueous media with use of the pulse radiolysis technique and transient ultraviolet-visible spectroscopy. N-rac or N-meso-CoL+ was produced by the hydrated electron reduction of N-rac or N-meso-CoL2+, with tert-butyl alcohol generally added to scavenge hydroxyl radicals. Reactions of both N-rac- and N-meso CoL+ are readily followed by the disappearance of intense ([epsilon] 1 x 104 M-1 cm-1) absorption bands

104

Stereoselective Binding of Ruthenium Complexes to Cytochrome c  

NLE Websites -- All DOE Office Websites (Extended Search)

Site-Dependent Stereoselective Binding of Ruthenium Aquobipyridine Site-Dependent Stereoselective Binding of Ruthenium Aquobipyridine Complexes to Histidine Side Chains in Horse Heart Cytochrome c Jian Luo, James F. Wishart, and Stephan S. Isied J. Am. Chem. Soc. 120, 12970-12971 (1998) [Find paper at ACS Publications] Abstract: Stereoselective covalent binding of the ruthenium complexes cis-[Ru(bpy)2(H2O)2]2+ (bpy = 2,2'-bipyridine) and cis-[Ru(dmbpy)2(H2O)2]2+ (dmbpy = 4,4'-dimethyl-2,2'-bipyridine) to the surface His 33 residue and the more buried His 26 residues of Horse heart cytochrome c (Hh cyt c) to form large enantiomeric excess of D-[Ru(dmbpy)2(H2O)]-His 26-cyt c (38%), but little or no excess of D-[Ru(bpy)2(H2O)]-His 26-cyt c (6%). At the surface exposed His 33 site, equal entiomeric excess of L-[Ru(dmbpy)2(H2O)]-His 33-cyt c and L-[Ru(bpy)2(H2O)]-His 33-cyt c (34%)

105

Angiotensin receptor binding and pressor effects in cat subretrofacial nucleus  

SciTech Connect

Central administration of angiotensin II (ANG II) increases arterial blood pressure via increased sympathetic activity. The authors have examined the possibility that one site of action of ANG II is the subretrofacial (SRF) nucleus in the rostral ventrolateral medulla, since this nucleus is known to play a critical role in the tonic and phasic control of arterial pressure. In vitro autoradiography, employing {sup 125}I-labeled (Sar{sup 1}, Ile{sup 8})ANG II as radioligand, was used to localize binding sites for ANG-II in the cat ventrolateral medulla. A high density of ANG II-receptor binding sites was found confined to the SRF nucleus. In a second group of experiments in anesthetized cats, microinjections of ANG II, in doses ranging from 10 to 50 pmol, were made into histologically identified sites within and outside the SRF nucleus. Microinjections into the nucleus resulted in a dose-dependent increase in arterial pressure, which was abolished by systemic administration of the ganglion-blocking drug hexamethonium bromide. In contrast, microinjections just outside the SRF nucleus had no effect on arterial pressure. It is concluded that activation of ANG II-receptor binding sites within the SRF nucleus leads to an increase in arterial pressure via increased sympathetic efferent activity.

Allen, A.M.; Dampney, R.A.L.; Mendelsohn, F.A.O. (Univ. of Melbourne (Australia) Univ. of Sydney (Australia))

1988-11-01T23:59:59.000Z

106

Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Danzhi Huang and Amedeo Caflisch*  

E-Print Network (OSTI)

Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation Danzhi Huang of the absolute free energy of binding. A predictive accuracy of about 1.0 kcal/mol is obtained for 13 and 29 into proteins of known structure require fast and accurate methods for the evaluation of binding free energies.1

Caflisch, Amedeo

107

Theory of Free Energy and Entropy in Noncovalent Binding Huan-Xiang Zhou*,  

E-Print Network (OSTI)

Theory of Free Energy and Entropy in Noncovalent Binding Huan-Xiang Zhou*, and Michael K. Gilson, Rockville, Maryland 20850 Received December 23, 2008 Contents 1. Introduction 4092 2. Free Energy, Partition.4. Solvation and a Temperature-Dependent Energy Function 4096 3. Binding Free Energy and Binding Constant 4096

Weston, Ken

108

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)  

E-Print Network (OSTI)

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method are described to predict the free energies of binding of a series of anaesthetic drugs to a recently. The correlation coefficient between computed and measured binding free energies is 70% with high statistical

109

Computational Investigation of Glycosylation Effects on a Family 1 Carbohydrate-Binding Module  

DOE Green Energy (OSTI)

Carbohydrate-binding modules (CBMs) are ubiquitous components of glycoside hydrolases, which degrade polysaccharides in nature. CBMs target specific polysaccharides, and CBM binding affinity to cellulose is known to be proportional to cellulase activity, such that increasing binding affinity is an important component of performance improvement. To ascertain the impact of protein and glycan engineering on CBM binding, we use molecular simulation to quantify cellulose binding of a natively glycosylated Family 1 CBM. To validate our approach, we first examine aromatic-carbohydrate interactions on binding, and our predictions are consistent with previous experiments, showing that a tyrosine to tryptophan mutation yields a 2-fold improvement in binding affinity. We then demonstrate that enhanced binding of 3-6-fold over a nonglycosylated CBM is achieved by the addition of a single, native mannose or a mannose dimer, respectively, which has not been considered previously. Furthermore, we show that the addition of a single, artificial glycan on the anterior of the CBM, with the native, posterior glycans also present, can have a dramatic impact on binding affinity in our model, increasing it up to 140-fold relative to the nonglycosylated CBM. These results suggest new directions in protein engineering, in that modifying glycosylation patterns via heterologous expression, manipulation of culture conditions, or introduction of artificial glycosylation sites, can alter CBM binding affinity to carbohydrates and may thus be a general strategy to enhance cellulase performance. Our results also suggest that CBM binding studies should consider the effects of glycosylation on binding and function.

Taylor, C. B.; Talib, M. F.; McCabe, C.; Bu, L.; Adney, W. S.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T.

2012-01-27T23:59:59.000Z

110

Reversibly Bound Chloride in the Atrial Natriuretic Peptide Receptor Hormone Binding Domain: Possible Allosteric Regulation and a Conserved Structural Motif for the Chloride-binding Site  

SciTech Connect

The binding of atrial natriuretic peptide (ANP) to its receptor requires chloride, and it is chloride concentration dependent. The extracellular domain (ECD) of the ANP receptor (ANPR) contains a chloride near the ANP-binding site, suggesting a possible regulatory role. The bound chloride, however, is completely buried in the polypeptide fold, and its functional role has remained unclear. Here, we have confirmed that chloride is necessary for ANP binding to the recombinant ECD or the full-length ANPR expressed in CHO cells. ECD without chloride (ECD(-)) did not bind ANP. Its binding activity was fully restored by bromide or chloride addition. A new X-ray structure of the bromide-bound ECD is essentially identical to that of the chloride-bound ECD. Furthermore, bromide atoms are localized at the same positions as chloride atoms both in the apo and in the ANP-bound structures, indicating exchangeable and reversible halide binding. Far-UV CD and thermal unfolding data show that ECD(-) largely retains the native structure. Sedimentation equilibrium in the absence of chloride shows that ECD(-) forms a strongly associated dimer, possibly preventing the structural rearrangement of the two monomers that is necessary for ANP binding. The primary and tertiary structures of the chloride-binding site in ANPR are highly conserved among receptor-guanylate cyclases and metabotropic glutamate receptors. The chloride-dependent ANP binding, reversible chloride binding, and the highly conserved chloride-binding site motif suggest a regulatory role for the receptor bound chloride. Chloride-dependent regulation of ANPR may operate in the kidney, modulating ANP-induced natriuresis.

Ogawa, H.; Qiu, Y; Philo, J; Arakawa, T; Ogata, C; Misono, K

2010-01-01T23:59:59.000Z

111

Tight-binding model for hydrogen-silicon interactions  

SciTech Connect

We have developed an empirical tight-binding model for use in molecular-dynamics simulations to study hydrogen-silicon systems. The hydrogen-silicon interaction is constructed to reproduce the electronic energy levels and vibration frequencies of silane (SiH{sub 4}). Further use of the model in the studies of disilane (Si{sub 2}H{sub 6}) and of hydrogen on the Si(111) surface also yields results in good agreement with first-principles calculations and experiments.

Min, B.J.; Lee, Y.H.; Wang, C.Z.; Chan, C.T.; Ho, K.M. (Microelectronics Research Center, Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States) Department of Physics and Astronomy, Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States))

1992-03-15T23:59:59.000Z

112

PHYS 551 Lecture #27 Title: Tight-Binding  

E-Print Network (OSTI)

PHYS 551 Lecture #27 Title: Tight-Binding Now that we have shown that (~k;~r) = P ~R ei~k~RA(~r ~R-function (~k;~r) must be normalized. Thus Z dV = 1 = j j2 X R X R0 ei~k~R ~R0 Z A(~r ~R0)A(~r ~R)dV Now for each ~R0, the sum over ~R must be the same since the crystal has the same distribution of neighbors

Winokur, Michael

113

Crystal Structure of the Chromodomain Helicase DNA-binding Protein 1 (Chd1) DNA-binding Domain in Complex with DNA  

Science Conference Proceedings (OSTI)

Chromatin remodelers are ATP-dependent machines that dynamically alter the chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. The structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet the details of how Chd1 recognized DNA were not known. Here we present the crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in complex with a DNA duplex. The bound DNA duplex is straight, consistent with the preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. Comparison of this structure with the recently solved ISW1a DNA-binding domain bound to DNA reveals that DNA lays across each protein at a distinct angle, yet contacts similar surfaces on the SANT and SLIDE domains. In contrast to the minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of the Chd1 DNA-binding domain contacts the DNA major groove. The majority of direct contacts with the phosphate backbone occur only on one DNA strand, suggesting that Chd1 may not strongly discriminate between major and minor grooves.

Sharma A.; Heroux A.; Jenkins K. R.; Bowman G. D.

2011-12-09T23:59:59.000Z

114

Relativistic Nuclear Energy Density Functionals: adjusting parameters to binding energies  

E-Print Network (OSTI)

We study a particular class of relativistic nuclear energy density functionals in which only nucleon degrees of freedom are explicitly used in the construction of effective interaction terms. Short-distance (high-momentum) correlations, as well as intermediate and long-range dynamics, are encoded in the medium (nucleon density) dependence of the strength functionals of an effective interaction Lagrangian. Guided by the density dependence of microscopic nucleon self-energies in nuclear matter, a phenomenological ansatz for the density-dependent coupling functionals is accurately determined in self-consistent mean-field calculations of binding energies of a large set of axially deformed nuclei. The relationship between the nuclear matter volume, surface and symmetry energies, and the corresponding predictions for nuclear masses is analyzed in detail. The resulting best-fit parametrization of the nuclear energy density functional is further tested in calculations of properties of spherical and deformed medium-heavy and heavy nuclei, including binding energies, charge radii, deformation parameters, neutron skin thickness, and excitation energies of giant multipole resonances.

T. Niksic; D. Vretenar; P. Ring

2008-09-08T23:59:59.000Z

115

Defining How Botulinum Toxin Binds to the Synaptotagmin Receptor and  

NLE Websites -- All DOE Office Websites (Extended Search)

Defining How Botulinum Toxin Binds to Defining How Botulinum Toxin Binds to the Synaptotagmin Receptor and Creating Improved Therapeutics to Block Toxicity Botulinum neurotoxin (BoNT), the most potent toxin known, induces a potentially fatal paralytic condition known as "botulism". Botulism can occur when toxin-producing bacteria infect wounds (wound botulism) or the intestinal tract (infant/intestinal botulism), or following the ingestion of contaminated food in which toxin has been produced (food-borne botulism). In the USA, infant botulism represents the most common manifestation of the disease, where its prevalence has led to speculation of a link to sudden infant death syndrome. BoNTs are subdivided into seven distinct serotypes (types A through G), and an increasingly large number of subtypes continue to be identified within each serotype, highlighting the need to produce broad-spectrum therapeutics. BoNT variants are an important biochemical set of tools for understanding nerve function, and important therapeutic agents in current clinical use to provide relief to patients with a wide spectrum of neurological disorders.

116

Dendroaspis natriuretic peptide binds to the natriuretic peptide clearance receptor  

SciTech Connect

Dendroaspis natriuretic peptide (DNP) is a newly-described natriuretic peptide which lowers blood pressure via vasodilation. The natriuretic peptide clearance receptor (NPR-C) removes natriuretic peptides from the circulation, but whether DNP interacts with human NPR-C directly is unknown. The purpose of this study was to test the hypothesis that DNP binds to NPR-C. ANP, BNP, CNP, and the NPR-C ligands AP-811 and cANP(4-23) displaced [{sup 125}I]-ANP from NPR-C with pM-to-nM K {sub i} values. DNP displaced [{sup 125}I]-ANP from NPR-C with nM potency, which represents the first direct demonstration of binding of DNP to human NPR-C. DNP showed high pM affinity for the GC-A receptor and no affinity for GC-B (K {sub i} > 1000 nM). DNP was nearly 10-fold more potent than ANP at stimulating cGMP production in GC-A expressing cells. Blockade of NPR-C might represent a novel therapeutic approach in augmenting the known beneficial actions of DNP in cardiovascular diseases such as hypertension and heart failure.

Johns, Douglas G. [Vascular Biology and Thrombosis Department, Cardiovascular and Urogenital Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States)]. E-mail: Douglas.G.Johns@gsk.com; Ao, Zhaohui [Vascular Biology and Thrombosis Department, Cardiovascular and Urogenital Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Heidrich, Bradley J. [Vascular Biology and Thrombosis Department, Cardiovascular and Urogenital Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Hunsberger, Gerald E. [Respiratory and Inflammatory Diseases Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Graham, Taylor [Gene Expression and Protein Biochemistry, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Payne, Lisa [Gene Expression and Protein Biochemistry, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Elshourbagy, Nabil [Gene Expression and Protein Biochemistry, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Lu, Quinn [Gene Expression and Protein Biochemistry, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Aiyar, Nambi [Vascular Biology and Thrombosis Department, Cardiovascular and Urogenital Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Douglas, Stephen A. [Vascular Biology and Thrombosis Department, Cardiovascular and Urogenital Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States)

2007-06-22T23:59:59.000Z

117

Structure, Function, and Evolution of Biogenic Amine-binding Proteins in Soft Ticks  

Science Conference Proceedings (OSTI)

Two highly abundant lipocalins, monomine and monotonin, have been isolated from the salivary gland of the soft tick Argas monolakensis and shown to bind histamine and 5-hydroxytryptamine (5-HT), respectively. The crystal structures of monomine and a paralog of monotonin were determined in the presence of ligands to compare the determinants of ligand binding. Both the structures and binding measurements indicate that the proteins have a single binding site rather than the two sites previously described for the female-specific histamine-binding protein (FS-HBP), the histamine-binding lipocalin of the tick Rhipicephalus appendiculatus. The binding sites of monomine and monotonin are similar to the lower, low affinity site of FS-HBP. The interaction of the protein with the aliphatic amine group of the ligand is very similar for the all of the proteins, whereas specificity is determined by interactions with the aromatic portion of the ligand. Interestingly, protein interaction with the imidazole ring of histamine differs significantly between the low affinity binding site of FS-HBP and monomine, suggesting that histamine binding has evolved independently in the two lineages. From the conserved features of these proteins, a tick lipocalin biogenic amine-binding motif could be derived that was used to predict biogenic amine-binding function in other tick lipocalins. Heterologous expression of genes from salivary gland libraries led to the discovery of biogenic amine-binding proteins in soft (Ornithodoros) and hard (Ixodes) tick genera. The data generated were used to reconstruct the most probable evolutionary pathway for the evolution of biogenic amine-binding in tick lipocalins.

Mans, Ben J.; Ribeiro, Jose M.C.; Andersen, John F. (NIH)

2008-08-19T23:59:59.000Z

118

In Vitro Evolution of a Peptide with a Hematite Binding Motif That May Constitute a Natural Metal-Oxide Binding Archetype  

DOE Green Energy (OSTI)

Phage-display technology was used to evolve peptides that selectively bind to the metal-oxide hematite (Fe2O3) from a library of approximately 3 billion different polypeptides. The sequences of these peptides contained the highly conserved amino acid motif, Ser/Thr-hydrophobic/aromatic-Ser/Thr-Pro-Ser/Thr. To better understand the nature of the peptide?metal oxide binding demonstrated by these experiments, molecular dynamics simulations were carried out for Ser-Pro-Ser at a hematite surface. These simulations show that hydrogen bonding occurs between the two serine amino acids and the hydroxylated hematite surface and that the presence of proline between the hydroxide residues restricts the peptide flexibility, thereby inducing a structural-binding motif. A search of published sequence data revealed that the binding motif (Ser/Thr-Pro-Ser/Thr) is adjacent to the terminal heme-binding domain of both OmcA and MtrC, which are outer membrane cytochromes from the metal-reducing bacterium Shewanella oneidensis MR-1. The entire five amino acid consensus sequence (Ser/Thr-hydrophobic/aromatic-Ser/Thr-Pro-Ser/Thr) was also found as multiple copies in the primary sequences of metal-oxide binding proteins Sil1 and Sil2 from Thalassiosira pseudonana. We suggest that this motif constitutes a natural metal-oxide binding archetype that could be exploited in enzyme-based biofuel cell design and approaches to synthesize tailored metal-oxide nanostructures.

Lower, Brian H.; Lins, Roberto D.; Oestreicher, Zachery W.; Straatsma, TP; Hochella Jr., Michael F.; Shi, Liang; Lower, Steven

2008-05-15T23:59:59.000Z

119

On the nuclear interaction. Potential, binding energy and fusion reaction  

E-Print Network (OSTI)

The nuclear interaction is responsible for keeping neutrons and protons joined in an atomic nucleus. Phenomenological nuclear potentials, fitted to experimental data, allow one to know about the nuclear behaviour with more or less success where quantum mechanics is hard to be used. A nuclear potential is suggested and an expression for the potential energy of two nuclear entities, either nuclei or nucleons, is developed. In order to estimate parameters in this expression, some nucleon additions to nuclei are considered and a model is suggested as a guide of the addition process. Coulomb barrier and energy for the addition of a proton to each one of several nuclei are estimated by taking into account both the nuclear and electrostatic components of energy. Studies on the binding energies of several nuclei and on the fusion reaction of two nuclei are carried out.

I. Casinos

2008-05-22T23:59:59.000Z

120

On the nuclear interaction. Potential, binding energy and fusion reaction  

E-Print Network (OSTI)

The nuclear interaction is responsible for keeping neutrons and protons joined in an atomic nucleus. Phenomenological nuclear potentials, fitted to experimental data, allow one to know about the nuclear behaviour with more or less success where quantum mechanics is hard to be used. A nuclear potential is suggested and an expression for the potential energy of two nuclear entities, either nuclei or nucleons, is developed. In order to estimate parameters in this expression, some nucleon additions to nuclei are considered and a model is suggested as a guide of the addition process. Coulomb barrier and energy for the addition of a proton to each one of several nuclei are estimated by taking into account both the nuclear and electrostatic components of energy. Studies on the binding energies of several nuclei and on the fusion reaction of two nuclei are carried out.

Casinos, I

2008-01-01T23:59:59.000Z

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121

Does nuclear matter bind at large $N_c$?  

E-Print Network (OSTI)

The existence of nuclear matter at large $N_c$ is investigated in the framework of effective hadronic models of the Walecka type. This issue is strongly related to the nucleon-nucleon attraction in the scalar channel, and thus to the nature of the light scalar mesons. Different scenarios for the light scalar sector correspond to different large $N_c$ scaling properties of the parameters of the hadronic models. In all realistic phenomenological scenarios for the light scalar field(s) responsible for the attraction in the scalar channel it is found that nuclear matter does not bind in the large $N_c$ world. We thus conclude that $N_c = 3$ is in this respect special: 3 is fortunately not large at all and allows for nuclear matter, while large $N_c$ would not.

Bonanno, Luca

2011-01-01T23:59:59.000Z

122

Unveiling Residual Molecular Binding in Triply Charged Hydrogen Bromide  

Science Conference Proceedings (OSTI)

We present an experimental and theoretical study of triply charged hydrogen bromide ions formed by photoionization of the inner 3d shell of Br. The experimental results, obtained by detecting the 3d photoelectron in coincidence with the two subsequent Auger electrons, are analyzed using calculated potential energy curves of HBr{sup 3+}. The competition between the short-range chemical binding potential and the Coulomb repulsion in the dissociative process is shown. Two different mechanisms are observed for double Auger decay: one, a direct process with simultaneous ejection of two Auger electrons to final HBr{sup 3+} ionic states and the other, a cascade process involving double Auger decay characterized by the autoionization of Br*{sup +} ion subsequent to the HBr{sup 2+} fragmentation.

Penent, F.; Lablanquie, P.; Palaudoux, J.; Gamblin, G.; Carniato, S. [UPMC, Universite Paris 06, LCPMR, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France)] [CNRS, LCPMR (UMR 7614), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Andric, L. [UPMC, Universite Paris 06, LCPMR, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France)] [CNRS, LCPMR (UMR 7614), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France)] [Universite Paris-Est, 5 boulevard Descartes, 77454 Marne-la-Vallee Cedex 2 (France); Hikosaka, Y. [Department of Environmental Science, Niigata University, Niigata 950-2181 (Japan); Ito, K. [Photon Factory, Institute of Materials Structure Science, Oho, Tsukuba 305-0801 (Japan)

2011-03-11T23:59:59.000Z

123

Characterization of Selective Binding of Alkali Cations with Carboxylate  

NLE Websites -- All DOE Office Websites (Extended Search)

Characterization of Selective Characterization of Selective Binding of Alkali Cations with Carboxylate Characterization of Selective Binding of Alkali Cations with Carboxylate Print Wednesday, 24 September 2008 00:00 During its lifetime, a cell spends a considerable fraction of its energy pumping sodium and calcium out and potassium in. This balancing process is similar to that found in the coils of the DNA double helix, where specific ions nestle and help stabilize this macromolecule. These are only two examples of selective ion interactions in biology; there are many others also vital to life. The existence of these interactions has been known since the early 20th century, when Franz Hofmeister observed that some salts (ionic compounds) aided the solution of proteins in egg, some caused proteins to destabilize and precipitate, and others ranged in activity between the two extremes. Hofmeister then ranked "salt-out" (destabilizing) ions versus "salt-in" (stabilizing) ions according to the magnitude of their effects (the "Hofmeister effects"). However, despite enormous effort, why certain interactions are preferred over others is not completely understood. Recently, a team of researchers from UC Berkeley used the model systems of acetate and formate (two simple carboxylic acids) with a series of cations to test predictions made in the literature for preferential interactions. Near-edge x-ray absorption fine structure (NEXAFS) spectroscopy was used as this technique is highly sensitive to the chemical environments around a molecule. Experiments at ALS Beamline 8.0.1 confirmed strengthening of the interaction between the cations and the carboxylate group in the following order: potassium, sodium, and lithium.

124

A = 4 0/sup +/ - 1/sup +/ binding-energy difference  

DOE Green Energy (OSTI)

The A = 4 ..lambda..-hypernuclei provide a rich source of information about the s-wave properties of the fundamental hyperon-nucleon (YN) force as well as offer a unique opportunity to investigate the complications that arise in calculations of the properties of bound systems in which one baryon (here the ..lambda..) with a given isospin couples strongly to another (the ..sigma..) with a different isospin. The ..lambda../sup 4/H - ..lambda../sup 4/He isodoublet ground-state energies are not consistent with a charge symmetry hypothesis for the YN interaction. The (spin-flip) excitation energies are quite sensitive to the ..lambda..N - ..sigma..N coupling of the YN interaction. In particular, when one represents the free YN interaction in terms of one-channel effective ..lambda..N potentials, the resulting 0/sup +/ (ground) state and 1/sup +/ (excited) spin-flip state are inversely ordered in terms of binding energies, the 1/sup +/ state being more bound. It is the ..sigma.. suppression that results from the reduced strength of the ..lambda..N - ..sigma..N off-diagonal coupling potential when the trinucleon core is restricted to isospin-1/2 which we study here. We find this spin-isospin suppression of the ..lambda..-..sigma.. conversion, which is due to the composite nature of the nuclear cores of the ..lambda../sup 4/H and ..lambda../sup 4/He hypernuclei, to be a significant factor in understanding the 0/sup +/ - 1 /sup +/ binding energy relationship.

Gibson, B.F.; Lehman, D.R.

1982-01-01T23:59:59.000Z

125

Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl Complexes with Glutarimidedioxime  

E-Print Network (OSTI)

data_request/cif. OECD, Uranium 2009: Resources, Productionthermodynamics of uranium, (H. Wanner and I. Forest,of California. Sequestering uranium from seawater: binding

Tian, Guoxin

2013-01-01T23:59:59.000Z

126

Functional characterization of acyl-CoA binding protein (ACBP) and oxysterol binding protein-related proteins (ORPS) from Cryptosporidium parvum.  

E-Print Network (OSTI)

??From opportunistic protist Cryptosporidium parvum we identified and functionally assayed a fatty acyl-CoA-binding protein (ACBP) gene. The CpACBP1 gene encodes a protein of 268 aa (more)

Zeng, Bin

2009-01-01T23:59:59.000Z

127

Using pre & post-processing methods to improve binding site predictions  

Science Conference Proceedings (OSTI)

Currently the best algorithms for transcription factor binding site prediction within sequences of regulatory DNA are severely limited in accuracy. In this paper, we integrate 12 original binding site prediction algorithms, and use a 'window' of consecutive ... Keywords: Feature selection, Filters, Support vector machines, Tomek link, Transcription factors

Yi Sun; Cristina Gonzlez Castellano; Mark Robinson; Rod Adams; Alistair G. Rust; Neil Davey

2009-09-01T23:59:59.000Z

128

Influence of transmembrane potential differences of renal tubular epithelial cell on ANG II binding  

SciTech Connect

Previous studies from this laboratory demonstrated specific high-affinity binding sites of rat renal brush-border membrane vesicles (BBMV). The time course of angiotensin II ((/sup 125/I) ANG II) binding in the presence of a NaCl gradient demonstrated an overshoot characteristic of electrogenic sodium-dependent d-(/sup 14/C) glucose uptake. The time course of ANG II binding to membrane vesicles equilibrated with NaCl did not exhibit such overshoot and was lower in magnitude. Therefore, studies were designed to test the hypothesis that ANG II binding to BBMV was enhanced by a transmembrane potential difference in a manner similar to sodium-dependent D-glucose uptake. The effects of sodium salts with differing rates of anion equilibration were compared on ANG II binding. ANG II binding in the presence of a KCl gradient was similar to NaCl. The overshoot was abolished in the presence of an inwardly directed KCl gradient plus valinomycin. Magnesium salts with differing rates of anion permeabilities had similar effects on binding, as did sodium salts. Scatchard analysis revealed that the receptor density was fourfold higher in the presence of an electrochemical gradient compared with nongradient conditions. These data are consistent with the conclusion that ANG II binding to BBMV is enhanced by a transmembrane potential difference, and suggest that this may be an important modulator of tubular epithelial responses to ANG II in vivo.

Brown, G.P.; Douglas, J.G.

1987-02-01T23:59:59.000Z

129

Distinct p53 genomic binding patterns in normal and cancer-derived human cells  

Science Conference Proceedings (OSTI)

We report here genome-wide analysis of the tumor suppressor p53 binding sites in normal human cells. 743 high-confidence ChIP-seq peaks representing putative genomic binding sites were identified in normal IMR90 fibroblasts using a reference chromatin sample. More than 40% were located within 2 kb of a transcription start site (TSS), a distribution similar to that documented for individually studied, functional p53 binding sites and, to date, not observed by previous p53 genome-wide studies. Nearly half of the high-confidence binding sites in the IMR90 cells reside in CpG islands, in marked contrast to sites reported in cancer-derived cells. The distinct genomic features of the IMR90 binding sites do not reflect a distinct preference for specific sequences, since the de novo developed p53 motif based on our study is similar to those reported by genome-wide studies of cancer cells. More likely, the different chromatin landscape in normal, compared with cancer-derived cells, influences p53 binding via modulating availability of the sites. We compared the IMR90 ChIPseq peaks to the recently published IMR90 methylome1 and demonstrated that they are enriched at hypomethylated DNA. Our study represents the first genome-wide, de novo mapping of p53 binding sites in normal human cells and reveals that p53 binding sites reside in distinct genomic landscapes in normal and cancer-derived human cells.

Botcheva K.; McCorkle S. R.; McCombie W. R.; Dunn J. J.; Anderson C. W.

2011-12-15T23:59:59.000Z

130

A new approach to the assessment of the quality of predictions of transcription factor binding sites  

Science Conference Proceedings (OSTI)

In this paper, we describe a novel method called Secondary Verification which assesses the quality of predictions of transcription factor binding sites. This method incorporates a distribution of prediction scores over positive examples (i.e. the actual ... Keywords: Mixture of PSSMs, Model assessment, Modeling dependencies, Motif finding, Predicting binding sites, Statistical significance

Szymon Nowakowski; Jerzy Tiuryn

2007-04-01T23:59:59.000Z

131

Paul D. Boyer, Adenosine Triphosphate (ATP), and the Binding Change  

Office of Scientific and Technical Information (OSTI)

Paul D. Boyer, Adenosine Triphosphate (ATP), and the Binding Change Mechanism Resources with Additional Information Paul D. Boyer Courtesy of UCLA 'For Paul Boyer, the Nobel Prize was "an unexpected pleasure." It had been 20 years since he formulated a hypothesis to describe what he calls "the most prominent chemical reaction in the whole world." It is the process by which molecules produce ATP (adenosine triphosphate), thereby transmuting light, air, water and food into the energy required for both plant and animal life. Boyer had been greeted with disbelief when he theorized that the previously mysterious process is the work of a "beautiful little machine" that operates within enzymes on the molecular level. ... Boyer experienced "one of the warmest moments of my life" when he learned that British biochemist John Walker had worked out the methodology required to demonstrate whether Boyer had been right or wrong. ... Using Walker's methodology, one of Boyer's former graduate students "did some elegant chemical work to demonstrate that the molecular rotation actually occurred." Boyer's hypothesis, finally, had been proven correct. For work that so enriched understanding of the life process itself, he and Walker were jointly awarded the Nobel prize [in Chemistry] in 1997.'

132

Structural basis of substrate discrimination and integrin binding by autotaxin  

SciTech Connect

Autotaxin (ATX, also known as ectonucleotide pyrophosphatase/phosphodiesterase-2, ENPP2) is a secreted lysophospholipase D that generates the lipid mediator lysophosphatidic acid (LPA), a mitogen and chemoattractant for many cell types. ATX-LPA signaling is involved in various pathologies including tumor progression and inflammation. However, the molecular basis of substrate recognition and catalysis by ATX and the mechanism by which it interacts with target cells are unclear. Here, we present the crystal structure of ATX, alone and in complex with a small-molecule inhibitor. We have identified a hydrophobic lipid-binding pocket and mapped key residues for catalysis and selection between nucleotide and phospholipid substrates. We have shown that ATX interacts with cell-surface integrins through its N-terminal somatomedin B-like domains, using an atypical mechanism. Our results define determinants of substrate discrimination by the ENPP family, suggest how ATX promotes localized LPA signaling and suggest new approaches for targeting ATX with small-molecule therapeutic agents.

Hausmann, Jens; Kamtekar, Satwik; Christodoulou, Evangelos; Day, Jacqueline E.; Wu, Tao; Fulkerson, Zachary; Albers, Harald M.H.G.; van Meeteren, Laurens A.; Houben, Anna J.S.; van Zeijl, Leonie; Jansen, Silvia; Andries, Maria; Hall, Troii; Pegg, Lyle E.; Benson, Timothy E.; Kasiem, Mobien; Harlos, Karl; Vander Kooi, Craig W.; Smyth, Susan S.; Ovaa, Huib; Bollen, Mathieu; Morris, Andrew J.; Moolenaar, Wouter H.; Perrakis, Anastassis (Pfizer); (Leuven); (Oxford); (NCI-Netherlands); (Kentucky)

2013-09-25T23:59:59.000Z

133

Position specific variation in the rate of evolution intranscription factor binding sites  

SciTech Connect

The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational methods have been developed to characterize transcription factor binding sites, they remain difficult to identify. Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution. Here we analyze the genome sequences of the budding yeasts Saccharomyces cerevisiae, S. bayanus, S. paradoxus and S. mikataeto study the evolution of transcription factor binding sites. As expected, we find that both experimentally characterized and computationally predicted binding sites evolve slower than surrounding sequence, consistent with the hypothesis that they are under purifying selection. We also observe position-specific variation in the rate of evolution within binding sites. We find that the position-specific rate of evolution is positively correlated with degeneracy among binding sites within S. cerevisiae. We test theoretical predictions for the rate of evolution at positions where the base frequencies deviate from background due to purifying selection and find reasonable agreement with the observed rates of evolution. Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artifacts of computational motif finding algorithms. As has been observed for protein sequences, the rate of evolution in transcription factor binding sites varies with position, suggesting that some regions are under stronger functional constraint than others. This variation likely reflects the varying importance of different positions in the formation of the protein-DNA complex. The characterization of the pattern of evolution in known binding sites will likely contribute to the effective use of comparative sequence data in the identification of transcription factor binding sites and is an important step toward understanding the evolution of functional non-coding DNA.

Moses, Alan M.; Chiang, Derek Y.; Kellis, Manolis; Lander, EricS.; Eisen, Michael B.

2003-08-28T23:59:59.000Z

134

Alterations in transcription factor binding in radioresistant human melanoma cells after ionizing radiation  

Science Conference Proceedings (OSTI)

We analyzed alterations in transcription factor binding to specific, known promoter DNA consensus sequences between irradiated and unirradiated radioresistant human melanoma (U1-Mel) cells. The goal of this study was to begin to investigate which transcription factors and DNA-binding sites are responsible for the induction of specific transcripts and proteins after ionizing radiation. Transcription factor binding was observed using DNA band-shift assays and oligonucleotide competition analyses. Confluence-arrested U1-Mel cells were irradiated (4.5 Gy) and harvested at 4 h. Double-stranded oligonucleotides containing known DNA-binding consensus sites for specific transcription factors were used. Increased DNA binding activity after ionizing radiation was noted with oligonucleotides containing the CREB, NF-kB and Sp1 consensus sites. No changes in protein binding to AP-1, AP-2, AP-3, or CTF/NF1, GRE or Oct-1 consensus sequences were noted. X-ray activation of select transcription factors, which bind certain consensus sites in promoters, may cause specific induction or repression of gene transcription. 22 refs., 2 figs.

Sahijdak, W.M.; Yang, Chin-Rang; Zuckerman, J.S.; Meyers, M.; Boothman, D.A. [Univ. of Wisconsin, Madison, WI (United States)

1994-04-01T23:59:59.000Z

135

Optimal register-type selection during resource binding in flip-flop/latch-based high-level synthesis  

Science Conference Proceedings (OSTI)

Flip-flop (FF)/latch-based design has advantages on such as area and power compared to single register-type design (only FFs or latches). Considering FF/latch-based design at high-level synthesis is necessary, because resource binding process significantly ... Keywords: FU binding, register binding, register-type selection

Keisuke Inoue; Mineo Kaneko

2012-05-01T23:59:59.000Z

136

Identifying Calcium-Binding Sites with Oxygen-Carbon Shell Geometric and Chemic Criteria-A Graph-Based Approach  

Science Conference Proceedings (OSTI)

Identifying calcium-binding sites in proteins help acknowledge protein functions. We thus developed a graph theory and geometry approach to improve the accuracy for predicting calcium-binding sites, we enhance our previous approach at a high level to ... Keywords: calcium-binding sites, graph theory, maximal cliques, prediction

Hui Liu; Hai Deng

2008-11-01T23:59:59.000Z

137

Mercury Binding Sites in Thiol-Functionalized Mesostructured Silica  

SciTech Connect

Thiol-functionalized mesostructured silica with anhydrous compositions of (SiO{sub 2}){sub 1-x}(LSiO{sub 1.5}){sub x}, where L is a mercaptopropyl group and x is the fraction of functionalized framework silicon centers, are effective trapping agents for the removal of mercuric(II) ions from water. In the present work, we investigate the mercury-binding mechanism for representative thiol-functionalized mesostructures by atomic pair distribution function (PDF) analysis of synchrotron X-ray powder diffraction data and by Raman spectroscopy. The mesostructures with wormhole framework structures and compositions corresponding to x = 0.30 and 0.50 were prepared by direct assembly methods in the presence of a structure-directing amine porogen. PDF analyses of five mercury-loaded compositions with Hg/S ratios of 0.50-1.30 provided evidence for the bridging of thiolate sulfur atoms to two metal ion centers and the formation of chain structures on the pore surfaces. We find no evidence for Hg-O bonds and can rule out oxygen coordination of the mercury at greater than the 10% level. The relative intensities of the PDF peaks corresponding to Hg-S and Hg-Hg atomic pairs indicate that the mercury centers cluster on the functionalized surfaces by virtue of thiolate bridging, regardless of the overall mercury loading. However, the Raman results indicate that the complexation of mercury centers by thiolate depends on the mercury loading. At low mercury loadings (Hg/S {le} 0.5), the dominant species is an electrically neutral complex in which mercury most likely is tetrahedrally coordinated to bridging thiolate ligands, as in Hg(SBu{sup t}){sub 2}. At higher loadings (Hg/S 1.0-1.3), mercury complex cations predominate, as evidenced by the presence of charge-balancing anions (nitrate) on the surface. This cationic form of bound mercury is assigned a linear coordination to two bridging thiolate ligands.

Billinge, Simon J.L.; McKimmey, Emily J.; Shatnawi, Mouath; Kim, HyunJeong; Petkov, Valeri; Wermeille, Didier; Pinnavaia, Thomas J. (MSU); (CMU); (Iowa State)

2010-07-13T23:59:59.000Z

138

V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

8: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw 8: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code December 31, 2012 - 6:58am Addthis PROBLEM: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code PLATFORM: Version(s): 6, 7, 8 ABSTRACT: A vulnerability was reported in Microsoft Internet Explorer. A remote user can cause arbitrary code to be executed on the target user's system. REFERENCE LINKS: SecurityTracker Alert ID: 1027930 Secunia Advisory SA51695 CVE-2012-4792 IMPACT ASSESSMENT: High DISCUSSION: A remote user can create specially crafted HTML that, when loaded by the target user, will trigger a memory corruption error and execute arbitrary

139

Analysis of variation at transcription factor binding sites in Drosophila and humans  

E-Print Network (OSTI)

Background: Advances in sequencing technology have boosted population genomics and made it possible to map the positions of transcription factor binding sites (TFBSs) with high precision. Here we investigate TFBS variability ...

Spivakov, Mikhail

140

NETL: CO2 Binding Organic Liquids Gas Capture with Polarity-Swing...  

