Sample records for jacobsen gene polik

  1. Steven D. Jacobsen BIOGRAPHICAL SKETCH

    E-Print Network [OSTI]

    Jacobsen, Steven D.

    -COMPRES. At Northwestern, he is Associate Master of the Public Affairs Residential College. In 2007 Jacobsen served in superhard materials. Jacobsen is active in science outreach and public dissemination of geophysical research matter physics, and planetary science. Jacobsen's research is currently supported by the NSF, DOE/NNSA

  2. nersc-brownbag-docker-jacobsen-canon.pptx

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del SolStrengtheningWildfires mayYuan T.External LinksDoug Jacobsen & Shane Canon

  3. Active Constraint Regions for Optimal Operation of Distillation Magnus G. Jacobsen and Sigurd Skogestad*

    E-Print Network [OSTI]

    Skogestad, Sigurd

    , NTNU, N-7491, Trondheim, Norway ABSTRACT: When designing the control structure of distillation columnsActive Constraint Regions for Optimal Operation of Distillation Columns Magnus G. Jacobsen presented in an earlier paper, to find how the active constraints for distillation columns change

  4. Active constraint regions for a natural gas liquefaction process Magnus G. Jacobsen a

    E-Print Network [OSTI]

    Skogestad, Sigurd

    processes. 2. Optimal operation of a PRICO liquefaction plant 2.1. Plant description The PRICO processActive constraint regions for a natural gas liquefaction process Magnus G. Jacobsen a , Sigurd Keywords: Self-optimizing control Liquefied natural gas LNG PRICO Disturbances Optimal operation a b s t r

  5. Doug Jacobsen

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625govInstrumentstdmadapInactiveVisitingContract ManagementDiscovering HowAna Moore Anne Jones DevensforDoubleDOE|Doug

  6. October2010Edition Jacobsen Lab

    E-Print Network [OSTI]

    Jacobsen, Steve

    ............780 Westwood Plaza Biomedical Sciences Research Bldg................................. F5............615 Charles. East Botany Bldg. ............................................................................. F5............618 Charles E. Young Dr. South Boyer Hall

  7. Douglas Jacobsen! NERSC User Services

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA : Papers69 FederalAdministrationDoug KotheRunning

  8. Abene, Cathy 6-3547 Energy Donatucci, Dana 4-8507 Waste Svcs/Recycling (363-6145) Jach, Dan 6-8579 U Construction (221-4269) Allen, John 5-6311 Haz-Mat (799-0712) Drews, Paul 6-0493 East Bank (290-2672) Jacobsen, Brad 5-2378 Energy

    E-Print Network [OSTI]

    Gulliver, Robert

    Abene, Cathy 6-3547 Energy Donatucci, Dana 4-8507 Waste Svcs/Recycling (363-6145) Jach, Dan 6-2692) Kluge, Nick 6-7176 Waste Svcs/Recy Berkowitz, Wendy 4-8886 Finance/Accounting Ford, Robert 5-5527 Energy-2672) Jacobsen, Brad 5-2378 Energy Anderson, Conrad 5-0689 StP/W (HellerH) (328-1586) Durushia, Ann 6-0291 U Svcs

  9. Douglas Jacobsen! NERSC Bioinformatics Computing Consultant

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA : Papers69 FederalAdministrationDoug Kothe About

  10. Douglas Jacobsen! NERSC Bioinformatics Computing Consultant

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA : Papers69 FederalAdministrationDoug Kothe

  11. Douglas Jacobsen! NERSC Bioinformatics Computing Consultant

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA : Papers69 FederalAdministrationDoug KotheRunning Jobs

  12. Douglas Jacobsen! NERSC User Services Group

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA : Papers69 FederalAdministrationDoug

  13. arne jacobsens ideas: Topics by E-print Network

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

    combines a kinetic Monte Carlo simulation for the thermal surface diffusion with a small scale molecular-dynamics simulation of every single deposition Sethna, James P. 23...

  14. Jacobsen of XSD Elected to American Physical Society Fellowship

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

    Appointed ALD for Photon Sciences APS, Other DOE Labs Help Develop New Cancer Fighting Drug APS News Archives: 2014 | 2013 2012 | 2011 | 2010 | 2009 2008 | 2007 | 2006 | 2005 2004...

  15. Douglas Jacobsen, Yushu Yao! NERSC User Services Group

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA : Papers69 FederalAdministrationDougSeptember 10, 2013

  16. Douglas Jacobsen, Yushu Yao! NERSC User Services Group

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA : Papers69 FederalAdministrationDougSeptember 10, 2013

  17. Douglas Jacobsen, Yushu Yao! NERSC User Services Group

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA : Papers69 FederalAdministrationDougSeptember 10,

  18. Evolution of Genes and Gene Networks in Filamentous Fungi 

    E-Print Network [OSTI]

    Greenwald, Charles Joaquin

    2011-10-21T23:59:59.000Z

    and Materials ................................................................... 15 Results ............................................................................................ 16 Discussion... .............................................................................. 46 14 Relative expression of conidiation-associated genes ................................. 49 15 Expression profiles for significantly regulated genes and FUNCAT category distributions...

  19. Microfluidic gene synthesis

    E-Print Network [OSTI]

    Kong, David Sun, 1979-

    2008-01-01T23:59:59.000Z

    The ability to synthesize custom de novo DNA constructs rapidly, accurately, and inexpensively is highly desired by researchers, as synthetic genes and longer DNA constructs are enabling to numerous powerful applications ...

  20. Spectral Clustering Gene Ontology Terms to Group Genes by Function

    E-Print Network [OSTI]

    Zell, Andreas

    Spectral Clustering Gene Ontology Terms to Group Genes by Function Nora Speer, Christian Spieth­12, 2005. c Springer-Verlag Berlin Heidelberg 2005 #12;2 N. Speer, C. Spieth, and A. Zell part-of is-a GO

  1. Differentially Coexpressed Genes

    E-Print Network [OSTI]

    Spang, Rainer

    Fine-tuning #12;Do these pattern exist in real data ? Acute Lymphoblastic Leukemia · About 1/3 of all) Classication, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression proling, Cancer Cell, 1(2), 133-43. #12;Differential coexpression in phil+ leukemia norm phil

  2. Partly Occupied Wannier Functions K. S. Thygesen, L. B. Hansen, and K. W. Jacobsen

    E-Print Network [OSTI]

    Thygesen, Kristian

    of representing the electronic ground state of a solid-state system in terms of localized orbitals dates back. In the upper panel only the occupied states are used and some of the resulting WFs clearly mix and characters

  3. Concurrency: The Next Generation Damian Dimmich, Christian Jacobsen and Matthew Jadud

    E-Print Network [OSTI]

    Kent, University of

    , to ensure that future software engineers have the skills required to use these new technologies. The need as a low level library. These libraries require developers to invest a large amount of energy to manually highly optimised native code[4, 5]. Making such a shift does not necessarily have adverse affects

  4. Euler-karakteristik af fusionskategorier for Chevalley-grupper Martin Wedel Jacobsen

    E-Print Network [OSTI]

    Møller, Jesper Michael

    for the Chevalley group (q) in the case where q is a power of p and is either A1 or A2. Finally I calculate mange eksempler p°a grupper der ikke er isomorfe, men alligvel har isomorfe Sylow

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

    DOE Patents [OSTI]

    Chen, Huei-Mei; Bissell, Mina

    2004-06-22T23:59:59.000Z

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

  6. A Gene Scrapbook A Tribute to Gene Loh

    E-Print Network [OSTI]

    A Gene Scrapbook A Tribute to Gene Loh on the Occasion of His Retirement Feb 22, 2003 #12;The Early visited such exotic destinations as Salt Lake City, Utah #12;Happy Retirement!!!! We wish you a happy retirement!!!! Although we are sure that you will not just be spending more time with your grandchildren #12;

  7. GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes

    SciTech Connect (OSTI)

    Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia; Ovchinnikova, Galina; Hooper, Sean D.; Lykidis, Athanasios; Kyrpides, Nikos C.

    2010-04-01T23:59:59.000Z

    We present 'gene prediction improvement pipeline' (GenePRIMP; http://geneprimp.jgi-psf.org/), a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start sites, missed genes and split genes. We found that manual curation of gene models using the anomaly reports generated by GenePRIMP improved their quality, and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome-sequencing and annotation technologies.

  8. Laboratory Directed Research and Development Program FY 2006

    E-Print Network [OSTI]

    Hansen Ed., Todd

    2007-01-01T23:59:59.000Z

    Spence, U. Weierstall, T. Beetz, C. Jacobsen, D. Shapiro; "Weierstall, D. Shapiro, T. Beetz, C. Jacobsen, E. Lima, A.

  9. Evolution of Genes and Gene Networks in Filamentous Fungi

    E-Print Network [OSTI]

    Greenwald, Charles Joaquin

    2011-10-21T23:59:59.000Z

    ........................................................................... 62 1 CHAPTER I INTRODUCTION The Pezizomycotina, a subphylum within the phylum Ascomycota, commonly known as the filamentous fungi, are a diverse group of important organisms. There are over 60,000 species representing between 210... in a secondary metabolite gene cluster responsible for roles in the loline biosynthetic pathway of Epichlo? and Neotyphodium species. Two genes lolC and lolD were of interest because: 1) lolines are unique to these closely related species; and 8 2...

  10. Statistical mechanics of gene competition 

    E-Print Network [OSTI]

    Venegas-Ortiz, Juan; Ortiz, Juan Venegas

    2013-11-28T23:59:59.000Z

    Statistical mechanics has been applied to a wide range of systems in physics, biology, medicine and even anthropology. This theory has been recently used to model the complex biochemical processes of gene expression and ...

  11. Nonviral Vectors for Gene Delivery

    E-Print Network [OSTI]

    Baoum, Abdulgader Ahmed

    2011-04-26T23:59:59.000Z

    optimized for gene delivery by varying particle surface chemistry using different coating materials that adsorb to the particle surface during formation. A variety of cationic coating materials were studied and compared to more conventional surfactants used...

  12. Metazoan Gene Families from Metazome

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

    Metazome is a joint project of the Department of Energy's Joint Genome Institute and the Center for Integrative Genomics to facilitate comparative genomic studies amongst metazoans. Clusters of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These clusters allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of version 2.0.4, Metazome provides access to twenty-four sequenced and annotated metazoan genomes, clustered at nine evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, Ensembl, and JGI are hyper-linked and searchable. The included organisms (by common name) are: Human, Mouse, Rat, Dog, Opossum, Chicken, Frog, Stickleback, Medaka, Fugu pufferfish; Zebrafish, Seasquirt - savignyi, Seasquirt - intestinalis, Amphioxus, Sea Urchin, Fruitfly, Mosquite, Yellow Fever Mosquito, Silkworm, Red Flour Beetle, Worm, Briggsae Worm, Owl limpet (snail), and Sea anemone. [Copied from Metazome Overview at http://www.metazome.net/Metazome_info.php

  13. Gene encoding plant asparagine synthetase

    DOE Patents [OSTI]

    Coruzzi, Gloria M. (New York, NY); Tsai, Fong-Ying (New York, NY)

    1993-10-26T23:59:59.000Z

    The identification and cloning of the gene(s) for plant asparagine synthetase (AS), an important enzyme involved in the formation of asparagine, a major nitrogen transport compound of higher plants is described. Expression vectors constructed with the AS coding sequence may be utilized to produce plant AS; to engineer herbicide resistant plants, salt/drought tolerant plants or pathogen resistant plants; as a dominant selectable marker; or to select for novel herbicides or compounds useful as agents that synchronize plant cells in culture. The promoter for plant AS, which directs high levels of gene expression and is induced in an organ specific manner and by darkness, is also described. The AS promoter may be used to direct the expression of heterologous coding sequences in appropriate hosts.