NLE Websites -- All DOE Office Websites (Extended Search)

CO2 Binding Organic Liquids Gas Capture with Polarity-Swing-Assisted Regeneration Project No.: DE-FE0007466 Battelle Pacific northwest Division is developing a new CO2 capture...

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


141

Screening SNPs residing in the microRNA-binding sites of Hepatocellular Carcinoma related genes  

Science Conference Proceedings (OSTI)

Single nucleotide polymorphisms located at miRNA-binding sites are likely to affect the expression of the miRNA targets and may contribute to the susceptibility of humans to common diseases. Here we selected 289 candidate Hepatocellular Carcinoma ...

Jun Ding; Yuzhen Gao; Yan He; Yifeng Zhou; Moli Huang; Haiyan Liu

2011-02-01T23:59:59.000Z

142

Crystal Structure of the Simian Virus 40 Large T-Antigen Origin-Binding Domain  

Science Conference Proceedings (OSTI)

The origins of replication of DNA tumor viruses have a highly conserved feature, namely, multiple binding sites for their respective initiator proteins arranged as inverted repeats. In the 1.45- Angstroms crystal structure of the simian virus 40 large T-antigen (T-ag) origin-binding domain (obd) reported herein, T-ag obd monomers form a left-handed spiral with an inner channel of 30 Angstroms having six monomers per turn. The inner surface of the spiral is positively charged and includes residues known to bind DNA. Residues implicated in hexamerization of full-length T-ag are located at the interface between adjacent T-ag obd monomers. These data provide a high-resolution model of the hexamer of origin-binding domains observed in electron microscopy studies and allow the obd's to be oriented relative to the hexamer of T-ag helicase domains to which they are connected.

Meinke,G.; Bullock, P.; Bohm, A.

2006-01-01T23:59:59.000Z

143

A hybrid model for prediction of peptide binding to MHC molecules  

Science Conference Proceedings (OSTI)

We propose a hybrid classification system for predicting peptide binding to major histocompatibility complex (MHC) molecules. This system combines Support Vector Machine (SVM) and Stabilized Matrix Method (SMM). Its performance was assessed using ROC ...

Ping Zhang; Vladimir Brusic; Kaye Basford

2008-11-01T23:59:59.000Z

144

Temperature-aware resource allocation and binding in high-level synthesis  

Science Conference Proceedings (OSTI)

Physical phenomena such as temperature have an increasingly important role in performance and reliability of modern process technologies. This trend will only strengthen with future generations. Attempts to minimize the design effort required for reaching ... Keywords: binding, leakage, switching, temperature

Rajarshi Mukherjee; Seda Ogrenci Memik; Gokhan Memik

2005-06-01T23:59:59.000Z

145

A generalized binding framework for the Low Level Reader Protocol (LLRP)  

E-Print Network (OSTI)

This Master of Engineering Thesis describes the design, implementation and testing of an XML binding framework for the RFID Low Level Reader Protocol (LLRP). LLRP is a recently released protocol which standardizes the ...

Poulopoulos, Dimitrios

2008-01-01T23:59:59.000Z

146

DensEl: An O(N) Tight Binding Code - TMS  

Science Conference Proceedings (OSTI)

Apr 3, 2008 ... DensEl is an O(N) (or linear scaling) tight binding code written in the first place by Chris Goringe with contributions by Paul Godwin and David...

147

A chromatin binding site in the tail domain of nuclear lamins that interacts with core histones  

E-Print Network (OSTI)

Abstract. Interaction of chromatin with the nuclear envelope and lamina is thought to help determine higher order chromosome organization in the interphase nucleus. Previous studies have shown that nuclear lamins bind chromatin directly. Here we have localized a chromatin binding site to the carboxyl-terminal tail domains of both A- and B-type mammalian lamins, and have characterized the biochemical properties of this binding in detail. Recombinant glutathione-S-transferase fusion proteins containing the tail domains of mammalian lamins C, BI, and B 2 were analyzed for their ability to associate with rat liver chromatin fragments immobi-lized on microtiter plate wells. We found that all three lamin tails specifically bind to chromatin with apparent Kds of 120-300 nM. By examining a series of deletion

Hideo Taniura; Charles Glass; Larry Gerace

1995-01-01T23:59:59.000Z

148

Structural and functional consequences of platinum anticancer drug binding to free and nucleosomal DNA  

E-Print Network (OSTI)

Cisplatin, carboplatin, and oxaliplatin are three FDA-approved members of the platinum anticancer drug family. These compounds induce apoptosis in tumor cells by binding to nuclear DNA, forming a variety of adducts, and ...

Todd, Ryan Christopher, 1981-

2010-01-01T23:59:59.000Z

149

2D IR spectroscopy and computational modeling : application to protein folding and binding  

E-Print Network (OSTI)

In this thesis, dynamics experiments are developed that can be used to study protein conformational changes such as folding and binding. Every functional motion of a protein is inextricably linked to conformational dynamics. ...

Ganim, Ziad

2010-01-01T23:59:59.000Z

150

Nucleotide Binding Site Communication in Arabidopsis thaliana Adenosine 5;-Phosphosulfate Kinase  

SciTech Connect

Adenosine 5{prime}-phosphosulfate kinase (APSK) catalyzes the ATP-dependent synthesis of adenosine 3{prime}-phosphate 5{prime}-phosphosulfate (PAPS), which is an essential metabolite for sulfur assimilation in prokaryotes and eukaryotes. Using APSK from Arabidopsis thaliana, we examine the energetics of nucleotide binary and ternary complex formation and probe active site features that coordinate the order of ligand addition. Calorimetric analysis shows that binding can occur first at either nucleotide site, but that initial interaction at the ATP/ADP site was favored and enhanced affinity for APS in the second site by 50-fold. The thermodynamics of the two possible binding models (i.e. ATP first versus APS first) differs and implies that active site structural changes guide the order of nucleotide addition. The ligand binding analysis also supports an earlier suggestion of intermolecular interactions in the dimeric APSK structure. Crystallographic, site-directed mutagenesis, and energetic analyses of oxyanion recognition by the P-loop in the ATP/ADP binding site and the role of Asp136, which bridges the ATP/ADP and APS/PAPS binding sites, suggest how the ordered nucleotide binding sequence and structural changes are dynamically coordinated for catalysis.

Ravilious, Geoffrey E.; Jez, Joseph M. (WU)

2012-08-31T23:59:59.000Z

151

Autoradiographic localization and characterization of angiotensin II binding sites in the spleen of rats and mice  

SciTech Connect

Specific binding sites for angiotensin II (Ang II) were localized in the red pulp of the spleen of rats and mice by quantitative autoradiography using /sup 125/I-Sar1-Ang II as a ligand. In the rat, the binding was saturable and specific, and the rank order for Ang II derivatives as competitors of /sup 125/I-Sar1-Ang II binding correlates well with their affinity for Ang II receptors in other tissues. Kinetic analysis in the rat spleen revealed a single class of binding sites with a KD of 1.11 nM and a Bmax value of 81.6 fmol/mg protein. Ang II binding sites were also localized on isolated rat spleen cells with similar affinity but with much lower Bmax, 9.75 fmol/mg protein. Ang II receptors were not detected in thymus sections from rats or mice, or on isolated rat thymocytes. The binding sites described here might represent a functional Ang II receptor with a role in the regulation of splenic volume and blood flow and in the modulation of the lymphocyte function.

Castren, E.; Kurihara, M.; Saavedra, J.M.

1987-07-01T23:59:59.000Z

152

Biochemical and Structural Characterization of Lysophosphatidic Acid Binding by a Humanized Monoclonal Antibody  

DOE Green Energy (OSTI)

Lysophosphatidic acid (LPA) is a common product of glycerophospholipid metabolism and an important mediator of signal transduction. Aberrantly high LPA concentrations accompany multiple disease states. One potential approach for treatment of these diseases, therefore, is the therapeutic application of antibodies that recognize and bind LPA as their antigen. We have determined the X-ray crystal structure of an anti-LPA antibody (LT3015) Fab fragment in its antigen-free form to 2.15 {angstrom} resolution and in complex with two LPA isotypes (14:0 and 18:2) to resolutions of 1.98 and 2.51 {angstrom}, respectively. The variable CDR (complementarity-determining region) loops at the antigen binding site adopt nearly identical conformations in the free and antigen-bound crystal structures. The crystallographic models reveal that the LT3015 antibody employs both heavy- and light-chain CDR loops to create a network of eight hydrogen bonds with the glycerophosphate head group of its LPA antigen. The head group is almost completely excluded from contact with solvent, while the hydrocarbon tail is partially solvent-exposed. In general, mutation of amino acid residues at the antigen binding site disrupts LPA binding. However, the introduction of particular mutations chosen strategically on the basis of the structures can positively influence LPA binding affinity. Finally, these structures elucidate the exquisite specificity demonstrated by an anti-lipid antibody for binding a structurally simple and seemingly unconstrained target molecule.

J Fleming; J Wojciak; M Campbell; T Huxford

2011-12-31T23:59:59.000Z

153

Cross-linking of atrial natriuretic peptide to binding sites in rat olfactory bulb membranes  

SciTech Connect

Binding sites for /sup 125/I-atrial natriuretic peptide (ANP)2 in rat olfactory bulb membranes have been studied using pharmacological and biochemical methods. Various unlabeled ANP-related peptides were tested for the ability to inhibit the binding of the radioligand in membrane binding assays. ANP(92-126) and ANP(99-126) were the most potent inhibitors tested, both exhibiting an IC50 value of 0.40 nM. ANP(103-126) and ANP(103-123) were 3 and 70 times less potent, respectively. ANP(111-126) was unable to inhibit the binding of the radioligand at a concentration of 1 microM. Several peptides unrelated to ANP were unable to inhibit the binding of the radioligand to rat olfactory bulb membranes. Membranes labeled with /sup 125/I-ANP were incubated with cross-linking agents and subjected to SDS-PAGE followed by autoradiography. A band possessing an apparent molecular mass of 116 kDa was identified. The labeling of this band was progressively decreased by increasing concentrations of unlabeled ANP(99-126) (IC50 = 0.6 nM) and by several other ANP-related peptides at nanomolar concentrations. For comparison purposes, ANP binding sites in rat aorta membranes were labeled with /sup 125/I-ANP and cross-linked using identical techniques. Three bands possessing molecular masses of 120, 72, and 62 kDa were identified. These results indicate that the ANP binding site in rat olfactory bulb membranes displays pharmacological and biochemical properties similar to peripheral ANP receptors.

Wildey, G.M.; Glembotski, C.C.

1986-12-01T23:59:59.000Z

154

In vitro receptor autoradiography reveals angiotensin IL (ANG II) binding associated with sensory and motor components of the vagus  

SciTech Connect

Specific, high affinity Ang II binding in the dog's dorsal medulla is concentrated in the area postrema, nucleus tractus solitarii (nTS) and dorsal motor nucleus of the vagus (dmnX). More recently Ang II binding sites were observed where bundles of vagal afferent fibers enter the dorsal medulla 6 mm rostral to obex and in the nodose ganglia and peripheral vagal nerves. Since Ang II binding in the nTS and dmnX overlies the distribution of vagal afferent fibers and efferent neurons, the effects of nodose ganglionectomy and cervical vagotomy on Ang II binding in the dorsal medulla were studied in rats and dogs using autoradiography after incubation of 14 ..mu..m coronal sections with 0.4 nM /sup 125/I-Ang II. Nonspecific binding was determined in the presence of 1 ..mu..m unlabeled Ang II. Two weeks after unilateral nodose ganglionectomy Ang II binding sites were absent ipsilaterally in the region where vagal afferent fibers enter the dorsal medulla. In the nTS and dmnX, binding near obex was reduced, while more rostrally these nuclei were almost completely devoid of Ang II binding on the denervated side. After cervical vagotomy, the loss of binding was restricted to the ipsilateral dmnX. These data are the first to reveal that Ang II binding in the dorsal medulla requires an intact vagal system.

Diz, D.I.; Barnes, K.L.; Ferrario, C.M.

1986-03-05T23:59:59.000Z

155

In vitro receptor autoradiography reveals angiotensin II (Ang II) binding associated with sensory and motor components of the vagus  

SciTech Connect

Specific, high affinity Ang II binding in the dog's dorsal medulla is concentrated in the area postrema, nucleus tractus solitarii (nTS) and dorsal motor nucleus of the vagus (dmnX). More recently Ang II binding sites were observed where bundles of vagal afferent fibers enter the dorsal medulla 6 mm rostral to obex and in the nodose ganglia and peripheral vagal nerves. Since Ang II binding in the nTS and dmnX overlies the distribution of vagal afferent fibers and efferent neurons, the effects of nodose ganglionectomy and cervical vagotomy on Ang II binding in the dorsal medulla were studied in rats and dogs using autoradiography after incubation of 14 ..mu..m coronal sections with 0.4 nM /sup 125/I-Ang II. Nonspecific binding was determined in the presence of 1 ..mu..M unlabeled Ang II. Two weeks after unilateral nodose ganglionectomy Ang II binding sites were absent ipsilaterally in the region where vagal afferent fibers enter the dorsal medulla. In the nTS and dmnX, binding near obex was reduced, while more rostrally these nuclei were almost completely devoid of Ang II binding on the denervated side. After cervical vagotomy, the loss of binding was restricted to the ipsilateral dmnX. These data are the first to reveal that Ang II binding in the dorsal medulla requires an intact vagal system.

Diz, D.I.; Barnes, K.L.; Ferrario, C.M.

1986-03-05T23:59:59.000Z

156

Ovine placental lactogen binds specifically to endometrial glands of the ovine uterus  

E-Print Network (OSTI)

A hormonal servomechanism has been proposed to regulate differentiation and function of the endometrial glandular epithelium (GE) in the ovine uterus during pregnancy that involves sequential actions of estrogen, progesterone, ovine interferon tau (IFN[T]), placental lactogen (oPL), and placental growth hormone (oGH). The biological actions of oPL in vitro are mediated by homodimerization of the PRL receptor (oPRLR) as well as heterodimerization of the oPRLR and oGH receptor (oGHR). The objectives of this study were to: (1) determine effects of intrauterine oPL, oGH and their combination on endometrial histoarchitecture and gene expression; (2) localize and characterize binding sites for oPL in the ovine uterus in vivo using an in situ ligand binding assay; and (3) determine temporal and spatial alterations in STAT 1, 3 and 5 expression in the pregnant ovine uterus. Intrauterine infusion of oPL and/or oGH following IFN[T] into ovariectomized ewes treated daily with progesterone differentially affected endometrial gland number and expression of uterine milk proteins and osteopontin. However, neither hormone affected PRLR, IGF-I or IGF-II mRNA levels in the endometrium. A chimeric protein of placental secretory alkaline phosphatase (SEAP) and oPL (SEAP-oPL) was used to identify and characterize binding sites for oPL in frozen sections of interplacentomal endometrium from pregnant ewes. Specific binding of SEAP-oPL was detected in the endometrial GE on Days 30, 60, 90, and 120 of pregnancy. In Day 90 endometrium, SEAP-oPL binding to the endometrial GE was displaced completely by oPL and oPRL, but only partially by oGH. Binding experiments using the extracellular domain of the oPRLR also showed that iodinated oPL binding could be competed by oPRL and oPL, but not by oGH. Collectively, results indicate that oPL binds to receptors in the endometrial glands and that PRL is more effective than GH for competing these binding sites. Thus, effects of oPL on the endometrial glands may be mediated by both PRLR and GHR.

Noel, Sekoni Daouda

2002-01-01T23:59:59.000Z

157

doi:10.1155/2011/839682 Review Article Haptenation: Chemical Reactivity and Protein Binding  

E-Print Network (OSTI)

Copyright 2011 Itai Chipinda et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Low molecular weight chemical (LMW) allergens are commonly referred to as haptens. Haptens must complex with proteins to be recognized by the immune system. The majority of occupationally related haptens are reactive, electrophilic chemicals, or are metabolized to reactive metabolites that form covalent bonds with nucleophilic centers on proteins. Nonelectrophilic protein binding may occur through disulfide exchange, coordinate covalent binding onto metal ions on metalloproteins or of metal allergens, themselves, to the major histocompatibility complex. Recent chemical reactivity kinetic studies suggest that the rate of protein binding is a major determinant of allergenic potency; however, electrophilic strength does not seem to predict the ability of a hapten to skew the response between Th1 and Th2. Modern proteomic mass spectrometry methods that allow detailed delineation of potential differences in protein binding sites may be valuable in predicting if a chemical will stimulate an immediate or delayed hypersensitivity. Chemical aspects related to both reactivity and protein-specific binding are discussed. 1.

Itai Chipinda; Justin M. Hettick; Paul D. Siegel

2011-01-01T23:59:59.000Z

158

Tau protein binds to microtubules through a flexible array of distributed weak sites. Z Cell Biol  

E-Print Network (OSTI)

Abstract. Tau protein plays a role in the extension and maintenance of neuronal processes through a direct association with microtubules. To characterize the nature of this association, we have synthesized a collection of tau protein fragments and studied their binding properties. The relatively weak affinity of tau protein for microtubules (ti10- ' M) is concentrated in a large region containing three or four 18 amino acid repeated binding elements. These are separated by apparently flexible but less conserved linker sequences of 13-14 amino acids that do not bind. Within the repeats, the binding energy for microtubules is delocalized and derives from a series of weak interactions contributed by small groups of amino acids. These unusual char acteristics suggest tau protein can assume multiple conformations and can pivot and perhaps migrate on the surface of the microtubule. The flexible structure of the tau protein binding interaction may allow it to be easily displaced from the microtubule lattice and may have important consequences for its function. TAU protein is a microtubule-associated protein present In brain and other neuronal tissues (Binder et al., 1985; Drubin et al., 1986; Weingarten et al., 1975). It is found in the axonal microtubules of mature neurons (Binder et al., 1985) and in the axonlike elongated neurite processes synthesized by differentiating neurons in culture

Karena Butner; Marc W. Kirschner

1991-01-01T23:59:59.000Z

159

T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

3: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets 3: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service May 31, 2011 - 3:35pm Addthis PROBLEM: A vulnerability was reported in BIND. A remote user can cause denial of service conditions. PLATFORM: BIND Version(s): 9.4-ESV-R3 and later, 9.6-ESV-R2 and later, 9.6.3, 9.7.1 and later, 9.8.0 and later; prior to 9.4-ESV-R4-P1, 9.6-ESV-R4-P1, 9.7.3-P1, 9.8.0-P2 ABSTRACT: A remote DNS server can supply very large RRSIG RRsets in a negative response to trigger an off-by-one error in a buffer size check and cause the target requesting named process to crash. A remote user can cause named to crash. reference LINKS: SecurityTracker Alert ID: 1025575 SecurityTracker Alert ID: 1025572

160

Characterization of angiotensin-binding sites in the bovine adrenal and the rat brain  

SciTech Connect

The first study was designed to determine whether systemically administered MSG affects neurons in the CVOs that are potentially important in mediating angiotensin-dependent responses. Rats were pretreated with MSG and the receptors for angiotensin II were assayed by radioligand binding in brain homogenates from the septum anteroventral third ventricular region (AV3V) and the thalamus/hypothalamus region using {sup 125}I-angiotensin II as the radioligand. The results of this experiment indicate that systematically administered MSG in the rat significantly reduced the number (Bmax) of Ang II receptors in a tissue sample which contained both extra blood-brain barrier organs as well as tissue within the blood-brain barrier with no change in the affinity (Kd) of the binding sites. The second chapter reports the successful solubilization of bovine adrenal {sup 125}I Ang II and {sup 125}I Sar{sup 1},Ile{sup 8}-Ang II binding sites with the detergent CHAPS. The results of our studies indicate the presence of two angiotensin binding sites. The one site is specific for naturally occurring angiotensins as well as sarcosine-1 substituted angiotensin analogues. The other site which can be optimally stabilized be re-addition of 0.3% CHAPS into the incubation assay binds sarcosine-1 substituted angiotensins exclusively. Hydrophobic interaction chromatography experiments suggest that these sites, possibly, represent distinct proteins. The third chapter discusses the successful solubilization and partial characterization of the rat brain angiotensin receptor.

Rogulja, I.

1989-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

Autoradiographic localization of (/sup 125/I)-angiotensin II binding sites in the rat adrenal gland  

SciTech Connect

To gain greater insight into sites of action of circulating angiotensin II (Ang II) within the adrenal, we have localized the (/sup 125/I)-Ang II binding site using in vitro autoradiography. Autoradiograms were generated either by apposition of isotope-sensitive film or with emulsion-coated coverslips to slide-mounted adrenal sections labeled in vitro with 1.0 nM (/sup 125/I)-Ang II. Analysis of the autoradiograms showed that Ang II binding sites were concentrated in a thin band in the outer cortex (over the cells of the zona glomerulosa) and in the adrenal medulla, which at higher power was seen as dense patches. Few sites were evident in the inner cortex. The existence of Ang II binding sites in the adrenal medulla was confirmed by conventional homogenate binding techniques which revealed a single class of high affinity Ang II binding site (K/sub d/ . 0.7nM, B/sub max/ . 168.7 fmol/mg). These results suggest that the adrenal medulla may be a target for direct receptor-mediated actions of Ang II.

Healy, D.P.; Maciejewski, A.R.; Printz, M.P.

1985-03-01T23:59:59.000Z

162

U-101: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding Use-After-Free  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

1: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding 1: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding Use-After-Free Vulnerability U-101: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding Use-After-Free Vulnerability February 13, 2012 - 7:00am Addthis PROBLEM: A vulnerability has been reported in multiple Mozilla products. PLATFORM: Mozilla Firefox 10.x Mozilla SeaMonkey 2.x Mozilla Thunderbird 10.x ABSTRACT: A vulnerability has been reported in multiple Mozilla products, which can be exploited by malicious people to compromise a user's system. reference LINKS: Vendor Advisory Secunia Advisory SA48008 CVE-2012-0452 IMPACT ASSESSMENT: High Discussion: A remote user can create HTML that, when loaded by the target user, will execute arbitrary code on the target user's system. The vulnerability is caused due to a use-after-free error in the

163

The Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A  

NLE Websites -- All DOE Office Websites (Extended Search)

Unique Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A Markus Alahuhta, Qi Xu, Yannick J. Bomble, Roman Brunecky, William S. Adney, Shi-You Ding, Michael E. Himmel and Vladimir V. Lunin⁎ National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401, USA Received 26 April 2010; received in revised form 12 July 2010; accepted 14 July 2010 Available online 21 July 2010 The crystal structure of the carbohydrate-binding module (CBM) 4 Ig fused domain from the cellulosomal cellulase cellobiohydrolase A (CbhA) of Clostridium thermocellum was solved in complex with cellobiose at 2.11 Å resolution. This is the first cellulosomal CBM4 crystal structure reported to date. It is similar to the previously solved noncellulosomal soluble oligosaccharide-binding CBM4 structures. However, this new structure possesses a significant

164

Molecular Determinants for Antibody Binding on Group 1 House Dust Mite Allergens  

SciTech Connect

House dust mites produce potent allergens, Der p 1 and Der f 1, that cause allergic sensitization and asthma. Der p 1 and Der f 1 are cysteine proteases that elicit IgE responses in 80% of mite-allergic subjects and have proinflammatory properties. Their antigenic structure is unknown. Here, we present crystal structures of natural Der p 1 and Der f 1 in complex with a monoclonal antibody, 4C1, which binds to a unique cross-reactive epitope on both allergens associated with IgE recognition. The 4C1 epitope is formed by almost identical amino acid sequences and contact residues. Mutations of the contact residues abrogate mAb 4C1 binding and reduce IgE antibody binding. These surface-exposed residues are molecular targets that can be exploited for development of recombinant allergen vaccines.

Chruszcz, Maksymilian; Poms, Anna; Glesner, Jill; Vailes, Lisa D.; Osinski, Tomasz; Porebski, Przemyslaw J.; Majorek, Karolina A.; Heymann, Peter W.; Platts-Mills, Thomas A.E.; Minor, Wladek; Chapman, Martin D. (INDOOR Bio.); (UV); (UVHS)

2012-07-11T23:59:59.000Z

165

Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint  

Science Conference Proceedings (OSTI)

Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.

Ramamurthy, Vidhyashankar; Krystek, Jr., Stanley R.; Bush, Alexander; Wei, Anzhi; Emanuel, Stuart L.; Gupta, Ruchira Das; Janjua, Ahsen; Cheng, Lin; Murdock, Melissa; Abramczyk, Bozena; Cohen, Daniel; Lin, Zheng; Morin, Paul; Davis, Jonathan H.; Dabritz, Michael; McLaughlin, Douglas C.; Russo, Katie A.; Chao, Ginger; Wright, Martin C.; Jenny, Victoria A.; Engle, Linda J.; Furfine, Eric; Sheriff, Steven (BMS)

2012-11-09T23:59:59.000Z

166

Statistical-mechanical lattice models for protein-DNA binding in chromatin  

E-Print Network (OSTI)

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quant...

Teif, Vladimir B

2010-01-01T23:59:59.000Z

167

Structural Analysis of Rtt106p Reveals a DNA Binding Role Required for Heterochromatin Silencing  

Science Conference Proceedings (OSTI)

Rtt106p is a Saccharomyces cerevisiae histone chaperone with roles in heterochromatin silencing and nucleosome assembly. The molecular mechanism by which Rtt106p engages in chromatin dynamics remains unclear. Here, we report the 2.5 {angstrom} crystal structure of the core domain of Rtt106p, which adopts an unusual 'double pleckstrin homology' domain architecture that represents a novel structural mode for histone chaperones. A histone H3-H4-binding region and a novel double-stranded DNA-binding region have been identified. Mutagenesis studies reveal that the histone and DNA binding activities of Rtt106p are involved in Sir protein-mediated heterochromatin formation. Our results uncover the structural basis of the diverse functions of Rtt106p and provide new insights into its cellular roles.

Liu, Y.; Huang, H; Zhou, B; Wang, S; Hu, Y; Li, X; Liu, J; Niu, L; Wu, J; et. al.

2010-01-01T23:59:59.000Z

168

LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins  

Science Conference Proceedings (OSTI)

Linker of nucleoskeleton and cytoskeleton (LINC) complexes span the nuclear envelope and are composed of KASH and SUN proteins residing in the outer and inner nuclear membrane, respectively. LINC formation relies on direct binding of KASH and SUN in the perinuclear space. Thereby, molecular tethers are formed that can transmit forces for chromosome movements, nuclear migration, and anchorage. We present crystal structures of the human SUN2-KASH1/2 complex, the core of the LINC complex. The SUN2 domain is rigidly attached to a trimeric coiled coil that prepositions it to bind three KASH peptides. The peptides bind in three deep and expansive grooves formed between adjacent SUN domains, effectively acting as molecular glue. In addition, a disulfide between conserved cysteines on SUN and KASH covalently links both proteins. The structure provides the basis of LINC complex formation and suggests a model for how LINC complexes might arrange into higher-order clusters to enhance force-coupling.

Sosa, Brian A.; Rothballer, Andrea; Kutay, Ulrike; Schwartz, Thomas U. (MIT); (ETH Zurich)

2012-08-31T23:59:59.000Z

169

New Mathematical Method Reveals Where Proteins Bind with DNA to Switch  

NLE Websites -- All DOE Office Websites (Extended Search)

Mathematical Mathematical Method Reveals Where Genes Switch On or Off New Mathematical Method Reveals Where Genes Switch On or Off "Compressed sensing" determines atomic-level energy potentials with accuracy approaching experimental measurement February 22, 2012 | Tags: Biological and Environmental Research (BER), Carver, Chemistry, Life Sciences, Math & Computer Science, NISE John Hules, JAHules@lbl.gov, +1 510 486 6008 Figure 1. Helix-turn-helix (HTH) proteins are the most widely distributed family of DNA-binding proteins, occurring in all biological kingdoms. This image shows a lambda repressor HTH transcription factor (green) binding to a lambda operator DNA sequence (blue and red) of the virus bacteriophage lambda. Image: Richard Wheeler, Wikipedia

170

Pyrazole-based cathepsin S inhibitors with arylalkynes as P1 binding elements  

SciTech Connect

A crystal structure of 1 bound to a Cys25Ser mutant of cathepsin S helped to elucidate the binding mode of a previously disclosed series of pyrazole-based CatS inhibitors and facilitated the design of a new class of arylalkyne analogs. Optimization of the alkyne and tetrahydropyridine portions of the pharmacophore provided potent CatS inhibitors (IC{sub 50} = 40-300 nM), and an X-ray structure of 32 revealed that the arylalkyne moiety binds in the S1 pocket of the enzyme.

Ameriks, Michael K.; Axe, Frank U.; Bembenek, Scott D.; Edwards, James P.; Gu, Yin; Karlsson, Lars; Randal, Mike; Sun, Siquan; Thurmond, Robin L.; Zhu, Jian; (J& J-PRD); (Sunesis)

2010-01-12T23:59:59.000Z

171

Isolation and characterization of a new zinc-binding protein from albacore tuna plasma  

SciTech Connect

The protein responsible for sequestering high levels of zinc in the plasma of the albacore tuna (Thunnus alalunga) has been isolated by sequential chromatography. The glycoprotein has a molecular weight of 66,000. Approximately 8.2% of its amino acid residues are histidines. Equilibrium dialysis experiments show it to bind 3 mol of zinc/mol of protein. The stoichiometric constant for the association of zinc with a binding site containing three histidines was determined to be 10/sup 9.4/. This protein is different from albumin and represents a previously uncharacterized zinc transport protein.

Dyke, B.; Hegenauer, J.; Saltman, P.; Laurs, R.M.

1987-06-02T23:59:59.000Z

172

Binding energy and fission of the heavy charged massive particle - nucleus bound state  

E-Print Network (OSTI)

We consider a possibility of capture of a heavy charged massive particle $\\chi^-$ by the nucleus leading to appearance of a bound state. A simple analytic formula allowing to calculate binding energies of the $N\\chi^-$ bound state for different nuclei is derived. If the binding energy is sufficiently large the particle $\\chi^-$ is stable inside the nucleus. The probabilities of the nuclear fissions for such states are calculated. It is shown that the bound states are more stable to a possible fission in comparison to the bare nucleus. This makes an observation of this hypothetical charged massive particle and the superheavy nuclei more probable.

V. V. Flambaum; G. McManus; S. G. Porsev

2010-08-20T23:59:59.000Z

173

JC3 Medium Impact Assessment Bulletins | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

3, 2012 3, 2012 U-227: bind-dyndb-ldap DN Escaping Flaw Lets Remote Users Deny Service A vulnerability has been reported in bind-dyndb-ldap, which can be exploited by malicious people to cause a DoS (Denial of Service). August 2, 2012 U-226: Linux Kernel SFC Driver TCP MSS Option Handling Denial of Service Vulnerability The Linux kernel is prone to a remote denial-of-service vulnerability. July 31, 2012 U-224: ISC DHCP Multiple Denial of Service Vulnerabilities ISC DHCP is prone to multiple denial-of-service vulnerabilities. July 25, 2012 U-220: Google Android DNS Resolver Randomization Flaw Lets Remote Users Poison the DNS Cache A remote user can poison the DNS cache. July 23, 2012 U-218: Cisco Linksys WMB54G TFTP Command Injection Vulnerability System access from local network

174

JC3 High Impact Assessment Bulletins | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

August 1, 2012 August 1, 2012 U-225: Citrix Access Gateway Plug-in for Windows nsepacom ActiveX Control Vulnerabilities Two vulnerabilities in Citrix Access Gateway Plug-in for Windows can be exploited by malicious people to compromise a user's system. July 30, 2012 U-223: Bugzilla May Disclose Confidential Information to Remote Users Two vulnerabilities were reported in Bugzilla. July 27, 2012 U-222: Apple Safari Bugs Let Remote Users Execute Arbitrary Code, Spoof the URL Address Bar, Conduct Cross-Site Scripting Attacks, and Obtain Potentially Sensitive Information Multiple vulnerabilities were reported in Apple Safari. July 26, 2012 U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability ISC BIND is prone to a denial-of-service vulnerability. July 24, 2012

175

On the possibility of binding of two electrons to dipole potentials  

Science Conference Proceedings (OSTI)

The possibility of binding two electrons by the fixed finite dipole (FFD) potential due to two point charges +qe and {minus}qe separated by the distance R is explored at the full configuration interaction level with extended basis sets. The critical value of the dipole moment {mu} = qR required to bind two electrons tends to infinity for small q (q {approx} 0.91e) and decreases precipitously as q increases. In the limit of very large q (and small R), this critical dipole moment seems to approach a limit below 2 Debyes (D). It is shown analytically that in the point dipole limit this critical dipole value will approach that for binding a single electron. An extension of the FFD model to include effects of inner-shell core electrons allows the Li{sup {minus}}, Na{sup {minus}}, and K{sup {minus}} cases (with a {minus} 1e charge at R) also to be examined. FFD-plus-core systems display even larger critical dipoles (113, 129, and 141 D, respectively) than does the +qe/{minus}qe FFD potential (92.2 D). These findings suggest that it will be difficult to find a real molecule that can bind (by {approx} 1 cm{sup {minus}1}) two electrons via its dipole potential. Finally, a simple electrostatic model is introduced which permits the critical dipole value of the FDD and its core-orbital extension to be evaluated rather well.

Skurski, P.; Gutowski, M.; Simons, J.

2000-01-15T23:59:59.000Z

176

Conservation analysis predicts in vivo occupancy of glucocorticoid receptor-binding sequences  

E-Print Network (OSTI)

Conservation analysis predicts in vivo occupancy of glucocorticoid receptor-binding sequences an individual GRE is highly conserved. In this study, we examined whether sequence conservation of sites re, we found that the level of conservation of these sites at genes up-regulated by glucocorticoids

Yamamoto, Keith

177

Kits and methods of detection using cellulose binding domain fusion proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL)

1998-01-01T23:59:59.000Z

178

Fundamental Cellular Processes Do Not Require Vertebrate-specific Sequences within the TATA-binding Protein*  

E-Print Network (OSTI)

, University of Utah, Salt Lake City, Utah 84112-5331 The 180-amino acid core of the TATA-binding proteinRNA (G2-specific). The mutation had no effect on tran- scription initiation site fidelity by either RNA to perform these functions. TBP acts in promoter recognition for transcription initiation by the Archaea RNA

Capecchi, Mario R.

179

A protein sequence meta-functional signature for calcium binding residue prediction  

Science Conference Proceedings (OSTI)

The diversity of characterized protein functions found amongst experimentally interrogated proteins suggests that a vast array of unknown functions remains undiscovered. These protein functions are imparted by specific geometric distributions of amino ... Keywords: Calcium, Functional signature, Protein binding site, Protein function prediction, Protein sequence analysis

Jeremy A. Horst; Ram Samudrala

2010-10-01T23:59:59.000Z

180

Theory of binless multi-state free energy estimation with applications to protein-ligand binding  

E-Print Network (OSTI)

Theory of binless multi-state free energy estimation with applications to protein-ligand binding Method (WHAM) is routinely used for com- puting free energies and expectations from multiple ensembles method, like WHAM, can be used not only to estimate free energies and equilibrium expectations, but also

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181

Structural Plasticity of Malaria Dihydroorotate Dehydrogenase Allows Selective Binding of Diverse Chemical Scaffolds  

SciTech Connect

Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes and to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.

Deng, Xiaoyi; Gujjar, Ramesh; El Mazouni, Farah; Kaminsky, Werner; Malmquist, Nicholas A.; Goldsmith, Elizabeth J.; Rathod, Pradipsinh K.; Phillips, Margaret A.; (UWASH); (UTSMC)

2010-01-20T23:59:59.000Z

182

An efficient motif discovery algorithm with unknown motif length and number of binding sites  

Science Conference Proceedings (OSTI)

Most motif discovery algorithms from DNA sequences require the motif's length as input. Styczynski et al. introduced the Extended (l,d)-Motif Problem (EMP) where the motif's length is not an input parameter. Unfortunately, ... Keywords: DNA sequences, binding sites, bioinformatics, consensus pattern, extended motif problem, gene expression data, gene regulatory networks, motif discovery, motif length, transcription factors

Henry C. M. Leung; Francis Y. L. Chin

2006-09-01T23:59:59.000Z

183

Memory access scheduling and binding considering energy minimization in multi-bank memory systems  

Science Conference Proceedings (OSTI)

Memory-related activity is one of the major sources of energy consumption in embedded systems. Many types of memories used in embedded systems allow multiple operating modes (e.g., active, standby, nap, power-down) to facilitate energy saving. Furthermore, ... Keywords: binding, low energy design, scheduling

Chun-Gi Lyuh; Taewhan Kim

2004-06-01T23:59:59.000Z

184

Timing variation-aware scheduling and resource binding in high-level synthesis  

Science Conference Proceedings (OSTI)

Due to technological scaling, process variations have increased significantly, resulting in large variations in the delay of the functional units. Hence, the worst-case approach is becoming increasingly pessimistic in meeting a certain performance yield. ... Keywords: HLS, ILP, binding, chaining, scheduling, variation-aware

Kartikey Mittal; Arpit Joshi; Madhu Mutyam

2011-10-01T23:59:59.000Z

185

Free energy screening of small ligands binding to an artificial protein cavity  

Science Conference Proceedings (OSTI)

The ?-dynamics simulation method was used to study the binding of 10 five-member ring heterocycle derivatives to an artificial cavity created inside cytochrome C peroxidase by mutagenesis. Application of ? dynamics using a multiple topology approach resulted in trapping in local minima. To extend the method to these cases

Shinichi Banba; Charles L. Brooks III

2000-01-01T23:59:59.000Z

186

Involvement of the Rab27 binding protein Slac2c/MyRIP in insulin exocytosis  

E-Print Network (OSTI)

Rab27a is a GTPase associated with insulin-containing secretory granules of pancreatic ?-cells. Selective reduction of Rab27a expression by RNA interference did not alter granule distribution and basal secretion but impaired exocytosis triggered by insulin secretagogues. Screening for potential effectors of the GTPase revealed that the Rab27a-binding protein Slac2c/MyRIP is associated with secretory granules of ?-cells. Attenuation of Slac2c/MyRIP expression by RNA interference did not modify basal secretion but severely impaired hormone release in response to secretagogues. Although ?-cells express Myosin-Va, a potential partner of Slac2c/MyRIP, no functional link between the two proteins could be demonstrated. In fact, overexpression of the Myosin-Va binding domain of Slac2c/MyRIP did not affect granule localization and hormone exocytosis. In contrast, overexpression of the actin-binding domain of Slac2c/MyRIP led to a potent inhibition of exocytosis without detectable alteration in granule distribution. This effect was prevented by point mutations that abolish actin binding. Taken together our data suggest that Rab27a and Slac2c/MyRIP are part of a complex mediating the interaction of secretory granules with cortical actin cytoskeleton and participate to the regulation of the final steps of insulin exocytosis.

Laurent Waselle; Mitsunori Fukuda; Mariella Iezzi; Aziz El-amraoui; Christine Petit; Romano Regazzi

2003-01-01T23:59:59.000Z

187

A flow cytometry-based dopamine transporter binding assay using antagonist-conjugated quantum dots  

SciTech Connect

Here we present the development and validation of a flow cytometry-based dopamine transporter (DAT) binding assay that uses antagonist-conjugated quantum dots (QDs).We anticipate that our QD-based assay is of immediate value to the high throughput screening of novel DAT modulators.

Kovtun, Oleg [Department of Chemistry, Vanderbilt University, 7300 Stevenson Ctr Ln, Nashville, TN 37235, USA.; Ross, Emily [Vanderbilt University; Tomlinson, Ian [Oak Ridge National Laboratory (ORNL); Rosenthal, Sandra [ORNL

2012-01-01T23:59:59.000Z

188

Structure of the Escherichia coli Phosphonate Binding Protein PhnD and Rationally Optimized Phosphonate Biosensors  

DOE Green Energy (OSTI)

The phnD gene of Escherichia coli encodes the periplasmic binding protein of the phosphonate (Pn) uptake and utilization pathway. We have crystallized and determined structures of E. coli PhnD (EcPhnD) in the absence of ligand and in complex with the environmentally abundant 2-aminoethylphosphonate (2AEP). Similar to other bacterial periplasmic binding proteins, 2AEP binds near the center of mass of EcPhnD in a cleft formed between two lobes. Comparison of the open, unliganded structure with the closed 2AEP-bound structure shows that the two lobes pivot around a hinge by {approx}70{sup o} between the two states. Extensive hydrogen bonding and electrostatic interactions stabilize 2AEP, which binds to EcPhnD with low nanomolar affinity. These structures provide insight into Pn uptake by bacteria and facilitated the rational design of high signal-to-noise Pn biosensors based on both coupled small-molecule dyes and autocatalytic fluorescent proteins.

Alicea, Ismael; Marvin, Jonathan S.; Miklos, Aleksandr E.; Ellington, Andrew D.; Looger, Loren L.; Schreiter, Eric R. (Puerto Rico); (HHMI); (Texas)

2012-09-17T23:59:59.000Z

189

Polymorphisms in Fibronectin Binding Protein A of Staphylococcus Aureus are Associated with Infection of Cardiovascular Devices  

Science Conference Proceedings (OSTI)

Medical implants, like cardiovascular devices, improve the quality of life for countless individuals but may become infected with bacteria like Staphylococcus aureus. Such infections take the form of a bio-film, a structured community of bacterial cells adherent to the surface of a solid substrate. Every bio-film begins with an attractive force or bond between bacterium and substratum. We used atomic force microscopy to probe experimentally forces between a fibronectin-coated surface (i.e., proxy for an implanted cardiac device) and fibronectin-binding receptors on the surface of individual living bacteria from each of 80 clinical isolates of S. aureus. These isolates originated from humans with infected cardiac devices (CDI; n = 26), uninfected cardiac devices (n = 20), and the anterior nares of asymptomatic subjects (n = 34). CDI isolates exhibited a distinct bindingforce signature and had speci!c single amino acid polymorphisms in fibronectin-binding protein A corresponding to E652D, H782Q, and K786N. In silico molecular dynamics simulations demonstrate that residues D652, Q782, and N786 in fibronectin-binding protein A form extra hydrogen bonds with fibronectin, complementing the higher binding force and energy measured by atomic force microscopy for the CDI isolates. This study is significant, because it links pathogenic bacteria biofilms from the length scale of bonds acting across a nanometer-scale space to the clinical presentation of disease at the human dimension.

Lower, Steven; Lamlertthon, Supaporn; Casillas-Ituarte, Nadia; Lins, Roberto D.; Yongsunthon, Ruchirej; Taylor, Eric S.; DiBartola, Alex; Edmondson, Catherine; McIntyre, Lauren M.; Reller, L. Barth; Que, Yok-Ai; Ros, Robert; Lower, Brian; Fowler, Vance

2011-11-08T23:59:59.000Z

190

Acetylation curtails nucleosome binding, not stable nucleosome remodeling, by FoxO1  

Science Conference Proceedings (OSTI)

Transcriptional activity of FoxO factors is controlled through the actions of multiple growth factors signaling through protein kinase B, whereby phosphorylation of FoxO factors inhibits FoxO-mediated transactivation by promoting nuclear export. Phosphorylation of FoxO factors is enhanced by p300-mediated acetylation, which decreases their affinity for DNA. The negative effect of acetylation on FoxO DNA binding, together with nuclear FoxO mobility, is eliminated by over-expression of the de-acetylase Sirt1, suggesting that acetylation mobilizes FoxO factors in chromatin for inducible gene expression. Here, we show that acetylation significantly curtails the affinity of FoxO1 for its binding sites in nucleosomal DNA but has no effect on either stable nucleosome binding or remodeling by this factor. We suggest that, while acetylation provides a first, essential step toward mobilizing FoxO factors for inducible gene repression, additional mechanisms exist for overcoming their inherent capacity to stably bind and remodel nuclear chromatin.

Hatta, M.; Liu, F. [Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226 (United States); Cirillo, L.A. [Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226 (United States)], E-mail: lcirillo@mcw.edu

2009-02-20T23:59:59.000Z

191

Kits and methods of detection using cellulose binding domain fusion proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

Shoseyov, O.; Yosef, K.

1998-04-14T23:59:59.000Z

192

Co Solid-State NMR as a New Probe for Elucidating Metal Binding in Polynucleotides  

E-Print Network (OSTI)

59 Co Solid-State NMR as a New Probe for Elucidating Metal Binding in Polynucleotides Christopher V for [Mg(H2O)6]2+ , and of high-resolution solid-state 59 Co NMR as a spectroscopic probe. Such strategy quenches fast cationic exchanges between bound and free states, while exploiting the superior NMR

Frydman, Lucio

193

Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase  

DOE Green Energy (OSTI)

The hydrophobic effect, the free-energetically favorable association of nonpolar solutes in water, makes a dominant contribution to binding of many systems of ligands and proteins. The objective of this study was to examine the hydrophobic effect in biomolecular recognition using two chemically different but structurally similar hydrophobic groups, aliphatic hydrocarbons and aliphatic fluorocarbons, and to determine whether the hydrophobicity of the two groups could be distinguished by thermodynamic and biostructural analysis. This paper uses isothermal titration calorimetry (ITC) to examine the thermodynamics of binding of benzenesulfonamides substituted in the para position with alkyl and fluoroalkyl chains (H{sub 2}NSO{sub 2}C{sub 6}H{sub 4}-CONHCH{sub 2}(CX{sub 2}){sub n}CX{sub 3}, n = 0-4, X = H, F) to human carbonic anhydrase II (HCA II). Both alkyl and fluoroalkyl substituents contribute favorably to the enthalpy and the entropy of binding; these contributions increase as the length of chain of the hydrophobic substituent increases. Crystallography of the protein-ligand complexes indicates that the benzenesulfonamide groups of all ligands examined bind with similar geometry, that the tail groups associate with the hydrophobic wall of HCA II (which is made up of the side chains of residues Phe131, Val135, Pro202, and Leu204), and that the structure of the protein is indistinguishable for all but one of the complexes (the longest member of the fluoroalkyl series). Analysis of the thermodynamics of binding as a function of structure is compatible with the hypothesis that hydrophobic binding of both alkyl and fluoroalkyl chains to hydrophobic surface of carbonic anhydrase is due primarily to the release of nonoptimally hydrogen-bonded water molecules that hydrate the binding cavity (including the hydrophobic wall) of HCA II and to the release of water molecules that surround the hydrophobic chain of the ligands. This study defines the balance of enthalpic and entropic contributions to the hydrophobic effect in this representative system of protein and ligand: hydrophobic interactions, here, seem to comprise approximately equal contributions from enthalpy (plausibly from strengthening networks of hydrogen bonds among molecules of water) and entropy (from release of water from configurationally restricted positions).

J Mecinovic; P Snyder; K Mirica; S Bai; E Mack; R Kwant; D Moustakas; A Heroux; G Whitesides

2011-12-31T23:59:59.000Z

194

Glycosylation Helps Cellulase Enzymes Bind to Plant Cell Walls (Fact Sheet)  

DOE Green Energy (OSTI)

Computer simulations suggest a new strategy to design enhanced enzymes for biofuels production. Large-scale computer simulations predict that the addition of glycosylation on carbohydrate-binding modules can dramatically improve the binding affinity of these protein domains over amino acid mutations alone. These simulations suggest that glycosylation can be used as a protein engineering tool to enhance the activity of cellulase enzymes, which are a key component in the conversion of cellulose to soluble sugars in the production of biofuels. Glycosylation is the covalent attachment of carbohydrate molecules to protein side chains, and is present in many proteins across all kingdoms of life. Moreover, glycosylation is known to serve a wide variety of functions in biological recognition, cell signaling, and metabolism. Cellulase enzymes, which are responsible for deconstructing cellulose found in plant cell walls to glucose, contain glycosylation that when modified can affect enzymatic activity-often in an unpredictable manner. To gain insight into the role of glycosylation on cellulase activity, scientists at the National Renewable Energy Laboratory (NREL) used computer simulation to predict that adding glycosylation on the carbohydrate-binding module of a cellulase enzyme dramatically boosts the binding affinity to cellulose-more than standard protein engineering approaches in which amino acids are mutated. Because it is known that higher binding affinity in cellulases leads to higher activity, this work suggests a new route to designing enhanced enzymes for biofuels production. More generally, this work suggests that tuning glycosylation in cellulase enzymes is a key factor to consider when engineering biochemical conversion processes, and that more work is needed to understand how glycosylation affects cellulase activity at the molecular level.

Not Available

2012-06-01T23:59:59.000Z

195

A nuclear cap-binding complex binds Balbiani ring pre-mRNA cotranscriptionally and accompanies the ribonucleoprotein particle during nuclear export  

E-Print Network (OSTI)

Abstract. In vertebrates, a nuclear cap-binding complex (CBC) formed by two cap-binding proteins, CBP20 and CBP80, is involved in several steps of RNA metabolism, including pre-mRNA splicing and nuclear export of some RNA polymerase II-transcribed U snRNAs. The CBC is highly conserved, and antibodies against human CBP20 cross-react with the CBP20 counterpart in the dipteran Chironomus tentans. Using immunoelectron microscopy, the in situ association of CBP20 with a specific pre-mRNP particle, the Balbiani ring particle, has been analyzed at different stages of pre-mRNA synthesis, maturation, and nucleo-cytoplasmic transport. We demonstrate that CBP20 binds to the nascent pre-mRNA shortly after transcription initiation, stays in the RNP particles after splicing has been completed, and remains attached to the 5 ' domain during translocation of the RNP through the nuclear pore complex (NPC). The rapid association of CBP20 with nascent RNA transcripts in situ is consistent with the role of CBC in splicing, and the retention of CBC on the RNP during translocation through the NPC supports its proposed involvement in RNA export. "~'N the nucleus of eukaryotic cells, messenger RNA pre-1 / cursors (pre-mRNAs) undergo a series of maturation- ~ reactions before they are exported to the cytoplasm where the mature messenger RNAs (mRNAs) can direct protein synthesis. One of these maturation events is the addition of a monomethylated guanosine residue to the first encoded nucleotide of the RNA via a 5'-5 ' triphosphate linkage (Shatkin, 1976). This reaction occurs on all transcripts synthesized by RNA polymerase II shortly after the start of transcription (Salditt-Georgieff et al., 1980; Rasmussen and Lis, 1993). The resulting cap structure is implicated in several aspects of pre-mRNA and mRNA metabolism. The cap structure increases RNA stability, and is required for efficient translation initiation, premRNA

Neus Visa; Elisa Izaurralde; Bertil Daneholt; Iain W. Mattaj

1996-01-01T23:59:59.000Z

196

Theory of Free Energy and Entropy in Noncovalent Binding HUAN-XIANG ZHOU AND MICHAEL K. GILSON  

E-Print Network (OSTI)

S1 Theory of Free Energy and Entropy in Noncovalent Binding HUAN-XIANG ZHOU AND MICHAEL K. GILSON 1 in a form that supports the present formulation of the theory of noncovalent binding. The free energy, F, provides a measure of the stability of a system at thermal equilibrium: the lower the free energy

Weston, Ken

197

2008 Special Issue: Combining experts in order to identify binding sites in yeast and mouse genomic data  

Science Conference Proceedings (OSTI)

The identification of cis-regulatory binding sites in DNA is a difficult problem in computational biology. To obtain a full understanding of the complex machinery embodied in genetic regulatory networks it is necessary to know both the identity of the ... Keywords: Computational biology, Imbalanced data, Sampling, Support vector machine, Transcription factor binding sites

Mark Robinson; Cristina Gonzlez Castellano; Faisal Rezwan; Rod Adams; Neil Davey; Alastair Rust; Yi Sun

2008-08-01T23:59:59.000Z

198

Free Energy Component Analysis for Drug Design: A Case Study of HIV-1 Protease-Inhibitor Binding  

E-Print Network (OSTI)

Free Energy Component Analysis for Drug Design: A Case Study of HIV-1 Protease-Inhibitor Binding of the free energies of binding of protein-ligand complexes is presented. The method formulated involves developing molecular dynamics trajectories of the enzyme, the inhibitor, and the complex, followed by a free

Jayaram, Bhyravabotla

199

Autoradiographic localization and characterization of atrial natriuretic peptide binding sites in the rat central nervous system and adrenal gland  

SciTech Connect

Atrial natriuretic peptides (ANP) have recently been identified in both heart and CNS. These peptides possess potent natriuretic, diuretic, and vasorelaxant activities, and are all apparently derived from a single prohormone. Specific ANP binding sites have been characterized in the adrenal zona glomerulosa and kidney cortex, and one study reported ANP binding sites in the CNS. However, a detailed examination of the localization of ANP binding sites throughout the brain has not been reported. In this study, quantitative autoradiography was employed to examine the distribution of ANP receptors in the rat CNS. The binding of (3-/sup 125/I-iodotyrosyl28) rat ANP-28 to binding sites in the rat CNS was saturable, specific for ANP-related peptides, and displayed high affinity (Kd = 600 pM). When the relative concentrations of ANP binding sites were determined throughout the rat brain, the highest levels of ANP binding were localized to the circumventricular organs, including the area postrema and subfornical organ, and the olfactory apparatus. Moderate levels of ANP binding sites were present throughout the midbrain and brain stem, while low levels were found in the forebrain, diencephalon, basal ganglia, cortex, and cerebellum. The presence of ANP binding sites in the subfornical organ and the area postrema, regions considered to be outside the blood-brain barrier, suggests that peripheral ANP levels may regulate some aspects of CNS control of salt and water balance. The possible functions of ANP binding sites in other regions of the rat brain are not known, but, like many other peptides, ANP may act as a neurotransmitter or neuromodulator at these loci.

Gibson, T.R.; Wildey, G.M.; Manaker, S.; Glembotski, C.C.

1986-07-01T23:59:59.000Z

200

Capture and release of mixed acid gasses with binding organic liquids  

DOE Patents (OSTI)

Reversible acid-gas binding organic liquid systems that permit separation and capture of one or more of several acid gases from a mixed gas stream, transport of the liquid, release of the acid gases from the ionic liquid and reuse of the liquid to bind more acid gas with significant energy savings compared to current aqueous systems. These systems utilize acid gas capture compounds made up of strong bases and weak acids that form salts when reacted with a selected acid gas, and which release these gases when a preselected triggering event occurs. The various new materials that make up this system can also be included in various other applications such as chemical sensors, chemical reactants, scrubbers, and separators that allow for the specific and separate removal of desired materials from a gas stream such as flue gas.

Heldebrant, David J. (Richland, WA); Yonker, Clement R. (Kennewick, WA)

2010-09-21T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
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We encourage you to perform a real-time search of NLEBeta
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201

Binding of stereognostically designed ligands to trivalent, pentavalent, and hexavalent f-block elements  

Science Conference Proceedings (OSTI)

Stability constants were determined for the complexes formed from two stereognostically designed ligands and the f-block elements Nd(III), Np(V), and Pu(VI). The ligands investigated were tris[3-(2-carboxyphenoxy)propyl]amine (NPB) and tris-N,N',N''-[2-(2-carboxy-4-ethyl-phenoxy)ethyl]-1,4,7-triazacyclononane (EETAC). A stereognostically blind ligand, nitrilotriacetic acid (NTA), was also investigated for comparison. The results suggest that there is no significant stereognostic effect for complexation of NPB or EETAC to Np(V). On the other hand, a modest stereognostic effect is seen for the NPB ligand when complexed to Pu(VI), leading to an approximately 8-fold increase in the binding strength. A more significant effect is observed for the EETAC system in which a 250-fold increase in binding is observed for Pu(VI) versus Nd(III).

Sinkov, Sergey I.; Lumetta, Gregg J.; Warner, Marvin G.; Pittman, Jonathan W.

2012-03-26T23:59:59.000Z

202

Decorin Core Protein (Decoron) Shape Complements Collagen Fibril Surface Structure and Mediates Its Binding  

Science Conference Proceedings (OSTI)

Decorin is the archetypal small leucine rich repeat proteoglycan of the vertebrate extracellular matrix (ECM). With its glycosaminoglycuronan chain, it is responsible for stabilizing inter-fibrillar organization. Type I collagen is the predominant member of the fibrillar collagen family, fulfilling both organizational and structural roles in animal ECMs. In this study, interactions between decoron (the decorin core protein) and binding sites in the d and e1 bands of the type I collagen fibril were investigated through molecular modeling of their respective X-ray diffraction structures. Previously, it was proposed that a model-based, highly curved concave decoron interacts with a single collagen molecule, which would form extensive van der Waals contacts and give rise to strong non-specific binding. However, the large well-ordered aggregate that is the collagen fibril places significant restraints on modes of ligand binding and necessitates multi-collagen molecular contacts. We present here a relatively high-resolution model of the decoron-fibril collagen complex. We find that the respective crystal structures complement each other well, although it is the monomeric form of decoron that shows the most appropriate shape complementarity with the fibril surface and favorable calculated energies of interaction. One molecule of decoron interacts with four to six collagen molecules, and the binding specificity relies on a large number of hydrogen bonds and electrostatic interactions, primarily with the collagen motifs KXGDRGE and AKGDRGE (d and e{sub 1} bands). This work helps us to understand collagen-decorin interactions and the molecular architecture of the fibrillar ECM in health and disease.

Orgel, Joseph P.R.O.; Eid, Aya; Antipova, Olga; Bella, Jordi; Scott, John E.; (IIT); (Manchester)

2010-02-11T23:59:59.000Z

203

Energy Employees Occupational Illness Compensation Program Act...  

Office of Science (SC) Website

Energy Employees Occupational Illness Compensation Program Act (EEOICPA) Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act...

204

DEVELOPMENT AND TESTING OF AN EXPERT SYSTEMUSING ARTIFICIAL NEURAL NETWORKS FOR AFORWARD IN-SITU COMBUSTION PROCESS.  

E-Print Network (OSTI)

??The main topic of the research is the enhanced oil recovery (EOR) method of forward dry in-situ combustion (ISC). ISC is an EOR method used (more)

Shihab, Rizvi

2011-01-01T23:59:59.000Z

205

T-677: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

7: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of 7: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service Vulnerability T-677: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service Vulnerability July 27, 2011 - 3:58pm Addthis PROBLEM: F5 has acknowledged a vulnerability in BIG-IP, which can be exploited by malicious people to cause a DoS (Denial of Service). PLATFORM: The vulnerability is reported in the following products and versions: BIG-IP LTM versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2 BIG-IP GTM versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2 BIG-IP ASM versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2 BIG-IP Link Controller versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2

206

Structural Basis of Ligand Binding by a C-di-GMP Riboswitch  

Science Conference Proceedings (OSTI)

The second messenger signaling molecule bis-(3{prime}-5{prime})-cyclic dimeric guanosine monophosphate (c-di-GMP) regulates many processes in bacteria, including motility, pathogenesis and biofilm formation. c-di-GMP-binding riboswitches are important downstream targets in this signaling pathway. Here we report the crystal structure, at 2.7 {angstrom} resolution, of a c-di-GMP riboswitch aptamer from Vibrio cholerae bound to c-di-GMP, showing that the ligand binds within a three-helix junction that involves base-pairing and extensive base-stacking. The symmetric c-di-GMP is recognized asymmetrically with respect to both the bases and the backbone. A mutant aptamer was engineered that preferentially binds the candidate signaling molecule c-di-AMP over c-di-GMP. Kinetic and structural data suggest that genetic regulation by the c-di-GMP riboswitch is kinetically controlled and that gene expression is modulated through the stabilization of a previously unidentified P1 helix, illustrating a direct mechanism for c-di-GMP signaling.

Smith, K.; Lipchock, S; Ames, T; Wang, J; Breaker, R; Strobel, S

2009-01-01T23:59:59.000Z

207

Collective Wage Setting When Wages Are Generally Binding: An Antitrust Perspective  

E-Print Network (OSTI)

This paper explores the anticompetitive effects that wage determination between an employers association and the industrys labor union may have when wages are generally binding. It is shown that employers associations can, under certain circumstances, use generally binding standard wages to raise rivals costs. In equilibrium, it may be optimal for the labor union to demand a wage rate which is either above or below the entry deterring limit wage. Hence, it might be the case that a strong labor union serves as an efficiency enhancing countervailing power, because it keeps the employers association from raising the standard wage up to the limit wage. The model is used to explain why both German employers associations and German labor unions appear to oppose the removal of a specific legal instrument provided for in the German labor law, the so-called Allgemeinverbindlicherklrung (AVE), which makes collectively negotiated employment contracts binding for an entire industry. The entry deterring effect of the AVE suggests that labor market organization is an important determinant of product market competition and should therefore be considered as part of antitrust policies.

Justus Haucap; Uwe Pauly; Christian Wey; Justus Haucap; Uwe Pauly; Christian Wey; Collective Wage Setting; Justus Haucap; Uwe Pauly; Christian Wey

2000-01-01T23:59:59.000Z

208

Atomic structure of nitrate-binding protein crucial for photosynthetic productivity  

DOE Green Energy (OSTI)

Cyanobacteria, blue-green algae, are the most abundant autotrophs in aquatic environments and form the base of all aquatic food chains by fixing carbon and nitrogen into cellular biomass. The single most important nutrient for photosynthesis and growth is nitrate, which is severely limiting in many aquatic environments particularly the open ocean (1, 2). It is therefore not surprising that NrtA, the solute-binding component of the high-affinity nitrate ABC transporter, is the single-most abundant protein in the plasma membrane of these bacteria (3). Here we describe the first structure of a nitratespecific receptor, NrtA from Synechocystis sp. PCC 6803, complexed with nitrate and determined to a resolution of 1.5. NrtA is significantly larger than other oxyanionbinding proteins, representing a new class of transport proteins. From sequence alignments, the only other solute-binding protein in this class is CmpA, a bicarbonatebinding protein. Therefore, these organisms created a novel solute-binding protein for two of the most important nutrients; inorganic nitrogen and carbon. The electrostatic charge distribution of NrtA appears to force the protein off of the membrane while the flexible tether facilitates the delivery of nitrate to the membrane pore. The structure not only details the determinants for nitrate selectivity in NrtA, but also the bicarbonate specificity in CmpA. Nitrate and bicarbonate transport are regulated by the cytoplasmic proteins NrtC and CmpC, respectively. Interestingly, the residues lining the ligand binding pockets suggest that they both bind nitrate. This implies that the nitrogen and carbon uptake pathways are synchronized by intracellular nitrate and nitrite.3 The nitrate ABC transporter of cyanobacteria is composed of four polypeptides (Figure 1): a high-affinity periplasmic solute-binding lipoprotein (NrtA), an integral membrane permease (NrtB), a cytoplasmic ATPase (NrtD), and a unique ATPase/solute-binding fusion protein (NrtC) that regulates transport (4). NrtA binds both nitrate and nitrite (Kd = 0.3 mM) and is necessary for cell survival when nitrate is the primary nitrogen source (5). The role of NrtA is to scavenge nitrate/nitrite from the periplasm for delivery to the membrane permease, NrtB. The passage of solute through the transmembrane pore is linked to ATP hydrolysis by NrtC and NrtD. NrtD consists of a single ATPase domain. In contrast, NrtC contains both an ATPase domain and a Cterminal solute-binding domain that shares 50% amino acid sequence similarity with NrtA, and is required for the ammonium-mediated inhibition of nitrate transport (6, 7). Aside from the homologous transporter for bicarbonate, CmpABCD, there are no other known examples of ABC transporters that have an ATPase/solute-binding fusion component. The specificity of the nitrate transporter is conferred by NrtA (4). NrtA is ~49% identical (60% similar) in amino acid sequence to the bicarbonate receptor CmpA. In its entirety, it does not have significant homology to any other known protein. To elucidate the molecular determinants of nitrate specificity, we determined the crystal structure of the Synechocystis 6803 NrtA to 1.5 . While the general shape of NrtA is akin to that of other solute binding proteins, NrtA clearly represents a new and unique structural variant of these C clamp proteins. From this structure and sequence alignments of other bicarbonate and nitrate transporters, the molecular basis for solute selectivity is clear and suggests that regulatory domains of both icarbonate and nitrate transport systems bind nitrate. Based on these findings, a model is presented that 4 demonstrates how such synergistic regulation of bicarbonate and nitrate transport is important in conserving energy during the process of carbon fixation and nitrogen assimilation.

Koropatkin, Nicole M.; Pakrasi, Himadri B.; Smith, Thomas J.

2006-06-27T23:59:59.000Z

209

Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Frauke Gra1ter,, Sonja M. Schwarzl,, Annick Dejaegere,| Stefan Fischer,*, and  

E-Print Network (OSTI)

Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics Frauke of the complexes are predicted (the "docking" problem) as well as in how the free energy is calculated from)solvation during the binding process.3 Typically, binding free energies calculated with these methods have average

Gräter, Frauke

210

Whole Genome Analysis of Functional Protein Binding Sites and DNA Methylation: Application to p53 and Low Dose Ionizing Radiation.  

NLE Websites -- All DOE Office Websites (Extended Search)

Whole Genome Analysis of Functional Protein Binding Sites and DNA Methylation: Whole Genome Analysis of Functional Protein Binding Sites and DNA Methylation: Application to p53 and Low Dose Ionizing Radiation. Krassimira Botcheva, John J. Dunn and Carl W. Anderson Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA The effects of exposure to low doses of ionizing radiation on humans results largely from changes in gene expression mediated by the activation of sequence-specific DNA binding proteins (transcription factors) as well as changes to other chromosomal proteins and perhaps to DNA. To develop a molecular understanding of the consequences of exposures to low doses of ionizing radiation, it will be necessary to understanding where radiation-activated transcription factors bind in whole genomes and how

211

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights  

E-Print Network (OSTI)

Background: Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding ...

Gordan, Raluca

212

Quantitative Estimates on the Binding Energy for Hydrogen in Non-Relativistic QED. II. The spin case  

E-Print Network (OSTI)

The hydrogen binding energy in the Pauli-Fierz model with the spin Zeeman term is determined up to the order alpha cube, where alpha denotes the fine-structure constant.

Jean-Marie Barbaroux; Semjon Vugalter

2013-06-19T23:59:59.000Z

213

Effect of localization in quantum wells and quantum wires on heavy-light hole mixing and acceptor binding energy  

Science Conference Proceedings (OSTI)

The variational method taking into account the complex valence band structure is used to study the effect of localization in quantum wells and quantum wires on the acceptor binding energy. Trial functions that make possible tracing of the transition from the bulk material to narrow quantum wells and quantum wires of small radius are constructed. The possibility of the appearance of an unsteadily varying dependence of the acceptor binding energy on the characteristic dimension of the system is shown.

Semina, M. A., E-mail: msemina@gmail.com; Suris, R. A. [Russian Academy of Sciences, Ioffe Physical Technical Institute (Russian Federation)

2011-07-15T23:59:59.000Z

214

Particle trap to sheath non-binding contact for a gas-insulated transmission line having a corrugated outer conductor  

DOE Patents (OSTI)

A non-binding particle trap to outer sheath contact for use in gas insulated transmission lines having a corrugated outer conductor. The non-binding feature of the contact according to the teachings of the invention is accomplished by having a lever arm rotatably attached to a particle trap by a pivot support axis disposed parallel to the direction of travel of the inner conductor/insulator/particle trap assembly.

Fischer, William H. (Pittsburgh, PA)

1984-04-24T23:59:59.000Z

215

Binding motifs in bacterial gene promoters modulate transcriptional effect of global regulators  

Science Conference Proceedings (OSTI)

Bacterial gene regulation involves transcription factors (TFs) that influence the expression of many genes. Global regulators, including CRP (cAMP Receptor Protein), ArcA, and FNR, can modulate the transcriptional activity of multiple operons. The similarity of a regulatory element s sequence to a TF s consensus binding site (BS) and the position of the regulatory element in an operon promoter are considered the most important determinants of this TF s regulatory influence. In this study we explore the hypothesis that the number of TFBS half-sites (where a half-site is one half of the palindromic BS consensus sequence, which we shall refer to as a binding motif or a BM) of a global regulator in an operon s promoter plays an important role in the operon s transcriptional regulation. We examine empirical data from transcriptional profiling of the CRP regulon in Shewanella oneidenses MR 1 and Escherichia coli, and of the ArcA regulon in S. oneidenses MR 1. We compare the power of CRP BM counts and of full, symmetrical CRP TFBS characteristics, namely similarity to consensus and location, to predict CRP-induced transcriptional activity. We find that CRP BM counts have a nonlinear effect on CRP-dependent transcriptional activity and predict this activity better than full-length TFBS quality or location. Regression analysis indicates that IHF (Integration Host Factor) and ArcA have synergistic effects on CRP-induced gene transcription, positive and negative, respectively. Based on these results, we propose that the fine-tuning of bacterial transcriptional activity by CRP may involves not only the bending of the operon promoter, facilitated by CRP in cooperation with the histone-like protein IHF, but also the cumulative binding affinity of multiple weak BMs.

Leuze, Michael Rex [ORNL; Karpinets, Tatiana V [ORNL; Syed, Mustafa H [ORNL; Beliaev, Alexander S [ORNL; Uberbacher, Edward C [ORNL

2012-01-01T23:59:59.000Z

216

Truncated atrial natriuretic peptide (ANP) analogs: relationship between receptor binding and cyclic GMP accumulation  

SciTech Connect

The authors have shown that cultured bovine aortic smooth muscle (BASM) cells contain high affinity receptor sites for the ANP, auriculin (ANP(4-28)). Furthermore, ANP(4-28) causes cyclic GMP (cGMP) levels to increase in BASM. In the present study, the authors synthesized a series of NH/sub 2/ and/or COOH truncated ANP(4-28) analogs and examined their ability to compete for /sup 125/I-ANP(4-28) binding to BASM and increase cGMP levels. ANP-mediated cGMP responses were reduced when amino acids were deleted from the NH/sub 2/ and/or COOH termini of ANP(4-28). Removal of the NH/sub 2/ terminal R, R-S, or R-S-S residues resulted in a 10X decrease in potency for cGMP stimulation. Deletion of the COOH terminal R-Y and F-R-Y residues resulted in a marked decline in potency. ANP's lacking the F-R-Y tripeptide were nearly inactive in stimulating cGMP accumulation. In contrast to the cGMP effects, NH/sub 2/ and/or COOH truncations of ANP(4-28) did not alter apparent receptor binding affinities (Ki(app)). All of these peptide analogs exhibited Ki(app)'s of 1-5 nM. Furthermore, peptides that bound effectively and failed to elicit cGMP responses did not antagonize ANP(4-28)-mediated cGMP increases. These binding and functional data suggest the presence of a single class of ANP receptors on BASM is insufficient to explain the actions of ANP's in these cells.

Scarborough, R.; Schenk, D.; Schwartz, K.; Kang, L.L.; McEnroe, G.; Arfsten, A.; Lewicki, J.

1986-03-01T23:59:59.000Z

217

Characterization of marine exopolymeric substance (EPS) responsible for binding of thorium (IV) isotopes  

E-Print Network (OSTI)

The functional group composition of acid polysaccharides was determined after isolation using cross-flow ultrafiltration, radiolabeling with 234Th(IV) and other isotopes, and separation using isoelectric focusing (IEF) and polyacrylamide gel electrophoresis (PAGE). Phosphate and sulphate concentrations were determined from cultured bacterial and phytoplankton colloid, particulate and colloidal samples collected from the Gulf of M??xico (GOM). Characterization of the 234Th(IV)-binding biomolecule was performed using ion chromatography (IC), and gas chromatography-mass spectrometry (GC-MS). Radiotracer experiments and culture experiments were conducted in determining the binding environment of the 234Th(IV)-binding ligand (i.e., sorption onto suspended particles), as well as the origin of the ligand in seawater systems. In all samples, 234Th(IV) isoelectric focusing profiles indicated that 49% to 65% of the 234Th(IV) labeled EPS from Roseobacter gallaeciensis, Sagittula stellata, Emiliania huxleyi, Synechococcus elongatus and GOM Station 4-72m was found at a pHIEF of 2 in the IEF spectrum. The carboxylic acid group appeared at the same pHIEF as 234Th(IV) for EPS from Roseobacter gallaeciensis, Emiliania huxleyi, Synechococcus elongatus and GOM colloidal organic matter sample. The phosphate group appeared at the same pHIEF as 234Th(IV) for EPS from Roseobacter gallaeciensis, and Synechococcus elongatus sample. The sulphate group was found at the same pHIEF as 234Th(IV) for EPS from S. elongatus and GOM colloidal organic matter sample. The total polysaccharide content was only 14% and 8%, uronic acids were approximately 5.4% and 87.1%, and total protein content was 2.6% and 6.2% of total carbon content of Sagittula stellata and Synechococcus elongatus, respectively. Monosaccharides identified in both Sagittula stellata and Synechococcus elongatus were galactose, glucose, and xylose in common. In addition, Sagittula stellata contained mannose and Synechococcus elongatus had galactoglucuronic acid. Thus, depending on the species, the size, structural composition, and functional groups of the 234Th(IV)-binding, acidic polysaccharides will vary. From these observations, it is concluded that the steric environment and not necessarily the exact functional group might actually be responsible for thorium-234 complexation to macromolecular organic matter. This research helped to improve our understanding of the observed variability in POC/234Th ratios in the ocean and provided insights into factors that regulate organic carbon export fluxes.

Alvarado Quiroz, Nicolas Gabriel

2003-05-01T23:59:59.000Z

218

ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes  

DOE Data Explorer (OSTI)

Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. This database of evolutionary conserved regions (ECRs) in vertebrate genomes features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and fugu genomes. (taken from paper in Journal: Bioinformatics, November 7, 2006, pp. 122-124

Loots, Gabriela G. (LLNL); Ovcharenko, I. (LLNL)

219

Determination of the Exciton Binding Energy in CdSe Quantum Dots  

Science Conference Proceedings (OSTI)

The exciton binding energy (EBE) in CdSe quantum dots (QDs) has been determined using x-ray spectroscopy. Using x-ray absorption and photoemission spectroscopy, the conduction band (CB) and valence band (VB) edge shifts as a function of particle size have been determined and combined to obtain the true band gap of the QDs (i.e. without and exciton). These values can be compared to the excitonic gap obtained using optical spectroscopy to determine the EBE. The experimental EBE results are compared with theoretical calculations on the EBE and show excellent agreement.

Meulenberg, R; Lee, J; Wolcott, A; Zhang, J; Terminello, L; van Buuren, T

2009-10-27T23:59:59.000Z

220

Two and three-body interatomic dispersion energy contributions to binding in molecules and solids.  

SciTech Connect

We present numerical estimates of the leading two- and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London and Axilrod-Teller-Muto expressions where the required interatomic dispersion energy coefficients, C{sub 6} and C{sub 9}, are computed 'on the fly' from the electron density. Inter- and intramolecular energy contributions are obtained using the Tang-Toennies (TT) damping function for short interatomic distances. The TT range parameters are equally extracted on the fly from the electron density using their linear relationship to van der Waals radii. This relationship is empiricially determined for all the combinations of He-Xe rare gas dimers, as well as for the He and Ar trimers. The investigated systems include the S22 database of noncovalent interactions, Ar, benzene and ice crystals, bilayer graphene, C{sub 60} dimer, a peptide (Ala{sub 10}), an intercalated drug-DNA model [ellipticine-d(CG){sub 2}], 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and 12 molecular crystal polymorphs from crystal structure prediction blind test studies. The two- and three-body interatomic dispersion energies are found to contribute significantly to binding and cohesive energies, for bilayer graphene the latter reaches 50% of experimentally derived binding energy. These results suggest that interatomic three-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems.

von Lilienfeld-Toal, Otto Anatole; Tkatchenko, Alexandre (Fritz-Haber-Institute)

2010-03-01T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

Involvement of RNA binding proteins AUF1 in mammary gland differentiation  

Science Conference Proceedings (OSTI)

The expression of many genes, such as {beta}-casein, c-myc, and cyclin D1, is altered by lactogenic hormone stimulation during mammary epithelial cell differentiation. Here, we demonstrate that post-transcriptional regulation plays an important role to establish gene expression required to initiate milk production as well as transcriptional control. AUF1 protein, a member of the AU-rich element (ARE)-binding protein family, plays a role in ARE-mRNA turnover by regulating mRNA stability and/or translational control. Cytoplasmic localization of AUF1 protein is critically linked to function. We show that as the mammary gland differentiates, AUF1 protein moves from the cytoplasm to the nucleus. Moreover, in mammary gland epithelial cells (HC11), stimulation by lactogenic hormone decreased cytoplasmic and increased nuclear AUF1 levels. Direct binding of AUF1 protein was observed on c-myc mRNA, but not {beta}-casein or cyclin D1 mRNA. AUF1 downregulation in HC11 cells increased the expression of {beta}-casein mRNA and decreased the expression of c-myc mRNA by lactogenic hormone. Conversely, overexpression of AUF1 inhibited these effects of lactogenic hormone stimulation in HC11 cells. These results suggest that AUF1 participates in mammary gland differentiation processes under the control of lactogenic hormone signals.

Nagaoka, Kentaro [Laboratory of Animal Breeding, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan)]. E-mail: akenaga@mail.ecc.u-tokyo.ac.jp; Tanaka, Tetsuya [Laboratory of Animal Breeding, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Imakawa, Kazuhiko [Laboratory of Animal Breeding, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Sakai, Senkiti [Laboratory of Animal Breeding, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan)

2007-08-01T23:59:59.000Z

222

Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites  

E-Print Network (OSTI)

Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97 % of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

Gregory A. Ross; Garrett M. Morris; Philip C. Biggin

2011-01-01T23:59:59.000Z

223

A Thousand Invisible Cords Binding Astronomy and High-Energy Physics  

E-Print Network (OSTI)

The traditional realm of astronomy is the observation and study of the largest objects in the Universe, while the traditional domain of high-energy physics is the study of the smallest things in nature. But these two sciences concerned with opposite ends of the size spectrum are, in Muir's words, bound fast by a thousand invisible cords that cannot be broken. In this essay I propose that collaborations of astronomers and high-energy physicists on common problems are beneficial for both fields, and that both astronomy and high-energy physics can advance by this close and still growing relationship. Dark matter and dark energy are two of the binding cords I will use to illustrate how collaborations of astronomers and high-energy physicists on large astronomical projects can be good for astronomy, and how discoveries in astronomy can guide high-energy physicists in their quest for understanding nature on the smallest scales. Of course, the fields have some different intellectual and collaborative traditions, neither of which is ideal. The cultures of the different fields cannot be judged to be right or wrong; they either work or they don't. When astronomers and high-energy physicists work together, the binding cords can either encourage or choke creativity. The challenge facing the astronomy and high-energy physics communities is to adopt the best traditions of both fields. It is up to us to choose wisely.