  14. GenePRIMP: Improving Microbial Gene Prediction Quality

    SciTech Connect (OSTI)

    Pati, Amrita [DOE Joint Genome Institute's Genome Biology group

    2009-05-29T23:59:59.000Z

    Amrita Pati of the DOE Joint Genome Institute's Genome Biology group talks about a computational pipeline that evaluates the accuracy of gene models in genomes and metagenomes at different stages of finishing at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  15. Essential Genes Are More Evolutionarily Conserved Than Are Nonessential Genes

    E-Print Network [OSTI]

    Jordan, King

    Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA Jordan, Igor B. Rogozin, Yuri I. Wolf, and Eugene V. Koonin1 National Center for Biotechnology functionally dispensable and/or redundant than are nonessential genes. Given the role of pu- rifying selection

  16. ascl1 target genes: Topics by E-print Network

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

    for postgenomic analysis of mammalian gene function is gene targeting McConnell, Susan 2 Infrared lasermediated gene induction in targeted Chemistry Websites Summary: a heat shock...

  17. abolishes gene targeting: Topics by E-print Network

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

    for postgenomic analysis of mammalian gene function is gene targeting McConnell, Susan 2 Infrared lasermediated gene induction in targeted Chemistry Websites Summary: a heat shock...

  18. ancestral gene relationships: Topics by E-print Network

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

    thought previously of entire genomes, rather than individual genes, on the basis of the analysis of gene orders. Human, mouse Batzoglou, Serafim 17 Analyzing gene relationships...

  19. 20Engineering Gene Circuits: Foundations

    E-Print Network [OSTI]

    You, Lingchong

    ................................................................. 20-363 20.2 Designing Gene Circuits............................................. 20-364 Modeling characterized as ``robustness.'' Based on extensive studies over the last several decades, much engineered switches [11­14], oscillators [15,16], logic gates [17­19], metabolic control [20], reengineered

  20. Regulation of the genes involved in nitrification.

    SciTech Connect (OSTI)

    Arp, D.J.; Sayavedra-Soto, L.A.

    2003-08-14T23:59:59.000Z

    OAK-B135 This project focuses on the characterization of the regulation of the genes involved in nitrification in the bacterium Nitrosomonas europaea. The key genes in the nitrification pathway, amo and hao, are present in multiple copies in the genome. The promoters for these genes were identified and characterized. It was shown that there were some differences in the transcriptional regulation of the copies of these genes.

  1. Plant nitrogen regulatory P-PII genes

    DOE Patents [OSTI]

    Coruzzi, Gloria M. (New York, NY); Lam, Hon-Ming (Hong Kong, HK); Hsieh, Ming-Hsiun (Woodside, NY)

    2001-01-01T23:59:59.000Z

    The present invention generally relates to plant nitrogen regulatory PII gene (hereinafter P-PII gene), a gene involved in regulating plant nitrogen metabolism. The invention provides P-PII nucleotide sequences, expression constructs comprising said nucleotide sequences, and host cells and plants having said constructs and, optionally expressing the P-PII gene from said constructs. The invention also provides substantially pure P-PII proteins. The P-PII nucleotide sequences and constructs of the

  2. Uses of antimicrobial genes from microbial genome

    DOE Patents [OSTI]

    Sorek, Rotem; Rubin, Edward M.

    2013-08-20T23:59:59.000Z

    We describe a method for mining microbial genomes to discover antimicrobial genes and proteins having broad spectrum of activity. Also described are antimicrobial genes and their expression products from various microbial genomes that were found using this method. The products of such genes can be used as antimicrobial agents or as tools for molecular biology.

  3. INVESTIGATION Gene Genealogies Within a Fixed Pedigree,

    E-Print Network [OSTI]

    INVESTIGATION Gene Genealogies Within a Fixed Pedigree, and the Robustness of Kingman's Coalescent, not as a random quantity. Gene genealogical models should describe the outcome of the percolation of genetic provide a surprisingly accurate description of gene genealogies on a fixed pedigree. We study

  4. Chapter 12 Gene Genealogies Noah A. Rosenberg

    E-Print Network [OSTI]

    Rosenberg, Noah

    Chapter 12 ­ Gene Genealogies Noah A. Rosenberg Program in Molecular and Computational Biology can be viewed as the result of mutations on a scaffold of genetic relationships ­ a gene genealogy, migration, species divergence, and changes in population size, an understanding of gene genealogies

  5. Short Specialist Review Gene structure prediction

    E-Print Network [OSTI]

    Brendel, Volker

    Short Specialist Review Gene structure prediction in plant genomes Volker Brendel Iowa State) within most genes makes the problem of computational gene structure prediction distinct from (and harder prediction in vertebrates. The second reason is pragmatic. Expressed Sequence Tag (EST) sequencing and whole

  6. Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions

    E-Print Network [OSTI]

    Ames, Ryan M.; Money, Daniel; Lovell, Simon C.

    2014-06-12T23:59:59.000Z

    The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological ...

  7. Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity

    SciTech Connect (OSTI)

    Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-08T23:59:59.000Z

    With the rising influence of the Gene On-tology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associ-ated with them. So far, these approaches have solely relied on the knowledge en-coded in the Gene Ontology and the gene annotations associated with the Gene On-tology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

  8. Thermostable cellulase from a thermomonospora gene

    DOE Patents [OSTI]

    Wilson, D.B.; Walker, L.P.; Zhang, S.

    1997-10-14T23:59:59.000Z

    The invention relates to a gene isolated from Thermomonospora fusca, wherein the gene encodes a thermostable cellulase. Disclosed is the nucleotide sequence of the T. fusca gene; and nucleic acid molecules comprising the gene, or a fragment of the gene, that can be used to recombinantly express the cellulase or a catalytically active polypeptide thereof, respectively. The isolated and purified recombinant cellulase or catalytically active polypeptide may be used to hydrolyze substrate either by itself; or in combination with other cellulases, with the resultant combination having unexpected hydrolytic activity. 3 figs.

  9. Method for determining gene knockouts

    DOE Patents [OSTI]

    Maranas, Costas D. (Port Matilda, PA); Burgard, Anthony R. (State College, PA); Pharkya, Priti (State College, PA)

    2011-09-27T23:59:59.000Z

    A method for determining candidates for gene deletions and additions using a model of a metabolic network associated with an organism, the model includes a plurality of metabolic reactions defining metabolite relationships, the method includes selecting a bioengineering objective for the organism, selecting at least one cellular objective, forming an optimization problem that couples the at least one cellular objective with the bioengineering objective, and solving the optimization problem to yield at least one candidate.

  10. Method for determining gene knockouts

    DOE Patents [OSTI]

    Maranas, Costa D; Burgard, Anthony R; Pharkya, Priti

    2013-06-04T23:59:59.000Z

    A method for determining candidates for gene deletions and additions using a model of a metabolic network associated with an organism, the model includes a plurality of metabolic reactions defining metabolite relationships, the method includes selecting a bioengineering objective for the organism, selecting at least one cellular objective, forming an optimization problem that couples the at least one cellular objective with the bioengineering objective, and solving the optimization problem to yield at least one candidate.

  11. Apolipoprotein gene involved in lipid metabolism

    DOE Patents [OSTI]

    Rubin, Edward (Berkeley, CA); Pennacchio, Len A. (Sebastopol, CA)

    2007-07-03T23:59:59.000Z

    Methods and materials for studying the effects of a newly identified human gene, APOAV, and the corresponding mouse gene apoAV. The sequences of the genes are given, and transgenic animals which either contain the gene or have the endogenous gene knocked out are described. In addition, single nucleotide polymorphisms (SNPs) in the gene are described and characterized. It is demonstrated that certain SNPs are associated with diseases involving lipids and triglycerides and other metabolic diseases. These SNPs may be used alone or with SNPs from other genes to study individual risk factors. Methods for intervention in lipid diseases, including the screening of drugs to treat lipid-related or diabetic diseases are also disclosed.

  12. Methods for monitoring multiple gene expression

    SciTech Connect (OSTI)

    Berka, Randy (Davis, CA); Bachkirova, Elena (Davis, CA); Rey, Michael (Davis, CA)

    2012-05-01T23:59:59.000Z

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

  13. Methods for monitoring multiple gene expression

    DOE Patents [OSTI]

    Berka, Randy; Bachkirova, Elena; Rey, Michael

    2013-10-01T23:59:59.000Z

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

  14. Gene expression abnormalities in the autistic brain

    E-Print Network [OSTI]

    Chow, Maggie Lok Mun

    2011-01-01T23:59:59.000Z

    lymphoblastoid cell lines (LCLs) derived from individualsby profiling gene expression in LCLs derived from livingsubjects. LCLs derived from (1) three monozygotic twin pairs

  15. THE JOURNAL OF GENE MEDICINE RESEARCH ARTICLE J Gene Med 2005; 7: 898907.

    E-Print Network [OSTI]

    Hemminki, Akseli

    THE JOURNAL OF GENE MEDICINE RESEARCH ARTICLE J Gene Med 2005; 7: 898­907. Published online 9 March Revised: 19 November 2004 Accepted: 24 November 2004 Abstract Background VP22 is a herpes simplex virus

  16. OpenGeneX:AToolkitforOpenSourceGeneExpressionInformatics Project Description Overview

    E-Print Network [OSTI]

    Weller, Jennifer Walsh

    interface (API), allowing them to interface specialized existing software to OpenGeneX, such as interactive standards by providing freely available reference implementations. A. Lessons from GeneXTM As stated above

  17. Statistical Measure of a Gene Evolution The Case of Glyceraldehyde-3-Phosphate Dehydrogenase Gene

    E-Print Network [OSTI]

    Chattopadhyay, S; Chakrabarti, J; Chattopadhyay, Sujay; Sahoo, Satyabrata; Chakrabarti, Jayprokas

    2000-01-01T23:59:59.000Z

    The enzyme Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) catalyses the decomposition of glucose. The gene that produces the GAPDH is therefore present in a wide class of organisms. We show that for this gene the average value of the fluctuations in nucleotide distribution in the codons, normalized to strand bias, provides a reasonable measure of how the gene has evolved in time.

  18. From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation

    E-Print Network [OSTI]

    Lässig, Michael

    From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation Michael L.e., if the protein produced from it is present in the cell. Genes interact by regulation: the protein of one gene can influence the production of protein from another gene. Gene regulation can take place during transcription

  19. Gene coding for the E1 endoglucanase

    DOE Patents [OSTI]

    Thomas, S.R.; Laymon, R.A.; Himmel, M.E.

    1996-07-16T23:59:59.000Z

    The gene encoding Acidothermus cellulolyticus E1 endoglucanase is cloned and expressed in heterologous microorganisms. A new modified E1 endoglucanase enzyme is produced along with variants of the gene and enzyme. The E1 endoglucanase is useful for hydrolyzing cellulose to sugars for simultaneous or later fermentation into alcohol. 6 figs.