Rocky Kolb

2007-08-09T23:59:59.000Z

224

Transcription Factors Bind Thousands of Active and InactiveRegions in the Drosophila Blastoderm  

SciTech Connect

Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. Here, we use whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior-posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched in bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over forty well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal-ventral patterning genes, whose expression we show to be quantitatively modulated by anterior-posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly-bound regions are not involved in early-embryonic transcriptional regulation, and a significant proportion may be nonfunctional. Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets.

Li, Xiao-Yong; MacArthur, Stewart; Bourgon, Richard; Nix, David; Pollard, Daniel A.; Iyer, Venky N.; Hechmer, Aaron; Simirenko, Lisa; Stapleton, Mark; Luengo Hendriks, Cris L.; Chu, Hou Cheng; Ogawa, Nobuo; Inwood, William; Sementchenko, Victor; Beaton, Amy; Weiszmann, Richard; Celniker, Susan E.; Knowles, David W.; Gingeras, Tom; Speed, Terence P.; Eisen, Michael B.; Biggin, Mark D.

2008-01-10T23:59:59.000Z

225

Structure of Human Toll-like Receptor 3 (TLR3) Ligand-binding Domain  

NLE Websites -- All DOE Office Websites (Extended Search)

Human Toll-like Receptor Human Toll-like Receptor 3 (TLR3) Ligand-binding Domain Jungwoo Choe1, Matthew S. Kelker1, and Ian A. Wilson1 1Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 Figure 1. Overall structure of human TLR3 ECD. The N-terminal region is colored blue, the 23 canonical LRRs are in yellow and the C-terminal region is in pink. N-linked sugars that are observed in the electron density maps are shown in ball-and-stick. (From Choe et al. 2005). Innate immunity is the front line host defense that acts within minutes of infection to counter invasion by microorganisms. Members of the Toll-like receptor (TLR) family recognize conserved pathogen-associated molecular

226

CO2-Binding Organic Liquids, an Integrated Acid Gas Capture System  

SciTech Connect

Amine systems are effective for CO2 capture, but they are still inefficient because the solvent regeneration energy is largely defined by the amount of water in the process. Most amines form heat-stable salts with SO2 and COS resulting in parasitic solvent loss and degradation. Stripping the CO2-rich solvent is energy intensive it requires temperatures above 100 ?C due to the high specific heat and heat of vaporization of water. CO2-capture processes could be much more energy efficient in a water free amine process. In addition, if the capture-material is chemically compatible with other acid gases, less solvent would be lost to heat-stable salts and the process economics would be further improved. One such system that can address these concerns is Binding Organic Liquids (BOLs), a class of switchable ionic liquids.

Heldebrant, David J.; Koech, Phillip K.; Rainbolt, James E.; Zheng, Feng

2011-04-01T23:59:59.000Z

227

Cloning and structure of the human corticotrophin releasing factor-binding protein gene (CRHBP)  

Science Conference Proceedings (OSTI)

The human CRF-binding protein gene has been cloned and mapped to the distal region of chromosome 13 and loci 5q in the mouse and human genomes, respectively. The gene consists of 7 exons and 6 introns. The mature protein has 10 cysteines and 5 tandem disulfide bridges 4 of which are contained within exons 3, 5, 6, and 7. One bridge is shared by exons 3 and 4. The signal peptide and the first 3 amino acids of the mature protein were coded for by an extreme 5[prime] exon. Primer extension analyses revealed the transcriptional initiation site to be located 32 bp downstream from a consensus TATA box. The promoter sequence contained a number of putative promoter elements including an AP-1 site, three ER-half sites, the immunoglobulin enhancer elements NF-kB and INF-1, and the liver-specific enhancers LFA1 and LFB1. 26 refs., 5 figs., 1 tab.

Behan, D.P.; Potter, E.; Lewis, K.A.; Vale, W.W. (Salk Inst., La Jolla, CA (United States)); Jenkins, N.A.; Copeland, N. (Frederick Cancer Research and Development Center, MD (United States)); Lowry, P.J. (Reading Univ. (United Kingdom))

1993-04-01T23:59:59.000Z

228

ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes  

SciTech Connect

Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes entitled ECRbase that is constructed from a collection of pairwise vertebrate genome alignments produced by the ECR Browser database. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a collection of promoters in all vertebrate genomes presented in the database. The database also contains a collection of annotated transcription factor binding sites (TFBS) in all ECRs and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and two pufferfish genomes. It is freely accessible at http://ECRbase.dcode.org.

Loots, G; Ovcharenko, I

2006-08-08T23:59:59.000Z

229

Hybrid Monte-Carlo simulation of interacting tight-binding model of graphene  

E-Print Network (OSTI)

In this work, results are presented of Hybrid-Monte-Carlo simulations of the tight-binding Hamiltonian of graphene, coupled to an instantaneous long-range two-body potential which is modeled by a Hubbard-Stratonovich auxiliary field. We present an investigation of the spontaneous breaking of the sublattice symmetry, which corresponds to a phase transition from a conducting to an insulating phase and which occurs when the effective fine-structure constant $\\alpha$ of the system crosses above a certain threshold $\\alpha_C$. Qualitative comparisons to earlier works on the subject (which used larger system sizes and higher statistics) are made and it is established that $\\alpha_C$ is of a plausible magnitude in our simulations. Also, we discuss differences between simulations using compact and non-compact variants of the Hubbard field and present a quantitative comparison of distinct discretization schemes of the Euclidean time-like dimension in the Fermion operator.

Dominik Smith; Lorenz von Smekal

2013-11-05T23:59:59.000Z

230

IQGAP Proteins Reveal an Atypical Phosphoinositide (aPI) Binding Domain with a Pseudo C2 Domain Fold  

SciTech Connect

Class I phosphoinositide (PI) 3-kinases act through effector proteins whose 3-PI selectivity is mediated by a limited repertoire of structurally defined, lipid recognition domains. We describe here the lipid preferences and crystal structure of a new class of PI binding modules exemplified by select IQGAPs (IQ motif containing GTPase-activating proteins) known to coordinate cellular signaling events and cytoskeletal dynamics. This module is defined by a C-terminal 105-107 amino acid region of which IQGAP1 and -2, but not IQGAP3, binds preferentially to phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3). The binding affinity for PtdInsP3, together with other, secondary target-recognition characteristics, are comparable with those of the pleckstrin homology domain of cytohesin-3 (general receptor for phosphoinositides 1), an established PtdInsP3 effector protein. Importantly, the IQGAP1 C-terminal domain and the cytohesin-3 pleckstrin homology domain, each tagged with enhanced green fluorescent protein, were both re-localized from the cytosol to the cell periphery following the activation of PI 3-kinase in Swiss 3T3 fibroblasts, consistent with their common, selective recognition of endogenous 3-PI(s). The crystal structure of the C-terminal IQGAP2 PI binding module reveals unexpected topological similarity to an integral fold of C2 domains, including a putative basic binding pocket. We propose that this module integrates select IQGAP proteins with PI 3-kinase signaling and constitutes a novel, atypical phosphoinositide binding domain that may represent the first of a larger group, each perhaps structurally unique but collectively dissimilar from the known PI recognition modules.

Dixon, Miles J.; Gray, Alexander; Schenning, Martijn; Agacan, Mark; Tempel, Wolfram; Tong, Yufeng; Nedyalkova, Lyudmila; Park, Hee-Won; Leslie, Nicholas R.; van Aalten, Daan M.F.; Downes, C. Peter; Batty, Ian H. (Toronto); (Dundee)

2012-10-16T23:59:59.000Z

231

Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger  

Science Conference Proceedings (OSTI)

Histone H3 lysine4 methylation (H3K4me) has been proposed as a critical component in regulating gene expression, epigenetic states, and cellular identities. The biological meaning of H3K4me is interpreted by conserved modules including plant homeodomain (PHD) fingers that recognize varied H3K4me states. The dysregulation of PHD fingers has been implicated in several human diseases, including cancers and immune or neurological disorders. Here we report that fusing an H3K4-trimethylation (H3K4me3)-binding PHD finger, such as the carboxy-terminal PHD finger of PHF23 or JARID1A (also known as KDM5A or RBBP2), to a common fusion partner nucleoporin-98 (NUP98) as identified in human leukaemias, generated potent oncoproteins that arrested haematopoietic differentiation and induced acute myeloid leukaemia in murine models. In these processes, a PHD finger that specifically recognizes H3K4me3/2 marks was essential for leukaemogenesis. Mutations in PHD fingers that abrogated H3K4me3 binding also abolished leukaemic transformation. NUP98-PHD fusion prevented the differentiation-associated removal of H3K4me3 at many loci encoding lineage-specific transcription factors (Hox(s), Gata3, Meis1, Eya1 and Pbx1), and enforced their active gene transcription in murine haematopoietic stem/progenitor cells. Mechanistically, NUP98-PHD fusions act as 'chromatin boundary factors', dominating over polycomb-mediated gene silencing to 'lock' developmentally critical loci into an active chromatin state (H3K4me3 with induced histone acetylation), a state that defined leukaemia stem cells. Collectively, our studies represent, to our knowledge, the first report that deregulation of the PHD finger, an 'effector' of specific histone modification, perturbs the epigenetic dynamics on developmentally critical loci, catastrophizes cellular fate decision-making, and even causes oncogenesis during mammalian development.

Wang, Gang G.; Song, Jikui; Wang, Zhanxin; Dormann, Holger L.; Casadio, Fabio; Li, Haitao; Luo, Jun-Li; Patel, Dinshaw J.; Allis, C. David; (MSKCC); (Scripps); (Rockefeller)

2009-07-21T23:59:59.000Z

232

Dependence of Nuclear Binding Energies on the Cutoff Momentum of Low-Momentum Nucleon-Nucleon Interaction  

E-Print Network (OSTI)

Binding energies of ^{3}H, ^{4}He, and ^{16}O are calculated, using low-momentum nucleon-nucleon interactions (V_{low-k}) for a wide range of the cutoff momentum \\Lambda. In addition, single-particle energies in nuclei around ^{16}O are computed. The dependence of the binding energies and the single-particle energies in these nuclei on the cutoff momentum \\Lambda of the V_{low-k} is examined. Furthermore, the availability of the V_{low-k} in nuclear structure calculations is discussed.

S. Fujii; H. Kamada; R. Okamoto; K. Suzuki

2004-06-30T23:59:59.000Z

233

Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values  

E-Print Network (OSTI)

The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande, J. Chem. Phys. ${\\bf 123}$, 084108 (2005)]. As an application, we perform the binding affinity calculations of six theophylline-related ligands with RNA aptamer. Basically, our method is applicable when using many compute nodes to accelerate simulations, thus a parallel computing system is also developed. To further reduce the computational cost, the adequate non-uniform intervals of coupling constant $\\lambda$, connecting two equilibrium states, namely bound and unbound, are determined. The absolute binding energies $\\Delta G$ thus obtained have effective linear relation between the computed and experimental values. If the results of two other different methods are compared, thermodynamic integration (TI) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) by the paper of Gouda $et al$ [H. Gouda, I. D. Kuntz, D. A. Case, and P. A. Kollman, Biopolymers ${\\bf 68}$, 16 (2003)], the predictive accuracy of the relative values $\\Delta\\Delta G$ is almost comparable to that of TI: the correlation coefficients (R) obtained are 0.99 (this work), 0.97 (TI), and 0.78 (MM-PBSA). On absolute binding energies meanwhile, a constant energy shift of $\\sim$ -7 kcal/mol against the experimental values is evident. To solve this problem, several presumable reasons are investigated.

Yoshiaki Tanida; Masakatsu Ito; Hideaki Fujitani

2007-08-06T23:59:59.000Z

234

T. E. Lowe R. W. Brill K. L. Cousins Blood oxygen-binding characteristics of bigeye tuna (Thunnus obesus),  

E-Print Network (OSTI)

T. E. Lowe á R. W. Brill á K. L. Cousins Blood oxygen-binding characteristics of bigeye tuna 1999 / Accepted: 18 December 1999 Abstract We found blood from bigeye tuna (Thunnus obesus) to have a signi®cantly higher O2 anity than blood from other tunas. Its P50 (partial pressure of oxygen, PO2

Hawai'i at Manoa, University of

235

Agonist-activated angiotensin II receptor is associated with a guanine nucleotide binding protein in bovine adrenal cortex  

SciTech Connect

Previous studies have shown that high affinity binding of the agonist Angiotensin II (Ang II) to adrenal cortex receptors was modulated by guanine nucleotides. In contrast, the antagonist (/sup 1/SAR,/sup 8/Ile) Ang II (SARILE) did not display any sensitivity toward guanine nucleotides. The authors have observed already after solubilization in octyl-glucoside and size-exclusion HPLC that agonist (/sup 131/I) (/sup 1/SAR) Ang II (SARANG)-stabilized receptor complex behaved as a larger protein than the antagonist (/sup 125/I)SARILE-stabilized receptor. Their purpose was to assay the direct association of a guanine nucleotide binding protein to the agonist-occupied Ang II receptor using (/sup 35/S) guanosine-thio-triphosphate (GTP-..gamma..-s) as a probe of the regulation protein. Adrenal cortical membrane receptors were activated with 10/sup -6/ M SARANG, solubilized and fraction marked on DEAE-agarose, then on size-exclusion HPLC. Fractionated samples were assayed with (/sup 35/S)-GTP-..gamma..-s. They found that a (/sup 35/S)GTP-..gamma..-s binding protein peak coeluted with the agonist-occupied receptor peak, while it disappeared in absence of agonist and eluted presumably free in a higher elution volume. Their results demonstrated directly the coupling of a guanine-nucleotide binding protein to the agonist-activated Ang II receptor.

Berardi, M.; Ong, H.; De Lean, A.

1986-03-05T23:59:59.000Z

236

Use of Cre/loxP recombination to swap cell binding motifs on the adenoviral capsid protein IX  

Science Conference Proceedings (OSTI)

We used Cre/loxP recombination to swap targeting ligands present on the adenoviral capsid protein IX (pIX). A loxP-flanked sequence encoding poly-lysine (pK-binds heparan sulfate proteoglycans) was engineered onto the 3'-terminus of pIX, and the resulting fusion protein allowed for routine virus propagation. Growth of this virus on Cre-expressing cells removed the pK coding sequence, generating virus that could only infect through alternative ligands, such as a tyrosine kinase receptor A (TrkA)-binding motif engineered into the capsid fibre protein for enhanced infection of neuronal cells. We used a similar approach to swap the pK motif on pIX for a sequence encoding a single-domain antibody directed towards CD66c for targeted infection of cancer cells; Cre-mediated removal of the pK-coding sequence simultaneously placed the single-domain antibody coding sequence in frame with pIX. Thus, we have developed a simple method to propagate virus lacking native viral tropism but containing cell-specific binding ligands. - Highlights: > We describe a method to grow virus lacking native tropism but containing novel cell-binding ligands. > Cre/loxP recombination was used to modify the adenovirus genome. > A targeting ligand present on capsid protein IX was removed or replaced using recombination. > Cre-loxP was also used to 'swap' the identity of the targeting ligand present on pIX.

Poulin, Kathy L. [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Tong, Grace; Vorobyova, Olga [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Pool, Madeline [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario (Canada); Kothary, Rashmi [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario (Canada); Department of Medicine, University of Ottawa, Ottawa, Ontario (Canada); Parks, Robin J., E-mail: rparks@ohri.ca [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Medicine, University of Ottawa, Ottawa, Ontario (Canada); Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario (Canada)

2011-11-25T23:59:59.000Z

237

Characterization of a baculovirus lacking the DBP (DNA-binding protein) gene  

Science Conference Proceedings (OSTI)

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) encodes two proteins that possess properties typical of single-stranded DNA-binding proteins (SSBs), late expression factor-3 (LEF-3), and a protein referred to as DNA-binding protein (DBP). Whereas LEF-3 is a multi-functional protein essential for viral DNA replication, transporting helicase into the nucleus, and forms a stable complex with the baculovirus alkaline nuclease, the role for DBP in baculovirus replication remains unclear. Therefore, to better understand the functional role of DBP in viral replication, a DBP knockout virus was generated from an AcMNPV bacmid and analyzed. The results of a growth curve analysis indicated that the dbp knockout construct was unable to produce budded virus indicating that dbp is essential. The lack of DBP does not cause a general shutdown of the expression of viral genes, as was revealed by accumulation of early (LEF-3), late (VP39), and very late (P10) proteins in cells transfected with the dbp knockout construct. To investigate the role of DBP in DNA replication, a real-time PCR-based assay was employed and showed that, although viral DNA synthesis occurred in cells transfected with the dbp knockout, the levels were less than that of the control virus suggesting that DBP is required for normal levels of DNA synthesis or for stability of nascent viral DNA. In addition, analysis of the viral DNA replicated by the dbp knockout by using field inversion gel electrophoresis failed to detect the presence of genome-length DNA. Furthermore, analysis of DBP from infected cells indicated that similar to LEF-3, DBP was tightly bound to viral chromatin. Assessment of the cellular localization of DBP relative to replicated viral DNA by immunoelectron microscopy indicated that, at 24 h post-infection, DBP co-localized with nascent DNA at distinct electron-dense regions within the nucleus. Finally, immunoelectron microscopic analysis of cells transfected with the dbp knockout revealed that DBP is required for the production of normal-appearing nucleocapsids and for the generation of the virogenic stroma.

Vanarsdall, Adam L. [Department of Microbiology, Nash Hall Room 220, Oregon State University, Corvallis, OR 97331-3804 (United States); Mikhailov, Victor S. [Department of Microbiology, Nash Hall Room 220, Oregon State University, Corvallis, OR 97331-3804 (United States); N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 117808 (Russian Federation); Rohrmann, George F. [Department of Microbiology, Nash Hall Room 220, Oregon State University, Corvallis, OR 97331-3804 (United States)]. E-mail: rohrmanng@orst.edu

2007-08-01T23:59:59.000Z

238

Synthesis, Characterization and Anion Binding Properties of Boron-based Lewis Acids  

E-Print Network (OSTI)

The recognition and capture of fluoride, cyanide and azide anions is attracting great deal of attention due to the negative effects of these anions on the environment and on human health. One of common methods used for the recognition and capture of these anions is based on triarylboranes, the Lewis acidity of which can be enhanced via variation the steric and electronic properties of the boron substituents. This dissertation is dedicated to the synthesis of novel boron-based anion receptors that, for the most part, feature an onium group bound to one of the aryl substituents. The presence of this group is shown to increase the anion affinity of the boron center via Coulombic effects. Another interesting effect is observed when the onium group is juxtaposed with the boron atom. This is for example the case of naphthalene-based compounds bearing a dimesitylboryl moiety at one of the peri-position and a sulfonium or telluronium unit at the other peri position. Fluoride anion complexation studies with these sulfonium or telluronium boranes, show that the boron-bound fluoride anion is further stabilized by formation of a B-F->Te/S bridge involving a lp(F)->sigma*(Te/S-C) donor acceptor interaction. Some of the sulfonium boranes investigated have been shown to efficiently capture fluoride anions from wet methanolic solutions. The resulting fluoride/sulfonium borane adducts can be triggered to release a "naked" fluoride equivalent in organic solution and thus show promise as new reagents for nucleophilic fluorination chemistry. Interestingly, the telluronium systems show a greater fluoride anion affinity than their sulfonium analogs. This increase is assigned to the greater spatial and energetic accessibility of the sigma* orbital on the tellurium atom which favors the formation of a strong B-F->Te interaction. This dissertation is concluded by an investigation of the Lewis acidic properties of B(C6Cl5)3. This borane, which has been reported to be non-Lewis acidic by other researchers, is found by us to bind fluoride, azide and cyanide anions in dichloromethane with large binding constants. This borane is also reactive toward neutral Lewis bases, such as p-dimethylaminopyridine, in organic solvents.

Zhao, Hai Yan

2012-05-01T23:59:59.000Z

239

New Method for Calculating the Absolute Free Energy of Binding: The Effect of a Mobile Loop on the Avidin/Biotin Complex  

E-Print Network (OSTI)

New Method for Calculating the Absolute Free Energy of Binding: The Effect of a Mobile Loop Hypothetical scanning molecular dynamics (HSMD) is a relatively new method for calculating the absolute free as a byproduct of the simulation. The binding mechanism of biotin to avidin involves a mobile loop

Meirovitch, Hagai

240

A New Heat Shock Protein That Binds Nucleic Acids* (Received for publication, August 20, 1998, and in revised form, September 28, 1998)  

E-Print Network (OSTI)

A New Heat Shock Protein That Binds Nucleic Acids* (Received for publication, August 20, 1998 describe the isolation of Hsp15, a new, very abun- dant heat shock protein that binds to DNA and RNA. Hsp15 category from that of many other heat shock proteins that act as mo- lecular chaperones or proteases

Bardwell, James

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241

f_Binding-Motifs-in-Bacterial-Gene-Promoters-Modulate-Transcriptional2_4335.pdf  

NLE Websites -- All DOE Office Websites (Extended Search)

Regulation and Systems Biology 2012:6 93-107 Regulation and Systems Biology 2012:6 93-107 doi: 10.4137/GRSB.S9357 This article is available from http://www.la-press.com. © the author(s), publisher and licensee Libertas Academica Ltd. This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. OPEN ACCESS Full open access to this and thousands of other papers at http://www.la-press.com. Gene Regulation and Systems Biology O R I G I N A L R E S E A R C H Gene Regulation and Systems Biology 2012:6 93 Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA Michael R. Leuze 1, *, Tatiana V. Karpinets 2,3, *, Mustafa H. Syed 2 , Alexander S. Beliaev 4 and Edward C. Uberbacher 2 1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.

242

The chlorophyll-binding protein CP47 in photosystem II. Progress report  

DOE Green Energy (OSTI)

The CP47 protein is encoded by the psbB gene, binds 10-20 chlorophyll and has an apparent molecular weight of about 47 kDa. Specific mutations can be introduced into this protein using the transformable, (photo)heterotrophic cyanobacterium Synechocystis sp. PCC 6803. This cyanobacterium takes up foreign DNA spontaneously, and can survive in the absence of PS II activity to take out the wild-type psbB gene and subsequently replace it by a construct containing the desired mutation(s) in psbB. The PS I-less Synechocystis system we are now utilizing for studies of His mutations in the CP47 protein is a very useful strain for detailed studies of pigment-protein interactions and of the effects of limited pheophytinization in the antenna on light-harvesting efficiency. This is providing new information on parameters influencing energy transfer efficiency in photosynthetic systems. Moreover, studies regarding the hydrophilic regions of the CP47 protein are contributing to an understanding of the role of this protein in optimizing water-splitting activity.

Vermaas, W.F.J.

1994-06-01T23:59:59.000Z

243

Noise Analysis in Ligand-Binding Reception for Molecular Communication in Nanonetworks  

E-Print Network (OSTI)

AbstractMolecular communication (MC) will enable the exchange of information among nanoscale devices. In this novel bioinspired communication paradigm, molecules are employed to encode, transmit and receive information. In the most general case, these molecules are propagated in the medium by means of free diffusion. An information theoretical analysis of diffusion-based MC is required to better understand the potential of this novel communication mechanism. The study and the modeling of the noise sources is of utmost importance for this analysis. The objective of this paper is to provide a mathematical study of the noise at the reception of the molecular information in a diffusion-based MC system when the ligand-binding reception is employed. The reference diffusion-based MC system for this analysis is the physical end-to-end model introduced in a previous work by the same authors, where the reception process is realized through ligandbinding chemical receptors. The reception noise is modeled in this paper by following two different approaches, namely, through the ligand-receptor kinetics and through the stochastic chemical kinetics. The ligand-receptor kinetics allows to simulate the random perturbations in the chemical processes of the reception, while the stochastic chemical kinetics provides the tools to derive a closedform solution to the modeling of the reception noise. The ligand-receptor kinetics model is expressed through a block scheme, while the stochastic chemical kinetics results in the characterization of the reception noise using stochastic differential equations. Numerical results are provided to demonstrate that the analytical formulation of the reception noise in terms of stochastic chemical kinetics is compliant with the reception noise behavior resulting from the ligand-receptor kinetics simulations. Index TermsChemical master equation, diffusion, ligand-receptor kinetics, molecular communication, nanonetworks, nanotechnology,

Massimiliano Pierobon; Ian F. Akyildiz

2010-01-01T23:59:59.000Z

244

Deep Atomic Binding (DAB) Hypothesis: A New Approach of Fission Product Chemistry  

SciTech Connect

Former studies assumed that, after fission process occurs, the highly ionized new born atoms (20-22 positive charge), ionize the media in which they pass through before becoming stable atoms in a manner similar to 4-MeV ?-particles. Via ordinary chemical reactions with the surroundings, each stable atom has a probability to form chemical compound. Since there are about 35 different elemental atoms created through fission processes, a large number of chemical species were suggested to be formed. But, these suggested chemical species were not found in the environment after actual releases of FP during accidents like TMI (USA, 1979), and Chernobyl (former USSR, 1986), also the models based on these suggested reactions and species could not interpret the behavior of these actual species. It is assumed here that the ionization states of the new born atoms and the long term high temperature were not dealt with in an appropriate way and they were the reasons of former models failure. Our new approach of Deep Atomic Binding (DAB) based on the following: 1-The new born atoms which are highly ionized, 10-12 electrons associated with each nucleus, having a large probability to create bonds between them to form molecules. These bonds are at the L, or M shells, and we call it DAB. 2-The molecules stay in the reactor at high temperatures for long periods, so they undergo many stages of composition and decomposition to form giant molecules. By applying DAB approach, field data from Chernobyl, TMI and nuclear detonations could be interpreted with a wide coincidence resulted. (author)

Ajlouni, Abdul-Wali M.S. [Ministry of Energy and Mineral Resources (Jordan)

2006-07-01T23:59:59.000Z

245

External and Internal Guest Binding of a Highly Charged Supramolecular Host in Water: Deconvoluting the Very Different Thermodynamics  

SciTech Connect

NMR, UV-vis and isothermal titration calorimetry (ITC) measurements probe different aspects of competing host-guest equilibria as simple alkylammonium guest molecules interact with both the exterior (ion-association) and interior (encapsulation) of the [Ga{sub 4}L{sub 6}]{sup 12-} supramolecular assembly in water. Data obtained by each independent technique measure different components of the host-guest equilibria and only when analyzed together does a complete picture of the solution thermodynamics emerge. Striking differences between the internal and external guest binding are found. External binding is enthalpy driven and mainly due to attractive interactions between the guests and the exterior surface of the assembly while encapsulation is entropy driven as a result of desolvation and release of solvent molecules from the host cavity.

Sgarlata, Carmelo; Mugridge, Jeffrey; Pluth, Michael; Tiedemann,, Bryan; Zito, Valeria; Arena, Giuseppe; Raymond, Kenneth N.

2009-07-22T23:59:59.000Z

246

Optimization of density functional tight-binding and classical reactive molecular dynamics for high-throughput simulations of carbon materials  

Science Conference Proceedings (OSTI)

Carbon materials and nanostructures (fullerenes, nanotubes) are promising building blocks of nanotechnology. Potential applications include optical and electronic devices, sensors, and nano-scale machines. The multiscale character of processes related ... Keywords: ACM proceedings, BLAS, Cray XT5, LAPACK, advanced materials, density-functional tight binding, high-throughput, linear algebra, material science, molecular dynamics, multiscale-modeling, quantum chemistry, scientific libraries, scientific-computing

Jacek Jakowski; Bilel Hadri; Steven J. Stuart; Predrag Krstic; Stephan Irle; Dulma Nugawela; Sophya Garashchuk

2012-07-01T23:59:59.000Z

247

Analysis of Mcm2-7 chromatin binding during anaphase and in the transition to quiescence in fission yeast  

Science Conference Proceedings (OSTI)

Mcm2-7 proteins are generally considered to function as a heterohexameric complex, providing helicase activity for the elongation step of DNA replication. These proteins are loaded onto replication origins in M-G1 phase in a process termed licensing or pre-replicative complex formation. It is likely that Mcm2-7 proteins are loaded onto chromatin simultaneously as a pre-formed hexamer although some studies suggest that subcomplexes are recruited sequentially. To analyze this process in fission yeast, we have compared the levels and chromatin binding of Mcm2-7 proteins during the fission yeast cell cycle. Mcm subunits are present at approximately 1 x 10{sup 4} molecules/cell and are bound with approximately equal stoichiometry on chromatin in G1/S phase cells. Using a single cell assay, we have correlated the timing of chromatin association of individual Mcm subunits with progression through mitosis. This showed that Mcm2, 4 and 7 associate with chromatin at about the same stage of anaphase, suggesting that licensing involves the simultaneous binding of these subunits. We also examined Mcm2-7 chromatin association when cells enter a G0-like quiescent state. Chromatin binding is lost in this transition in a process that does not require DNA replication or the selective degradation of specific subunits.

Namdar, Mandana [Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS (United Kingdom); Kearsey, Stephen E. [Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS (United Kingdom)]. E-mail: stephen.kearsey@zoo.ox.ac.uk

2006-10-15T23:59:59.000Z

248

Characterization and Segmental Distribution of 251-Bolton-Hunterlabeled Substance P Binding Sites in Rat Spinal Cord  

E-Print Network (OSTI)

Substance P (SP) is widely distributed in the spinal cord and has been implicated as a neurotransmitter in several spinal cord neuronal systems. To investigate SP receptors in the spinal cord, 1251-Bolton-Hunter-SP (*I-BH-SP) was used to identify and characterize spinal cord binding sites for the peptide. The binding of *%BH-SP had the following characteristics: high affinity; time, temperature, and membrane concentration dependent; reversible; and saturable. The KS0 of SP in whole spinal cord was 0.46 nM as compared with 0.95, 60, and 150 nM for physalaemin, eledoisin, and kassinin. Four putative antagonists of SP were e 0.0001 times as potent as SP in inhibiting *%BH-SP binding. lCsos were 5, 7.5, 7.0, and 45 PM for D-Pro*, D-Trp73s-SP; D-Pro*, D-Phe, D-Trp-SP; D-Arg, D-Pro*, D-Tqfss, Leu-SP; and D-Pro4, D-Trp7Vs30-SP(4-1 I), respectively.

Clivel G. Charlton; Cinda; J. Helke

1984-01-01T23:59:59.000Z

249

Genetic probes of structure/function relationships in the Q{sub B} binding site of the photosynthetic reaction center  

SciTech Connect

In photosynthetic reaction centers, a quinone molecule, Q{sub B}, is the terminal acceptor in light-induced electron transfer. The crystal structure of the reaction center implicates the protonatable amiho acid residues L212Glu and L213Asp in the binding of Q{sub B} to the reaction center and in proton transfer to the anionic forms of Q{sub B} generated by electron transfer from Q{sub A}. Here we report the construction of the double mutant L212Ala-L213Ala by site-specific mutagenesis, and the isolation and preliminary biophysical characterization of revertant and suppressor strains that have regained the ability to grow under photosynthetic conditions. Our results show that neither L212Glu nor L213Asp is essential for efficient light-induced electron or proton transfer in Rhodobacter capsulatus and that second-site mutations, located within the QB binding pocket or at a more distant site, can compensate for mutations at L212 and L213. Acquisition of a single negatively charged residue (at position L213, or on the other side of the binding pocket at position L225) or loss of a positively charged residue (at position M231) is sufficient to restore activity to the complex.

Hanson, D.K.; Tiede, D.M.; Nance, S.L.; Chang, Chong-Hwan; Schiffer, M.

1991-06-25T23:59:59.000Z

250

The chlorophyll-binding protein CP47 in photosystem II. Final report  

DOE Green Energy (OSTI)

Generally, light-harvesting chlorophyll-binding proteins (LHCP) of the Cab family that are prevalent antenna systems in plants are thought to be absent in cyanobacteria. Therefore, it often is tacitly assumed that in cyanobacteria all chlorophyll is associated with the PS II and PS I core antenna. For this reason, it was of interest to investigate what the effect would be of genetic deletion of both the PS I core complex and the PS II core antenna in Synechocystis. Therefore, a mutant was made in which the psaAB genes for the PS I core were deleted, in addition to deletion or inactivation of psbB and/or psbC (coding for CP43). In this series of mutants, also apcE was deleted. In the absence of both CP47 and CP43, also the PS II reaction center proteins D1 and D2 were not detectable in the thylakoid membrane. Thus, both PS II and PS I were deleted in the resulting strains. Nonetheless, a significant amount of chlorophyll (about 15% of that present when PS II was left intact) was found to remain in the PS I-less, psbB{sup {minus}}, psbC{sup {minus}}, apcE{sup {minus}} mutant. This chlorophyll had fluorescence characteristics resembling those of LHC II in higher plants, with a 678 nm emission maximum at 77 K. The properties of this chlorophyll remaining in the absence of PS II and PS I in Synechocystis did not resemble those of chlorophyll bound to a CP43-like protein that has been found in cyanobacteria and that is expressed under iron-stress conditions. However, some similarities in terms of fluorescence emission were observed with the isolated 22 kDa protein encoded by psbS. The role and association of the remaining chlorophyll in the PS I-less, psbB{sup {minus}}, psbC{sup {minus}}, apcE{sup {minus}} mutant remains unclear, however, this chlorophyll protein is expected to be functionally connected to PS II when this photosystem is present.

Vermaas, W.F.J.

1995-12-31T23:59:59.000Z

251

Effects of chloroquine and hepatic stimulator substance on cellular accumulation and nuclear binding of sup 125 I-epidermal growth factor in primary culture of adult rat hepatocytes  

SciTech Connect

The effects of chloroquine and hepatic stimulator substance (HSS) on cellular accumulation and nuclear binding of {sup 125}I-epidermal growth factor (EGF) were examined in primary culture of adult rat hepatocytes. When intact hepatocytes were incubated at 37{degrees}C with {sup 125}I-EGF, the cellular accumulation and the nuclear binding reached a peak at 1 h and declined thereafter, where the nuclear binding was 2.49% at 1 h and 2.53% at 2 h. Chloroquine resulted in a time-dependent increase in the cellular accumulation and the nuclear binding was 3.37% at 1 h and 3.72% at 2 h. In contrast, HSS produced no change in each value, suggesting that HSS does not modulate EGF receptors in plasma membrane and nucleus.

Murawaki, Y.; Storkenmaier, R.; Fleig, W.E.; Hahn, E.G. (Tottori Univ. School of Medicine, Yonago (Japan))

1990-07-01T23:59:59.000Z

252

Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens  

SciTech Connect

The thanatos (the Greek god of death)-associated protein (THAP) domain is a sequence-specific DNA-binding domain that contains a C2-CH (Cys-Xaa{sub 2-4}-Cys-Xaa{sub 35-50}-Cys-Xaa{sub 2}-His) zinc finger that is similar to the DNA domain of the P element transposase from Drosophila. THAP-containing proteins have been observed in the proteome of humans, pigs, cows, chickens, zebrafish, Drosophila, C. elegans, and Xenopus. To date, there are no known THAP domain proteins in plants, yeast, or bacteria. There are 12 identified human THAP domain-containing proteins (THAP0-11). In all human THAP protein, the THAP domain is located at the N-terminus and is {approx}90 residues in length. Although all of the human THAP-containing proteins have a homologous N-terminus, there is extensive variation in both the predicted structure and length of the remaining protein. Even though the exact function of these THAP proteins is not well defined, there is evidence that they play a role in cell proliferation, apoptosis, cell cycle modulation, chromatin modification, and transcriptional regulation. THAP-containing proteins have also been implicated in a number of human disease states including heart disease, neurological defects, and several types of cancers. Human THAP4 is a 577-residue protein of unknown function that is proposed to bind DNA in a sequence-specific manner similar to THAP1 and has been found to be upregulated in response to heat shock. THAP4 is expressed in a relatively uniform manner in a broad range of tissues and appears to be upregulated in lymphoma cells and highly expressed in heart cells. The C-terminal domain of THAP4 (residues 415-577), designated here as cTHAP4, is evolutionarily conserved and is observed in all known THAP4 orthologs. Several single-domain proteins lacking a THAP domain are found in plants and bacteria and show significant levels of homology to cTHAP4. It appears that cTHAP4 belongs to a large class of proteins that have yet to be fully functionally characterized. On the basis of prior work, we predicted that cTHAP4 is composed of a heme-binding nitrobindin domain, making THAP4 the only human THAP protein predicted to bind a cofactor. Nitrobindin, a recently characterized protein from Arabidopsis thaliana, is structurally similar and exhibits nitric oxide (NO)-binding properties that resemble the heme-binding nitrophorins. Nitrophorins use a heme moiety to store, transport, and release NO in a pH-specific manner. Although the exact function of nitrobindin is not fully known, the similarities between the well-characterized nitrophorins imply a role in NO transport, sensing, or metabolism. To better elucidate the possible function of THAP4, we solved the hemebound structure of cTHAP4 to a resolution of 1.79 {angstrom}.

Bianchetti, Christopher M.; Bingman, Craig A.; Phillips, Jr., George N. (UW)

2012-03-15T23:59:59.000Z

253

Non-hinge-binding pyrazolo[1,5-a]pyrimidines as potent B-Raf kinase inhibitors  

SciTech Connect

As part of our research effort to discover B-Raf kinase inhibitors, we prepared a series of C-3 substituted N-(3-(pyrazolo[1,5-a]pyrimidin-7-yl)phenyl)-3-(trifluoromethyl)benzamides. X-ray crystallography studies revealed that one of the more potent inhibitors (10n) bound to B-Raf kinase without forming a hinge-binding hydrogen bond. With basic amine residues appended to C-3 aryl residues, cellular activity and solubility were enhanced over previously described compounds of this class.

Berger, Dan M.; Torres, Nancy; Dutia, Minu; Powell, Dennis; Ciszewski, Greg; Gopalsamy, Ariamala; Levin, Jeremy I.; Kim, Kyung-Hee; Xu, Weixin; Wilhelm, James; Hu, YongBo; Collins, Karen; Feldberg, Larry; Kim, Steven; Frommer, Eileen; Wojciechowicz, Donald; Mallon, Robert; (Wyeth)

2010-11-19T23:59:59.000Z

254

High energy nuclear quasielastic reactions: Decisive tests of nuclear binding/pion models of the EMC effect  

SciTech Connect

The light-cone nucleon momentum distributions obtained from non- relativistic spectral functions or given by nuclear binding/pion models are often used to analyze high Q{sup 2} quasi-elastic and deep-inelastic (e,e{prime}) reactions. We demonstrate that in such models the presence of non-nucleonic components causes the scattering from forward and backward moving target protons to be significantly different. Other models do not have this property. The sensitivity of current (e,e{prime}p) and (p,pp) color transparency experiments is sufficient to observe these differences.

Frankfurt, L; Strikman, M [Washington Univ., Seattle, WA (United States). Inst. for Nuclear Theory AN SSSR, Leningrad (USSR). Inst. Yadernoj Fiziki; Miller, G A [Washington Univ., Seattle, WA (United States). Inst. for Nuclear Theory

1991-01-01T23:59:59.000Z

255

Cell-surface changes in cadmium-resistant Euglena: Studies using lectin-binding techniques and flow cytometry  

Science Conference Proceedings (OSTI)

Most in vitro studies on contaminants focus on the short-term effects of pollutants on cells, without regard to long-term effects and the ability of cells or microorganisms to develop a specific resistance to a pollutant. Cadmium is ubiquitous environmental contaminant. This heavy metal enters the aquatic environment mainly through vapor emissions and fallout during smelting operations. Diverse mechanisms of algal resistance to toxic metals are known. Among these, the most general mechanism is the development of metal-binding proteins. In cadmium-resistant unicellular Euglena gracilis Z algae cells, the metal did not appear to be sequestered on soluble metal-binding ligands. Previous experiments have shown that resistance development is related to a diminution of cadmium penetration into cells, implicating cell surface or membrane alteration. This research investigates the mechanisms of development of cadmium resistance in Euglena cells at the cell-surface level. Sugar chains of glycoproteins and glycolipids are a predominant feature of the surface of cells. Moreover, the cell-response to environmental changes is often orchestrated through surface macromolecules such as glycoproteins. In this study, we applied this lectin method to investigate surface carbohydrate expression during and after resistance development. Our interest was twofold: (1) to learn more about the carbohydrate composition of the cell-surface of Euglena; and (2) to determine whether transition from wild cells to Cd-resistant cells changes the expression of cell-surface carbohydrates. 13 refs., 2 figs., 1 tab.

Bonaly, J.; Brochiero, E. [Faculte de Pharmacie, Chatenay-Malabry (France)

1994-01-01T23:59:59.000Z

256

Non-binding conductor load bearing roller for a gas-insulated transmission line having a corrugated outer conductor  

DOE Patents (OSTI)

A gas-insulated transmission line includes a corrugated outer conductor, an inner conductor disposed within and insulated from the outer conductor by means of support insulators and an insulating gas, and a non-binding transport device for supporting and permitting movement of the inner conductor/insulating support assembly axially along the corrugated outer conductor without radial displacement and for moving without binding along corrugations of any slope less than vertical. The transport device includes two movable contacts, such as skids or rollers, supported on a common pivot lever, the pivot lever being rotatably disposed about a pivot lever axis, which pivot lever axis is in turn disposed on the periphery of a support insulator or particle trap if one is used. The movable contacts are separated axially a distance equal to the axial distance between the peaks and valleys of the corrugations of the outer conductor and separated radially a distance equal to the radial distance between the peaks and valleys of the corrugations of the outer conductor. The transport device has the pivot lever axis disposed parallel to the motion of travel of the inner conductor/insulating support assembly.

Fischer, William H. (Pittsburgh, PA)

1984-01-01T23:59:59.000Z

257

Interaction of the 4S polycyclic hydrocarbon-binding protein with the cytochrome P450c gene  

SciTech Connect

The 4S polycyclic hydrocarbon binding protein has been purified from rat liver and its properties examined. The protein was incubated with subclones from the P450c gene; it specifically interacted with a plasmid that contained the 5'-half of intron 1, exon 1 and 5'-flanking sequences. Exonuclease foot-printing after binding of the 4S protein to portions of the P450c gene showed protection at -200 and -400 bp from exon 1. The region -882 to +2545bp was constructed before a reporter, chloramphenicol acetyl transferase (CAT) gene in a plasmid that contained the SV40 ori, polyA signals, ampicillin resist gene. The P450c region contained promoter and putative regulatory sequences. The construct was transfected into rat hepatocytes, RL-PR-C and into rat hepatoma cells, H-4-11-E. After addition of 3-methylcholanthrene (3MC), CAT expression was induced. When the plasmid was constructed with the P450c fragment inverted, no CAT expression was seen. Deletion of -95 to -665 or from -238 to -660 bp eliminated the expression of CAT in response to 3MC. These experiments indicated the importance of this region in the induction of P450c by 3MC.

Houser, W.H.; Cunningham, C.K.; Hines, R.N.; Bresnick, E.

1987-05-01T23:59:59.000Z

258

The Influence of Spatial Variation in Chromatin Density Determined by X-ray Tomograms on the Time to Find DNA Binding Sites  

E-Print Network (OSTI)

In this work we examine how volume exclusion caused by regions of high chromatin density might influence the time required for proteins to find specific DNA binding sites. The spatial variation of chromatin density within mouse olfactory sensory neurons is determined from soft X-ray tomography reconstructions of five nuclei. We show that there is a division of the nuclear space into regions of low-density euchromatin and high-density heterochromatin. Volume exclusion experienced by a diffusing protein caused by this varying density of chromatin is modeled by a repulsive potential. The value of the potential at a given point in space is chosen to be proportional to the density of chromatin at that location. The constant of proportionality, called the volume exclusivity, provides a model parameter that determines the strength of volume exclusion. Numerical simulations demonstrate that the mean time for a protein to locate a binding site localized in euchromatin is minimized for a finite, non-zero volume exclusivity. For binding sites in heterochromatin, the mean time is minimized when the volume exclusivity is zero (the protein experiences no volume exclusion). An analytical theory is developed to explain these results. The theory suggests that for binding sites in euchromatin there is an optimal level of volume exclusivity that balances a reduction in the volume searched in finding the binding site, with the height of effective potential barriers the protein must cross during the search process.

Samuel A. Isaacson; Carolyn A. Larabell; Mark A. Le Gros; David M. McQueen; Charles S. Peskin

2013-07-15T23:59:59.000Z

259

Symmetry-related mutants in the quinone binding sites of the reaction center -- The effects of changes in charge distribution  

Science Conference Proceedings (OSTI)

To probe the structural elements that contribute to the functional asymmetries of the two ubiquinone{sub 10}binding pockets in the reaction center of Rhodobacter capsulatus, the authors targeted the L212Glu-L213Asp (near Q{sub B}) and the M246Ala-M247Ala (near Q{sub A}) pairs of symmetry-related residues for site-specific mutagenesis. They have constructed site-specific mutants that eliminate the sequence differences at these positions (L212Glu-L213Asp{yields}Ala-Ala or M246Ala-M247Ala{yields}Glu-Asp), and have reversed that asymmetry by constructing a quadruple-mutant strain, RQ (L212Glu-L213Asp-M246Ala-M247Ala{yields}Ala-Ala-Glu-Asp). The mutations were designed to change the charge distribution in the quinone-binding region of the reaction center; none of the strains is capable of photosynthetic growth. In photocomponent phenotypic revertants of the RQ strain, second-site mutations which affect Q{sub B} function are coupled to mutations in the Q{sub A} site which restore an Ala or substitute a Tyr at the M247 site; one strain carries an additional Met{yields}Glu substitution at M260 near Q{sub A}. All of the RQ revertants retain the engineered M246Ala{yields}Glu mutation in the Q{sub A} site as well as the L212Ala-L213Ala mutations in the Q{sub B} site. Kinetic characterization of the RQ revertants will give them an idea of what structural and functional elements are important for restoring efficiency to electron and proton transfer pathways in the RQRC, which is far from native. To date, these preliminary results underscore the importance of an asymmetric distribution of polar amino acids in the quinone binding pockets and its influence on the functional properties of the reaction center.

Hanson, D.K.; Schiffer, M. [Argonne National Lab., IL (United States). Center for Mechanistic Biology and Biotechnology

1997-09-01T23:59:59.000Z

260

Roles of the Tetrahymena thermophila type I element binding factor, TIF1, in DNA replication and genome stability  

E-Print Network (OSTI)

The Tetrahymena thermophila rDNA minichromosome has been used as a model system for studying DNA replication. Previous studies have identified cis-acting replication determinants within the rDNA origin and promoter region including the type I element that is essential for replication initiation, fork progression and promoter activation. TIF1 is a non-ORC single strand-binding protein that binds the type I element in vivo. TIF1 binds opposing strands at the origin and promoter regions indicating that it may play a role in selectively marking these regions. In this dissertation, I use gene disruption to elucidate the role of TIF1 in replication. This work reveals that TIF1 represses rDNA origin firing, and is required for proper macronuclear S phase progression and division. Replication at the rDNA origin initiates precociously despite the observation that TIF1 mutants exhibit an elongated macronuclear S phase and a diminished rate of DNA replication. The amitotic macronucleus also displays delayed and abnormal division even though cells exit S phase with a wild-type macronuclear DNA content. Nuclear defects are also evident in the diploid micronucleus as TIF1 mutants contain fewer micronuclear chromosomes and are unable to pass genetic information to progeny. This defect is progressive as clonal mutant lines exhibit micronuclear instability during subsequent vegetative cell cycling. This work reveals that these macro- and micronuclear phenotypes may be the result of DNA damage as TIF1 mutants are hypersensitive to DNA damaging agents. This suggests that TIF1 mutants may have defects in the DNA damage response pathway. TIF1-deficient cells also incur DNA damage with no exogenous damaging agents. I propose that micro- and macronuclear defects witnessed in TIF1 mutant cells result from cells exiting S phase with compromised chromosomes due to the accumulation of DNA damage. Furthermore, TIF1 appears to play a role in the prevention, recognition or repair of DNA damage in addition to regulating rDNA replication and cell cycle progression and division. Additionally, TIF1 plays an essential role in the faithful propagation of both the macro- and micronuclear genomes.

Morrison, Tara Laine

2005-08-01T23:59:59.000Z

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261

An Object-Oriented Tcl/Tk Binding for Interpreted Control of the NIST Express Toolkit in the NIST STEP Application Protocol Development Environment  

E-Print Network (OSTI)

The National Institute of Standards and Technology (NIST) has built numerous software toolkits and applications for manipulating STEP and EXPRESS data. These toolkits are traditionally used as compiled libraries which are linked to other compiled modules. This paper describes a binding allowing the toolkit interfaces to be called from interpreted scripts. This significantly reduces the time required to construct and compile new applications. An X11 extension allows the construction of graphic elements, providing easy creation and integration of existing applications into X graphic user interfaces. We describe how the combination of bindings has been used to construct a STEP Application Protocol Development Environment. Keywords: Tcl; Tk; EXPRESS; Object Oriented; National PDES Testbed; PDES; STEP; APDE; Development Environment Reprinted from Proceedings of the EXPRESS User Group Workshop (EUG `95), Grenoble, France, October 21-22, 1995. An Object-Oriented Tcl/Tk Binding for Interpr...

An Object-oriented; Don Libes; Stephen N. Clark

1995-01-01T23:59:59.000Z

262

In Silico Design, Extended Molecular Dynamic Simulations and Binding Energy Calculations for a New Series of Dually Acting Inhibitors against EGFR and HER2  

E-Print Network (OSTI)

Starting from the lead structure we have identified in our previous works, we are extending our insight understanding of its potential inhibitory effect against both EGFR and HER2 receptors. Herein and using extended molecular dynamic simulations and different scoring techniques, we are providing plausible explanations for the observed inhibitory effect. Also, we are comparing the binding mechanism in addition to the dynamics of binding with two other approved inhibitors against EGFR (Lapatinib) and HER2 (SYR). Based on this information, we are also designing and in silico screening new potential inhibitors sharing the same scaffold of the lead structure. We have chosen the best scoring inhibitor for additional in silico investigation against both the wild-type and T790M mutant strain of EGFR. It seems that certain substitution pattern guarantees the binding to the conserved water molecule commonly observed with kinase crystal structures. Also, the new inhibitors seem to form a stable interaction with the mut...

Ahmed, Marawan; Abouzid, Khaled A; Wang, Feng

2013-01-01T23:59:59.000Z

263

The binding of herbicidal halovinyl anilides to the photosystem II Q sub B site and the relationship between affinities and molecular characteristics  

SciTech Connect

A new class of herbicidal halovinyl anilides, which inhibit photosynthetic electron transport, have been shown to inhibit {sup 14}C-atrazine binding in spinach thylakoid membranes. A scatchard analysis of the {sup 14}C-atrazine binding inhibition of the lead compound, LY221204, has shown it to be a competitive inhibitor. Preliminary QSAR (quantitative structure activity relationship) studies suggested that 75-80% of the variance in vivo activity could be explained by size and electronic properties and that activity increased with smaller and more electron releasing substituents. To analyze the effects of these properties on intrinsic activity, a larger QSAR study was undertaken. Atrazine binding inhibition data was generated for a group of substituted, non-conjugated vinyl anilides at 1 and 10 {mu}M concentrations and plotted as a function of physicochemical parameters. The results will be presented.

Eilers, R.J.; Crouse, G.D.; Durst, G.L.; Streusand, V.J.; Manly, C.J.; Webster, J.D. (DowElanco, Greenfield, IN (USA))

1990-05-01T23:59:59.000Z

264

Crystal structure of the N-terminal region of human Ash2L shows a winged-helix motif involved in DNA binding  

Science Conference Proceedings (OSTI)

Ash2L is a core component of the MLL family histone methyltransferases and has an important role in regulating the methylation of histone H3 on lysine 4. Here, we report the crystal structure of the N-terminal domain of Ash2L and reveal a new function of Ash2L. The structure shows that Ash2L contains an atypical PHD finger that does not have histone tail-binding activity. Unexpectedly, the structure shows a previously unrecognized winged-helix motif that directly binds to DNA. The DNA-binding-deficient mutants of Ash2L reduced Ash2L localization to the HOX locus. Strikingly, a single mutation in Ash2L{sub WH} (K131A) breaks the chromatin domain boundary, suggesting that Ash2L also has a role in chromosome demarcation.

Chen, Yong; Wan, Bingbing; Wang, Kevin C.; Cao, Fang; Yang, Yuting; Protacio, Angeline; Dou, Yali; Chang, Howard Y.; Lei, Ming (Michigan-Med); (HHMI)

2011-09-06T23:59:59.000Z

265

Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel May Affect Cellobiohydrolase Directional Specificity  

NLE Websites -- All DOE Office Websites (Extended Search)

Initial Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel May Affect Cellobiohydrolase Directional Specificity Pavan K. GhattyVenkataKrishna, †‡ Emal M. Alekozai, §{ Gregg T. Beckham, k ** Roland Schulz, {‡‡ Michael F. Crowley, ‡†† * Edward C. Uberbacher, †‡ * and Xiaolin Cheng ‡{‡‡ * † Computational Biology and Bioinformatics Group and ‡ BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; § Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg Germany; { UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee; k National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado; **Department of Chemical Engineering, Colorado School of Mines, Golden, Colorado; †† Biosciences Center, National

266

Apo and InsP[subscript 3]-bound crystal structures of the ligand-binding domain of an InsP[subscript 3] receptor  

Science Conference Proceedings (OSTI)

We report the crystal structures of the ligand-binding domain (LBD) of a rat inositol 1,4,5-trisphosphate receptor (InsP{sub 3}R) in its apo and InsP{sub 3}-bound conformations. Comparison of these two conformations reveals that LBD's first {beta}-trefoil fold ({beta}-TF1) and armadillo repeat fold (ARF) move together as a unit relative to its second {beta}-trefoil fold ({beta}-TF2). Whereas apo LBD may spontaneously transition between gating conformations, InsP{sub 3} binding shifts this equilibrium toward the active state.

Lin, Chun-Chi; Baek, Kyuwon; Lu, Zhe (UPENN)

2012-05-08T23:59:59.000Z

267

V-008: Debian Security Advisory | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

8: Debian Security Advisory 8: Debian Security Advisory V-008: Debian Security Advisory October 23, 2012 - 6:00am Addthis PROBLEM: Debian Security Advisory PLATFORM: Debian GNU/Linux 6.0 ABSTRACT: Debian update for bind9 REFERENCE LINKS: Debian Security Advisory DSA-2560-1 Debian bugtracking system: Bug 690118 ISC Reference Number: AA-00801 Secunia Advisory SA51054 CVE-2012-5166 IMPACT ASSESSMENT: Medium DISCUSSION: was discovered that BIND, a DNS server, hangs while constructing the additional section of a DNS reply, when certain combinations of resource records are present. This vulnerability affects both recursive and authoritative servers. For the stable distribution (squeeze), this problem has been fixed in version 1:9.7.3.dfsg-1~squeeze8. IMPACT: Debian has issued an update for bind9. This fixes a vulnerability, which

268

V-008: Debian Security Advisory | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

08: Debian Security Advisory 08: Debian Security Advisory V-008: Debian Security Advisory October 23, 2012 - 6:00am Addthis PROBLEM: Debian Security Advisory PLATFORM: Debian GNU/Linux 6.0 ABSTRACT: Debian update for bind9 REFERENCE LINKS: Debian Security Advisory DSA-2560-1 Debian bugtracking system: Bug 690118 ISC Reference Number: AA-00801 Secunia Advisory SA51054 CVE-2012-5166 IMPACT ASSESSMENT: Medium DISCUSSION: was discovered that BIND, a DNS server, hangs while constructing the additional section of a DNS reply, when certain combinations of resource records are present. This vulnerability affects both recursive and authoritative servers. For the stable distribution (squeeze), this problem has been fixed in version 1:9.7.3.dfsg-1~squeeze8. IMPACT: Debian has issued an update for bind9. This fixes a vulnerability, which

269

Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs  

E-Print Network (OSTI)

MicroRNAs (miRNAs) are 1922-nucleotide noncoding RNAs that post-transcriptionally regulate mRNA targets. We have identified endogenous miRNA binding sites in mouse embryonic stem cells (mESCs), by performing photo-cross-linking ...

Leung, Anthony K. L.

270

HH Domain of Alzheimers Disease Ab Provides Structural Basis for Neuronal Binding in PC12 and Mouse Cortical/Hippocampal Neurons  

E-Print Network (OSTI)

A key question in understanding AD is whether extracellular Ab deposition of parenchymal amyloid plaques or intraneuronal Ab accumulation initiates the AD process. Amyloid precursor protein (APP) is endocytosed from the cell surface into endosomes where it is cleaved to produce soluble Ab which is then released into the brain interstitial fluid. Intraneuronal Ab accumulation is hypothesized to predominate from the neuronal uptake of this soluble extracellular Ab rather than from ER/Golgi processing of APP. We demonstrate that substitution of the two adjacent histidine residues of Ab40 results in a significant decrease in its binding with PC12 cells and mouse cortical/hippocampal neurons. These substitutions also result in a dramatic enhancement of both thioflavin-T positive fibril formation and binding to preformed Ab fibrils while maintaining its plaque-binding ability in AD transgenic mice. Hence, alteration of the histidine domain of Ab prevented neuronal binding and drove Ab to enhanced fibril formation and subsequent amyloid plaque deposition- a potential mechanism for removing toxic species of Ab. Substitution or even masking of these Ab histidine residues might provide a new therapeutic direction for minimizing neuronal uptake and subsequent neuronal degeneration and

Joseph F. Poduslo; Emily J. Gilles; Muthu Ramakrishnan; Kyle G. Howell; Thomas M. Wengenack; Geoffry L. Curran; Karunya K. K

2010-01-01T23:59:59.000Z

271

J. Phys. Chem. 1994, 98, 5113-5111 5773 Free Energy of Solvation, Interaction, and Binding of Arbitrary Charge Distributions Imbedded in  

E-Print Network (OSTI)

J. Phys. Chem. 1994, 98, 5113-5111 5773 Free Energy of Solvation, Interaction, and Binding in a continuum solvent. Background Attempts seeking analytical solutions to the hydration free energies solvation free energies of arbitrary charge distributions with an overall spherical symmetry. This theory

Jayaram, Bhyravabotla

272

Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation  

SciTech Connect

The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an important chromatin modifying complex that can both acetylate and deubiquitinate histones. Sgf29 is a novel component of the SAGA complex. Here, we report the crystal structures of the tandem Tudor domains of Saccharomyces cerevisiae and human Sgf29 and their complexes with H3K4me2 and H3K4me3 peptides, respectively, and show that Sgf29 selectively binds H3K4me2/3 marks. Our crystal structures reveal that Sgf29 harbours unique tandem Tudor domains in its C-terminus. The tandem Tudor domains in Sgf29 tightly pack against each other face-to-face with each Tudor domain harbouring a negatively charged pocket accommodating the first residue alanine and methylated K4 residue of histone H3, respectively. The H3A1 and K4me3 binding pockets and the limited binding cleft length between these two binding pockets are the structural determinants in conferring the ability of Sgf29 to selectively recognize H3K4me2/3. Our in vitro and in vivo functional assays show that Sgf29 recognizes methylated H3K4 to recruit the SAGA complex to its targets sites and mediates histone H3 acetylation, underscoring the importance of Sgf29 in gene regulation.

Bian, Chuanbing; Xu, Chao; Ruan, Jianbin; Lee, Kenneth K.; Burke, Tara L.; Tempel, Wolfram; Barsyte, Dalia; Li, Jing; Wu, Minhao; Zhou, Bo O.; Fleharty, Brian E.; Paulson, Ariel; Allali-Hassani, Abdellah; Zhou, Jin-Qiu; Mer, Georges; Grant, Patrick A.; Workman, Jerry L.; Zang, Jianye; Min, Jinrong (Toronto); (Stowers); (UST - China); (UV); (Chinese Aca. Sci.); (MCCM)

2011-09-28T23:59:59.000Z

273

Detection of Multiple-Duty-Related Security Leakage in ...  

Science Conference Proceedings (OSTI)

... ARCHON is a digital library that federates physics ... on Software Engineering (ICSE 2005), pages ... formation Security Conference (ISC 2005), pages ...

2009-11-16T23:59:59.000Z

274

What can be learned from binding energy differences about nuclear structure: the example of delta V_{pn}  

E-Print Network (OSTI)

We perform an analysis of a binding energy difference called delta V_{pn}(N,Z) =- 1/4(E(Z,N)-E(Z,N-2)-E(Z-2,N)+ E(Z-2,N-2) in the framework of a realistic nuclear model. Using the angular-momentum and particle-number projected generator coordinate method and the Skyrme interaction SLy4, we analyze the contribution brought to delta V_{pn} by static deformation and dynamic fluctuations around the mean-field ground state. Our method gives a good overall description of delta V_{pn} throughout the chart of nuclei with the exception of the anomaly related to the Wigner energy along the N=Z line. The main conclusions of our analysis are that (i) the structures seen in the systematics of delta V_{pn} throughout the chart of nuclei can be easily explained combining a smooth background related to the symmetry energy and correlation energies due to deformation and collective fluctuations; (ii) the characteristic pattern of delta V_{pn} around a doubly-magic nucleus is a trivial consequence of the asymmetric definition o...

Bender, Michael

2011-01-01T23:59:59.000Z

275

The adenovirus E4 11 k protein binds and relocalizes the cytoplasmic P-body component Ddx6 to aggresomes  

Science Conference Proceedings (OSTI)

The adenovirus E4 11 k protein, product of E4 ORF3, is required in infection for processes including normal accumulation of viral late mRNAs. 11 k restructures both the nucleus and cytoplasm of infected cells by relocalizing specific host cell target proteins, most strikingly components of nuclear PML oncogenic domains. It is likely that in many cases relocalization inactivates target proteins to produce 11 k's effects, although the mechanism and targets for stimulation of late mRNA accumulation is unknown. We have identified a new set of proteins relocalized by 11 k: at least five protein components of cytoplasmic mRNA processing bodies (p-bodies) are found in 11 k-induced cytoplasmic aggresomes, sites where proteins are inactivated or destroyed. One of these p-body proteins, RNA helicase Ddx6, binds 11 k, suggesting a mechanism for relocalization. Because p-bodies are sites for mRNA degradation, their modification by 11 k may provide an explanation for the role of 11 k in viral late mRNA accumulation.

Greer, Amy E. [Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore MD 21205 (United States); Hearing, Patrick [Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, Stony Brook, NY 11794 (United States); Ketner, Gary, E-mail: gketner@jhsph.edu [W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore MD 21205 (United States)

2011-08-15T23:59:59.000Z

276

Nbs1-dependent binding of Mre11 to adenovirus E4 mutant viral DNA is important for inhibiting DNA replication  

Science Conference Proceedings (OSTI)

Adenovirus (Ad) infections stimulate the activation of cellular DNA damage response and repair pathways. Ad early regulatory proteins prevent activation of DNA damage responses by targeting the MRN complex, composed of the Mre11, Rad50 and Nbs1 proteins, for relocalization and degradation. In the absence of these viral proteins, Mre11 colocalizes with viral DNA replication foci. Mre11 foci formation at DNA damage induced by ionizing radiation depends on the Nbs1 component of the MRN complex and is stabilized by the mediator of DNA damage checkpoint protein 1 (Mdc1). We find that Nbs1 is required for Mre11 localization at DNA replication foci in Ad E4 mutant infections. Mre11 is important for Mdc1 foci formation in infected cells, consistent with its role as a sensor of DNA damage. Chromatin immunoprecipitation assays indicate that both Mre11 and Mdc1 are physically bound to viral DNA, which could account for their localization in viral DNA containing foci. Efficient binding of Mre11 to E4 mutant DNA depends on the presence of Nbs1, and is correlated with a significant E4 mutant DNA replication defect. Our results are consistent with a model in which physical interaction of Mre11 with viral DNA is mediated by Nbs1, and interferes with viral DNA replication.

Mathew, Shomita S. [Department of Microbiology, 32 Pearson Hall, Miami University, Oxford OH 45056 (United States); Bridge, Eileen [Department of Microbiology, 32 Pearson Hall, Miami University, Oxford OH 45056 (United States)], E-mail: BridgeE@muohio.edu

2008-04-25T23:59:59.000Z

277

Chain-specific Protein Kinase C Activity by a Direct Interaction: Identification of the 143-3 Binding Domain  

E-Print Network (OSTI)

Myosin II heavy chain (MHC) specific protein kinase C (MHC-PKC), isolated from Dictyostelium discoideum, regulates myosin II assembly and localization in response to the chemoattractant cyclic AMP. Immunoprecipitation of MHC-PKC revealed that it resides as a complex with several proteins. We show herein that one of these proteins is a homologue of the 143-3 protein (Dd143-3). This protein has recently been implicated in the regulation of intracellular signaling pathways via its interaction with several signaling proteins, such as PKC and Raf-1 kinase. We demonstrate that the mammalian 143-3 ? isoform inhibits the MHC-PKC activity in vitro and that this inhibition is carried out by a direct interaction between the two proteins. Furthermore, we found that the cytosolic MHC-PKC, which is inactive, formed a complex with Dd143-3 in the cytosol in a cyclic AMP-dependent manner, whereas the membrane-bound active MHC-PKC was not found in a complex with Dd143-3. This suggests that Dd143-3 inhibits the MHC-PKC in vivo. We further show that MHC-PKC binds Dd143-3 as well as 143-3? through its C1 domain, and the interaction between these two proteins does not involve a peptide containing phosphoserine as was found for Raf-1 kinase. Our experiments thus show an in vivo function for a member of the 143-3 family and demonstrate that MHC-PKC interacts directly with Dd143-3 and 143-3 ? through its C1 domain both in vitro and in vivo, resulting in the inhibition of the kinase.

Meirav Matto-yelin; Alastair Aitken; Shoshana Ravid; James A. Spudich

1997-01-01T23:59:59.000Z

278

Allosteric Activation of E2-RING Finger-Mediated Ubiquitylation by a Structurally Defined Specific E2-Binding Region of gp78  

SciTech Connect

The activity of RING finger ubiquitin ligases (E3) is dependent on their ability to facilitate transfer of ubiquitin from ubiquitin-conjugating enzymes (E2) to substrates. The G2BR domain within the E3 gp78 binds selectively and with high affinity to the E2 Ube2g2. Through structural and functional analyses, we determine that this occurs on a region of Ube2g2 distinct from binding sites for ubiquitin-activating enzyme (E1) and RING fingers. Binding to the G2BR results in conformational changes in Ube2g2 that affect ubiquitin loading. The Ube2g2:G2BR interaction also causes an 50-fold increase in affinity between the E2 and RING finger. This results in markedly increased ubiquitylation by Ube2g2 and the gp78 RING finger. The significance of this G2BR effect is underscored by enhanced ubiquitylation observed when Ube2g2 is paired with other RING finger E3s. These findings uncover a mechanism whereby allosteric effects on an E2 enhance E2-RING finger interactions and, consequently, ubiquitylation.

Das, Ranabir; Mariano, Jennifer; Tsai, Yien Che; Kalathur, Ravi C.; Kostova, Zlatka; Li, Jess; Tarasov, Sergey G.; McFeeters, Robert L.; Altieri, Amanda S.; Ji, Xinhua; Byrd, R. Andrew; Weissman, Allan M.; (NCI)

2010-11-12T23:59:59.000Z

279

Binding of the Respiratory Chain Inhibitor Antimycin to theMitochondrial bc1 Complex: A New Crystal Structure Reveals an AlteredIntramolecular Hydrogen-Bonding Pattern  

DOE Green Energy (OSTI)

Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex.Structure-activity-relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc1 complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc1 complex at 2.28Angstrom resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cyt b, and the formylamino O H-bonds via a water molecule to Lys227. A strong density the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alpha-A helix.

Huang, Li-shar; Cobessi, David; Tung, Eric Y.; Berry, Edward A.

2005-05-10T23:59:59.000Z

280

XAFS Studies of Cobalt(II) Binding by Solid Peat and Soil-derived Humic Acids and Plant-derived Humic Acid-like Substances  

SciTech Connect

This work has examined cobalt(II) binding by a variety of solid humic acids (HAs) isolated from peat, plant and soil sources at temperatures down to 60 K. The results confirm that X-ray absorption near-edge spectroscopy (XANES) measurements cannot distinguish between aquo and carboxylato ligands in the inner coordination sphere of Co(II). However, between 1 and 2 inner-sphere carboxylato ligands can be detected in all the peat, plant and soil-derived HA samples by extended X-ray absorption fine structure (EXAFS) measurements, indicating inner-sphere coordination of HA-bound Co(II). The precision of C(carboxylate) detection is limited by the extent and quality of the data and the contribution from inner-sphere O to the Fourier transformed peaks used to detect carbon. Putative chelate ring formation is consistent with a relatively negative entropy change in step A, the stronger Co(II) binding step by HA functional groups, and could relate to 'non-exchangeable' metal binding by HSs.

Ghabbour,E.; Scheinost, A.; Davies, G.

2007-01-01T23:59:59.000Z

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281

Proteomic analysis of the nuclear matrix in the early stages of rat liver carcinogenesis: Identification of differentially expressed and MAR-binding proteins  

Science Conference Proceedings (OSTI)

Tumor progression is characterized by definite changes in the protein composition of the nuclear matrix (NM). The interactions of chromatin with the NM occur via specific DNA sequences called MARs (matrix attachment regions). In the present study, we applied a proteomic approach along with a Southwestern assay to detect both differentially expressed and MAR-binding NM proteins, in persistent hepatocyte nodules (PHN) in respect with normal hepatocytes (NH). In PHN, the NM undergoes changes both in morphology and in protein composition. We detected over 500 protein spots in each two dimensional map and 44 spots were identified. Twenty-three proteins were differentially expressed; among these, 15 spots were under-expressed and 8 spots were over-expressed in PHN compared to NH. These changes were synchronous with several modifications in both NM morphology and the ability of NM proteins to bind nuclear RNA and/or DNA containing MARs sequences. In PHN, we observed a general decrease in the expression of the basic proteins that bound nuclear RNA and the over-expression of two species of Mw 135 kDa and 81 kDa and pI 6.7-7.0 and 6.2-7.4, respectively, which exclusively bind to MARs. These results suggest that the deregulated expression of these species might be related to large-scale chromatin reorganization observed in the process of carcinogenesis by modulating the interaction between MARs and the scaffold structure.

Barboro, Paola [Istituto Nazionale per la Ricerca sul Cancro, Largo Rosanna Benzi, 10 - 16132 Genova (Italy); D'Arrigo, Cristina [C.N.R., Istituto per lo Studio delle Macromolecole, ISMAC, Sezione di Genova, Via De Marini, 6 - 16149 Genova (Italy); Repaci, Erica [Istituto Nazionale per la Ricerca sul Cancro, Largo Rosanna Benzi, 10 - 16132 Genova (Italy); Bagnasco, Luca [Istituto Nazionale per la Ricerca sul Cancro, Largo Rosanna Benzi, 10 - 16132 Genova (Italy); Dipartimento di Oncologia, Biologia e Genetica, Universita di Genova, Largo R. Benzi, 10 - 16132 Genova (Italy); Orecchia, Paola; Carnemolla, Barbara [Istituto Nazionale per la Ricerca sul Cancro, Largo Rosanna Benzi, 10 - 16132 Genova (Italy); Patrone, Eligio [C.N.R., Istituto per lo Studio delle Macromolecole, ISMAC, Sezione di Genova, Via De Marini, 6 - 16149 Genova (Italy); Balbi, Cecilia [Istituto Nazionale per la Ricerca sul Cancro, Largo Rosanna Benzi, 10 - 16132 Genova (Italy)], E-mail: cecilia.balbi@istge.it

2009-01-15T23:59:59.000Z

282

What can be learned from binding energy differences about nuclear structure: The example of {delta}V{sub pn}  

Science Conference Proceedings (OSTI)

We perform an analysis of a binding energy difference called {delta}V{sub pn}(N,Z){identical_to}-(1/4)[E(Z,N)-E(Z,N-2)-E(Z-2,N)+E(Z-2,N-2)] in the framework of a realistic nuclear model. It has been suggested that {delta}V{sub pn} values provide a sensitive probe of nuclear structure, and it has been put forward as a primary motivation for the measurement of specific nuclear masses. Using the angular momentum and particle-number projected generator coordinate method and the Skyrme interaction SLy4, we analyze the contribution brought to {delta}V{sub pn} by static deformation and dynamic fluctuations around the mean-field ground state. Our method gives a good overall description of {delta}V{sub pn} throughout the chart of nuclei with the exception of the anomaly related to the Wigner energy along the N=Z line. The main conclusions of our analysis of {delta}V{sub pn}, which are at variance with its standard interpretation, are that (i) the structures seen in the systematics of {delta}V{sub pn} throughout the chart of nuclei can be easily explained combining a smooth background related to the symmetry energy and correlation energies due to deformation and collective fluctuations, (ii) the characteristic pattern of {delta}V{sub pn} having a much larger size for nuclei that add only particles or only holes to a doubly magic nucleus than for nuclei that add particles for one nucleon species and holes for the other is a trivial consequence of the asymmetric definition of {delta}V{sub pn} and not due to a the different structure of these nuclei, (iii) {delta}V{sub pn} does not provide a very reliable indicator for structural changes, (iv){delta}V{sub pn} does not provide a reliable measure of the proton-neutron interaction in the nuclear energy density functional (EDF) or of that between the last filled orbits or of the one summed over all orbits, and (v) {delta}V{sub pn} does not provide a conclusive benchmark for nuclear EDF methods that is superior or complementary to other mass filters such as two-nucleon separation energies or Q values.

Bender, M. [Centre d'Etudes Nucleaires de Bordeaux Gradignan, UMR5797, Universite Bordeaux, F-33175 Gradignan (France); CNRS/IN2P3, Centre d'Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France); Heenen, P.-H. [Physique Nucleaire Theorique, CP229, Universite Libre de Bruxelles, B-1050 Bruxelles (Belgium)

2011-06-15T23:59:59.000Z

283

On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H ?): WFT and DFT Calculations  

DOE Green Energy (OSTI)

The strengths of noncovalent interactions are generally very sensitive to a number of geometric parameters. Among the most important of these parameters is the separation between the interacting moieties (in the case of an intermolecular interaction, this would be the intermolecular separation). Most works seeking to characterize the properties of intermolecular interactions are mainly concerned with binding energies obtained at the potential energy minimum (as determined at some particular level of theory). In this work, in order to extend our understanding of these types of noncovalent interactions, we investigate the distance dependence of several types of intermolecular interactions, these are hydrogen bonds, stacking interactions, dispersion interactions, and X-H ? interactions. There are several methods that have traditionally been used to treat noncovalent interactions as well as many new methods that have emerged within the past three or four years. Here we obtain reference data using estimated CCSD(T) values at the complete basis set limit (using the CBS(T) method); potential energy curves are also produced using several other methods thought to be accurate for intermolecular interactions, these are MP2/ccpVTZ, MP2/aug-cc-pVDZ,MP2/6-31G*(0.25), SCS(MI)-MP2/cc-pVTZ, estimated MP2.5/CBS, DFT-SAPT/ aug-cc-pVTZ, DFT/M06-2X/6-311+G(2df,2p), and DFT-D/TPSS/6-311++G(3df,3pd). The basis set superposition error is systematically considered throughout the study. It is found that the MP2.5 and DFTSAPT methods, which are both quite computationally intensive, produce potential energy curves that are in very good agreement to those of the reference method. Among the MP2 techniques, which can be said to be of medium computational expense, the best results are obtained with MP2/cc-pVTZ and SCS(MI)-MP2/cc-pVTZ. DFT-D/TPSS/6-311++G(3df,3pd) is the DFT-based method that can be said to give the most well-balanced description of intermolecular interactions.

Riley, Kevin E.; Pitonak, Michal; Cerny, Jiri; Hobza, Pavel

2009-12-09T23:59:59.000Z

284

JC3 Medium Impact Assessment Bulletins | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

November 6, 2012 November 6, 2012 V-017: Apache Tomcat Security Bypass and Denial of Service Vulnerabilities Two vulnerabilities were reported in Apache Tomcat October 23, 2012 V-008: Debian Security Advisory Debian update for bind9 October 22, 2012 V-007: McAfee Firewall Enterprise ISC BIND Record Handling Lockup Vulnerability McAfee has acknowledged a vulnerability in McAfee Firewall Enterprise, which can be exploited by malicious people to cause a DoS (Denial of Service). October 18, 2012 V-005: ModSecurity Multipart Message Parsing Security Bypass Vulnerability SEC Consult has reported a vulnerability in ModSecurity, which can be exploited by malicious people to bypass certain security restrictions. October 15, 2012 V-002: EMC NetWorker Module for Microsoft Applications Lets Remote Users

285

Rotations of the 2B Sub-domain of E. coli UvrD Helicase/Translocase Coupled to Nucleotide and DNA Binding  

Science Conference Proceedings (OSTI)

Escherichia coli UvrD is a superfamily 1 DNA helicase and single-stranded DNA (ssDNA) translocase that functions in DNA repair and plasmid replication and as an anti-recombinase by removing RecA protein from ssDNA. UvrD couples ATP binding and hydrolysis to unwind double-stranded DNA and translocate along ssDNA with 3'-to-5' directionality. Although a UvrD monomer is able to translocate along ssDNA rapidly and processively, DNA helicase activity in vitro requires a minimum of a UvrD dimer. Previous crystal structures of UvrD bound to a ssDNA/duplex DNA junction show that its 2B sub-domain exists in a 'closed' state and interacts with the duplex DNA. Here, we report a crystal structure of an apo form of UvrD in which the 2B sub-domain is in an 'open' state that differs by an {approx} 160{sup o} rotation of the 2B sub-domain. To study the rotational conformational states of the 2B sub-domain in various ligation states, we constructed a series of double-cysteine UvrD mutants and labeled them with fluorophores such that rotation of the 2B sub-domain results in changes in fluorescence resonance energy transfer. These studies show that the open and closed forms can interconvert in solution, with low salt favoring the closed conformation and high salt favoring the open conformation in the absence of DNA. Binding of UvrD to DNA and ATP binding and hydrolysis also affect the rotational conformational state of the 2B sub-domain, suggesting that 2B sub-domain rotation is coupled to the function of this nucleic acid motor enzyme.