  20. WHAT IS A GENE? DEPARTMENT OF GENETICS,

    E-Print Network [OSTI]

    Batzoglou, Serafim

    . Studies of the effect of x-ray radiation and of unstable genes are the best means now availableWHAT IS A GENE? M. DEMEREC DEPARTMENT OF GENETICS, CARNEGIE INSTITUTION OF WASHINGTON, COLD SPRING Scholarly Publishing Project http://www.esp.org The original work, upon which this electronic edition

  1. Computational Diagnostics based on Large Scale Gene

    E-Print Network [OSTI]

    Spang, Rainer

    Computational Diagnostics based on Large Scale Gene Expression Profiles using MCMC Rainer Spang = Data Loadings Singular values Expression levels of super genes, orthogonal matrix #12;)( genessuperall- #12;Given the Few Profiles With Known Diagnosis: · The uncertainty on the right model is high

  2. Nucleotide Frequency Variation Across Human Genes

    E-Print Network [OSTI]

    Majewski, Jacek

    Nucleotide Frequency Variation Across Human Genes Elizabeth Louie, Jurg Ott, and Jacek Majewski1 The Rockefeller University, New York, New York 10021, USA The frequencies of individual nucleotides exhibit significant fluctuations across eukaryotic genes. In this paper, we investigate nucleotide variation across

  3. Assignment of Orthologous Genes via Genome Rearrangement

    E-Print Network [OSTI]

    Lonardi, Stefano

    Assignment of Orthologous Genes via Genome Rearrangement Xin Chen, Jie Zheng, Zheng Fu, Peng Nan of genomes is a fundamental and challenging problem in comparative genomics. Existing methods that assign sequence similarity and evolutionary events at a genome level, where orthologous genes are assumed

  4. Tissue-specific gene silencing monitored in circulating RNA

    E-Print Network [OSTI]

    Sehgal, Alfica

    Pharmacologic target gene modulation is the primary objective for RNA antagonist strategies and gene therapy. Here we show that mRNAs encoding tissue-specific gene transcripts can be detected in biological fluids and that ...

  5. Interacting models of cooperative gene regulation Debopriya Das*, Nilanjana Banerjee*

    E-Print Network [OSTI]

    Interacting models of cooperative gene regulation Debopriya Das*, Nilanjana Banerjee* , and Michael, especially mammals, where cooperative control of gene regulation is absolutely essential. cooperativity control in gene regulation networks. It requires cooperative binding of multiple transcription factors

  6. apoptosis related gene: Topics by E-print Network

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

    of protein Barkai, Naama 10 Inference of Gene Relations from Microarray Data by Abduction Computer Technologies and Information Sciences Websites Summary: Inference of Gene...

  7. apoptosis related genes: Topics by E-print Network

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

    of protein Barkai, Naama 10 Inference of Gene Relations from Microarray Data by Abduction Computer Technologies and Information Sciences Websites Summary: Inference of Gene...

  8. albumin gene expression: Topics by E-print Network

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

    biology, and multiple orthogonal gene switches are needed Zhao, Huimin 223 Metabolic load and heterologous gene expression CiteSeer Summary: The expression of a foreign...

  9. at1 receptor gene: Topics by E-print Network

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

    28 The axon guidance receptor gene ROBO1 is a candidate gene for developmental dyslexia CiteSeer Summary: Dyslexia, or specific reading disability, is the most common...

  10. angiotensin receptor gene: Topics by E-print Network

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

    36 The axon guidance receptor gene ROBO1 is a candidate gene for developmental dyslexia CiteSeer Summary: Dyslexia, or specific reading disability, is the most common...

  11. arthritis candidate genes: Topics by E-print Network

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

    37 The axon guidance receptor gene ROBO1 is a candidate gene for developmental dyslexia CiteSeer Summary: Dyslexia, or specific reading disability, is the most common...

  12. Organization and evolution of the rat tyrosine hydroxylase gene

    SciTech Connect (OSTI)

    Brown, E.R.; Coker, G.T. III; O'Malley, K.L.

    1987-08-11T23:59:59.000Z

    This report describes the organization of the rat tyrosine hydroxylase (TH) gene and compares its structure with the human phenylalanine hydroxylase gene. Both genes are single copy and contain 13 exons separated by 12 introns. Remarkably, the positions of 10 out 12 intron/exon boundaries are identical for the two genes. These results support the idea that these hydroxylases genes are members of a gene family which has a common evolutionary origin. The authors predict that this ancestral gene would have encoded exons similar to those of TH prior to evolutionary drift to other members of this gene family.

  13. The specificity and evolution of gene regulatory elements

    E-Print Network [OSTI]

    Friedman, Robin Carl

    2010-01-01T23:59:59.000Z

    The regulation of gene expression underlies the morphological, physiological, and functional differences between human cell types, developmental stages, and healthy and disease states. Gene regulation in eukaryotes is ...

  14. agnostic gene coding: Topics by E-print Network

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

    25 Next Page Last Page Topic Index 21 Associating Genes with Gene Ontology Codes Using a Maximum Entropy Analysis of Biology and Medicine Websites Summary: and select appropriate...

  15. BESC Submits 32 Gene Disclosures for Patents | ORNL

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

    invention disclosures for 32 different genes that can help improve the yield of ethanol from cellulosic biomass. These genes or their variants function to overcome...

  16. Radiation-induced gene responses

    SciTech Connect (OSTI)

    Woloschak, G.E.; Paunesku, T.; Shearin-Jones, P.; Oryhon, J.

    1996-12-31T23:59:59.000Z

    In the process of identifying genes that are differentially regulated in cells exposed to ultraviolet radiation (UV), we identified a transcript that was repressed following the exposure of cells to a combination of UV and salicylate, a known inhibitor of NF-kappaB. Sequencing this band determined that it has identify to lactate dehydrogenase, and Northern blots confirmed the initial expression pattern. Analysis of the sequence of the LDH 5` region established the presence of NF-kappaB, Sp1, and two Ap-2 elements; two partial AP- 1; one partial RE, and two halves of E-UV elements were also found. Electromobility shift assays were then performed for the AP-1, NF- kappaB, and E-UV elements. These experiments revealed that binding to NF-kappaB was induced by UV but repressed with salicylic acid; UV did not affect AP-1 binding, but salicylic acid inhibited it alone or following UV exposure; and E-UV binding was repressed by UV, and salicylic acid had little effect. Since the binding of no single element correlated with the expression pattern of LDH, it is likely that multiple elements govern UV/salicylate-mediated expression.

  17. Distance matters: the impact of gene proximity in bacterial gene regulation

    E-Print Network [OSTI]

    Otto Pulkkinen; Ralf Metzler

    2013-05-13T23:59:59.000Z

    Following recent discoveries of colocalization of downstream-regulating genes in living cells, the impact of the spatial distance between such genes on the kinetics of gene product formation is increasingly recognized. We here show from analytical and numerical analysis that the distance between a transcription factor (TF) gene and its target gene drastically affects the speed and reliability of transcriptional regulation in bacterial cells. For an explicit model system we develop a general theory for the interactions between a TF and a transcription unit. The observed variations in regulation efficiency are linked to the magnitude of the variation of the TF concentration peaks as a function of the binding site distance from the signal source. Our results support the role of rapid binding site search for gene colocalization and emphasize the role of local concentration differences.

  18. Gene expression profiles in irradiated cancer cells

    SciTech Connect (OSTI)

    Minafra, L.; Bravatà, V.; Russo, G.; Ripamonti, M.; Gilardi, M. C. [IBFM CNR - LATO, Cefalù, Segrate (Italy)] [IBFM CNR - LATO, Cefalù, Segrate (Italy)

    2013-07-26T23:59:59.000Z

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

  19. Parallel gene synthesis in a microfluidic device

    E-Print Network [OSTI]

    Kong, David S.

    The ability to synthesize custom de novo DNA constructs rapidly, accurately and inexpensively is highly desired by researchers, as synthetic genes and longer DNA constructs are enabling to numerous powerful applications ...

  20. Predicting gene function from images of cells

    E-Print Network [OSTI]

    Jones, Thouis Raymond, 1971-

    2007-01-01T23:59:59.000Z

    This dissertation shows that biologically meaningful predictions can be made by analyzing images of cells. In particular, groups of related genes and their biological functions can be predicted using images from large ...

  1. Characterization of a unique embedded gene

    E-Print Network [OSTI]

    Zhang, Ning

    1999-01-01T23:59:59.000Z

    ). Plasmids were either transformed into host cells or stored in ? 20'C as water solutions. The oligonucleotides were purchased from Gene Technologies Laboratory (GTL) in the Department of Biology at Texas A&M University (TAMU). In all experiments involving...

  2. Control of gene expression by cell size

    E-Print Network [OSTI]

    Wu, Chia-Yung

    2010-01-01T23:59:59.000Z

    Polyploidy, increased copy number of whole chromosome sets in the genome, is a common cellular state in evolution, development and disease. Polyploidy enlarges cell size and alters gene expression, producing novel phenotypes ...

  3. INVESTIGATION Coding Gene Single Nucleotide Polymorphism

    E-Print Network [OSTI]

    Bernatchez, Louis

    INVESTIGATION Coding Gene Single Nucleotide Polymorphism Mapping and Quantitative Trait Loci QTL detection single nucleotide polymorphisms (SNP) reproduction Salvelinus fontinalis Linkages maps such as microsatellites and single nucleotide polymorphisms (SNPs). Also, compared with previ- ous methods based

  4. Characterization of the Bovine Cathelicidin Gene Family

    E-Print Network [OSTI]

    Flores, Erin Gillenwaters

    2012-10-19T23:59:59.000Z

    genome assembly (Btau_4.0) confirmed current gene order. Comparative sequence analysis for 10 domestic cattle breeds representing both Bos taurus taurus and Bos taurus indicus revealed 60 SNPs, 7 of which were nonsynonymous, and 5 indel mutations. Data...

  5. Gene-environment interactions in genetic epidemiology

    E-Print Network [OSTI]

    Spinka, Christine Marie

    2005-02-17T23:59:59.000Z

    joint linkage disequilibrium and linkage mapping of quantitative trait loci is developed. Subsequently, methods are needed to determine the interaction, if any, between these genes and environmental risk factors. Many of these factors, such as weight... . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Mapping Quantitative Trait Loci Using Complex Pedigrees 2 1.3 Gene-environment Interactions . . . . . . . . . . . . . . . 3 II JOINT LINKAGE DISEQUILIBRIUM AND LINKAGE MAP- PING FOR COMPLEX PEDIGREES . . . . . . . . . . . . . . . 5 2...

  6. GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes

    E-Print Network [OSTI]

    Pati, Amrita

    2012-01-01T23:59:59.000Z

    PRediction IMprovement Pipeline for Amrita Pati 1 , NataliaGene Prediction IMprovement Pipeline, http://geneprimp.jgi-based post-processing pipeline that identifies erroneously

  7. NEED AND METHODS OF GENE CONSERVATION IN ANIMAL BREEDING (*)

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    new useful variation. The available methods of gene conservation were discussed, the main attention being paid to the maintenance of small nuclei of most breeds and strains, to the establishment of gene of genes is deter- mined by several groups of factors, e. g. theoccurrence of actual gene losses

  8. Interactive 3D Gene Expression Viewer Victor E. Gerth*

    E-Print Network [OSTI]

    Vize, Peter D.

    Interactive 3D Gene Expression Viewer Victor E. Gerth* University of Calgary, Department. The Interactive Gene Expression viewer provides a way to view spatial relationships between different gene expression patterns and anatomic features. Web based 3D enabled technologies such as the Interactive Gene

  9. Gene for ataxia-telangiectasia complementation group D (ATDC)

    DOE Patents [OSTI]

    Murnane, J.P.; Painter, R.B.; Kapp, L.N.; Yu, L.C.