Jia, Haifeng; Korolev, Sergey; Niedziela-Majka, Anita; Maluf, Nasib K.; Gauss, George H.; Myong, Sua; Ha, Taekjip; Waksman, Gabriel; Lohman, Timothy M. (UIUC); (St. Louis-MED); (WU-MED); (UCL)

2011-11-02T23:59:59.000Z

286

[3H]Azidodantrolene photoaffinity labeling, synthetic domain peptides and monoclonal antibody reactivity identify the dantrolene binding sequence on RyR1  

DOE Green Energy (OSTI)

Dantrolene is a drug that suppresses intracellular Ca2+ release from sarcoplasmic reticulum in normal skeletal muscle and is used as a therapeutic agent in individuals susceptible to malignant hyperthermia. Though its precise mechanism of action has not been elucidated, we have identified the N-terminal region (amino acids 1-1400) of the skeletal muscle isoform of the ryanodine receptor (RyR1), the primary Ca2+ release channel in sarcoplasmic reticulum, as a molecular target for dantrolene using the photoaffinity analog [3H]azidodantrolene(1). Here, we demonstrate that heterologously expressed RyR1 retains its capacity to be specifically labeled with [3H]azidodantrolene,indicating that muscle specific factors are not required for this ligand-receptor interaction. Synthetic domain peptides of RyR1, previously shown to affect RyR1 function in vitro and in vivo, were exploited as potential drug binding site mimics and used in photoaffinity labeling experiments. Only DP1 and DP1-2, peptide s containing the amino acid sequence corresponding to RyR1 residues 590-609, were specifically labeled by [3H]azidodantrolene. A monoclonal anti-RyR1 antibody which recognizes RyR1 and its 1400 amino acid N-terminal fragment, recognizes DP1 and DP1-2 in both Western blots and immunoprecipitation assays, and specifically inhibits [3H]azidodantrolene photolabeling of RyR1 and its N-terminal fragment in sarcoplasmic reticulum. Our results indicate that synthetic domain peptides can mimic a native, ligand binding conformation in vitro, and that the dantrolene binding site and the epitope for the monoclonal antibody on RyR1 are equivalent and composed of amino-acids 590-609.

Paul-Pletzer, Kalanethee; Yamamoto, Takeshi; Bhat, Manju B.; Ma, Jianjie; Ikemoto, Noriaki; Jimenez, Leslie S.; Morimoto, Hiromi; Williams, Philip G.; Parness, Jerome

2002-06-14T23:59:59.000Z

287

COOH-terminal truncation of flightin decreases myofilament lattice organization, cross-bridge binding, and power output in Drosophila indirect flight muscle  

Science Conference Proceedings (OSTI)

The indirect flight muscle (IFM) of insects is characterized by a near crystalline myofilament lattice structure that likely evolved to achieve high power output. In Drosophila IFM, the myosin rod binding protein flightin plays a crucial role in thick filament organization and sarcomere integrity. Here we investigate the extent to which the COOH terminus of flightin contributes to IFM structure and mechanical performance using transgenic Drosophila expressing a truncated flightin lacking the 44 COOH-terminal amino acids (fln{sup {Delta}C44}). Electron microscopy and X-ray diffraction measurements show decreased myofilament lattice order in the fln{sup {Delta}C44} line compared with control, a transgenic flightin-null rescued line (fln{sup +}). fln{sup {Delta}C44} fibers produced roughly 1/3 the oscillatory work and power of fln{sup +}, with reduced frequencies of maximum work (123 Hz vs. 154 Hz) and power (139 Hz vs. 187 Hz) output, indicating slower myosin cycling kinetics. These reductions in work and power stem from a slower rate of cross-bridge recruitment and decreased cross-bridge binding in fln{sup {Delta}C44} fibers, although the mean duration of cross-bridge attachment was not different between both lines. The decreases in lattice order and myosin kinetics resulted in fln{sup {Delta}C44} flies being unable to beat their wings. These results indicate that the COOH terminus of flightin is necessary for normal myofilament lattice organization, thereby facilitating the cross-bridge binding required to achieve high power output for flight.

Tanner, Bertrand C.W.; Miller, Mark S.; Miller, Becky M.; Lekkas, Panagiotis; Irving, Thomas C.; Maughan, David W.; Vigoreaux, Jim O. (IIT); (Vermont)

2011-08-26T23:59:59.000Z

288

Structure of an Odorant-Vinding Protein form the Mosquito Aedes aegypti Suggests a Binding Pocket Covered by a pH-Sensitive  

Science Conference Proceedings (OSTI)

The yellow fever mosquito, Aedes aegypti, is the primary vector for the viruses that cause yellow fever, mostly in tropical regions of Africa and in parts of South America, and human dengue, which infects 100 million people yearly in the tropics and subtropics. A better understanding of the structural biology of olfactory proteins may pave the way for the development of environmentally-friendly mosquito attractants and repellents, which may ultimately contribute to reduction of mosquito biting and disease transmission. Previously, we isolated and cloned a major, female-enriched odorant-binding protein (OBP) from the yellow fever mosquito, AaegOBP1, which was later inadvertently renamed AaegOBP39. We prepared recombinant samples of AaegOBP1 by using an expression system that allows proper formation of disulfide bridges and generates functional OBPs, which are indistinguishable from native OBPs. We crystallized AaegOBP1 and determined its three-dimensional structure at 1.85 {angstrom} resolution by molecular replacement based on the structure of the malaria mosquito OBP, AgamOBP1, the only mosquito OBP structure known to date. The structure of AaegOBP1 (= AaegOBP39) shares the common fold of insect OBPs with six {alpha}-helices knitted by three disulfide bonds. A long molecule of polyethylene glycol (PEG) was built into the electron-density maps identified in a long tunnel formed by a crystallographic dimer of AaegOBP1. Circular dichroism analysis indicated that delipidated AaegOBP1 undergoes a pH-dependent conformational change, which may lead to release of odorant at low pH (as in the environment in the vicinity of odorant receptors). A C-terminal loop covers the binding cavity and this 'lid' may be opened by disruption of an array of acid-labile hydrogen bonds thus explaining reduced or no binding affinity at low pH.

N Leite; R Krogh; W Xu; Y Ishida; J Iulek; W Leal; G Oliva

2011-12-31T23:59:59.000Z

289

Scalar and Spinor Particles with Low Binding Energy in the Strong Stationary Magnetic Field Studied by Means of Two-and Three-Dimensional Models  

E-Print Network (OSTI)

On the basis of analytic solutions of Schrodinger and Pauli equations for a uniform magnetic field and a single attractive $\\delta({\\bf r})$-potential the equations for the bound one-active electron states are discussed. It is vary important that ground electron states in the magnetic field essentially different from the analog state of spin-0 particles that binding energy has been intensively studied at more then forty years ago. We show that binding energy equations for spin-1/2 particles can be obtained without using of a well-known language of boundary conditions in the model of $\\delta$-potential that has been developed in pioneering works. Obtained equations are used for the analytically calculation of the energy level displacements, which demonstrate nonlinear dependencies on field intensities. It is shown that in a case of the weak intensity a magnetic field indeed plays a stabilizing role in considering systems. However the strong magnetic field shows the opposite action. We are expected that these properties can be of importance for real quantum mechanical fermionic systems in two- and three-dimensional cases.

V. N. Rodionov

2007-02-22T23:59:59.000Z

290

X-ray crystallographic analysis of adipocyte fatty acid binding protein (aP2) modified with 4-hydroxy-2-nonenal  

SciTech Connect

Fatty acid binding proteins (FABP) have been characterized as facilitating the intracellular solubilization and transport of long-chain fatty acyl carboxylates via noncovalent interactions. More recent work has shown that the adipocyte FABP is also covalently modified in vivo on Cys117 with 4-hydroxy-2-nonenal (4-HNE), a bioactive aldehyde linked to oxidative stress and inflammation. To evaluate 4-HNE binding and modification, the crystal structures of adipocyte FABP covalently and noncovalently bound to 4-HNE have been solved to 1.9 {angstrom} and 2.3 {angstrom} resolution, respectively. While the 4-HNE in the noncovalently modified protein is coordinated similarly to a carboxylate of a fatty acid, the covalent form show a novel coordination through a water molecule at the polar end of the lipid. Other defining features between the two structures with 4-HNE and previously solved structures of the protein include a peptide flip between residues Ala36 and Lys37 and the rotation of the side chain of Phe57 into its closed conformation. Representing the first structure of an endogenous target protein covalently modified by 4-HNE, these results define a new class of in vivo ligands for FABPs and extend their physiological substrates to include bioactive aldehydes.

Hellberg, Kristina; Grimsrud, Paul A.; Kruse, Andrew C.; Banaszak, Leonard J.; Ohlendorf, Douglas H.; Bernlohr, David A. (UMM)

2012-07-11T23:59:59.000Z

291

Ion binding compounds, radionuclide complexes, methods of making radionuclide complexes, methods of extracting radionuclides, and methods of delivering radionuclides to target locations  

DOE Patents (OSTI)

The invention pertains to compounds for binding lanthanide ions and actinide ions. The invention further pertains to compounds for binding radionuclides, and to methods of making radionuclide complexes. Also, the invention pertains to methods of extracting radionuclides. Additionally, the invention pertains to methods of delivering radionuclides to target locations. In one aspect, the invention includes a compound comprising: a) a calix[n]arene group, wherein n is an integer greater than 3, the calix[n]arene group comprising an upper rim and a lower rim; b) at least one ionizable group attached to the lower rim; and c) an ion selected from the group consisting of lanthanide and actinide elements bound to the ionizable group. In another aspect, the invention includes a method of extracting a radionuclide, comprising: a) providing a sample comprising a radionuclide; b) providing a calix[n]arene compound in contact with the sample, wherein n is an integer greater than 3; and c) extracting radionuclide from the sample into the calix[n]arene compound. In yet another aspect, the invention includes a method of delivering a radionuclide to a target location, comprising: a) providing a calix[n]arene compound, wherein n is an integer greater than 3, the calix[n]arene compound comprising at least one ionizable group; b) providing a radionuclide bound to the calix[n]arene compound; and c) providing an antibody attached to the calix[n]arene compound, the antibody being specific for a material found at the target location.

Chen, Xiaoyuan (Syracuse, NY); Wai, Chien M. (Moscow, ID); Fisher, Darrell R. (Richland, WA)

2000-01-01T23:59:59.000Z

292

BMC Molecular Biology BioMed Central Research article A Xenopus Dbf4 homolog is required for Cdc7 chromatin binding and DNA replication  

E-Print Network (OSTI)

2004 Jares et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. Background: Early in the cell cycle a pre-replicative complex (pre-RC) is assembled at each replication origin. This process involves the sequential assembly of the Origin Recognition Complex (ORC), Cdc6, Cdt1 and the MiniChromosome Maintenance (Mcm2-7) proteins onto chromatin to license the origin for use in the subsequent S phase. Licensed origins must then be activated by S phase-inducing cyclin-dependent kinases (S-CDKs) and the Dbf4/Cdc7 kinase. Results: We have cloned a Xenopus homologue of Dbf4 (XDbf4), the sequence of which confirms the results of Furukhori et al. We have analysed the role of XDbf4 in DNA replication using cellfree extracts of Xenopus eggs. Our results indicate that XDbf4 is the regulatory subunit of XCdc7 required for DNA replication. We show that XDbf4 binds to chromatin during interphase, but unlike XCdc7, its chromatin association is independent of pre-RC formation, occurring in the absence of licensing, XCdc6 and XORC. Moreover, we show that the binding of XCdc7 to chromatin is dependent on the presence of XDbf4, whilst under certain circumstances XDbf4 can

Pedro Jares; M Gloria Luciani; J Julian Blow

2004-01-01T23:59:59.000Z

293

Briefly Bound to Activate: Transient Binding of a Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis  

SciTech Connect

We have determined high-resolution crystal structures of a CDK2/Cyclin A transition state complex bound to ADP, substrate peptide, and MgF{sub 3}{sup -}. Compared to previous structures of active CDK2, the catalytic subunit of the kinase adopts a more closed conformation around the active site and now allows observation of a second Mg{sup 2+} ion in the active site. Coupled with a strong [Mg{sup 2+}] effect on in vitro kinase activity, the structures suggest that the transient binding of the second Mg{sup 2+} ion is necessary to achieve maximum rate enhancement of the chemical reaction, and Mg{sup 2+} concentration could represent an important regulator of CDK2 activity in vivo. Molecular dynamics simulations illustrate how the simultaneous binding of substrate peptide, ATP, and two Mg{sup 2+} ions is able to induce a more rigid and closed organization of the active site that functions to orient the phosphates, stabilize the buildup of negative charge, and shield the subsequently activated {gamma}-phosphate from solvent.

Bao, Zhao Qin; Jacobsen, Douglas M.; Young, Matthew A. (Michigan-Med)

2012-03-15T23:59:59.000Z

294

A Regulatory Mechanism Involving TBP-1/Tat-Binding Protein 1 and Akt/PKB in the Control of Cell Proliferation  

E-Print Network (OSTI)

TBP-1 /Tat-Binding Protein 1 (also named Rpt-5, S6a or PSMC3) is a multifunctional protein, originally identified as a regulator of HIV-1-Tat mediated transcription. It is an AAA-ATPase component of the 19S regulative subunit of the proteasome and, as other members of this protein family, fulfils different cellular functions including proteolysis and transcriptional regulation. We and others reported that over expression of TBP-1 diminishes cell proliferation in different cellular contexts with mechanisms yet to be defined. Accordingly, we demonstrated that TBP-1 binds to and stabilizes the p14ARF oncosuppressor increasing its anti-oncogenic functions. However, TBP-1 restrains cell proliferation also in the absence of ARF, raising the question of what are the molecular pathways involved. Herein we demonstrate that stable knock-down of TBP-1 in human immortalized fibroblasts increases cell proliferation, migration and resistance to apoptosis induced by serum deprivation. We observe that TBP-1 silencing causes activation of the Akt/PKB kinase and that in turn TBP-1, itself, is a downstream target of Akt/PKB. Moreover, MDM2, a known Akt target, plays a major role in this regulation. Altogether, our data suggest the existence of a

Maria Sepe; Luisa Festa; Fabio Tolino; Luca Bellucci; Luca Sisto; Daniela Alfano; Pia Ragno; Viola Calabr; Vittorio De Franciscis; Girolama La Mantia; Ra Pollice

2010-01-01T23:59:59.000Z

295

Crystallographic Analysis of Murine Constitutive Androstane Receptor Ligand-Binding Domain Complexed with 5[alpha]-androst-16-en-3[alpha]-ol  

Science Conference Proceedings (OSTI)

The constitutive androstane receptor (CAR) is a member of the nuclear receptor superfamily. In contrast to classical nuclear receptors, which possess small-molecule ligand-inducible activity, CAR exhibits constitutive transcriptional activity in the apparent absence of ligand. CAR is among the most important transcription factors; it coordinately regulates the expression of microsomal cytochrome P450 genes and other drug-metabolizing enzymes. The murine CAR ligand-binding domain (LBD) was coexpressed with the steroid receptor coactivator protein (SRC-1) receptor-interacting domain (RID) in Escherichia coli. The mCAR LBD subunit was purified away from SRC-1 by affinity, anion-exchange and size-exclusion chromatography, crystallized with androstenol and the structure of the complex determined by molecular replacement.

Vincent, J.; Shan, L.; Fan, M.; Brunzelle, J.S.; Forman, B.M.; Fernandez, E.J. (Tennessee-K); (NWU); (CHNMC)

2010-03-08T23:59:59.000Z

296

Carcinogenic heavy metals replace Ca{sup 2+} for DNA binding and annealing activities of mono-ubiquitinated annexin A1 homodimer  

Science Conference Proceedings (OSTI)

Mono-ubiquitinated annexin A1 was purified from rat liver nuclei. The homodimer form of mono-ubiquitinated annexin A1 was able to unwind dsDNA in a Mg{sup 2+}- and ATP-dependent manner, and to anneal ssDNA in a Ca{sup 2+}-dependent manner. Phospholipids decreased the concentration of Ca{sup 2+} required for maximal annealing activity. Heavy metals such as As{sup 3+}, Cr{sup 6+}, Pb{sup 2+} and Cd{sup 2+} substituted for Ca{sup 2+} in the ssDNA binding and annealing activities of annexin A1. While these metals inhibited the unwinding of dsDNA by nuclear annexin A1 in the presence of Mg{sup 2+} and ATP, they enhanced dsDNA-dependent ATPase activity of annexin A1. Heavy metals may have produced dsDNA, a substrate for the DNA unwinding reaction, via the DNA annealing reaction. DNA synthesomes were isolated from L5178Y tk(+/-) mouse lymphoma cells in exponential growth, and were found to contain helicase activities. The As{sup 3+}- or Cr{sup 6+}-induced increases in ssDNA binding activity of DNA synthesomes were reduced by a mono-specific anti-annexin A1 antibody, but not by anti-Ig antibody. Anti-annexin A1 antibody also blocked the inhibitory and stimulatory effects of As{sup 3+} or Cr{sup 6+} towards DNA unwinding and annealing activities of DNA synthesomes. Based on these observations, it can be concluded that the effects of heavy metals on DNA annealing and unwinding activities are mediated, at least in substantial part, through actions of the mono-ubiquitinated annexin A1 homodimer.

Hirata, Aiko; Corcoran, George B.; Hirata, Fusao, E-mail: fhirata@wayne.ed

2010-10-01T23:59:59.000Z

297

{sup 13}C and {sup 17}O NMR binding constant studies of uranyl carbonate complexes in near-neutral aqueous solution. Yucca Mountain Project Milestone Report 3351  

SciTech Connect

Valuable structural information, much of it unavailable by other methods, can be obtained about complexes in solution through NMR spectroscopy. From chemical shift and intensity measurements of complexed species, NMR can serve as a species-specific structural probe for molecules in solution and can be used to validate thermodynamic constants used in geochemical modeling. Fourier-transform nuclear magnetic resonance (FT-NMR) spectroscopy has been employed to study the speciation of uranium(VI) ions in aqueous carbonate solutions as a function of pH, ionic strength, carbonate concentration, uranium concentration, and temperature. Carbon-13 and oxygen-17 NMR spectroscopy were used to monitor the fractions, and hence thermodynamic binding constants of two different uranyl species U0{sub 2}(CO{sub 3}){sub 3}{sup 4{minus}} and (UO{sub 2}){sub 3}(CO{sub 3}){sub 6}{sup 6{minus}} in aqueous solution. Synthetic buffer solutions were prepared under the ionic strength conditions used in the NMR studies in order to obtain an accurate measure of the hydrogen ion concentration, and a discussion of pH = {minus}log(a{sub H}{sup +}) versus p[H] = {minus}log[H+] is provided. It is shown that for quantitative studies, the quantity p[H] needs to be used. Fourteen uranium(VI) binding constants recommended by the OECD NEA literature review were corrected to the ionic strengths employed in the NMR study using specific ion interaction theory (SIT), and the predicted species distributions were compared with the actual species observed by multinuclear NMR. Agreement between observed and predicted stability fields is excellent. This establishes the utility of multinuclear NMR as a species-specific tool for the study of the actinide carbonate complexation constants, and serves as a means for validating the recommendations provided by the OECD NEA.

Clark, D.L.; Newton, T.W.; Palmer, P.D.; Zwick, B.D.

1995-01-01T23:59:59.000Z

298

JC3 Bulletin Archive | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

22, 2012 22, 2012 V-007: McAfee Firewall Enterprise ISC BIND Record Handling Lockup Vulnerability McAfee has acknowledged a vulnerability in McAfee Firewall Enterprise, which can be exploited by malicious people to cause a DoS (Denial of Service). October 19, 2012 V-006: CA ARCserve Backup Flaws Let Remote Users Execute Arbitrary Code and Deny Service Two vulnerabilities were reported in CA ARCserve Backup. A remote user can execute arbitrary code on the target system. A remote user can cause denial of service conditions. October 18, 2012 V-005: ModSecurity Multipart Message Parsing Security Bypass Vulnerability SEC Consult has reported a vulnerability in ModSecurity, which can be exploited by malicious people to bypass certain security restrictions. October 17, 2012

299

Assignment of human myocyte-specific enhancer binding factor 2C (hMEF2C) to human chromosome 5q14 and evidence that MEF2C is evolutionarily conserved  

SciTech Connect

Human myocyte-specific enhancer binding factor 2C (hMEF2C) belongs to the MEF2 subfamily of the MADS (MCM1, AGAMOUS, DEF A, serum response factor) family of transcription factors. Members of the MADS family share a conserved domain - the MADS domain - that is necessary for DNA binding. Highly conserved versions of the MADS domain and of an adjacent domain that is known as the MEF2 domain are found in members of the MEF2 subfamily. Both of these domains are necessary for binding to the MEF2 regulatory element. This regulatory element is known to be functionally important in a variety of muscle-specific genes and possibly in the brain creatine kinase gene. The MEF2C gene product activates transcription by binding to the MEF2 element. hMEF2C is expressed at high levels in postmitotic neurons in the brain, where it is most abundant in the cerebral cortex, and is also expressed in differentiated myotubes. Several lines of evidence suggest the existence of a rat homologue of MEF2C, and a mouse homologue has been cloned. The mouse gene was mapped to mouse chromosome 13 in a region that is syntenic to human 5q13-q15. 12 refs., 1 fig.

Krainc, D.; Lipton, S.A. [Harvard Medical School, Boston, MA (United States); Haas, M.; Ward, D.C. [Yale Univ. School of Medicine, New Haven, CT (United States)] [and others

1995-10-10T23:59:59.000Z

300

Purification, crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding region of the Streptococcus gordonii adhesin GspB  

Science Conference Proceedings (OSTI)

The carbohydrate-binding region of the bacterial adhesin GspB from Streptococcus gordonii strain M99 (GspB{sub BR}) was expressed in Escherichia coli and purified using affinity and size-exclusion chromatography. Separate sparse-matrix screening of GspB{sub BR} buffered in either 20 mM Tris pH 7.4 or 20 mM HEPES pH 7.5 resulted in different crystallographic behavior such that different precipitants, salts and additives supported crystallization of GspB{sub BR} in each buffer. While both sets of conditions supported crystal growth in space group P2{sub 1}2{sub 1}2{sub 1}, the crystals had distinct unit-cell parameters of a = 33.3, b = 86.7, c = 117.9 {angstrom} for crystal form 1 and a = 34.6, b = 98.3, c = 99.0 {angstrom} for crystal form 2. Additive screening improved the crystals grown in both conditions such that diffraction extended to beyond 2 {angstrom} resolution. A complete data set has been collected to 1.3 {angstrom} resolution with an overall R{sub merge} value of 0.04 and an R{sub merge} value of 0.33 in the highest resolution shell.

Pyburn, Tasia M.; Yankovskaya, Victoria; Bensing, Barbara A.; Cecchini, Gary; Sullam, Paul M.; Iverson, T.M. (VA); (Vanderbilt); (UCSF)

2012-07-11T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
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to obtain the most current and comprehensive results.


301

The adsorption effect of C{sub 6}H{sub 5} on density of states for double wall carbon nanotubes by tight binding model  

SciTech Connect

A theoretical approach based on a tight-binding model is developed to study the effects of the adsorption of finite concentrations of C{sub 6}H{sub 5} gas molecules on double-walled carbon nanotube (DWCNT) electronic properties. To obtain proper hopping integrals and random on-site energies for the case of one molecule adsorption, the local density of states for various hopping integrals and random on-site energies are calculated. Since C{sub 6}H{sub 5} molecule is a donor with respect to the carbon nanotubes and their states should appear near the conduction band of the system, effects of various hopping integral deviations and on-site energies for one molecule adsorption are considered to find proper hopping and on-site energies consistent with expected n-type semiconductor. We found that adsorption of C{sub 6}H{sub 5} gas molecules could lead to a (8.0)-(20.0) DWCNT n-type semiconductor. The width of impurity adsorbed gas states in the density of states could be controlled by adsorbed gas concentration.

Fathalian, A., E-mail: a.fathalian@gmail.com [Razi University, Department of Physics (Iran, Islamic Republic of)

2012-06-15T23:59:59.000Z

302

Unveiling N-Protonation and Anion-Binding Effects on Fe/N/C Catalysts for O2 Reduction in Proton-Exchange-Membrane Fuel Cells  

Science Conference Proceedings (OSTI)

The high cost of proton-exchange-membrane fuel cells would be considerably reduced if platinum-based catalysts were replaced by iron-based substitutes, which have recently demonstrated comparable activity for oxygen reduction but whose cause of activity decay in acidic medium has been elusive. Here, we reveal that the activity of Fe/N/C catalysts prepared through a pyrolysis in NH{sub 3} is mostly imparted by acid-resistant FeN{sub 4} sites whose turnover frequency for the O{sub 2} reduction can be regulated by fine chemical changes of the catalyst surface. We show that surface N-groups protonate at pH 1 and subsequently bind anions. This results in decreased activity for the O{sub 2} reduction. The anions can be removed chemically or thermally, which restores the activity of acid-resistant FeN{sub 4} sites. These results are interpreted as an increased turnover frequency of FeN{sub 4} sites when specific surface N-groups protonate. These unprecedented findings provide a new perspective for stabilizing the most active Fe/N/C catalysts known to date.

J Herranz; F Jaouen; M Lefevre; U Kramm; E Proietti; J Dodelet; P Bogdanoff; S Fiechter; I Abs-Wurbach; et al.

2011-12-31T23:59:59.000Z

303

Alpha-2 adrenergic activity of bromocriptine and quinpirole in chicken pineal gland. Effects on melatonin synthesis and ( sup 3 H)rauwolscine binding  

SciTech Connect

In the pineal gland and retina of chickens, serotonin N-acetyl-transferase (NAT) activity and melatonin content are modulated by different receptors, alpha-2 adrenergic receptors in pineal gland and D2-dopamine receptors in retina. The effect of two D2-dopamine receptor agonists, bromocriptine and quinpirole (LY 171555), on melatonin synthesis in these tissues was investigated. Systemic administrations of bromocriptine and quinpirole decreased nocturnal NAT activity and melatonin content of both pineal gland and retina. Bromocriptine was equipotent in the two tissues, whereas quinpirole was approximately 100-fold more potent in retina than in pineal gland. In pineal gland, the suppressive effects of bromocriptine and quinpirole on NAT activity were blocked by yohimbine, a selective alpha-2 adrenergic receptor antagonist, but not by spiperone, a D2-dopamine receptor antagonist. In contrast, bromocriptine- and quinpirole-induced decreases of the enzyme activity in retina were antagonized by spiperone, and not affected by yohimbine. The nocturnal increase of NAT activity of pineal glands in vitro was inhibited with an order of potency clonidine greater than bromocriptine greater than quinpirole. Additionally, bromocriptine and quinpirole displaced the specific binding of (3H)rauwolscine, an alpha-2 adrenergic receptor antagonist, to membranes from chicken pineal gland, with potencies comparable to those observed for inhibition of NAT activity in vitro. It is suggested that bromocriptine and quinpirole, in addition to their D2-dopaminergic activity, can stimulate alpha-2 adrenergic receptors in pineal gland of chicken.

Zawilska, J.; Iuvone, P.M. (Emory Univ. School of Medicine, Atlanta, GA (USA))

1990-12-01T23:59:59.000Z

304

Study of the Mn-binding sites in photosystem II using antibodies raised against lumenal regions of the D1 and D2 reaction center proteins  

DOE Green Energy (OSTI)

The experiments discussed in this thesis focus on identifying the protein segments or specific amino acids which provide ligands to the Mn cluster of photosystem II (PS II). This Mn cluster plays a central role in the oxygen-evolving complex (OEC) of PS II. The Mn cluster is thought to be bound by lumenal regions of the PS II reaction center proteins known as D1 and D2. First, several peptides were synthesized which correspond to specific lumenal segments of the D1 and D2 proteins. Next, polyclonal antibodies were successfully elicited using three of these peptides. The peptides recognized by these antibodies correspond to protein segments of the spinach reaction center proteins: Ile-321 to Ala-344 of D1 (D1-a), Asp-319 to Arg-334 of D1 (D1-b), and Val-300 to Asn-319 of D2 (D2-a). These antibodies were then used in assays which were developed to structurally or functionally probe the potential Mn-binding regions of the D1 and D2 proteins.

Dalmasso, E.A.

1992-04-01T23:59:59.000Z

305

Heat shock factor 1 upregulates transcription of Epstein-Barr Virus nuclear antigen 1 by binding to a heat shock element within the BamHI-Q promoter  

SciTech Connect

Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) is essential for maintenance of the episome and establishment of latency. In this study, we observed that heat treatment effectively induced EBNA1 transcription in EBV-transformed B95-8 and human LCL cell lines. Although Cp is considered as the sole promoter used for the expression of EBNA1 transcripts in the lymphoblastoid cell lines, the RT-PCR results showed that the EBNA1 transcripts induced by heat treatment arise from Qp-initiated transcripts. Using bioinformatics, a high affinity and functional heat shock factor 1 (HSF1)-binding element within the - 17/+4 oligonucleotide of the Qp was found, and was determined by electrophoretic mobility shift assay and chromatin immunoprecipitation assay. Moreover, heat shock and exogenous HSF1 expression induced Qp activity in reporter assays. Further, RNA interference-mediated HSF1 gene silencing attenuated heat-induced EBNA1 expression in B95-8 cells. These results provide evidence that EBNA1 is a new target for the transcription factor HSF1.

Wang, Feng-Wei [The State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-Sen University, Guangzhou (China)] [The State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-Sen University, Guangzhou (China); Wu, Xian-Rui [Department of Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou (China)] [Department of Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou (China); Liu, Wen-Ju; Liao, Yi-Ji [The State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-Sen University, Guangzhou (China)] [The State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-Sen University, Guangzhou (China); Lin, Sheng [Laboratory of Integrated Biosciences, School of Life Science, Sun Yat-sen University, Guangzhou (China)] [Laboratory of Integrated Biosciences, School of Life Science, Sun Yat-sen University, Guangzhou (China); Zong, Yong-Sheng; Zeng, Mu-Sheng; Zeng, Yi-Xin [The State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-Sen University, Guangzhou (China)] [The State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-Sen University, Guangzhou (China); Mai, Shi-Juan, E-mail: maishj@sysucc.org.cn [The State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-Sen University, Guangzhou (China)] [The State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-Sen University, Guangzhou (China); Xie, Dan, E-mail: xied@mail.sysu.edu.cn [The State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-Sen University, Guangzhou (China)] [The State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-Sen University, Guangzhou (China)

2011-12-20T23:59:59.000Z

306

High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor binding domain of botulinum neurotoxin serotype D  

SciTech Connect

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and can cause neuroparalytic disease botulism. Due to the limitations of production and manipulation of holoenzymes, expressing non-toxic heavy chain receptor binding domains (HCR) has become a common strategy for vaccine and antibody development. Meanwhile, large quantities and highly purified soluble proteins are required for research areas such as antibody maturation and structural biology. We present high level expression and purification of the BoNT serotype D HCR in E. coli using a codon-optimized cDNA. By varying expression conditions, especially at low temperature, the protein was expressed at a high level with high solubility. About 150-200 mg protein was purified to >90% purity from 1 L cell culture. The recombinant D_HCR was crystallized and the crystals diffracted to 1.65 resolution. The crystals belong to space group P212121 with unit cell dimensions a = 60.8 , b = 89.7 , c = 93.9 . Preliminary crystallographic data analysis revealed one molecule in asymmetric unit.

Zhang, Yanfeng; Gao, Xiaoli; Qin, Lin; Buchko, Garry W.; Robinson, Howard; Varnum, Susan M.

2010-12-01T23:59:59.000Z

307

CSSPAB Meeting September 17, 2002  

Science Conference Proceedings (OSTI)

... and sharing of information and that ISC's are expected ... NIST has a digital data preservation laboratory. ... with other Federal agencies' libraries as well ...

2007-09-26T23:59:59.000Z

308

Comprehensive Comparison of Hardware Performance of ...  

Science Conference Proceedings (OSTI)

... used as a part of a digital signature used ... low-level tool options; the same library of basic ... Y. Frankel, 5th International Conference, ISC 2002, Sao ...

2012-05-30T23:59:59.000Z

309

Publications Portal  

Science Conference Proceedings (OSTI)

... Information Security - 10th International Conference, ISC 2007 Published: 10/12/2007 Author ... SP 823-XX: Integrated Services Digital Network Series.

2012-09-17T23:59:59.000Z

310

25th Annual Conference  

Science Conference Proceedings (OSTI)

... Skills Gap Panel Marc Noble, (ISC)2 (moderator ... 00 9:30 am Keynote Digital Persona Protection ... On a Budget Joe Garrity, Library of Congress ...

2012-03-27T23:59:59.000Z

311

Special Publication 800-81-2 (PRE-PUBLICATION), Secure ...  

Science Conference Proceedings (OSTI)

... just been established) then verifies the digital signature to ... vulnerabilities page at http://www.isc.org/products ... microsoft.com/en-us/library/cc422472(v ...

2013-09-12T23:59:59.000Z

312

FISSEA Newsletter - Sept. 1998  

Science Conference Proceedings (OSTI)

... specializes in electronics and digital systems, and he ... (ISC ) 2 offers the Certified Information Systems ... etc.), PTA meetings, local library lecture series ...

313

Design of Hybrid Steam-In Situ Combustion Bitumen Recovery ...  

Science Conference Proceedings (OSTI)

Steam-assisted gravity drainage (SAGD) is the most widely used ..... Temperature (C) distribution of hybrid alternating SAGDISC process at reservoir cross.

314

Optimization of in-situ combustion| Maximizing production and reducing CO2 footprint.  

E-Print Network (OSTI)

?? The in-situ combustion (ISC) process is an enhanced oil recovery (EOR) method that utilizes fuel in place to upgrade and displace the hydrocarbons in (more)

Liu, Zhenshuo

2011-01-01T23:59:59.000Z

315

Sheltering in Place | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Sheltering in Place Emergency Information Emergency Information Home Public Notifications Emergency Vocabulary Sheltering in Place Evacuation ISC Home Sheltering in Place Print...

316

Method of binding structural material  

DOE Patents (OSTI)

A structural material of a polystyrene base and the reaction product of the polystyrene base and a solid phosphate ceramic. The ceramic is applied as a slurry which includes one or more of a metal oxide or a metal hydroxide with a source of phosphate to produce a phosphate ceramic and a poly (acrylic acid or acrylate) or combinations or salts thereof and polystyrene or MgO applied to the polystyrene base and allowed to cure so that the dried aqueous slurry chemically bonds to the polystyrene base. A method is also disclosed of applying the slurry to the polystyrene base.

Wagh, Arun S. (Orland Park, IL); Antink, Allison L. (Bolingbrook, IL)

2007-12-25T23:59:59.000Z

317

Rat MHC-linked peptide transporter alleles strongly influence peptide binding by HLA-B27 but not B27-associated inflammatory disease  

SciTech Connect

Rats transgenic for the human MHC molecule HLA-B27 were used to study the effect of two alleles, cim{sup a} and cim{sup b}, which are associated with peptide transport by the MHC-encoded Tap2 transporter, on the function of HLA-B27 as a restriction element for CTL recognition of the male H-Y minor H Ag and on the multisystem inflammatory disease characteristic of B27 transgenic rats. Anti-H-Y CTL generated in cim{sup a} B27 transgenic rats lysed male B27 cim{sup b/b} targets significantly less well than cim{sup a/a} or cim{sup a/b} targets. Addition of exogenous H-Y peptides to male B27 cim{sup b/b} targets increased susceptibility to lysis to the level of cim{sup a/a} targets sensitized with exogenous H-Y peptides. {sup 3}H-labeled peptides eluted from B27 molecules of lymphoblasts from rats of two cim{sup b} and three cim{sup a} RT1 haplotypes showed that the cim{sup b} peptide pool favors comparatively longer and/or more hydrophobic peptides. These results indicate that RT1-linked Tap2 polymorphism in the rat strongly influences peptide loading of HLA-B27. Nonetheless, the prevalence and severity of multisystem inflammatory lesions were comparable in backcross rats bearing either cim{sup a/b} or cim{sup b/b}. It thus appears either that binding of specific peptides to B27 is unimportant in the pathogenesis of B27-associated disease or that the critical peptides, unlike H-Y and many others, are not influenced by Tap transporter polymorphism. 42 refs., 6 figs., 3 tabs.

Simmons, W.A.; Satumtira, Nimman; Taurog, J.D. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States)] [and others

1996-02-15T23:59:59.000Z

318

Binding and Direct Electrochemistry of OmcA, an Outer-Membrane Cytochrome from an Iron Reducing Bacterium, with Oxide Electrodes: A Candidate Biofuel Cell System  

SciTech Connect

Dissimilatory iron-reducing bacteria transfer electrons to solid ferric respiratory electron acceptors. Outer-membrane cytochromes expressed by these organisms are of interest in both microbial fuel cells and biofuel cells. We use optical waveguide lightmode spectroscopy (OWLS) to show that OmcA, an 85 kDa decaheme outer-membrane c-type cytochrome from Shewanella oneidensis MR-1, adsorbs to isostructural Al2O3 and Fe2O3 in similar amounts. Adsorption is ionic-strength and pH dependent (peak adsorption at pH 6.57.0). The thickness of the OmcA layer on Al2O3 at pH 7.0 [5.8 1.1 (2r) nm] from OWLS is similar, within error, to that observed using atomic force microscopy (4.8 2 nm). The highest adsorption density observed was 334 ng cm 2 (2.4 1012 molecules cm 2), corresponding to a monolayer or 9.9 nm diameter spheres or submonolayer coverage by smaller molecules. Direct electrochemistry of OmcA on Fe2O3 electrodes was observed using cyclic voltammetry, with cathodic peak potentials of 380 to 320 mV versus Ag/AgCl. Variations in the cathodic peak positions are speculatively attributed to redox-linked conformation change or changes in molecular orientation. OmcA can exchange electrons with ITO electrodes at higher current densities than with Fe2O3. Overall, OmcA can bind to and exchange electrons with several oxides, and thus its utility in fuel cells is not restricted to Fe2O3.