    1995-03-07T23:59:59.000Z

    Disclosed herein is a new gene, an AT gene for complementation group D, the ATDC gene and fragments thereof. Nucleic acid probes for the gene are provided as well as proteins encoded by the gene, cDNA therefrom, preferably a 3 kilobase (kb) cDNA, and recombinant nucleic acid molecules for expression of the proteins. Further disclosed are methods to detect mutations in the gene, preferably methods employing the polymerase chain reaction (PCR). Also disclosed are methods to detect AT genes from other AT complementation groups. 30 figs.

  10. Gene Lopez Edgar Howard Gene Lopez and Edgar Howard both taught Mathematics at San Diego State for over 30 years.

    E-Print Network [OSTI]

    Gallo, Linda C.

    Gene Lopez Edgar Howard Gene Lopez and Edgar Howard both taught Mathematics at San Diego State and Computer Sciences is establishing The Gene Lopez and Edgar Howard Memorial Fund Donations to this fund that this is especially appropriate as a memorial to Gene and Edgar since each of them contributed significantly

  11. Low Rates of Expression Profile Divergence in Highly Expressed Genes and Tissue-Specific Genes During Mammalian Evolution

    E-Print Network [OSTI]

    Zhang, Jianzhi

    Low Rates of Expression Profile Divergence in Highly Expressed Genes and Tissue-Specific Genes specificity influence the divergence of expression profiles between orthologous genes. Here we address expression profile change during evolution is negatively correlated with the level of gene expression

  12. GeneTracer: Gene Sequence Analysis of Disease Mutations VAST 2010 Mini Challenge 3 Award: Excellent Process Explanation

    E-Print Network [OSTI]

    Stasko, John T.

    GeneTracer: Gene Sequence Analysis of Disease Mutations VAST 2010 Mini Challenge 3 Award: ExcellentTracer, developed for the VAST 2010 genetic sequence mini challenge, visualizes gene sequences of cur- rent outbreaks and native sequences along with disease character- istics. We successfully used Gene

  13. Gene Expression Patterns and Gene Copy Number Changes in Dermatofibrosarcoma Protuberans

    E-Print Network [OSTI]

    Botstein, David

    of Anatomic Pathology,¶ Cleveland Clinic Foundation, Cleveland, Ohio Dermatofibrosarcoma protuberans (DFSP:22), which fuses the COL1A1 and PDGF genes. We determined the characteristic gene expression profile of DFSP and characterized DNA copy number changes in DFSP by array-based comparative genomic hybridization (ar- ray CGH

  14. Id-1 gene and gene products as therapeutic targets for treatment of breast cancer and other types of carcinoma

    SciTech Connect (OSTI)

    Desprez, Pierre-Yves; Campisi, Judith

    2014-08-19T23:59:59.000Z

    A method for treatment of breast cancer and other types of cancer. The method comprises targeting and modulating Id-1 gene expression, if any, for the Id-1 gene, or gene products in breast or other epithelial cancers in a patient by delivering products that modulate Id-1 gene expression. When expressed, Id-1 gene is a prognostic indicator that cancer cells are invasive and metastatic.

  15. Pathogenicity island mobility and gene content.

    SciTech Connect (OSTI)

    Williams, Kelly Porter

    2013-10-01T23:59:59.000Z

    Key goals towards national biosecurity include methods for analyzing pathogens, predicting their emergence, and developing countermeasures. These goals are served by studying bacterial genes that promote pathogenicity and the pathogenicity islands that mobilize them. Cyberinfrastructure promoting an island database advances this field and enables deeper bioinformatic analysis that may identify novel pathogenicity genes. New automated methods and rich visualizations were developed for identifying pathogenicity islands, based on the principle that islands occur sporadically among closely related strains. The chromosomally-ordered pan-genome organizes all genes from a clade of strains; gaps in this visualization indicate islands, and decorations of the gene matrix facilitate exploration of island gene functions. A %E2%80%9Clearned phyloblocks%E2%80%9D method was developed for automated island identification, that trains on the phylogenetic patterns of islands identified by other methods. Learned phyloblocks better defined termini of previously identified islands in multidrug-resistant Klebsiella pneumoniae ATCC BAA-2146, and found its only antibiotic resistance island.

  16. Universal light-switchable gene promoter system

    DOE Patents [OSTI]

    Quail, Peter H.; Huq, Enamul; Tepperman, James; Sato, Sae

    2005-02-22T23:59:59.000Z

    An artificial promoter system that can be fused upstream of any desired gene enabling reversible induction or repression of the expression of the gene at will in any suitable host cell or organisms by light is described. The design of the system is such that a molecule of the plant photoreceptor phytochrome is targeted to the specific DNA binding site in the promoter by a protein domain that is fused to the phytochrome and that specifically recognizes this binding site. This bound phytochrome, upon activation by light, recruits a second fusion protein consisting of a protein that binds to phytochrome only upon light activation and a transcriptional activation domain that activates expression of the gene downstream of the promoter.

  17. Correction of human. beta. sup S -globin gene by gene targeting

    SciTech Connect (OSTI)

    Shesely, E.G.; Hyungsuk Kim; Shehee, W.R.; Smithies, O. (Univ. of North Carolina, Chapel Hill (United States)); Papayannopoulou, T. (Univ. of Washington, Seattle (United States)); Popovich, B.W. (Children's Hospital, San Diego, CA (United States))

    1991-05-15T23:59:59.000Z

    As a step toward using gene targeting for gene therapy, the authors have corrected a human {beta}{sup S}-globin gene to the normal {beta}{sup A} allele by homologous recombination in the mouse-human hybrid cell line BSM. BSM is derived from a mouse erythroleukemia cell line and carries a single human chromosome 11 with the {beta}{sup S}-globin allele. A {beta}{sup A}-globin targeting construct containing a unique oligomer and a neomycin-resistance gene was electroporated into the BSM cells, which were then placed under G418 selection. Then 126 resulting pools containing a total {approx}29,000 G418-resistant clones were screened by PCR for the presence of a targeted recombinant: 3 positive pools were identified. A targeted clone was isolated by replating one of the positive pools into smaller pools and rescreening by PCR, followed by dilution cloning. Southern blot analysis demonstrated that the isolated clone had been targeted as planned. The correction of the {beta}{sup S} allele to {beta}{sup A} was confirmed both by allele-specific PCR and by allele-specific antibodies. Expression studies comparing the uninduced and induced RNA levels in unmodified BSM cells and in the targeted clone showed no significant alteration in the ability of the targeted clone to undergo induction, despite the potentially disrupting presence of a transcriptionally active neomycin gene 5{prime} to the human {beta}{sup A}-globin gene. Thus gene targeting can correct a {beta}{sup S} allele to {beta}{sup A}, and the use of a selectable helper gene need not significantly interfere with the induction of the corrected gene.

  18. Regulation of methane genes and genome expression

    SciTech Connect (OSTI)

    John N. Reeve

    2009-09-09T23:59:59.000Z

    At the start of this project, it was known that methanogens were Archaeabacteria (now Archaea) and were therefore predicted to have gene expression and regulatory systems different from Bacteria, but few of the molecular biology details were established. The goals were then to establish the structures and organizations of genes in methanogens, and to develop the genetic technologies needed to investigate and dissect methanogen gene expression and regulation in vivo. By cloning and sequencing, we established the gene and operon structures of all of the “methane” genes that encode the enzymes that catalyze methane biosynthesis from carbon dioxide and hydrogen. This work identified unique sequences in the methane gene that we designated mcrA, that encodes the largest subunit of methyl-coenzyme M reductase, that could be used to identify methanogen DNA and establish methanogen phylogenetic relationships. McrA sequences are now the accepted standard and used extensively as hybridization probes to identify and quantify methanogens in environmental research. With the methane genes in hand, we used northern blot and then later whole-genome microarray hybridization analyses to establish how growth phase and substrate availability regulated methane gene expression in Methanobacterium thermautotrophicus ?H (now Methanothermobacter thermautotrophicus). Isoenzymes or pairs of functionally equivalent enzymes catalyze several steps in the hydrogen-dependent reduction of carbon dioxide to methane. We established that hydrogen availability determine which of these pairs of methane genes is expressed and therefore which of the alternative enzymes is employed to catalyze methane biosynthesis under different environmental conditions. As were unable to establish a reliable genetic system for M. thermautotrophicus, we developed in vitro transcription as an alternative system to investigate methanogen gene expression and regulation. This led to the discovery that an archaeal protein, designated TFE, that had sequences in common with the eukaryotic general transcription factor TFIIE, stimulated archaeal transcription initiation and that the archaeal TATA-box binding protein (TBP) remained attached to the promoter region whereas the transcription factor TFB dissociated from the template DNA following initiation. DNA sequences that directed the localized assembly of archaeal histones into archaeal nucleosomes were identified, and we established that transcription by an archaeal RNA polymerase was slowed but not blocked by archaeal nucleosomes. We developed a new protocol to purify archaeal RNA polymerases and with this enzyme and additional improvements to the in vitro transcription system, we established the template requirements for archaeal transcription termination, investigated the activities of proteins predicted to be methane gene regulators, and established how TrpY, a novel archaeal regulator of expression of the tryptophan biosynthetic operon functions in M. thermautotrophicus. This also resulted in the discovery that almost all M. thermautotrophicus mutants isolated as spontaneously resistant to 5-methyl tryptophan (5MTR) had mutations in trpY and were therefore 5MTR through de-repressed trp operon expression. This established a very simple, practical procedure to determine and quantify the DNA sequence changes that result from exposure of this Archaeon to any experimental mutagenesis protocol. Following the discovery that the Thermococcus kodakaraensis was amenable to genetic manipulation, we established this technology at OSU and subsequently added plasmid expression, a reporter system and additional genetic selections to the T. kodakaraensis genetic toolbox. We established that transcription and translation are coupled in this Archaeon, and by combining in vitro transcription and in vivo genetics, we documented that both TFB1 and TFB2 support transcription initiation in T. kodakaraensis. We quantified the roles of ribosome binding sequences and alternative initiation codons in translation initiation, established that polarity e

  19. What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

    E-Print Network [OSTI]

    Barkley, Noelle A.; Krueger, Robert R.; Federici, Claire T.; Roose, Mikeal L.

    2009-01-01T23:59:59.000Z

    What phylogeny and gene genealogy analyses reveal aboutAdditionally, gene genealogies (networks) were constructedtaxa. Networks/gene genealogies TCS version 1.13 (Clement et

  20. Gene Expression in the Stallion Testes

    E-Print Network [OSTI]

    Laughlin, Andy M.

    2011-08-08T23:59:59.000Z

    genes were differentially expressed (122 in fertile tissue, 111 in subfertile tissue). Of these, phosphodiesterase 3B (PDE3B), steroidogenic acute regulatory (StAR) protein, and outer dense fiber of sperm tails 2 (ODF2) mRNAs, were localized...

  1. Gene duplications, robustness and evolutionary innovations

    E-Print Network [OSTI]

    Wagner, Andreas

    , flowering plant evolution and heart development, which encompass some of the most striking innovationsGene duplications, robustness and evolutionary innovations Andreas Wagner1,2,3 Summary Mutational with evolutionary innovation is thus a special case of a general mechanism linking innovation to robustness

  2. Gene encoding acetyl-coenzyme A carboxylase

    DOE Patents [OSTI]

    Roessler, Paul G. (Golden, CO); Ohlrogge, John B. (Okemos, MI)

    1996-01-01T23:59:59.000Z

    A DNA encoding an acetyl-coenzyme A carboxylase (ACCase) from a photosynthetic organism and functional derivatives thereof which are resistant to inhibition from certain herbicides. This gene can be placed in organisms to increase their fatty acid content or to render them resistant to certain herbicides.

  3. Gene encoding acetyl-coenzyme A carboxylase

    DOE Patents [OSTI]

    Roessler, P.G.; Ohlrogge, J.B.

    1996-09-24T23:59:59.000Z

    A DNA encoding an acetyl-coenzyme A carboxylase (ACCase) from a photosynthetic organism and functional derivatives are disclosed which are resistant to inhibition from certain herbicides. This gene can be placed in organisms to increase their fatty acid content or to render them resistant to certain herbicides. 5 figs.

  4. SHORT REVIEW Ecological genomics: understanding gene and

    E-Print Network [OSTI]

    Kaufman, Glennis A.

    SHORT REVIEW Ecological genomics: understanding gene and genome function in the natural environment MC Ungerer, LC Johnson and MA Herman Division of Biology, Ecological Genomics Institute, Kansas State University, Manhattan, KS, USA The field of ecological genomics seeks to understand the genetic mechanisms

  5. ORIGINAL ARTICLE Viral photosynthetic reaction center genes

    E-Print Network [OSTI]

    Mandel-Gutfreund, Yael

    , Technion--Israel Institute of Technology, Haifa, Israel; 3 Inter-Departmental Program for Biotechnology. The discovery of genes (psbA, psbD) that encode key photosystem II proteins (D1, D2) in the genomes of phages the infection process. Here, using metagenomic data in natural ocean samples, we show that about 60% of the psb

  6. COMPUTATIONAL COMPARATIVE GENOMICS: GENES, REGULATION, EVOLUTION

    E-Print Network [OSTI]

    Kellis, Manolis

    COMPUTATIONAL COMPARATIVE GENOMICS: GENES, REGULATION, EVOLUTION by Manolis (Kellis) Kamvysselis B.S. Electrical Engineering and Computer Science; M. Eng. Computer Science and Engineering Massachusetts Institute at the Massachusetts Institute of Technology June 2003 © 2003 Massachusetts Institute of Technology All rights reserved

  7. BIOINFORMATICS Comparative Evaluation of Reverse Engineering Gene

    E-Print Network [OSTI]

    Babu, M. Madan

    BIOINFORMATICS Comparative Evaluation of Reverse Engineering Gene Regulatory Networks of Statistics, University of Dortmund, Germany ABSTRACT Motivation: An important problem in systems biology into account. This suggests that the higher computational costs of infe- rence with BNs over GGMs and RNs

  8. Cross-regulation and interaction between eukaryotic gene regulatory processes

    E-Print Network [OSTI]

    Spies, Noah (Noah Walter Benjamin)

    2012-01-01T23:59:59.000Z

    Regulation of genes is fundamental to all living processes and can be exerted at many sequential steps. We studied several eukaryotic gene regulatory mechanisms with an emphasis on understanding the interplay between ...

  9. Text Mining in Cancer Gene and Pathway Prioritization

    E-Print Network [OSTI]

    Riedlinger, Gregory

    Prioritization of cancer implicated genes has received growing attention as an effective way to reduce wet lab cost by computational analysis that ranks candidate genes according to the likelihood that experimental ...

  10. Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes

    E-Print Network [OSTI]

    Babu, M. Madan

    Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes Sarath. Although it is known that eukaryotic transcriptional regulation is complex and requires an intricate-order organization of genes across and within chromosomes that is constrained by transcriptional regulation

  11. asthma candidate genes: Topics by E-print Network

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

    F.C. 38 The axon guidance receptor gene ROBO1 is a candidate gene for developmental dyslexia CiteSeer Summary: Dyslexia, or specific reading disability, is the most common...

  12. autism candidate gene: Topics by E-print Network

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

    F.C. 46 The axon guidance receptor gene ROBO1 is a candidate gene for developmental dyslexia CiteSeer Summary: Dyslexia, or specific reading disability, is the most common...

  13. adhd candidate gene: Topics by E-print Network

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

    F.C. 34 The axon guidance receptor gene ROBO1 is a candidate gene for developmental dyslexia CiteSeer Summary: Dyslexia, or specific reading disability, is the most common...

  14. axon guidance gene: Topics by E-print Network

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

    Index 1 The axon guidance receptor gene ROBO1 is a candidate gene for developmental dyslexia CiteSeer Summary: Dyslexia, or specific reading disability, is the most common...

  15. asthma susceptibility gene: Topics by E-print Network

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

    in the IL13 gene and atopy in all three populations (and with asthma 2005-01-01 6 The Dyslexia Susceptibility Genes and Neurodevelopment. Open Access Theses and Dissertations...

  16. amoa gene analysis: Topics by E-print Network

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

    applied to determine the core cell cycle genes in the recently Gent, Universiteit 264 Graeber et al. 2013 -Roles of Lepidium Seed Dormancy Genes 1 Spatio-temporal Seed Development...

  17. analysis reveals genes: Topics by E-print Network

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

    applied to determine the core cell cycle genes in the recently Gent, Universiteit 466 Graeber et al. 2013 -Roles of Lepidium Seed Dormancy Genes 1 Spatio-temporal Seed Development...

  18. analysis identifies genes: Topics by E-print Network

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

    applied to determine the core cell cycle genes in the recently Gent, Universiteit 490 Graeber et al. 2013 -Roles of Lepidium Seed Dormancy Genes 1 Spatio-temporal Seed Development...

  19. Gene-supplemented collagen scaffolds for non-viral gene delivery for brain tissue engineering

    E-Print Network [OSTI]

    Bolliet, Catherine

    2007-01-01T23:59:59.000Z

    Recent advances in tissue engineering, combining an extracellular matrix (ECM)-like vehicle with therapeutic molecules, cells and/or genes has yielded promising results for brain injury repair. The purpose of this thesis ...

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

    SciTech Connect (OSTI)

    Salem, Tamer Z. [Department of Entomology, Michigan State University, East Lansing, MI 48824 (United States) [Department of Entomology, Michigan State University, East Lansing, MI 48824 (United States); Department of Microbial Molecular Biology, AGERI, Agricultural Research Center, Giza 12619 (Egypt); Division of Biomedical Sciences, Zewail University, Zewail City of Science and Technology, Giza 12588 (Egypt); Zhang, Fengrui [Department of Entomology, Michigan State University, East Lansing, MI 48824 (United States)] [Department of Entomology, Michigan State University, East Lansing, MI 48824 (United States); Thiem, Suzanne M., E-mail: smthiem@msu.edu [Department of Entomology, Michigan State University, East Lansing, MI 48824 (United States); Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 (United States)

    2013-01-20T23:59:59.000Z

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

  1. Gene Expression Analyses and Association Studies of Wood Development Genes in Loblolly Pine (Pinus taeda L.)

    E-Print Network [OSTI]

    Palle, Sreenath Reddy

    2011-10-21T23:59:59.000Z

    ............................................................ 58 7 Model of the association between the AIP and PRT genes ........................ 64 8 Pathways demonstrating the indirect role of CGS and the direct role of CAD in lignin biosynthesis... complex and therefore the molecular mechanisms governing the differentiation of wood tissues are complicated. Several researchers have identified a number of genes involved in the biosynthesis of polysaccharides, lignins and cell wall proteins in forest...

  2. Gene co-expression network analysis in Rhodobacter capsulatus...

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

    annotation. We identified R. capsulatus modules enriched with genes for ribosomal proteins, porphyrin and bacteriochlorophyll anabolism, and biosynthesis of secondary...

  3. Message from ISCB Getting Started in Gene Orthology and Functional

    E-Print Network [OSTI]

    Gerstein, Mark

    . Each genome consists of a unique gene inventory, which determines the specific phenotype species by analyzing compositions of gene inventories therefore opens the door to the rich branch can only be identified when the whole gene inventories from all the involved species are examined

  4. Generator based Modeling CP Game for Gene Regulatory Network

    E-Print Network [OSTI]

    Lescanne, Pierre

    introduces a framework based on game theory that models gene regulation activities. Strategic games which are the basic model in game theory was successfully applied to gene regulation networks and molecular networks be established. One of the main issue when a gene regulation system is analyzed through a model is to decompose

  5. 2005 Nature Publishing Group Photosynthesis genes in marine viruses yield

    E-Print Network [OSTI]

    Church, George M.

    © 2005 Nature Publishing Group Photosynthesis genes in marine viruses yield proteins during host­6 probably influences the genetic and functional diversity of both. For example, photosynthesis genes period. We also show that the expression of host photosynthesis genes declines over the course

  6. Efficient and Robust Algorithms for Statistical Inference in Gene Regulatory Networks

    E-Print Network [OSTI]

    Noor, Amina

    2013-12-10T23:59:59.000Z

    Inferring gene regulatory networks (GRNs) is of profound importance in the ?eld of computational biology and bioinformatics. Understanding the gene-gene and gene- transcription factor (TF) interactions has the potential of providing an insight...

  7. Identification of novel lung genes in bronchial epithelium by serial analysis of gene Kim M. Lonergan*1

    E-Print Network [OSTI]

    Ng, Raymond T.

    1 Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression of human bronchial epithelium should provide a basis for studying lung diseases including cancer. We have deduced global gene expression profiles of bronchial epithelium and lung parenchyma, based upon a vast

  8. DNA methylation map of mouse and human brain identifies target genes in Alzheimer's disease

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

    al. Figure 3 Epigenetic deregulation of target genes in the3027 Figure 2 Epigenetic deregulation of target genes in

  9. The Role of Multiple Transcription Factors In Archaeal Gene Expression

    SciTech Connect (OSTI)

    Charles J. Daniels

    2008-09-23T23:59:59.000Z

    Since the inception of this research program, the project has focused on two central questions: What is the relationship between the 'eukaryal-like' transcription machinery of archaeal cells and its counterparts in eukaryal cells? And, how does the archaeal cell control gene expression using its mosaic of eukaryal core transcription machinery and its bacterial-like transcription regulatory proteins? During the grant period we have addressed these questions using a variety of in vivo approaches and have sought to specifically define the roles of the multiple TATA binding protein (TBP) and TFIIB-like (TFB) proteins in controlling gene expression in Haloferax volcanii. H. volcanii was initially chosen as a model for the Archaea based on the availability of suitable genetic tools; however, later studies showed that all haloarchaea possessed multiple tbp and tfb genes, which led to the proposal that multiple TBP and TFB proteins may function in a manner similar to alternative sigma factors in bacterial cells. In vivo transcription and promoter analysis established a clear relationship between the promoter requirements of haloarchaeal genes and those of the eukaryal RNA polymerase II promoter. Studies on heat shock gene promoters, and the demonstration that specific tfb genes were induced by heat shock, provided the first indication that TFB proteins may direct expression of specific gene families. The construction of strains lacking tbp or tfb genes, coupled with the finding that many of these genes are differentially expressed under varying growth conditions, provided further support for this model. Genetic tools were also developed that led to the construction of insertion and deletion mutants, and a novel gene expression scheme was designed that allowed the controlled expression of these genes in vivo. More recent studies have used a whole genome array to examine the expression of these genes and we have established a linkage between the expression of specific tfb genes and the regulation of nitrogen metabolism and other global cellular responses.