Eggleston, Carrick M.; Voros, Janos; Shi, Liang; Lower, Brian H.; Droubay, Timothy; Colberg, Patricia J.

2008-02-15T23:59:59.000Z

319

Low p53 Binding Protein 1 (53BP1) Expression Is Associated With Increased Local Recurrence in Breast Cancer Patients Treated With Breast-Conserving Surgery and Radiotherapy  

SciTech Connect

Purpose: To investigate whether the expression of p53 binding protein 1 (53BP1) has prognostic significance in a cohort of early-stage breast cancer patients treated with breast-conserving surgery and radiotherapy (BCS+RT). Methods and Materials: A tissue microarray of early-stage breast cancer treated with BCS+RT from a cohort of 514 women was assayed for 53BP1, estrogen receptor, progesterone receptor, and HER2 expression by immunohistochemistry. Through log-rank tests and univariate and multivariate models, the staining profile of each tumor was correlated with clinical endpoints, including ipsilateral breast recurrence-free survival (IBRFS), distant metastasis-free survival (DMFS), cause-specific survival (CSS), recurrence-free survival (RFS), and overall survival (OS). Results: Of the 477 (93%) evaluable tumors, 63 (13%) were scored as low. Low expression of 53BP1 was associated with worse outcomes for all endpoints studied, including 10-year IBRFS (76.8% vs. 90.5%; P=.01), OS (66.4% vs. 81.7%; P=.02), CSS (66.0% vs. 87.4%; P<.01), DMFS (55.9% vs. 87.0%; P<.01), and RFS (45.2% vs. 80.6%; P<.01). Multivariate analysis incorporating various clinico-pathologic markers and 53BP1 expression found that 53BP1 expression was again an independent predictor of all endpoints (IBRFS: P=.0254; OS: P=.0094; CSS: P=.0033; DMFS: P=.0006; RFS: P=.0002). Low 53BP1 expression was also found to correlate with triple-negative (TN) phenotype (P<.01). Furthermore, in subset analysis of all TN breast cancer, negative 53BP1 expression trended for lower IBRFS (72.3% vs. 93.9%; P=.0361) and was significant for worse DMFS (48.2% vs. 86.8%; P=.0035) and RFS (37.8% vs. 83.7%; P=.0014). Conclusion: Our data indicate that low 53BP1 expression is an independent prognostic indicator for local relapse among other endpoints in early-stage breast cancer and TN breast cancer patients treated with BCS+RT. These results should be verified in larger cohorts of patients to validate their clinical significance.

Neboori, Hanmanth J.R. [Department of Radiation Oncology, Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States)] [Department of Radiation Oncology, Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States); Haffty, Bruce G., E-mail: hafftybg@umdnj.edu [Department of Radiation Oncology, The Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States); Wu Hao [Department of Radiation Oncology, Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States)] [Department of Radiation Oncology, Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States); Yang Qifeng [Department of Breast Surgery, Qilu Hospital, Shandong University, Ji'nan (China)] [Department of Breast Surgery, Qilu Hospital, Shandong University, Ji'nan (China); Aly, Amal [Division of Medical Oncology, The Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States)] [Division of Medical Oncology, The Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States); Goyal, Sharad; Schiff, Devora [Department of Radiation Oncology, Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States)] [Department of Radiation Oncology, Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States); Moran, Meena S. [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT (United States)] [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT (United States); Golhar, Ryan [Department of Radiation Oncology, Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States)] [Department of Radiation Oncology, Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States); Chen Chunxia; Moore, Dirk [Department of Biostatistics, The Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States)] [Department of Biostatistics, The Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ (United States); and others

2012-08-01T23:59:59.000Z

320

Structural Insights into the Functional Role of the Hcn Sub-domain of the Receptor-Binding Domain of the Botulinum Neurotoxin Mosaic Serotype C/D  

SciTech Connect

Botulinum neurotoxin (BoNT), the causative agent of the deadly neuroparalytic disease botulism, is the most poisonous protein known for humans. Produced by different strains of the anaerobic bacterium Clostridium botulinum, BoNT effects cellular intoxication via a multistep mechanism executed by the three modules of the activated protein. Endocytosis, the first step of cellular intoxication, is triggered by the ~50 kDa, heavy-chain receptor-binding module (HCR) that is specific for a ganglioside and a protein receptor on neuronal cell surfaces. This dual receptor recognition mechanism between BoNT and the host cells membrane is well documented and occurs via specific intermolecular interactions with the C-terminal sub-domain, Hcc, of BoNT-HCR. The N-terminal sub-domain of BoNT-HCR, Hcn, comprises ~50% of BoNT-HCR and adopts a B-sheet jelly roll fold. While suspected in assisting cell surface recognition, no unambiguous function for the Hcn sub-domain in BoNT has been indentified. To obtain insights into the potential function of the Hcn sub-domain in BoNT, the first crystal structure of a BoNT with an organic ligand bound to the Hcn sub-domain has been obtained. Here, we describe the crystal structure of BoNT/CD-HCR determined at 1.70 resolution with a tetraethylene glycol (PG4) molecule bound in an hydrophobic cleft between B-strands in the B-sheet jelly fold roll of the Hcn sub-domain. The molecule is completely engulfed in the cleft, making numerous hydrophobic (Y932, S959, W966, and D1042) and hydrophilic (S935, W977, L979, N1013, and I1066) contacts with the proteins side chain and backbone that may mimic in vivo interactions with the phospholipid membranes on neuronal cell surfaces. A sulfate ion was also observed bound to residues T1176, D1177, K1196, and R1243 in the Hcc sub-domain of BoNT/CD-HCR. In the crystal structure of a similar protein, BoNT/D-HCR, a sialic acid

Zhang, Yanfeng; Gardberg, Anna; Edwards, Tom E.; Sankaran, Banumathi; Robinson, Howard; Varnum, Susan M.; Buchko, Garry W.

2013-07-01T23:59:59.000Z

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321

Participation of Glutamate-354 of the CP43 Polypeptide in the Ligation of Mn and the Binding of Substrate Water in Photosystem II  

Science Conference Proceedings (OSTI)

In the current X-ray crystallographic structural models of photosystem II, Glu354 of the CP43 polypeptide is the only amino acid ligand of the oxygen-evolving Mn4Ca cluster that is not provided by the D1 polypeptide. To further explore the influence of this structurally unique residue on the properties of the Mn4Ca cluster, the CP43-E354Q mutant of the cyanobacterium Synechocystis sp. PCC 6803 was characterized with a variety of biophysical and spectroscopic methods, including polarography, EPR, X-ray Absorption, FTIR, and mass spectrometry. The kinetics of oxygen release in the mutant were essentially unchanged from those in wild-type. In addition, the oxygen flash-yields exhibited normal period-four oscillations having normal S state parameters, although the yields were lower, correlating with the mutant?s lower steady-state rate (approx. 20percent compared to wild-type). Experiments conducted with H218O showed that the fast and slow phases of substrate water exchange in CP43-E354Q thylakoid membranes were accelerated 8.5- and 1.8-fold, respectively, in the S3 state compared to wild-type. Purified oxygen-evolving CP43-E354Q PSII core complexes exhibited a slightly altered S1 state Mn-EXAFS spectrum, a slightly altered S2 state multiline EPR signal, a substantially altered S2-minus-S1 FTIR difference spectrum, and an unusually long lifetime for the S2 state (> 10 hours) in a substantial fraction of reaction centers. In contrast, the S2 state Mn-EXAFS spectrum was nearly indistinguishable from that of wild-type. The S2-minus-S1 FTIR difference spectrum showed alterations throughout the amide and carboxylate stretching regions. Global labeling with 15N and specific labeling with L-[1-13C]alanine revealed that the mutation perturbs both amide II and carboxylate stretching modes and shifts the symmetric carboxylate stretching modes of the ?-COO? group of D1-Ala344 (the C-terminus of the D1 polypeptide) to higher frequencies by 3 ? 4 cm-1 in both the S1 and S2 states. The EPR and FTIR data implied that 76 -82 percent of CP43-E354Q PSII centers can achieve the S2 state and that most of these can achieve the S3 state, but no evidence for advancement beyond the S3 state was observed in the FTIR data, at least not in a majority of PSII centers. Although the X-ray absorption and EPR data showed that the CP43-E354Q mutation only subtly perturbs the structure and spin state of the Mn4Ca cluster in the S2 state, the FTIR and H218O exchange data show that the mutation strongly influences other properties of the Mn4Ca cluster, altering the response of numerous carboxylate and amide groups to the increased positive charge that develops on the cluster during the S1 to S2 transition and weakening the binding of both substrate water molecules (or water derived ligands), especially the one that exchanges rapidly in the S3 state. The FTIR data provide evidence that CP43-Glu354 coordinates to the Mn4Ca cluster in the S1 state as a bridging ligand between two metal ions, but provide no compelling evidence that this residue changes its coordination mode during the S1 to S2 transition. The H218O exchange data provide evidence that CP43-Glu354 interacts with the Mn ion that ligates the substrate water molecule (or water-derived ligand) that is in rapid exchange in the S3 state.

Service, Rachel; Yano, Junko; McConnell, Iain; Hwang, Hong Jin; Niks, Dimitri; Hille, Russ; Wydrzynski, Tom; Burnap, Robert; Hillier, Warwick; Debus, Richard

2010-09-30T23:59:59.000Z

322

FOIA Request Form | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

About » Field Offices » ISC Home » Freedom of About » Field Offices » ISC Home » Freedom of Information Act (FOIA) » How to Submit a FOIA Request » FOIA Request Form Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Advisory Exemptions How to Submit a FOIA Request FOIA Request Form Fee Waiver and Reduction Criteria Electronic Reading Room ISC Conventional Reading Rooms Reference Links Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 How to Submit a FOIA Request FOIA Request Form Print Text Size: A A A RSS Feeds FeedbackShare Page

323

Synthesis and electrochemical and spectroscopic properties of a series of binuclear and trinuclear ruthenium and palladium complexes based on a new bridging ligand containing terpyridyl and catechol binding sites  

Science Conference Proceedings (OSTI)

The ligand 4{prime}-(3,4-dimethoxyphenyl)-2,2{prime}:6{prime},2{double_prime}-terpyridine (L{sup 2}), containing a terpyridyl binding site and a masked catechol binding site, was prepared by a standard Kroehnke-type synthesis. From this the complexes [Ru(terpy)-(L{sup 2})][PF{sub 6}]{sub 2} (1) and [Ru(L{sup 2}){sub 2}][PF{sub 6}]{sub 2} (2), containing one and two dimethoxyphenyl substituents, were prepared: demethylation with BBr{sub 3} afforded [Ru(terpy)(H{sub 2}L{sup 1})][PF{sub 6}]{sub 2} (3) and [Ru(H{sub 2}L{sup 1}){sub 2}][PF{sub 6}]{sub 2} (4), respectively, which have one or two free catechol binding sites pendant from the [Ru(terpy){sub 2}]{sup 2+} core. Binuclear complexes (based on 3) and trinuclear complexes (based on 4) were then prepared by attachment of other metal fragments at the catechol sites. In [Ru(terpy)({mu}-L{sup 1})Ru(bipy){sub 2}][PF{sub 6}]{sub 3} (5) and [Ru({mu}-L{sup 1}){sub 2}(Ru(bipy){sub 2}){sub 2}][PF{sub 6}]{sub 4} (6) the pendant (Ru(bipy){sub 2}(O-O)){sup n+} sites (O-O = catecholate, n = 0; o-benzosemiquinone, n = 1; o-benzoquinone, n = 2) are redox active and may be reversibly interconverted between the three oxidation levels. In [Ru(terpy)({mu}-L{sup 1})Pd(bipy)][PF{sub 6}]{sub 2} (7), [Ru({mu}-L{sup 1}){sub 2}(Pd(bipy)){sub 2}][PF{sub 6}]{sub 2} (8), [Ru(terpy)({mu}-L{sup 1})Pd(4,4{prime}-{sup t}Bu{sub 2}-bipy)][PF{sub 6}]{sub 2} (9), and [Ru({mu}-L{sup 1}){sub 2}(Pd(4,4{prime}-{sup t}Bu{sub 2}-bipy)){sub 2}][PF{sub 6}]{sub 2} (10) the pendant (Pd(bipy)(catecholate)) fragments are known to be photocatalysts for production of {sup 1}O{sub 2} in their own right. Electrochemical and UV/vis studies were performed on all complexes and consistently indicate the presence of interactions between the components in 5-10. The EPR spectrum of 6 (which contains two semiquinone radicals) shows that the two spins are coupled by an exchange interaction.

Whittle, B.; Everest, N.S.; Howard, C.; Ward, M.D. [Univ. of Bristol (United Kingdom)

1995-04-12T23:59:59.000Z

324

Optimized procedures for extractioin, purification and characterization of exopolymeric substances (eps) from two bacteria (sagittula stellata and pseudomonas fluorescens biovar ii) with relevance to the study of actinide binding in aquatic environments  

E-Print Network (OSTI)

The extracellular polymeric substances (EPS) of marine bacterium Sagittula stellata and soil bacterium Pseudomonas fluorescens Biovar II, were extracted by six methods referred to the bibliography, efficacies of which were compared based on the EPS yield, composition as well as cell disturbance. Purification methods on these EPS were also improved, which proved to be more cost-effective and involve less interference from broth, compared to previous methods. Size exclusion chromatography (SEC) proved to be a useful tool, providing the fingerprints of the EPS extracted by different methods or after each purification step. Studies of the EPS production and composition at different growth stages provided abundant information and a basis for further in-depth studies. Results from SEC demonstrated that bacterial EPS had a constant molecular weight distribution all through the life but with various polymers in different proportions. Three fractions were successfully isolated by a combination of SEC and anion exchange chromatography for non-attched EPS produced by Pseudomonas flurorescens Biovar II. Protein turned out to be a major component of EPS in their native states, which was mixed with the broth material and couldnt be recognized previously. The EPS harvested at the optimal time of the bacterial life was purified according to the improved method and was more enriched in polysaccharides, with small amounts of proteins, giving the molecules amphiphilic properties. In addition, simultaneous determination of neutral sugars and uronic acids by GC-EI-MS provided more information on the monosaccharide composition of the exopolysaccharides. Isoelectric focusing (IEF) spectra of the bacterial EPS spiked with Pu/Th, and Pu-enriched Rocky Flats Environmental Technology Site (RFETS) soil organic colloid spiked with Th showed similar activity distributions of both actinides along the pH gradient, with the activities of both actinides focusing on the low pH region. Characterizations of this Pu-enriched IEF extract from RFETS soil by spectrophotometric methods and ATR-FTIR indicated the co-presence of lipids, proteins and polysaccharides, in contrast to the bacterial EPS, which showed a simpler composition. This suggests that Th/Pu binding to organic macromolecules is more determined by the availability of binding functional groups rather than the exact specific compounds.

Xu, Chen

2007-12-01T23:59:59.000Z

325

Binding Organic Liquids - Energy Innovation Portal  

Applications and Industries This technology has potential application in the chemical, energy and utilities, and oil and gas industries. Patents and Patent Applications.

326

Analysis of Holliday junction-binding compounds  

E-Print Network (OSTI)

G. Lloyd (2004). "RecG helicase promotes DNA double-strandby RecG helicase. . 74III Fork remodeling RecG helicase Blooms Syndrome helicase (

Rideout, Marc Christoffer

2011-01-01T23:59:59.000Z

327

Tight-Binding Parameters for the Elements  

Science Conference Proceedings (OSTI)

Apr 9, 2007 ... search ... total energy method for transition and noble metals: Elastic constants, vacancies, and surfaces of monatomic metals ," Phys. Rev.

328

BINDING HASH TECHNIQUE FOR XML QUERY OPTIMIZATION.  

E-Print Network (OSTI)

??XML is a format that allows the storage and exchange of information across the World Wide Web. XML is a semi-structured markup language containing recursively-nested (more)

BRANT, MICHAEL J

2006-01-01T23:59:59.000Z

329

Tuning Genetic Clocks Employing DNA Binding Sites  

E-Print Network (OSTI)

Periodic oscillations play a key role in cell physiology from the cell cycle to circadian clocks. The interplay of positive and negative feedback loops among genes and proteins is ubiquitous in these networks. Often, delays ...

Del Vecchio, Domitilla

330

Minimizing Binding Errors Using Learned Conjunctive Features  

Science Conference Proceedings (OSTI)

We have studied some of the design trade-offs governing visual representations based on spatially invariant conjunctive feature detectors, with an emphasis on the susceptibility of such systems to false-positive recognition errorsMalsburg's classical ...

Bartlett W. Mel; Jzsef W. Fiser

2000-02-01T23:59:59.000Z

331

Minimizing Binding Errors Using Learned Conjunctive Features  

Science Conference Proceedings (OSTI)

We have studied some of the design trade-offs governing visual representations based on spatially invariant conjunctive feature detectors, with an emphasis on the susceptibility of such systems to false-positive recognition errorsMalsburgs ...

Bartlett W. Mel; Jsef W. Fiser

2000-04-01T23:59:59.000Z

332

XANES Study of Cu2+ -Binding Sites  

E-Print Network (OSTI)

.; Solera, J. A.; Chaboy, J.; Proietti, M. G.; Garcia, J. Phys. Rev. B 1997, 56, 2447-2452. (30) Croue´, J

Frenkel, Anatoly

333

Binding of Proteins to Copolymers of Varying  

E-Print Network (OSTI)

based on the free energy of transfer of hydro- carbons from aqueous solution to apolar solvent), hydro- phobic interactions between protein and stationary phase polymer are central to the protein of concrete evidence. However, in some cases, hydro- phobic contribution to protein­polymer interactions may

Dubin, Paul D.

334

Structure of the human gene encoding sterol regulatory element binding protein-1 (SREBF1) and localization of SREBF1 and SREBF2 to chromosomes 17p11.2 and 22q13  

Science Conference Proceedings (OSTI)

Sterol regulatory element binding protein-1 (SREBP1) and SREBP2 are structurally related proteins that control cholesterol homeostasis by stimulating transcription of sterol-regulated genes, including those encoding the low-density lipoprotein (LDL) receptor and 3-hydroxy-3-methylglutaryl CoA synthase. SREBP1 and SREBP2 are 47% identical, and they share a novel structure comprising a transcriptionally active NH{sub 2}-terminal basic helix-loop-helix-leucine zipper (bHLH-Zip) domain followed by a membrane attachment domain. Cleavage by a sterol-regulated protease frees the bHLH-Zip domain from the membrane and allows it to enter the nucleus. SREBP1 exists in several forms, possibly as a result of alternative splicing at both the 5{prime} and the 3{prime} ends of the mRNA. The genes for SREBP1 (SREBF1) and SREBP2 (SREBF2) have not been studied. In this paper we describe the cloning and characterization of the human SREBF1 gene. The gene is 26 kb in length and has 22 exons and 20 introns. The 5{prime} and 3{prime} sequences that differ between the two SREBP1 cDNAs are encoded by discrete exons, conforming the hypothesis that they result from alternative splicing. The chromosomal locations of human SREBF1 and SREBF2 were determined by analysis of human-rodent somatic cell hybrids and fluorescence in situ hybridization. The SREBF1 gene mapped to the proximal short arm of chromosome 17 (17p11.2), and the SREBF2 gene was localized to the long arm of chromosome 22 (22q13). 22 refs., 3 figs., 2 tabs.

Hua, X.; Wu, J.; Goldstein, J.L. [Univ. of Texas, Dallas, TX (United States)] [and others] [Univ. of Texas, Dallas, TX (United States); and others

1995-02-10T23:59:59.000Z

335

Radionuclide-binding compound, a radionuclide delivery system, a method of making a radium complexing compound, a method of extracting a radionuclide, and a method of delivering a radionuclide  

DOE Patents (OSTI)

The invention pertains to compounds which specifically bind radionuclides, and to methods of making radionuclide complexing compounds. In one aspect, the invention includes a radionuclide delivery system comprising: a) a calix[n]arene-crown-[m]-ether compound, wherein n is an integer greater than 3, and wherein m is an integer greater than 3, the calix[n]arene-crown-[m]-ether compound comprising at least two ionizable groups; and b) an antibody attached to the calix[n]arene-crown-[m]-ether compound. In another aspect, the invention includes a method of making a radium complexing compound, comprising: a) providing a calix[n]arene compound, wherein n is an integer greater than 3, the calix[n]arene compound comprising n phenolic hydroxyl groups; b) providing a crown ether precursor, the crown ether precursor comprising a pair of tosylated ends; c) reacting the pair of tosylated ends with a pair of the phenolic hydroxyl groups to convert said pair of phenolic hydroxyl groups to ether linkages, the ether linkages connecting the crown ether precursor to the calix[n]arene to form a calix[n]arene-crown-[m]-ether compound, wherein m is an integer greater than 3; d) converting remaining phenolic hydroxyl groups to esters; e) converting the esters to acids, the acids being proximate a crown-[m]-ether portion of the calix[n]arene-crown-[m]-ether compound; and f) providing a Ra.sup.2+ ion within the crown-[m]-ether portion of the calix[n]arene-crown-[m]-ether compound.

Fisher, Darrell R. (Richland, WA); Wai, Chien M. (Moscow, ID); Chen, Xiaoyuan (Moscow, ID)

2000-01-01T23:59:59.000Z

336

How to Submit a FOIA Request | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

How to Submit a FOIA Request How to Submit a FOIA Request Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Advisory Exemptions How to Submit a FOIA Request FOIA Request Form Fee Waiver and Reduction Criteria Electronic Reading Room ISC Conventional Reading Rooms Reference Links Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Freedom of Information Act (FOIA) How to Submit a FOIA Request Print Text Size: A A A RSS Feeds FeedbackShare Page Related Links Electronic FOIA Request Form Office of Science Integrated Support Center (ISC)

337

Real Property Management | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Real Property Management Real Property Management Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Real Property Management Print Text Size: A A A RSS Feeds FeedbackShare Page Real Property Management provides a consistent approach for all real property transactions throughout the Office of Science (SC). The ISC advises on and reviews real estate transactions to assure compliance with applicable requirements to the SC complex. The ISC ensures that the government and the contractor real property transactions comply with

338

Mesoscale Convective Complexes over the Indian Monsoon Region  

Science Conference Proceedings (OSTI)

Full disk infrared satellite imagery from the Indian National Satellite System (INSAT) geostationary meteorological satellite was examined to determine if mesoscale convective complexes (MCCs) frequent the Indian subcontinent (ISC) region. Using ...

Arlenf G. Laing; J. Michael Fritsch

1993-05-01T23:59:59.000Z

339

Environment, Safety and Health (ES&H) | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Environment, Safety and Health (ES&H) Environment, Safety and Health (ES&H) Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Environment, Safety and Health (ES&H) Print Text Size: A A A RSS Feeds FeedbackShare Page Environment, Safety and Health is a vital component within the ISC that helps Office of Science's line managers perform their responsibilities, while protecting the Department's assets and resources. The ISC assists management and ensures environment, safety, and health performance

340

Budget and Finance | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Budget and Finance Budget and Finance Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Budget and Finance Print Text Size: A A A RSS Feeds FeedbackShare Page The ISC Budget and Financial Management staffs ensure that the Office of Science is exemplary in stewardship of fiscal resources. ISC budget and financial staff support the ten Office of Science site offices, the Science budget office and program offices by distributing funds in an efficient and

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

Use dispersion modeling update  

SciTech Connect

This paper discusses EPA's long-awaited update to the Industrial Source Complex (ISC) dispersion models which provides computer-software to comply with National Ambient Air Quality Standards. Moreover, the ISC2 models's Fortran codes are available from EPA at no cost, in a form compatible with desktop computers. This is a plus for hydrocarbon processing industry (HPI) environmental control professionals. ISC2 will be used for all future regulatory applications where dispersion modeling is required for facilities in simple terrain. Process engineers sometimes use ISC models and are often called upon to assist in developing emissions estimates that the program uses to calculate air quality impacts. The model challenges users because it can represent a variety of configurations for emissions sources. Title III of the Clean Air Act Amendments is an entirely new section dealing with air toxics such as those in the HPI. EPA is required to develop a list of maximum achievable control technologies (MACT) for these compounds.

Freiman, J.P.; Hill, J. (Bechtel Environmental, Inc., Houston, TX (US))

1992-08-01T23:59:59.000Z

342

Manual  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

DOE U.S. Department of Energy ES&H Environment, Safety, and Health FEL Free Electron Laser FM&L Facilities Management and Logistics HSS Office of Health, Safety and Security ISC...

343

Impact of chemical reactions in the gas phase on the in-situ combustion process: an experimental study.  

E-Print Network (OSTI)

??In-Situ Combustion (ISC) is a thermal enhanced oil recovery method. Therefore, air or oxygen-enriched air is injected in the reservoir. The oxygen reacts with part (more)

Hoekstra, B.E.

2011-01-01T23:59:59.000Z

344

Preliminary Investigation of Methods for Correcting for Variations in Solar Spectrum under Clear Skies  

DOE Green Energy (OSTI)

Study of two methods for correcting Isc of PV modules for variations in solar spectrum: empirical relationships based on air mass, and spectral irradiance models and PV module spectral response data.

Marion, B.

2010-03-01T23:59:59.000Z

345

Relating metal binding to DNA binding in the nickel regulatory protein NikR  

E-Print Network (OSTI)

The concentration of transition metals within the cell must be tightly regulated. If the concentration of a given transition metal is too low the cell may not be able to perform life-sustaining processes, while high levels ...

Phillips, Christine M. (Christine Marie)

2010-01-01T23:59:59.000Z

346

Exemptions | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Exemptions Exemptions Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Advisory Exemptions How to Submit a FOIA Request Fee Waiver and Reduction Criteria Electronic Reading Room ISC Conventional Reading Rooms Reference Links Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Freedom of Information Act (FOIA) Exemptions Print Text Size: A A A RSS Feeds FeedbackShare Page Exemption 1: National Security Information This exemption protects from disclosure all national security information concerning the national defense or foreign policy that has been properly

347

Quality Management | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Quality Management Quality Management Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Quality Management Print Text Size: A A A RSS Feeds FeedbackShare Page The ISC provides quality assurance expertise to the Office of Science's site offices in support of their federal oversight of the national laboratories. Effective quality assurance (QA) programs are essential for achieving a high level of efficiency and excellence in the design, construction, operation and maintenance of laboratory facilities, and in

348

Freedom of Information Act (FOIA) | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Freedom of Freedom of Information Act (FOIA) Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Advisory Exemptions How to Submit a FOIA Request Fee Waiver and Reduction Criteria Electronic Reading Room ISC Conventional Reading Rooms Reference Links Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Freedom of Information Act (FOIA) Print Text Size: A A A RSS Feeds FeedbackShare Page On September 4, 1966, Public Law 89-554, enacted into law Title 5 of the U.S. Code entitled , "Government Organization and Employees", and

349

JC3 Tools | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

JC3 Tools JC3 Tools JC3 Tools NMAP Nmap ("Network Mapper") is a free and open source (license) utility for network exploration or security auditing. Many systems and network administrators also find it useful for tasks such as network inventory, managing service upgrade schedules, and monitoring host or service uptime. WireShark Wireshark is a network protocol analyzer. It lets you capture and interactively browse the traffic running on a computer network. Microsoft Network Monitor Network Monitor 3.4 is a protocol analyzer. It allows you to capture network traffic, view and analyze it.Solar Winds IP Address Tracker ISC SANS The ISC was created in 2001 following the successful detection, analysis, and widespread warning of the Li0n worm. Today, the ISC provides a free

350

Jobs | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

About » About » Jobs Integrated Support Center (ISC) ISC Home About Jobs Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 About Jobs Print Text Size: A A A Subscribe FeedbackShare Page Current Open Federal Positions The ISC is a virtual organization comprised of the combined support capabilities of offices in Chicago, Illinois, and Oak Ridge, Tennessee. All open federal positions listed below are posted on USAJobs.gov External link . (Chicago Organization Chart .pdf file (84KB) | Oak Ridge Organization

351

Small Business Program Management | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Small Business Program Management Small Business Program Management Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Small Business Program Management Print Text Size: A A A RSS Feeds FeedbackShare Page Related Links Federal Acquisition Regulations External link DOE Small Business Program U.S. Small Business Administration External link Small Businesses are vital to our country's continued growth and it is important to the ISC that small business is provided the maximum practical

352

Human Resources | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Human Resources Human Resources Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Human Resources Print Text Size: A A A RSS Feeds FeedbackShare Page Related Links Forms External link Office of Chief Human Capital Officer USA Jobs External link The ISC Human Resources Services develops and implements a comprehensive human capital program to facilitate the acquisition, development and retention of a technically competent, diverse workforce that meets the

353

Reference Links | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Reference Links Reference Links Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Advisory Exemptions How to Submit a FOIA Request Fee Waiver and Reduction Criteria Electronic Reading Room ISC Conventional Reading Rooms Reference Links Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Freedom of Information Act (FOIA) Reference Links Print Text Size: A A A RSS Feeds FeedbackShare Page FOIA, 5 U.S.C. Sec. 552, As Amended by Public Law No. 104-231, 110 Stat. 2422 External link DOE Implementing Regulations, 10 CFR 1004 External link

354

Fee Waiver and Reduction Criteria | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Fee Waiver and Reduction Criteria Fee Waiver and Reduction Criteria Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Advisory Exemptions How to Submit a FOIA Request Fee Waiver and Reduction Criteria Electronic Reading Room ISC Conventional Reading Rooms Reference Links Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Freedom of Information Act (FOIA) Fee Waiver and Reduction Criteria Print Text Size: A A A RSS Feeds FeedbackShare Page The FOIA generally requires that requesters pay fees for processing their requests. In accordance with 5 U.S.C 552(a)(4)(A)(iv), an agency is

355

Public Affairs and Intergovernmental Relations | U.S. DOE Office of Science  

NLE Websites -- All DOE Office Websites (Extended Search)

Public Affairs and Intergovernmental Relations Public Affairs and Intergovernmental Relations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Public Affairs and Intergovernmental Relations Print Text Size: A A A RSS Feeds FeedbackShare Page The ISC's Public Affairs and Intergovernmental Relations divisions develop and implement communication strategies and advise officials within the Department how to best communicate issues and priorities of public and internal interest. In addition, the division oversees news media relations,

356

Privacy Act Advisory | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Privacy Act Advisory Privacy Act Advisory Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Advisory Exemptions How to Submit a FOIA Request Fee Waiver and Reduction Criteria Electronic Reading Room ISC Conventional Reading Rooms Reference Links Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Freedom of Information Act (FOIA) Privacy Act Advisory Print Text Size: A A A RSS Feeds FeedbackShare Page To Contact Us Freedom of Information Act/Privacy Act Officer U.S. Department of Energy SC Integrated Support Center - Chicago

357

Personal Property Management | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Personal Property Management Personal Property Management Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Personal Property Management Print Text Size: A A A RSS Feeds FeedbackShare Page The ISC's Personal Property Management ensures the Department utilizes the most efficient and effective processes in acquiring, managing, and disposing of personal property assets as it conducts its missions. Personnel provide procedural guidance, conduct oversight and periodic

358

Information Management | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Information Management Information Management Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Information Management Print Text Size: A A A RSS Feeds FeedbackShare Page Integrated Support Center information management professionals are an integral part of the Science Information Technology Modernized Organization. Staff in the ISC collaborate closely with the Site Offices and the SC Chief Information Officer to ensure federal staff in the field have the right products and services to efficiently fulfill the mission.

359

CX-006810: Categorical Exclusion Determination | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

6810: Categorical Exclusion Determination 6810: Categorical Exclusion Determination CX-006810: Categorical Exclusion Determination International lndustrial Energy Efficiency Training and Deployment (IIEETD) CX(s) Applied: A9, A11 Date: 09/15/2011 Location(s): Vermont Office(s): Energy Efficiency and Renewable Energy, Golden Field Office Institute for Sustainable Communities (ISC) would use Department of Energy (DOE) funding for energy efficiency education and outreach activities directed at industrial energy efficiency in China and India. ISC would retain subject matter experts to collaborate with United States (U.S.) companies to disseminate best practices to their manufacturing facilities in China and India. ISC would adapt DOE energy assessment and management tools and technologies to the Chinese and Indian contexts, targeting the

360

Identification of DNA-Binding Proteins and Protein-Protein ...  

Science Conference Proceedings (OSTI)

The regulation may be either activation, stimulation, inhibition or suppression. ... genes is mediated by well-coordinated proteinprotein interactions between...

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


361

Motifs, binding, and expression : computational studies of transcriptional regulation  

E-Print Network (OSTI)

Organisms must control gene expression in response to developmental, nutritional, or other environmental cues. This process is known as transcriptional regulation and occurs through complex networks of proteins interacting ...

MacIsaac, Kenzie D. (Kenzie Daniel), 1975-

2009-01-01T23:59:59.000Z

362

Analysis of the Vertebrate Insulator Protein CTCF-Binding  

E-Print Network (OSTI)

Research, Department of Cellular and Molecular Medicine, University of California, San Diego School Present address: Department of Genetics, Yale University School of Medicine, 333 Cedar Street, SHMI 142B as protocadherin g (pcdhg), T cell receptor a/d, loci (tcra/d and tcrb), and light-chain l locus (igll; Fig- ure S4

363

Structural signatures of antibiotic binding sites on the ribosome  

E-Print Network (OSTI)

that this pocket could be a good candidate for a novel drug. CONCLUSIONS In an attempt to better understand the atomic and struc- tural features that could elucidate the druggability of ABSs on the ribosome, we

Mandel-Gutfreund, Yael

364

Thermodynamics of Binding Biomass to Cellulases for Renewable...  

NLE Websites -- All DOE Office Websites (Extended Search)

synthesis and conversion will enable experimental design approaches in a rational design paradigm both to develop superior enzymes and less recalcitrant plant-based...

365

Engineered biomolecular interactions with inorganic materials : sequence, binding, and assembly  

E-Print Network (OSTI)

Nanobiotechnology aims to exploit biomolecular recognition and self-assembly capabilities for integrating advanced materials into medicine and electronics. In particular, peptides have exhibited the ability to specifically ...

Peelle, Beau R

2005-01-01T23:59:59.000Z

366

Hypoglycemia due to insulin binding antibodies in a patient with ...  

Science Conference Proceedings (OSTI)

autoimmune diseases, some drugs, such as methimazole. [3]. ... She accepted oral antidiabetic drugs ... University School of Medicine, China 280# MoHe Road,

367

The importance of metal binding in metalloprotein inhibitors  

E-Print Network (OSTI)

the requirement of a catechol moiety Quercetin Diketoon C-3 making the MBG a catechol; RCD-12 contains a methoxyRCD-9S, -9S2), catechol (RCD-11), hydroxyquinolines (RCD-

Agrawal, Arpita

2011-01-01T23:59:59.000Z

368

Identification and Characterization of the Drosophila Inverted Repeat Binding Complex  

E-Print Network (OSTI)

D. H. (1990). A novel RNA helicase gene tightly linked toLiu, Z. R. (2009). P68 RNA helicase is a nucleocytoplasmicand Ira, G. (2008). Sgs1 helicase and two nucleases Dna2 and

Francis, Malik Joseph

2011-01-01T23:59:59.000Z

369

Probing Product Binding in Cellulase Enzymes (Fact Sheet)  

DOE Green Energy (OSTI)

Simulations uncover potential new strategies for increasing the desired effects of enzymes for biofuels.

Not Available

2012-08-01T23:59:59.000Z

370

Making Sense of Non-Binding Retail-Price Recommendations  

E-Print Network (OSTI)

information about production costs, we show that RPRs may beis independent of production costs and punishment strategiesabout their own production costs than retailers. This seems

Grtner, Dennis L; Buehler, Stefan

2009-01-01T23:59:59.000Z

371

PRELIMINARY STUDY OF METHODS TO CHEMICALLY BIND ZINC  

DOE Green Energy (OSTI)

To address the {sup 65}Zn contamination issue in the TEF, a multi-task experimental program was initiated. The first two experimental tasks were completed. The results of the third experimental task are reported here. This task was conducted to determine if the zinc vapors could be chemically bound on two non hydrogen active substrates. Based on a thermodynamic study copper and cobalt were the most favorable for capturing zinc without forming hydrides. Within the experimental parameters tested, which include temperatures of 350, 400, and 450 C at pressures of nominally 20-40 millitorr, the zinc deposited on the both copper screen and cobalt rods but did not react to form a compound. The conditions that were tested are not prototypic and additional testing under higher vacuum conditions, i.e., .01 millitorr, may enhance the reactivity of the surfaces and is recommended.

Korinko, P.

2011-06-10T23:59:59.000Z

372

A Nanocube Plasmonic Sensor for Molecular Binding on Membrane ...  

junctions at T-cell synapses.22,23 The detection strategy ... ized hot spots of ampli?ed intensity which extend ap-proximately 10 nm beyond the metal ...

373

New Mathematical Method Reveals Where Proteins Bind with DNA...  

NLE Websites -- All DOE Office Websites (Extended Search)

computing resources at the U.S. Department of Energy's National Energy Research Scientific Computing Center (NERSC), have taken a new mathematical method used in signal...

374

Probing Product Binding in Cellulase Enzymes (Fact Sheet), NREL...  

NLE Websites -- All DOE Office Websites (Extended Search)

uncover potential new strategies for increasing the desired effects of enzymes for biofuels. Large-scale computer simulations offer a new interpretation for the discrepancy in...

375

Glycosylation Helps Cellulase Enzymes Bind to Plant Cell Walls...  

NLE Websites -- All DOE Office Websites (Extended Search)

simulations suggest a new strategy to design enhanced enzymes for biofuels production. Large-scale computer simulations predict that the addition of glycosylation on...

376

Breaking the ties that bind: New hope for biomass fuels  

NLE Websites -- All DOE Office Websites (Extended Search)

viable process for making biofuels from cellulosic biomass," adds Langan, director of the biofuels project. Funding for the project comes from Laboratory-Directed Research and...

377

Molecular Characterization of a Novel Class of DNA Binding Proteins  

E-Print Network (OSTI)

Current Protocols in Molecular Biology. Wiley, New York, NY.1997. Biological and molecular features of the relationshipsand G. Darai. 2002. Molecular anatomy of Chilo iridescent

Spears, Tatsinda Verity

2010-01-01T23:59:59.000Z

378

The Formation and Binding of Gold Nanoparticles onto Wool Fibres  

SciTech Connect

This paper presents the novel use of nanosize gold with different plasmon resonance colours, as stable colourfast colourants on wool fibres for use in high quality fabrics and textiles. The gold nanoparticles are synthesised by the controlled reduction of Au{sup 3+} in the AuCl{sub 4}{sup -} complex to Au{sup 0} onto the surface of the wool where they attach to the S in the cystine amino acids in wool keratin proteins. Scanning electronmicroscopy shows the nanoparticles are present on the cuticles of the fibre surface and are concentrated at the edges of these cuticles. EDS analysis shows a strong correlation of Au with S and X-ray photoelectron spectroscopy suggests Au-S bond formation. Hence the nanogold colourants are chemically bound to the wool fibre surface and do not fade as traditional organic dyes do. A range of coloured fibres have been produced.