  10. Gene Calling Standards (GSC8 Meeting)

    ScienceCinema (OSTI)

    Kyrpides, Nikos [Genome Biology Program, DOE JGI

    2011-04-28T23:59:59.000Z

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Nikos Kyrpides of the DOE Joint Genome Institute discusses gene calling standards at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

  11. Engineering disease resistance with pectate lyase-like genes

    DOE Patents [OSTI]

    Vogel, John; Somerville, Shauna

    2005-03-08T23:59:59.000Z

    A mutant gene coding for pectate lyase and homologs thereof is provided, which when incorporated in transgenic plants effect an increased level disease resistance in such plants. Also is provided the polypeptide sequence for the pectate lyase of the present invention. Methods of obtaining the mutant gene, producing transgenic plants which include the nucleotide sequence for the mutant gene and producing improved disease resistance in a crop of such transgenic plants are also provided.

  12. Petascale Debugging via Allinea DDT for IBM Blue Gene /P

    E-Print Network [OSTI]

    Kemner, Ken

    Petascale Debugging via Allinea DDT for IBM Blue Gene /P and IBM Blue Gene /Q Ian Lumb petascaling Allinea DDT Petascaling Allinea DDT for IBM Blue Gene /x Getting Started with Allinea DDT #12;0 50,000 100,000 150,000 200,000 0 0.02 0.04 0.06 0.08 0.1 0.12 DDT 3.0 Performance Figures Jaguar Cray

  13. was nonrandom, localized to genes and within particular regions of genes, much like sense tran-

    E-Print Network [OSTI]

    Xie, Xiaoliang Sunney

    number of genes. References and Notes 1. P. O. Brown, D. Botstein, Nat. Genet. 21, 33 (1999). 2. V. E (2002). 10. B. Lehner, G. Williams, R. D. Campbell, C. M. Sanderson, Trends Genet. 18, 63 (2002). 11. J Acids Res. 32, 4812 (2004). 9. M. E. Fahey, T. F. Moore, D. G. Higgins, Comp. Funct. Genomics 3, 244

  14. Candidate genes affecting Drosophila life span identified by integrating microarray gene expression analysis and QTL mapping

    E-Print Network [OSTI]

    Mackay, Trudy F.C.

    University, Boston, MA 02111, United States b Department of Genetics and W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695-7614, United States Received 4 April 2006, short-lived animal models are essential to identifying the mechanisms and genes that affect the rate

  15. acquired resistance genes: Topics by E-print Network

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

    and fractionation resistance Biology and Medicine Websites Summary: in Paramecium, Gout et al. 10 identify a clear relationship between high WGD duplicate gene retention...

  16. adenovirus early gene: Topics by E-print Network

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

    of Kupffer cell activation and viral gene expression in early liver toxicity after infusion of recombinant adenovirus vectors CiteSeer Summary: Systemic application of...

  17. autoimmunity susceptibility gene: Topics by E-print Network

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

    curable by the removal of culpable antibodies and antigens. 1. unknown authors 5 The Dyslexia Susceptibility Genes and Neurodevelopment. Open Access Theses and Dissertations...

  18. autism susceptibility genes: Topics by E-print Network

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

    the susceptibility for autism. To this end, 267 subjects with autism spectrum 3 The Dyslexia Susceptibility Genes and Neurodevelopment. Open Access Theses and Dissertations...

  19. arthritis susceptibility genes: Topics by E-print Network

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

    worldwide will be able to access these treatments. Yuti Chernajovsky 2005-01-01 7 The Dyslexia Susceptibility Genes and Neurodevelopment. Open Access Theses and Dissertations...

  20. Mutator gene and hereditary non-polyposis colorectal cancer

    DOE Patents [OSTI]

    de la Chapelle, Albert (Helsingfors, FI); Vogelstein, Bert (Baltimore, MD); Kinzler, Kenneth W. (Baltimore, MD)

    2008-02-05T23:59:59.000Z

    The human MSH2 gene, responsible for hereditary non-polyposis colorectal cancer, was identified by virtue of its homology to the MutS class of genes, which are involved in DNA mismatch repair. The sequence of cDNA clones of the human gene are provided, and the sequence of the gene can be used to demonstrate the existence of germ line mutations in hereditary non-polyposis colorectal cancer (HNPCC) kindreds, as well as in replication error.sup.+ (RER.sup.+) tumor cells.

  1. acid gene cluster: Topics by E-print Network

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

    the application of a novel clustering algorithm, Super-Paramagnetic Clustering (SPC) to analysis of gene expression profiles that were generated recently during a study of...

  2. apoptosis gene profiling: Topics by E-print Network

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

    the application of a novel clustering algorithm, Super-Paramagnetic Clustering (SPC) to analysis of gene expression profiles that were generated recently during a study of...

  3. arom gene cluster: Topics by E-print Network

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

    the application of a novel clustering algorithm, Super-Paramagnetic Clustering (SPC) to analysis of gene expression profiles that were generated recently during a study of...

  4. almt1 gene cluster: Topics by E-print Network

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

    the application of a novel clustering algorithm, Super-Paramagnetic Clustering (SPC) to analysis of gene expression profiles that were generated recently during a study of...

  5. Genomics, Gene Expression and Other Studies in Soybean Rust

    E-Print Network [OSTI]

    Posada-Buitrago, Martha Lucia

    2005-01-01T23:59:59.000Z

    Joint Genome Institute Genomics, Gene Expression and otherRust Martha Lucía Posada-Buitrago Ph.D Genomics DivisionEvolutionary Genomics DOE- Joint Genome Institute Lawrence

  6. aurata hemoglobin genes: Topics by E-print Network

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

    chain reaction and in situ hybridization, the expression of the prolactin (PRL) gene was determined during development in gilthead sea bream (Sparus aurata) for the...

  7. aspartyl proteinase gene: Topics by E-print Network

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

    and pathogen Edinburgh, University of - Research Archive Summary: Parasite nematode genomics is a relatively new field9, but already two of the most interesting gene families to...

  8. GENE 7360: Teaching Internship in Genetics Instructor: Rodney Mauricio

    E-Print Network [OSTI]

    Arnold, Jonathan

    GENE 7360: Teaching Internship in Genetics Instructor: Rodney Mauricio Fall 2004 COURSE DESCRIPTION to serve as a formal internship in the teaching of Genetics. Through close faculty supervision

  9. Nonlinear effects in kinetic resolutions

    E-Print Network [OSTI]

    Johnson, Derrell W.

    1999-01-01T23:59:59.000Z

    KTRIC AMPLIFICATION IN THE JACOBSEN HYDROLYTIC KINET RESOLUTION OF RACEMIC EPOXIDES 20 Applicability of Homocompetitive Reaction Kinetics to the Jacobsen HKR Effect of Catalyst EE and Choice of Epoxide on Amplification in the Jacobsen HKR.... . . . . . . . . . . . . . . . . . Effect of Temperature on Amplification and Reaction Rate in the Jacobsen HKR . Effect of Low EE Catalyst Generation on Amplification in the Jacobsen HKR. . . . 21 21 25 26 27 30 31 TABLE OF CONTENTS (Continued) CHAPTER Page V AS...

  10. Interference and k-point sampling in the supercell approach to phase-coherent transport K. S. Thygesen and K. W. Jacobsen

    E-Print Network [OSTI]

    Thygesen, Kristian

    tight-binding model to show that interference be- tween the repeated images is a small effect compared the re- peated images. As the transverse dimensions of the supercell are increased the interference of k-point sam- pling and interference on the transmission function by means of two examples. The first

  11. Variant translocation of the bcl-2 gene to immunoglobulin. lambda. light chain gene in chronic lymphocytic leukemia

    SciTech Connect (OSTI)

    Adachi, M.; Cossman, J.; Longo, D.; Croce, C.M.; Tsujimoto, Y. (Wistar Institute of Anatomy and Biology, Philadelphia, PA (USA))

    1989-04-01T23:59:59.000Z

    The bcl-2 gene has been identified as a gene directly involved in the consistent chromosome translocation t(14;18), which is found in {approx} 90% of human follicular lymphoma cases, and is a prime candidate for the oncogene playing a crucial role in follicular lymphomagenesis. In this paper, the authors describe a case of chronic lymphocytic leukemia showing the juxtaposition of the bcl-2 gene on chromosome 18 to immunoglobulin {lambda} light chain (Ig{lambda}) gene on chromosome 22 in a head-to-head configuration. Sequencing analysis of the joining site of the bcl-2 gene and Ig{lambda} gene has shown that the breakpoint is within the 5{prime} flanking region of the bcl-2 gene and about 2.2 kilobases 5{prime} to the joining segment of Ig{lambda} locus in a germ-line configuration. The extranucleotide, commonly appearing at the joining site of the t(14;18) translocation involving the IgH locus, is absent from the joining site of bcl-2 and Ig{lambda}. The lack of extranucleotide suggests that the juxtaposition of the bcl-2 and Ig{lambda} genes occurred during physiological rearrangement of the Ig{lambda} gene since it has been shown that the rearrangement of the Ig{lambda} locus is not accompanied by extranucleotides.

  12. Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph

    SciTech Connect (OSTI)

    Daniel J Arp

    2005-06-15T23:59:59.000Z

    Nitrosomonas europaea is an aerobic lithoautotrophic bacterium that uses ammonia (NH3) as its energy source. As a nitrifier, it is an important participant in the nitrogen cycle, which can also influence the carbon cycle. The focus of this work was to explore the genetic structure and mechanisms underlying the lithoautotrophic growth style of N. europaea. Whole genome gene expression. The gene expression profile of cells in exponential growth and during starvation was analyzed using microarrays. During growth, 98% of the genes increased in expression at least two fold compared to starvation conditions. In growing cells, approximately 30% of the genes were expressed eight fold higher, Approximately 10% were expressed more than 15 fold higher. Approximately 3% (91 genes) were expressed to more than 20 fold of their levels in starved cells. Carbon fixation gene expression. N. europaea fixes carbon via the Calvin-Benson-Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). This study showed that transcription of cbb genes was up-regulated when the carbon source was limited, while amo, hao and other energy harvesting related genes were down-regulated. Iron related gene expression. Because N. europaea has a relatively high content of hemes, sufficient Fe must be available in the medium for it to grow. The genome revealed that approximately 5% of the coding genes in N. europaea are dedicated to Fe transport and assimilation. Nonetheless, with the exception of citrate biosynthesis genes, N. europaea lacks genes for siderophore production. The Fe requirements for growth and the expression of the putative membrane siderophore receptors were determined. The N. europaea genome has over 100 putative genes ({approx}5% of the coding genes) related to Fe uptake and its siderophore receptors could be grouped phylogenetically in four clusters. Fe related genes, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and enterobactin, and diffusion protein OmpC were expressed to higher levels under Fe limitation. N. europaea has a high Fe requirement and under Fe limiting conditions (0.2 ?M), is capable to assimilate up to 70% of the available Fe without the ability to produce siderophores.