Johnston, James H.; Burridge, Kerstin A.; Kelly, Fern M. [School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140 (New Zealand)

2009-07-23T23:59:59.000Z

379

Boron compounds as anion binding agents for nonaqueous battery electrolytes  

DOE Patents (OSTI)

Novel fluorinated boron-based compounds which act as anion receptors in non-aqueous battery electrolytes are provided. When added to non-aqueous battery electrolytes, the fluorinated boron-based compounds of the invention enhance ionic conductivity and cation transference number of non-aqueous electrolytes. The fluorinated boron-based anion receptors include borane and borate compounds bearing different fluorinated alkyl and aryl groups.

Lee, Hung Sui (East Setauket, NY); Yang, Xia-Oing (Port Jefferson Station, NY); McBreen, James (Bellport, NY); Xiang, Caili (Upton, NY)

2000-02-08T23:59:59.000Z

380

The Ties that Bind Metals to Proteins | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

Nanobio Catalyst for Biofuels Multiple Crystal Cavities for Unlimited X-ray Energy Resolution and Coherence An Intriguing Twist in the Structure of a Cobalt Oxide Catalyst Breaking...

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


381

Comparative analysis of MTF-1 binding sites between human and ...  

Science Conference Proceedings (OSTI)

cedure such as chromatin immunoprecipitation followed by either genomic microchip hybridization (ChIP-on-Chip) or deep sequencing (ChIP and Sequencing)...

382

Ties that Bind: Policies to Promote (Good) Patent Pools  

E-Print Network (OSTI)

incentives for invention and disclosure. The patent systemin return for greater invention and disclosure of patented

Gilbert, Richard J

2009-01-01T23:59:59.000Z

383

Identification of Hydrogen Trapping Sites, Binding Energies, and ...  

Science Conference Proceedings (OSTI)

Environmentally Assisted Cracking of Carbon Steel in High Temperature Geothermal Well Evaluation of the Susceptibility to Hydrogen Assisted Cracking in...

384

Mining characteristic relations bind to RNA secondary structures  

Science Conference Proceedings (OSTI)

The identification of RNA secondary structures has been among the most exciting recent developments in biology and medical science. It has been recognized that there is an abundance of functional structures with frameshifting, regulation of translation, ... Keywords: H-pseudoknot, association group, function, probability matrix, secondary structure

Qingfeng Chen; Yi-Ping Phoebe Chen

2010-01-01T23:59:59.000Z

385

DNA polymerase having modified nucleotide binding site for DNA sequencing  

DOE Patents (OSTI)

A modified gene encoding a modified DNA polymerase is disclosed. The modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase. 6 figs.

Tabor, S.; Richardson, C.

1997-03-25T23:59:59.000Z

386

Influence of proteolytic enzymes and calcium-binding agents on ...  

Science Conference Proceedings (OSTI)

Department of Histology, Karolinska Institutet, Stockholm, Sweden; and Laboratory for Cell Biology and Histology,. University of Leiden, Leiden, The Netherlands.

387

Binding sites of quinones in photosynthetic bacterial reaction centers investigated by light-induced FTIR difference spectroscopy: Symmetry of the carbonyl interactions and close equivalence of the Q{sub B} vibrations in Rhodobacter sphaeroides and Rhodopseudomonas viridis probed by isotope labeling  

Science Conference Proceedings (OSTI)

The photoreduction of the secondary quinone acceptor Q{sub B} in reaction centers (RCs) of the photosynthetic bacteria Rhodobacter sphaeroides and Rhodopseudomonas viridis has been investigated by light-induced FTIR difference spectroscopy of RCs reconstituted with several isotopically labeled ubiquinones. The labels used were {sup 18}O on both carbonyls and {sup 13}C either uniformly or selectively at the 1- or the 4-position, i.e., on either one of the two carbonyls. The Q{sub B}{sup {minus}}/Q{sub B} spectra of RCs reconstituted with the isotopically labeled and unlabeled quinones as well as the double differences calculated form these spectra exhibit distinct isotopic shifts for a numer of bands attributed to vibrations of Q{sub B} and Q{sub B}{sup {minus}}. The vibrational modes of the quinone in the Q{sub B} site are compared to those of ubiquinone in vitro, leading to band assignments for the C{double_bond}O and C{double_bond}C vibrations of the neutral Q{sub B} and for the C---O and C---C of the semiquinone. The C{double_bond}O frequency of each of the carbonyls of the unlabeled quinone is revealed at 1641 cm{sup {minus}1} for both species. This demonstrates symmetrical and weak hydrogen bonding of the two C{double_bond}O groups to the protein at the Q{sub B} site. In contrast, the C{double_bond}C vibrations are not equivalent for selective labeling at C{sub 1} or at C{sub 4}, although they both contribute to the {approximately}1611-cm{sup {minus}1} band in the Q{sub B}{sup {minus}}/Q{sub B} spectra of the two species. Compared to the vibrations of isolated ubiquinone, the C{double_bond}C mode of Q{sub B} does not involve displacement of the C{sub 4} carbon atom, while the motion of C{sub 1} is not hindered. Further analysis of the spectra suggests that the protein at the binding site imposes a specific constraint on the methoxy and/or the methyl group proximal to the C{sub 4} carbonyl. 49 refs., 5 figs.

Breton, J.; Berger, G.; Nabedryk, E. [SBE/DBCM and SMM/DBCM, CEA-Saclay (France)] [and others

1995-09-12T23:59:59.000Z

388

R&D: Cyberterrorism: A look into the future  

Science Conference Proceedings (OSTI)

Cyberterrorism might mean different things to different people, but one thing is certain - it needs to be taken incredibly seriously. What are we dealing with? How can we defend our nation? How will cyberterrorists of the future look to attack? The (ISC)^2 ...

2009-09-01T23:59:59.000Z

389

Estimation of Biomass Heat Storage Using Thermal Infrared Imagery: Application to a Walnut Orchard  

E-Print Network (OSTI)

biomass. The speci?c heat capacity (C p,trunk ), thermalFisch 1986). The speci?c heat capacity of leaves C p,leaf isC p,trunk is the speci?c heat capacity of the trunk, T trunk

Garai, Anirban; Kleissl, Jan; Llewellyn Smith, Stefan G.

2010-01-01T23:59:59.000Z

390

Industrial strength COMPASS: A comprehensive algorithm and software for optimization via simulation  

Science Conference Proceedings (OSTI)

Industrial Strength COMPASS (ISC) is a particular implementation of a general framework for optimizing the expected value of a performance measure of a stochastic simulation with respect to integer-ordered decision variables in a finite (but typically ... Keywords: Optimization via simulation, random search, ranking and selection

Jie Xu; Barry L. Nelson; JEFF L. Hong

2010-01-01T23:59:59.000Z

391

Cissp video mentor, First edition  

Science Conference Proceedings (OSTI)

Learn exam essentials from the Expert The fast, powerful way to prepare for your CISSP exam! Get the hands-on training you need to pass the (ISC)2 globally recognized CISSP exam, get certified, and give your IT career a lift! In these videos, the world's ...

Shon Harris

2009-12-01T23:59:59.000Z

392

106 Home Power #78 August / September 2000 Code Corner  

E-Print Network (OSTI)

at 1.56 Isc, but Section 110.3 says to follow the product labels. Any installer facing this quandary from the National Fire Protection Association (NFPA) · 800-344-3555 or 617-770-3000 · www.nfpa.org www

Johnson, Eric E.

393

Suspension Polymerization of Polystyrene Clayton Barrix, Dr. Matthew Ray, University of Wisconsin-Stout  

E-Print Network (OSTI)

at 1.56 Isc, but Section 110.3 says to follow the product labels. Any installer facing this quandary from the National Fire Protection Association (NFPA) · 800-344-3555 or 617-770-3000 · www.nfpa.org www

Wu, Mingshen

394

Beauty is in the Eye of the Inspector  

E-Print Network (OSTI)

at 1.56 Isc, but Section 110.3 says to follow the product labels. Any installer facing this quandary from the National Fire Protection Association (NFPA) · 800-344-3555 or 617-770-3000 · www.nfpa.org www

Johnson, Eric E.

395

Improvements to the EPA Industrial Source Complex Dispersion Model  

Science Conference Proceedings (OSTI)

Air quality models are a key component in determining air pollution control requirements. The Industrial Source Complex (ISC2) model is a steady-state Gaussian plume model that is used for modeling point, area, volume, and line sources. Since its ...

Dennis G. Atkinson; Desmond T. Bailey; John S. Irwin; Jawad S. Touma

1997-08-01T23:59:59.000Z

396

Dispersion modeling of ground-level area sources of particulate  

E-Print Network (OSTI)

The use of dispersion modeling by State Air Pollution hics. Regulatory Agencies (SAPRAS) is increasing. Dispersion modeling provides a quick and efficient means of determining the downwind impact of pollutant release from a source. The SAPRAS are charged with the task of insuring that public exposure levels of these pollutants are less than the standards set by the United States Environmental Protection Agency (US EPA). Estimating the concentration of pollutant at some distance downwind, in most cases the property line, allows that SAPRAS to determine whether or not a source needs to install additional means of control in order to decrease the rate of pollutant release. One set of models approved for regulatory use by the US EPA is Industrial Source Complex (ISC). ISC includes SCREEN: which is a simple screening model with imbedded meteorological data, and ST3 which is a more refined model requiring meteorological data to be provided. ISC models are based on the concept of Gaussian dispersion. The concentration determined using the ISC models are a result of determining concentrations based on a single wind speed and direction for a one hour time period. The first step in the formulation of a new model was to incorporate smaller time periods into the concentration predictions, in order to account for variation or wind speed and direction within an hour period. For ground-level sources, the vertical distribution involves mathematically dispersing the pollutant underground, then reflecting it back up. The next step taken in the new model development was the incorporation of a triangular distribution in the Medical plane. The triangular distribution is entirely above ground. Once the new model was formulated, a sample modeling procedure was performed in order to compare the behavior of the new model as compared to ISC ST3. Examination of the characteristics of the two models, the meteorological data, and the output from the modeling procedures allows the comparison and contrast of the behavioral characteristics of the two models.

Fritz, Bradley Keith

1998-01-01T23:59:59.000Z

397

Energy Savings Performance Contracts (ESPCs) | U.S. DOE Office of Science  

NLE Websites -- All DOE Office Websites (Extended Search)

Energy Savings Performance Contracts (ESPCs) Energy Savings Performance Contracts (ESPCs) Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Energy Savings Performance Contracts (ESPCs) Print Text Size: A A A RSS Feeds FeedbackShare Page Energy Savings Contracts (Utility Energy Savings Contracts [UESCs] and Energy Savings Performance Contracts [ESPCs]) allow federal agencies to accomplish energy projects for their facilities without depending on special appropriations to pay for the improvements. The contractor conducts

398

How to Submit a Privacy Act Request | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

How to Submit a Privacy Act Request How to Submit a Privacy Act Request Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Compilation of Systems of Records Energy Employees Occupational Illness Compensation Program Act (EEOICPA) How to Submit a Privacy Act Request Privacy Act Request Form .pdf file (99KB) Reference Links Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Privacy Act How to Submit a Privacy Act Request Print Text Size: A A A RSS Feeds FeedbackShare Page Related Links Privacy Act Request Form .pdf file (99KB) You may request your own Privacy Act records by submitting a request in

399

Oak Ridge National Laboratory Site Office CX Determinations | U.S. DOE  

NLE Websites -- All DOE Office Websites (Extended Search)

Oak Ridge National Laboratory Site Office Oak Ridge National Laboratory Site Office CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations Oak Ridge National Laboratory Site Office CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link 12/11/2013 Demolition and Replacement of Building 7018 at the Oak Ridge National Laboratory (3790CXD) .pdf file (100KB) B1.15; B1.23

400

Microsoft Word - DOE-ID-INL-13-020.doc  

NLE Websites -- All DOE Office Websites (Extended Search)

0 0 SECTION A. Project Title: Interim Storage Area for Interim Storage Containers (ISCs) at the Radioactive Scrap and Waste Facility (RSWF) SECTION B. Project Description: Currently, dedicated space is unavailable for above-grade storage of Interim Storage Containers (ISCs) containing 55-gal drums of remote handled transuranic waste (RH-TRU). In the past this waste was packaged in specially constructed liners and placed into the RSWF. When ready for transfer this waste would then be removed from RSWF and transferred to CH2M-WG Idaho, LLC (CWI) where it was sorted and repackaged for shipment to Waste Isolation Pilot Plant (WIPP). The construction of this new interim storage area is needed to eliminate special packaging and placement into RSWF in order to reduce costs and exposure associated with repackaging

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

Breaking Down the Barriers  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Breaking Down the Barriers Breaking Down the Barriers Engaging Agency Legal Resources to be Part of the Solution Daniel Gore US Coast Guard Energy Manager X ESPC ISC Kodiak ESPC/UESC Unit Contract Type Coast Guard Alternatively Financed Project Status Estimated Contract Value (Millions) Under Consideration Initial Proposal Delayed by lack of Contracting Officer or Champion Detailed Design Study Recently Awarded TRACEN Cape May ESPC X TRACEN Petaluma PPA X X ISC San Pedro UESC X X CG Academy ESPC X TRACEN Cape May UESC X Air Station Borenquin ESPC X X Sector New York (3 sites) ESPC X X CG Yard (BAMF) ESPC X E-City ESPC X West Coast - 9 Sites ESPC X Five Essentials for Alt. Financed Project * Site approval * Technical Champion * Contracting Officer * Financial Analyst * Legal Support

402

Services | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Services Services Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Print Text Size: A A A RSS Feeds FeedbackShare Page Service Plan of the SC Integrated Support Center .pdf file (4.2MB) Human Resources Acquisition and Assistance Energy Savings Performance Contracts (ESPCs) Contractor Human Resources Personal Property Management Real Property Management Small Business Program Management Budget and Finance Public Affairs and Intergovernmental Relations

403

Chicago Office CX Determinations | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Chicago Office CX Determinations Chicago Office CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations Chicago Office CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link 07/17/2013 Generic Categorical Exclusion Determination for Financial Assistance Awards .pdf file (905KB) Various

404

New Brunswick Laboratory CX Determinations | U.S. DOE Office of Science  

NLE Websites -- All DOE Office Websites (Extended Search)

New Brunswick Laboratory CX Determinations New Brunswick Laboratory CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations New Brunswick Laboratory CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link 06/08/2012 NBL-17 GENERIC CATEGORICAL EXCLUSION (CX) FOR THE NBL: Indoor Bench Scale Research Projects and Conventional Laboratory Operations .pdf file (617KB) B3.6

405

Argonne Site Office CX Determinations | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Argonne Site Office CX Determinations Argonne Site Office CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations Argonne Site Office CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link 12/12/2013 Operation of the 50 MeV Electron LINAC Accelerator (ASO-CX-300) .pdf file (177KB) B3.10

406

SLAC Site Office CX Determinations | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

SLAC Site Office CX Determinations SLAC Site Office CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations SLAC Site Office CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page CX Determinations prior to October 2009 should be requested from David Osugi. Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link

407

Princeton Site Office CX Determinations | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Princeton Site Office CX Determinations Princeton Site Office CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations Princeton Site Office CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page Note: ARRA is the American Recovery and Reinvestment Act of 2009 Funded Projects. PSO CX Posting Statement .pdf file (73KB) Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link

408

Oak Ridge Office CX Determinations | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Office CX Determinations Office CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations Oak Ridge Office CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link 09/25/2013 Office of Secure Transportation Multiple Actions (CX-ORR-13-009) .pdf file (65KB) B1.2, B1.3, B1.11, B1.15

409

Acquisition and Assistance | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Services » Services » Acquisition and Assistance Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Acquisition and Assistance Print Text Size: A A A RSS Feeds FeedbackShare Page Related Links Current Contract Solicitations Major Contracts Awarded Funding Opportunity Announcements (FOAs): - Open FOAs - Closed FOAs DOE National Laboratory Announcements: - Open Lab Announcements - Closed Lab Announcements Financial Assistance & Interagency Agreement Award Search

410

Thomas Jefferson Site Office CX Determinations | U.S. DOE Office of Science  

Office of Science (SC) Website

Thomas Jefferson Site Office CX Thomas Jefferson Site Office CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations Thomas Jefferson Site Office CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page As of October 31, 2010, there have been no CX determinations made. Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link

411

Ames Site Office CX Determinations | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Ames Site Office CX Determinations Ames Site Office CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations Ames Site Office CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link 07/10/2013 Sensitive Instrument Facility .pdf file (792KB) B3.6

412

Compilation of Systems of Records | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Compilation of Systems of Records Compilation of Systems of Records Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Compilation of Systems of Records Energy Employees Occupational Illness Compensation Program Act (EEOICPA) How to Submit a Privacy Act Request Reference Links Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Privacy Act Compilation of Systems of Records Print Text Size: A A A RSS Feeds FeedbackShare Page DOE publishes compilations of Privacy Act systems of records notices (SORNs) periodically in the Federal Register as the SORNS are updated. The

413

Employee Concerns Program | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Employee Concerns Program Employee Concerns Program Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Employee Concerns Program Print Text Size: A A A RSS Feeds FeedbackShare Page Related Links Energy Department Employee Concerns Program Order Employee Concerns Program Guide Secretarial Employee Concerns Program Statement Reporting Employee Concerns is an important part of our work. Office of Science employees and any contractor or subcontractor fulfilling our

414

Categorical Exclusion (CX) Determinations | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Categorical Categorical Exclusion (CX) Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page On October 2, 2009, a Secretarial Memorandum outlined the Department's policy for transparency, openness and participation, especially with regards to the NEPA process. The current policy is for website posting of Categorical Exclusions determined from Subpart D of Title 10 of the Code of

415

Privacy Act | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Privacy Act Privacy Act Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Compilation of Systems of Records Energy Employees Occupational Illness Compensation Program Act (EEOICPA) How to Submit a Privacy Act Request Reference Links Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Privacy Act Print Text Size: A A A RSS Feeds FeedbackShare Page General Disclaimer This system is made available by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of

416

JC3 Bulletin Archive | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

2, 2012 2, 2012 U-226: Linux Kernel SFC Driver TCP MSS Option Handling Denial of Service Vulnerability The Linux kernel is prone to a remote denial-of-service vulnerability. August 1, 2012 U-225: Citrix Access Gateway Plug-in for Windows nsepacom ActiveX Control Vulnerabilities Two vulnerabilities in Citrix Access Gateway Plug-in for Windows can be exploited by malicious people to compromise a user's system. July 31, 2012 U-224: ISC DHCP Multiple Denial of Service Vulnerabilities ISC DHCP is prone to multiple denial-of-service vulnerabilities. July 30, 2012 U-223: Bugzilla May Disclose Confidential Information to Remote Users Two vulnerabilities were reported in Bugzilla. July 27, 2012 U-222: Apple Safari Bugs Let Remote Users Execute Arbitrary Code, Spoof the URL Address Bar, Conduct Cross-Site Scripting Attacks, and Obtain

417

Safeguards & Security | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Safeguards & Security Safeguards & Security Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Safeguards & Security Print Text Size: A A A RSS Feeds FeedbackShare Page Security and Emergency Management staff ensures the people, materials, and information at DOE sites remain safe and secure. The Office of Science complex contains some of the U.S. Department of Energy's most important assets, and these organizations ensure the security of these crucial and

418

Brookhaven Site Office CX Determinations | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Brookhaven Site Office CX Determinations Brookhaven Site Office CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations Brookhaven Site Office CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link 04/29/2013 This generic CX covers removal and transfer of beamlines from Brookhaven National Laboratory to other federal agencies or scientific laboratories. This activity will involve disassembly of beamlines and transport via tractor trailers over public roads. .pdf file (14KB) B1.30

419

Reference Links | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Reference Links Reference Links Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Compilation of Systems of Records Energy Employees Occupational Illness Compensation Program Act (EEOICPA) How to Submit a Privacy Act Request Reference Links Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Privacy Act Reference Links Print Text Size: A A A RSS Feeds FeedbackShare Page Privacy Act of 1974 and Amendments, 5 USC 552a External link DOE Implementing Regulations, 10 CFR 1008 External link DOE Privacy Act Compilation External link

420

Berkeley Site Office CX Determinations | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Berkeley Site Office CX Determinations Berkeley Site Office CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations Berkeley Site Office CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link 09/05/2013 Joint BioEnergy Institute Lease and Operations of Greenhouses at UC Davis .pdf file (77KB) B1.24; B3.6

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


421

Current Contract Solicitations | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Acquisition and Assistance » Current Contract Solicitations Acquisition and Assistance » Current Contract Solicitations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Acquisition and Assistance Current Contract Solicitations Print Text Size: A A A RSS Feeds FeedbackShare Page « Return to Acquisition and Assistance Current solicitations can be viewed until awarded. Recently awarded contracts will be listed in the Major Contracts Awarded section. Awards utilized by other DOE offices and other agencies will be listed for the

422

Pacific Northwest Site Office CX Determinations | U.S. DOE Office of  

Office of Science (SC) Website

Pacific Northwest Site Office CX Pacific Northwest Site Office CX Determinations Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Categorical Exclusion (CX) Determinations Pacific Northwest Site Office CX Determinations Print Text Size: A A A RSS Feeds FeedbackShare Page Categorical Exclusion Determination Documents (CX Determinations): * Determination Date Name of Action: Description Categorical Exclusion Number External link 08/01/2012 CX for Routine Maintenance .pdf file (517KB) B3.3

423

Reservation Management | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Reservation Management Reservation Management Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Services Reservation Management Print Text Size: A A A RSS Feeds FeedbackShare Page Related Links Emergency Information The Department of Energy's Oak Ridge Reservation is home to a world-leading research and manufacturing park, with major federal programs in the areas of science, environmental management, energy efficiency, nuclear energy, and national security. In addition to its role as the SC

424

About | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

About About Integrated Support Center (ISC) ISC Home About Jobs Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 About Print Text Size: A A A RSS Feeds FeedbackShare Page Mission We provide specialized professional services essential to the success of the Office of Science and the Department of Energy. Vision We provide quality innovative solutions that ensure customer success. Values We believe people are our most important resource and should be treated with fairness, respect, and dignity. We exist to serve our customer needs.

425

US-China Partnership for Climate Action | Open Energy Information  

Open Energy Info (EERE)

US-China Partnership for Climate Action US-China Partnership for Climate Action Jump to: navigation, search Name US-China Partnership for Climate Action Agency/Company /Organization Institute for Sustainable Communities (ISC), World Resources Institute (WRI) Sector Climate, Energy Focus Area Non-renewable Energy, Greenhouse Gas, Industry Topics Background analysis Website http://www.iscvt.org/where_we_ Program Start 2009 Country China, United States Eastern Asia, Northern America References http://www.iscvt.org/where_we_work/china/ "In the fall of 2009, Institute for Sustainable Communities (ISC) launched the US-China Partnership for Climate Action (PCA)[1] with its partner, the World Resources Institute (WRI). This program will leverage resources and best practices from both countries to achieve significant and lasting

426

Microsoft Word - DOE-ID-INL-13-020.doc  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

20 20 SECTION A. Project Title: Interim Storage Area for Interim Storage Containers (ISCs) at the Radioactive Scrap and Waste Facility (RSWF) SECTION B. Project Description: Currently, dedicated space is unavailable for above-grade storage of Interim Storage Containers (ISCs) containing 55-gal drums of remote handled transuranic waste (RH-TRU). In the past this waste was packaged in specially constructed liners and placed into the RSWF. When ready for transfer this waste would then be removed from RSWF and transferred to CH2M-WG Idaho, LLC (CWI) where it was sorted and repackaged for shipment to Waste Isolation Pilot Plant (WIPP). The construction of this new interim storage area is needed to eliminate special packaging and placement into RSWF in order to reduce costs and exposure associated with repackaging

427

September 18, 2013, FTCP Face to Face Meeting Presentation - NTC Briefing  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

September 18th, 2012 September 18th, 2012 Discussion Topics Discussion Topics NTC T h l * NTC Technology * Nuclear Safety Training Program y g g * Safeguards & Security Training Program Program NTC Technology gy * eLearning - SAF-200DE: Safety Conscious Work Environment Prerequisite - PHY-210DE: Facility Security Officer Orientation SAF 330DE: Accident Investigation Refresher - SAF-330DE: Accident Investigation Refresher * Distance Learning - SAF-720: Hazard Identification - SAF-725: Hazard Categorization ISC 202: Legal Aspects of Inquiries - ISC-202: Legal Aspects of Inquiries NTC Technology gy * Continuing Education - SAF-340DV NELT: Differing Professional Opinions and Employee Concerns - SAF-340DV NELT: Environmental Sustainability and Compliance - SAF-340DV NELT: Managing the Safety Basis - SAF-785DV: Technical Safety Requirements

428

Stabilization of High Efficiency CdTe Photovoltaic Modules in Controlled Indoor Light Soaking  

Science Conference Proceedings (OSTI)

The performance and stabilization of large-area, high-efficiency 9%, CdTe photovoltaic (PV) modules maintained under controlled light-soaking nominally at 800 Watts/m2 irradiance and 65C module temperature are investigated. Degradation of module performance occurs predominantly in the first few hundred hours of exposure under these conditions; these symptoms included losses in fill factor (FF), open-circuit voltage (Voc), and short-circuit current (Isc), which amount to between 7% and 15% total loss in performance. Higher stabilized performance was achieved with lower copper content in the back contact. Transient effects in module Voc and Isc were observed, suggesting partial annealing thereof when stored under low-light levels. Performance changes are analyzed, aided by monitoring the current-voltage characteristics in situ during exposure.

del Cueto, J. A.; Pruett, J.; Cunningham, D.

2003-05-01T23:59:59.000Z

429

Experimental Investigation and High Resolution Simulator of In-Situ Combustion Processes  

SciTech Connect

Accurate simulation of in-situ combustion processes is computationally very challenging because the spatial and temporal scales over which the combustion process takes place are very small. In this current and eleventh report, we report on the development of a virtual kinetic cell (VKC) that aids the study of the interaction between kinetics and phase behavior. The VKC also provides an excellent tool for developing and testing specialized solvers for the stiff kinetics encountered in ISC processes.

Margot Gerritsen; Anthony R. Kovscek

2006-07-01T23:59:59.000Z

430

Effect of Initial Oil Saturation on In-Situ Combustion Performance of a Canadian Bitumen  

E-Print Network (OSTI)

In-Situ Combustion (ISC) is a very complex thermal recovery process that is strongly affected by the chemical composition and physical properties of reservoir rock and fluids. Stability of the process depends on the amount of heat continuously generated from the chemical reactions between fuel formed during ISC and injected oxygen. Heat generation depends on the amount of fuel formed, which, in turn, is affected by initial oil saturation (IOS). Thus, in this study, ISC process dynamics were investigated at various saturations on 7.5 API Peace River bitumen, under 3.4 l/min air injection rate. Through one-dimensional combustion tube experiments higher combustion front temperatures were observed for increased IOS. The degree of bitumen upgrading was determined in terms of viscosity and API gravity changes. Correlations for hydrogen-carbon ratio, air requirement, consumed fuel, and combustion front velocity were obtained. Good burning characteristics of Peace River bitumen resulted in stable self-sustained combustion with 26.01% IOS. However, an experiment with 13.39% IOS failed because of insufficient fuel generation. Furthermore, X-Ray cross-sectional images were taken along the combustion tube after each run to support and enhance the interpretation of experimental results. Particularly, fluctuations in concentrations of produced gas composition were explained with computed tomography (CT) data.

Aleksandrov, Denis

2013-08-01T23:59:59.000Z

431

Role of the inclusion survey contractor in the Uranium Mill Tailings Remedial Action Program  

Science Conference Proceedings (OSTI)

Twenty-four former uranium mills are involved in the Department of Energy's Uranium Mill Tailings Remedial Action Program (UMTRAP). The Radiological Survey Activities project at Oak Ridge National Laboratory serves as the Inclusion Survey Contractor (ISC) in the UMTRA program. Responsibilities of the ISC are: (1) to identify potentially contaminated sites in the vicinity of these former uranium mills; (2) conduct radiological surveys to assess whether the property is contaminated with material originating from the mill in excess of Environmental Protection Agency criteria formulated specifically for the UMTRA program (40 CFR 192); and (3) provide recommendations to DOE regarding remedial action. Properties are identified by the ISC using historical information, serial and ground-level gamma scanning, and surveying erosional pathways (wind and water movement of contamination from primary sources). Currently, over 8000 vicinity properties have been identified that warrant further investigation. Once identified, an inclusion survey is conducted to assess whether a property is sufficiently contaminated to warrant inclusion into the UMTRA program. The inclusion survey includes a complete gamma scan of the surfaces of the property outdoors and the lowest habitable level indoors, and collection of soil samples outdoors and/or radon daughter samples indoors if required. Survey methods are described. 8 references.

Berven, B.A.; Little, C.A.

1985-01-01T23:59:59.000Z

432

A New DNA Binding Protein Highly Conserved in Diverse Crenarchaeal Viruses  

DOE Green Energy (OSTI)

Sulfolobus turreted icosahedral virus (STIV) infects Sulfolobus species found in the hot springs of Yellowstone National Park. Its 37 open reading frames (ORFs) generally lack sequence similarity to other genes. One exception, however, is ORF B116. While its function is unknown, orthologs are found in three additional crenarchaeal viral families. Due to the central importance of this protein family to crenarchaeal viruses, we have undertaken structural and biochemical studies of B116. The structure reveals a previously unobserved fold consisting of a five-stranded beta-sheet flanked on one side by three alpha helices. Two subunits come together to form a homodimer with a 10-stranded mixed beta-sheet, where the topology of the central strands resembles an unclosed beta-barrel. Highly conserved loops rise above the surface of the saddle-shaped protein and suggest an interaction with the major groove of DNA. The predicted B116-DNA interaction is confirmed by electrophoretic mobility shift assays.

Larson, E.T.; Eilers, B.J.; Reiter, D.; Ortmann, A.C.; Young, M.J.; Lawrence, C.M.; /Montana State U. /Tubingen U.

2007-07-09T23:59:59.000Z

433

Binding of the Anticonvulsant Drug Lamotrigine and the Neurotoxin Batrachotoxin to Voltage-gated Sodium Channels  

E-Print Network (OSTI)

and PHAST gels were from Amersham Biosciences and polyvinylidene fluoride membranes were from BDH Laboratory). The gel was calibrated using standards ranging from 53 to 220 kDa. The 4­15% gradient PHAST acrylamide

Wallace, Bonnie Ann

434

Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates  

E-Print Network (OSTI)

conducted by the Joint BioEnergy Institute was supported byDivision, Joint BioEnergy Institute, Emeryville, CA 94608,Panicum virgatum L. ). BioEnergy Research 2010, 3:134145.

2013-01-01T23:59:59.000Z

435

Investigating the mechanotransduction by two-photon fluorescence microscopy measurement of intracellular free energy of binding  

E-Print Network (OSTI)

Force, due either to haemodynamic shear stress or relayed directly to the cell through adhesion complexes, is transmitted and translated into biological signals. This process is known as mechanotransduction. Extensive ...

Abdul Rahim, Nur Aida

2008-01-01T23:59:59.000Z

436

Movement of `gating charge' is coupled to ligand binding in a G-protein-coupled receptor  

E-Print Network (OSTI)

by the demonstration that a depol- arization-induced shift of m2R from high to low affinity has a crucial role

Bezanilla, Francisco

437

Coupling of Protein Relaxation to Ligand Binding and Migration in Myoglobin  

E-Print Network (OSTI)

and temperature dependence to any kinetic model (Frauenfelder et al., 2002). In the usual chemical kinetic presented here is of intermediate complexity, between simple chemical kinetics and atomic- detail molecular. Transient kinetics of chemical reactions with bounded diffusion perpendicular to the reaction co- ordinate

Agmon, Noam

438

Water growth on metals and oxides: binding, dissociation and role of hydroxyl groups  

E-Print Network (OSTI)

Sci. Rep. 63, 169 (2008) S. Wendt, J. Matthiesen, R. Schaub,Lett. 96, 066107 (2006). S. Wendt, R. Schaub, J. Matthiesen,

Salmeron, M.

2008-01-01T23:59:59.000Z

439

Using computational alchemy to predict protein-ligand binding free energies  

E-Print Network (OSTI)

integration (IT-TI) free energy changes for biomolecular systems:Integration Free Energy Changes for Biomolecular Systems:Integration Free Energy Changes for Biomolecular Systems:

Lawrenz, Morgan

2011-01-01T23:59:59.000Z

440

A quantitative model of transcriptional regulation reveals the influence binding location on expression  

E-Print Network (OSTI)

Understanding the mechanistic basis of transcriptional regulation has been a central focus of molecular biology since its inception. New high-throughput chromatin immunoprecipitation experiments have revealed that most ...

MacIsaac, Kenzie Daniel

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
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441

Implementing Multi-Vendor Home Network System with Vendor-Neutral Services and Dynamic Service Binding  

Science Conference Proceedings (OSTI)

The home network system (HNS) consists of networked household appliances, intended to provide value-added services. The conventional HNS has been built on the single-vendor system, which severely limits potential of the HNS. To overcome the problem, ...

Masahide Nakamura; Yusuke Fukuoka; Hiroshi Igaki; Ken-ichi Matsumoto

2008-07-01T23:59:59.000Z

442

Ties That Do Not Bind: Russia and the International Liberal Order  

E-Print Network (OSTI)

it less dependent on Russian gas, such as LNG and shale gas.in the extraction of shale gas, which is extracted fromboast large reserves of shale gas. A report by the Baker

Krickovic, Andrej

2012-01-01T23:59:59.000Z

443

Lithium Diisopropylamide Solvated by Monodentate and Bidentate Ligands: Solution Structures and Ligand Binding  

E-Print Network (OSTI)

Lithium Diisopropylamide Solvated by Monodentate and Bidentate Ligands: Solution Structures, 1997X Abstract: 6Li and 15N NMR spectroscopic studies of lithium diisopropylamide ([6Li]LDA and [6Li,15 are correlated with those obtained previously for lithium hexamethyldisilazide. Introduction Despite

Collum, David B.

444

Calnuc binds to Alzheimer's beta-amyloid precursor protein and affects its biogenesis.  

E-Print Network (OSTI)

protein; Ab, amyloid-b peptide; CNG, calnuc-GFP; Co-IP, co-levels of APP. Calnuc-GFP (CNG) or GFP constructs werestably expressing calnuc- GFP (CNG) or GFP were lysed. Equal

2007-01-01T23:59:59.000Z

445

Neural model of auditory cortex for binding sound intensity and frequency information in bat's echolocation  

Science Conference Proceedings (OSTI)

Most species of bats making echolocation use the sound pressure level (SPL) and Doppler-shifted frequency of ultrasonic echo pulse to measure the size and velocity of target. The neural circuits for detecting these target features are specialized for ... Keywords: SPL amplitude, auditory system, echolocation, frequency tuning, neural model

Yoshitaka Mutoh; Yoshiki Kashimori

2011-11-01T23:59:59.000Z

446

Ties That Do Not Bind: Russia and the International Liberal Order  

E-Print Network (OSTI)

China supports the development of national champions in key strategic industries such as renewable

Krickovic, Andrej

2012-01-01T23:59:59.000Z

447

Estimating ProteinLigand Binding Free Energy: Atomic Solvation Parameters for Partition Coefficient and  

E-Print Network (OSTI)

cancer. Nat Genet 39:638­644. 5. Easton DF, et al.; SEARCH collaborators; kConFab; AOCS Management Group

Luhua, Lai

448

Parametric modeling of protein-DNA binding kinetics: A discrete event based simulation approach  

Science Conference Proceedings (OSTI)

To understand the stochastic behavior of biological systems, we adopt an ''in silico'' stochastic event based simulation methodology that can determine the temporal dynamics of different molecules. The main requirement for this technique is the event ... Keywords: Biophysics, Collision theory, Stochastic modeling, Systems biology

Preetam Ghosh; Samik Ghosh; Kalyan Basu; Sajal Das

2009-05-01T23:59:59.000Z

449

Nucleotide sequences and modifications that determine RIG-I/RNA binding and signaling activities  

E-Print Network (OSTI)

Cytoplasmic viral RNAs with 5? triphosphates (5?ppp) are detected by the RNA helicase RIG-I, initiating downstream signaling and alpha/beta interferon (IFN-?/?) expression that establish an antiviral state. We demonstrate ...

Urzi, Dina

450

Structure and selectivity trends in crystalline urea-functionalized anion-binding capsules  

Science Conference Proceedings (OSTI)

A tripodal trisurea receptor (L1) persistently self-assembles with various divalent oxoanion salts M{sub n}X (M = Na, K, Mg, Ca, Cd; X = SO{sub 4}{sup 2-}, SO{sub 3}{sup 2-}, SeO{sub 4}{sup 2-}, CrO{sub 4}{sup 2-}) into isomorphous series of crystalline frameworks in three different compositions: MX(L1){sub 2}(H{sub 2}O){sub 6} (M = Mg, Ca, Cd) (1), Na{sub 2}X(L1){sub 2}(H{sub 2}O){sub 4} (2) and K{sub 2}X(L1){sub 2}(H{sub 2}O){sub 2} (3). Single-crystal X-ray structural analysis revealed that all three series of structures adopt a NaCl-type topology, consisting of alternating anionic X(L1){sub 2}{sup 2-} capsules and M(H{sub 2}O){sub 6}{sup 2+}, Na{sub 2}(H{sub 2}O){sub 4}{sup 2+} or K{sub 2}(H{sub 2}O){sub 2}{sup 2+} hydrated cations. The capsules provide a complementary environment to tetrahedral oxoanions via 12 hydrogen bonds from six urea groups lining the cavities of the capsules. The persistent formation of the capsules facilitated the investigation of structural trends and structure-selectivity relationships across series 1-3. First, it was found that the size of the capsules is relatively unresponsive to the change in the encapsulated anion, resulting in good shape and size recognition in the separation of anions by competitive crystallizations. Second, it was found that the size of the capsules varies linearly with the size of the external cation, which provides a way for tuning the anion encapsulation selectivity. However, no straightforward dependence was found between the size of the capsules and the relative selectivity for different-sized tetrahedral oxoanions in competitive crystallizations.

Rajbanshi, Arbin [Oak Ridge National Laboratory (ORNL); Custelcean, Radu [ORNL

2012-01-01T23:59:59.000Z

451

The ties that bind : Iran and Hamas' principal-agent relationship.  

E-Print Network (OSTI)

??The evolution of the Iran-Hamas relationship can be mapped using Principal-Agent analysis. It is a cost-benefit approach based on rational choice theory. In contrast to (more)

Thomson, Amy

2012-01-01T23:59:59.000Z