  13. Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph

    SciTech Connect (OSTI)

    Daniel J. Arp

    2005-05-25T23:59:59.000Z

    Nitrosomonas europaea is an aerobic lithoautotrophic bacterium that uses ammonia (NH3) as its energy source. As a nitrifier, it is an important participant in the nitrogen cycle, which can also influence the carbon cycle. The focus of this work was to explore the genetic structure and mechanisms underlying the lithoautotrophic growth style of N. europaea. Whole genome gene expression: The gene expression profile of cells in exponential growth and during starvation was analyzed using microarrays. During growth, 98% of the genes increased in expression at least two fold compared to starvation conditions. In growing cells, approximately 30% of the genes were expressed eight fold higher, Approximately 10% were expressed more than 15 fold higher. Approximately 3% (91 genes) were expressed to more than 20 fold of their levels in starved cells. Carbon fixation gene expression: N. europaea fixes carbon via the Calvin-Benson-Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). This study showed that transcription of cbb genes was up-regulated when the carbon source was limited, while amo, hao and other energy harvesting related genes were down-regulated. Iron related gene expression: Because N. europaea has a relatively high content of hemes, sufficient Fe must be available in the medium for it to grow. The genome revealed that approximately 5% of the coding genes in N. europaea are dedicated to Fe transport and assimilation. Nonetheless, with the exception of citrate biosynthesis genes, N. europaea lacks genes for siderophore production. The Fe requirements for growth and the expression of the putative membrane siderophore receptors were determined. The N. europaea genome has over 100 putative genes ({approx}5% of the coding genes) related to Fe uptake and its siderophore receptors could be grouped phylogenetically in four clusters. Fe related genes, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and enterobactin, and diffusion protein OmpC were expressed to higher levels under Fe limitation. N. europaea has a high Fe requirement and under Fe limiting conditions (0.2 {micro}M), is capable to assimilate up to 70% of the available Fe without the ability to produce siderophores.

  14. Interferon-Stimulated Genes in the Pregnant Mouse Uterus

    E-Print Network [OSTI]

    Tilford, Sarah

    2008-08-24T23:59:59.000Z

    INTERFERON-STIMULATED GENES IN THE PREGNANT MOUSE UTERUS A Senior Honors Thesis by SARAH TILFORD Submitted to the Office of Honors Programs Texas A&M University In partial... fulfillment of the requirements of the UNIVERSITY UNDERGRADUATE RESEARCH FELLOWS May 2008 Major: Biomedical Science and Chemistry ii ABSTRACT Interferon-Stimulated Genes in the Pregnant Mouse Uterus (May 2008) Sarah Tilford Department...

  15. Kinetics of gene derepression by ERK signaling , Nria Samperb

    E-Print Network [OSTI]

    Shvartsman, Stanislav "Stas"

    Kinetics of gene derepression by ERK signaling Bomyi Lima , Núria Samperb , Hang Luc , Christine February 25, 2013) ERK controls gene expression in development, but mechanisms that link ERK activation to study transcriptional interpretation of ERK signaling during Dro- sophila embryogenesis, at a stage when

  16. Uncorrected Proof Copy Finding Genes by Using Computational Tools 85

    E-Print Network [OSTI]

    Uncorrected Proof Copy Finding Genes by Using Computational Tools 85 Job: Plant Functional Genomics/Rev.02.03 Uncorrected Proof Copy #12;Uncorrected Proof Copy Finding Genes by Using Computational Tools 87 Computational Tools 89 Job: Plant Functional Genomics--Grotewold Compositor: Nettype Chapter: Chapter 6 Date: 3

  17. NEWS AND VIEWS Modeling gene expression control using Omes Law

    E-Print Network [OSTI]

    Nguyen, Dat H.

    NEWS AND VIEWS Modeling gene expression control using Omes Law Harmen J Bussemaker Department class of methods that fit simple mathematical models of transcription regulation to DNA microarray data factors (TFs) to specific sites in the genome is a crucial step in the molecular process controlling gene

  18. RESEARCH Open Access Transient receptor potential genes, smoking,

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    RESEARCH Open Access Transient receptor potential genes, smoking, occupational exposures and cough chemicals and may play an important role in the pathogenesis of cough. The aim was to study the influence of single nucleotide polymorphisms (SNPs) in TRP genes and irritant exposures on cough. Methods: Nocturnal

  19. Visualization of Gene Combinations Christian Tominski & Heidrun Schumann

    E-Print Network [OSTI]

    Tominski, Christian

    expression or gene regulation) in different experi- ments or at different time steps. A variety of approaches- ing combinations for further investigation. Our approach manifests in an analysis pipeline, we describe the follow- ing concepts in more detail: · a pipeline for the visual analysis of gene

  20. INTRODUCTION Cascades of gene interactions are critical for the establishment

    E-Print Network [OSTI]

    Quake, Stephen R.

    along the anterior- posterior axis, predominantly where cuticle defects are seen in embryos that lack homeotic proteins control animal development. In particular, the basis for differential regulation of target genes must be learned. Target genes can be activated by some homeotic proteins and repressed

  1. Identification of Human Gene Core Promoters Michael Q. Zhang1

    E-Print Network [OSTI]

    Identification of Human Gene Core Promoters in Silico Michael Q. Zhang1 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 USA Identification of the 5 -end of human genes requires--CorePromoter. Our experiments indicate that when given a 1- to 2-kb extended promoter, CorePromoter will correctly

  2. GenePRIMP: A software quality control tool

    SciTech Connect (OSTI)

    Amrita Pati

    2010-05-05T23:59:59.000Z

    Amrita Pati of the DOE Joint Genome Institute's Genome Biology group describes the software tool GenePRIMP and how it fits into the quality control pipeline for microbial genomics. Further details regarding GenePRIMP appear in a paper published online May 2, 2010 in Nature Methods.

  3. Hotspots of Biased Nucleotide Substitutions in Human Genes

    E-Print Network [OSTI]

    Sorenson, Michael

    Hotspots of Biased Nucleotide Substitutions in Human Genes Jonas Berglund1 , Katherine S. Pollard2) Hotspots of biased nucleotide substitutions in human genes. PLoS Biol 7(1): e1000026. doi:10.1371/journal selection in the human lineage. However, HARs tend to have biased patterns of nucleotide substitution

  4. GenePRIMP: A software quality control tool

    ScienceCinema (OSTI)

    Amrita Pati

    2010-09-01T23:59:59.000Z

    Amrita Pati of the DOE Joint Genome Institute's Genome Biology group describes the software tool GenePRIMP and how it fits into the quality control pipeline for microbial genomics. Further details regarding GenePRIMP appear in a paper published online May 2, 2010 in Nature Methods.

  5. Photoacoustic microscopy of tyrosinase reporter gene in vivo

    E-Print Network [OSTI]

    Wang, Lihong

    Photoacoustic microscopy of tyrosinase reporter gene in vivo Arie Krumholz Sarah J. Van microscopy of tyrosinase reporter gene in vivo Arie Krumholz,a Sarah J. VanVickle-Chavez,b Junjie Yao for tyrosinase, the primary enzyme responsible for expression of melanin in melanogenic cells. Optical res

  6. Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions

    E-Print Network [OSTI]

    Ames, Ryan M.; Money, Daniel; Lovell, Simon C.

    2014-06-12T23:59:59.000Z

    new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We...

  7. HumanMouse Gene Identification by Comparative Evidence Integration and

    E-Print Network [OSTI]

    Pavlovic, Vladimir

    The identification of genes in the human genome remains a challenge, as the actual predictions appear to disagree of genes in the human genome by using a reference, such as mouse genome. However, this comparative genome. In particular, it is not clear whether the mouse is at the correct evolutionary distance from

  8. Lung Disease in Pediatrics: is it all in the Genes?

    E-Print Network [OSTI]

    Lung Disease in Pediatrics: is it all in the Genes? Jay K. Kolls, M.D.Jay K. Kolls, M.D. Chair with CF do worse than other? #12;· Outcomes are better at CF centers · There is huge variation in lung with the same mutation do worse than others? · Modifier genes ­ lung disease ­ Tgfb1 ­ Irfd1 ­ neutrophil

  9. Diversity of gene expression in adenocarcinoma of the lung

    E-Print Network [OSTI]

    Botstein, David

    Diversity of gene expression in adenocarcinoma of the lung Mitchell E. Garber*, Olga G. Troyanskaya Contributed by David Botstein, September 21, 2001 The global gene expression profiles for 67 human lung tumors pathologic analysis. Four main histologic subtypes of lung cancer are regularly distinguished by tumor

  10. Mutational analysis of the lambda S gene

    E-Print Network [OSTI]

    Neal, Gregory Scott

    1984-01-01T23:59:59.000Z

    , the early stages of gene expression 1n the lytic cycle are not germane to this d1scussion. Late protein synthes1s is programmed from transcr1pts initiated at a single promoter, Pr'. This promoter is controlled by termination at the term1nator trz, and 1t... p JG13 pJH2 pZ150 pZ152 pGN200 pGN201 CSH57B met+ lacIQI lacZ+ ~tr + su- CQ21 F'~ro lacIQI lacZ Tn5 (PI) F'tra036, proAB+, lacZm15, lacI/ a~lac ro, thi, strtr, endA, ~scB15, , ~su E AmpR TetR lacPO (in pBR322) AmpR lacPO Sam7 R+Rz+ (in p...

  11. Prediction of epigenetically regulated genes in breast cancer cell lines

    SciTech Connect (OSTI)

    Loss, Leandro A; Sadanandam, Anguraj; Durinck, Steffen; Nautiyal, Shivani; Flaucher, Diane; Carlton, Victoria EH; Moorhead, Martin; Lu, Yontao; Gray, Joe W; Faham, Malek; Spellman, Paul; Parvin, Bahram

    2010-05-04T23:59:59.000Z

    Methylation of CpG islands within the DNA promoter regions is one mechanism that leads to aberrant gene expression in cancer. In particular, the abnormal methylation of CpG islands may silence associated genes. Therefore, using high-throughput microarrays to measure CpG island methylation will lead to better understanding of tumor pathobiology and progression, while revealing potentially new biomarkers. We have examined a recently developed high-throughput technology for measuring genome-wide methylation patterns called mTACL. Here, we propose a computational pipeline for integrating gene expression and CpG island methylation profles to identify epigenetically regulated genes for a panel of 45 breast cancer cell lines, which is widely used in the Integrative Cancer Biology Program (ICBP). The pipeline (i) reduces the dimensionality of the methylation data, (ii) associates the reduced methylation data with gene expression data, and (iii) ranks methylation-expression associations according to their epigenetic regulation. Dimensionality reduction is performed in two steps: (i) methylation sites are grouped across the genome to identify regions of interest, and (ii) methylation profles are clustered within each region. Associations between the clustered methylation and the gene expression data sets generate candidate matches within a fxed neighborhood around each gene. Finally, the methylation-expression associations are ranked through a logistic regression, and their significance is quantified through permutation analysis. Our two-step dimensionality reduction compressed 90% of the original data, reducing 137,688 methylation sites to 14,505 clusters. Methylation-expression associations produced 18,312 correspondences, which were used to further analyze epigenetic regulation. Logistic regression was used to identify 58 genes from these correspondences that showed a statistically signifcant negative correlation between methylation profles and gene expression in the panel of breast cancer cell lines. Subnetwork enrichment of these genes has identifed 35 common regulators with 6 or more predicted markers. In addition to identifying epigenetically regulated genes, we show evidence of differentially expressed methylation patterns between the basal and luminal subtypes. Our results indicate that the proposed computational protocol is a viable platform for identifying epigenetically regulated genes. Our protocol has generated a list of predictors including COL1A2, TOP2A, TFF1, and VAV3, genes whose key roles in epigenetic regulation is documented in the literature. Subnetwork enrichment of these predicted markers further suggests that epigenetic regulation of individual genes occurs in a coordinated fashion and through common regulators.

  12. Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae

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

    Hunsperger, Heather M.; Randhawa, Tejinder; Cattolico, Rose Ann

    2015-01-01T23:59:59.000Z

    Two non-homologous, isofunctional enzymes catalyze the penultimate step of chlorophyll a synthesis in oxygenic photosynthetic organisms such as cyanobacteria, eukaryotic algae and land plants: the light independent (LIPOR) and light-dependent (POR) protochlorophyllide oxidoreductases. Whereas the distribution of these enzymes in cyanobacteria and land plants is well understood, the presence, loss, duplication, and replacement of these genes have not been surveyed in the polyphyletic and remarkably diverse eukaryotic algal lineages.

  13. Genomic Analyses of Bacterial Porin-Cytochrome Gene Clusters

    SciTech Connect (OSTI)

    Shi, Liang; Fredrickson, Jim K.; Zachara, John M.

    2014-11-26T23:59:59.000Z

    The porin-cytochrome (Pcc) protein complex is responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III) by the dissimilatory metal-reducing bacterium Geobacter sulfurreducens PCA. The identified and characterized Pcc complex of G. sulfurreducens PCA consists of a porin-like outer-membrane protein, a periplasmic 8-heme c type cytochrome (c-Cyt) and an outer-membrane 12-heme c-Cyt, and the genes encoding the Pcc proteins are clustered in the same regions of genome (i.e., the pcc gene clusters) of G. sulfurreducens PCA. A survey of additionally microbial genomes has identified the pcc gene clusters in all sequenced Geobacter spp. and other bacteria from six different phyla, including Anaeromyxobacter dehalogenans 2CP-1, A. dehalogenans 2CP-C, Anaeromyxobacter sp. K, Candidatus Kuenenia stuttgartiensis, Denitrovibrio acetiphilus DSM 12809, Desulfurispirillum indicum S5, Desulfurivibrio alkaliphilus AHT2, Desulfurobacterium thermolithotrophum DSM 11699, Desulfuromonas acetoxidans DSM 684, Ignavibacterium album JCM 16511, and Thermovibrio ammonificans HB-1. The numbers of genes in the pcc gene clusters vary, ranging from two to nine. Similar to the metal-reducing (Mtr) gene clusters of other Fe(III)-reducing bacteria, such as Shewanella spp., additional genes that encode putative c-Cyts with predicted cellular localizations at the cytoplasmic membrane, periplasm and outer membrane often associate with the pcc gene clusters. This suggests that the Pcc-associated c-Cyts may be part of the pathways for extracellular electron transfer reactions. The presence of pcc gene clusters in the microorganisms that do not reduce solid-phase Fe(III) and Mn(IV) oxides, such as D. alkaliphilus AHT2 and I. album JCM 16511, also suggests that some of the pcc gene clusters may be involved in extracellular electron transfer reactions with the substrates other than Fe(III) and Mn(IV) oxides.

  14. Edinburgh Research Explorer High-resolution gene expression profiling for simultaneous

    E-Print Network [OSTI]

    Millar, Andrew J.

    Edinburgh Research Explorer High-resolution gene expression profiling for simultaneous kinetic, UH 2008, 'High-resolution gene expression profiling for simultaneous kinetic parameter analysis date: 16. Jun. 2014 #12;METHOD High-resolution gene expression profiling for simultaneous kinetic

  15. Functional replacement of a primary metabolic pathway via multiple independent eukaryote-to-eukaryote gene transfers

    E-Print Network [OSTI]

    Nedelcu, Aurora M.

    Functional replacement of a primary metabolic pathway via multiple independent eukaryote can be added to the recipient's gene complement (gene additions) or simply replace existing endogenous counterparts (functional replacements). The recruitment of novel genes is thought to allow the recipient

  16. Multiple gene genealogies and microsatellite markers reflect relationships between morphotypes of Sphaeropsis sapinea

    E-Print Network [OSTI]

    Multiple gene genealogies and microsatellite markers reflect relationships between morphotypes between isolates representing different S. sapinea morphotypes, using multiple gene genealogies inferred from partial sequences of six protein-coding genes and six microsatellite loci. Genealogies generated

  17. Modulation of Gene Expression by Polymer Nanocapsule Delivery of DNA Cassettes Encoding Small RNAs.

    E-Print Network [OSTI]

    Yan, M; Wen, J; Liang, M; Lu, Y; Kamata, M; Chen, IS

    2015-01-01T23:59:59.000Z

    of Gene Expression by Polymer Nanocapsule S5 Fig. Stabilityof Gene Expression by Polymer Nanocapsule Rao D, Vorhies J,of Gene Expression by Polymer Nanocapsule Delivery of DNA

  18. Toward epigenetic and gene regulation models of specific language impairment: looking for links among growth, genes, and impairments

    E-Print Network [OSTI]

    Rice, Mabel L.

    2012-11-24T23:59:59.000Z

    for candidate genes. Regulatory regions of the genes may be involved. Behavioral growth models of language development of children with SLI reveal that the onset of language is delayed, and the growth trajectories of children with SLI parallel those of younger...

  19. An adaptive radiation model for the origin of new gene functions

    E-Print Network [OSTI]

    Francino, M. Pilar

    2005-01-01T23:59:59.000Z

    An adaptive radiation model for the origin of new genePreadaptation Adaptive radiation Competition among closefor a specific niche Adaptive radiation model Adaptive gene

  20. Low-Oxygen Induction of Normally Cryptic psbA Genes in Cyanobacteria...

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

    Oxygen Induction of Normally Cryptic psbA Genes in Cyanobacteria. Low-Oxygen Induction of Normally Cryptic psbA Genes in Cyanobacteria. Abstract: Microarray analysis indicated...

  1. Targeting gene expression to tumor cells with loss of wild-type p53 function

    E-Print Network [OSTI]

    Tian, Weidong

    of the carcinoembryonic antigen and -fetoprotein genes for hepatocarcinoma4,5 and of the tyrosinase gene for mel- anoma,6

  2. Mutational analysis of the [phi] X174 E Gene

    E-Print Network [OSTI]

    Morham, Scott Garton

    1985-01-01T23:59:59.000Z

    for the rapid isolation and sequencing of E gene mutants from the screening vector pSM120 has been developed. Two nonsense mutations have been isolated which totally inactivate the E gene product. A variety of amino acids have been inserted at these non... Hydroxylami ne mutagenesis Transformation 13 16 18 19 29 29 30 30 32 33 33 36 38 38 TABLE OF CONTENTS (continued) Selection of gene E mutations in pSM120 M13 cloning and dideoxy sequencing 3. RESULTS Characterization of deletion clones...

  3. Sorghum Ma5 and Ma6 maturity genes

    E-Print Network [OSTI]

    Brady, Jeffrey Alan

    2009-05-15T23:59:59.000Z

    the precise mechanism of function for the A. thaliana circadian clock is not fully established, at least three genes appear to be involved in the central circadian oscillator mechanism. These genes are TIMING OF CHLOROPHYLL A/B BINDING PROTEIN 1 (TOC1... the expression of CCA1 and LHY, and the gene encoding it is a target for repression by CCA1 and LHY proteins. The protein is an A. thaliana pseudo response regulator (APRR) called TIMING OF CHLOROPHYLL A/B BINDING PROTEIN 1 (TOC1), and its transcript levels...

  4. LATERAL GENE TRANSFER AND THE HISTORY OF BACTERIAL GENOMES

    SciTech Connect (OSTI)

    Howard Ochman

    2006-02-22T23:59:59.000Z

    The aims of this research were to elucidate the role and extent of lateral transfer in the differentiation of bacterial strains and species, and to assess the impact of gene transfer on the evolution of bacterial genomes. The ultimate goal of the project is to examine the dynamics of a core set of protein-coding genes (i.e., those that are distributed universally among Bacteria) by developing conserved primers that would allow their amplification and sequencing in any bacterial taxa. In addition, we adopted a bioinformatic approach to elucidate the extent of lateral gene transfer in sequenced genome.

  5. Hot prospect for new gene amplifier

    SciTech Connect (OSTI)

    Not Available

    1991-11-29T23:59:59.000Z

    Molecular biologist Francis Barany is investigating one of the hottest areas in biotechnology: a gene-amplification technique called ligase chain reaction, or LCR. Already scientists have used LCR to detect the tiny mutation that causes sickle cell anemia and have adapted it to screen for a handful of other genetic diseases simultaneously - in a single test-tube. Some experts, in fact, are predicting that LCR will supplement the polymerase chain reaction (PCR), and in some cases even supplant it. LCR could revolutionize DNA diagnostics just as PCR transformed basic molecular biology following its introduction 6 years ago. With its ease of automation and ability to produce useful quantitative results, LCR could become a major player in the rapidly growing market for DNA diagnostics. LCR, like PCR, uses snippets of nucleic acid, or oligonucleotides, that anneal to a specific, complementary sequence on the target DNA to be amplified. But where PCR uses oligos that bracket the stretch to be amplified, LCR uses pairs of oligos that completely cover the target sequence.

  6. Determination of the linkage relationships and the gene-centromere genetic distances for endopeptidase structural genes in hexaploid wheat

    E-Print Network [OSTI]

    McMillin, David Edwin

    1977-01-01T23:59:59.000Z

    . The linkage relationships for the (EP) structural gene are shown below. centromere 42. 17 ~E -Blv 13. 04 7AL ~E-Ale 6. 67 ~E-Al 3. 90 10. 67 ACKNOMLF. DGT'KNT S Sincere gratitude is extended to all members of my graduate committee for. their guidance..., or KP-BlZ and their chromosome constitut on Linkage relationships for three (EP) structural genes on 7AL Chi square test for independence of EP-Aj. y and ~E-Alx Chi square testing the hypothesis that two independently segregating genes in FI...

  7. High-throughput comparison of gene fitness among related bacteria

    E-Print Network [OSTI]

    2012-01-01T23:59:59.000Z

    licenses/by/2.0), which permits unrestricted use,Mutations in this gene permit second site mutations in hnsIt is known that rpoS mutants permit mutations in hns in

  8. antagonist gene polymorphism: Topics by E-print Network

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

    processing, short-term memory 57 Association of Common Polymorphisms in GLUT9 Gene with Gout but Not with Coronary Artery Disease in a Large Case-Control Study CiteSeer Summary:...

  9. antigen-4 gene polymorphisms: Topics by E-print Network

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

    processing, short-term memory 55 Association of Common Polymorphisms in GLUT9 Gene with Gout but Not with Coronary Artery Disease in a Large Case-Control Study CiteSeer Summary:...

  10. antagonist gene polymorphisms: Topics by E-print Network

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

    processing, short-term memory 57 Association of Common Polymorphisms in GLUT9 Gene with Gout but Not with Coronary Artery Disease in a Large Case-Control Study CiteSeer Summary:...

  11. alpha gene polymorphisms: Topics by E-print Network

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

    processing, short-term memory 60 Association of Common Polymorphisms in GLUT9 Gene with Gout but Not with Coronary Artery Disease in a Large Case-Control Study CiteSeer Summary:...

  12. ORIGINAL PAPER Identifying differentially expressed genes in human acute leukemia

    E-Print Network [OSTI]

    Gu, Xun

    ORIGINAL PAPER Identifying differentially expressed genes in human acute leukemia and mouse brain the experimental-wise false discovery rate. A human acute leukemia dataset corrected from 38 leukemia patients

  13. adipose tissue gene: Topics by E-print Network

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

    the expression of the UCP1 gene 293 D. Norepinephrine is an apoptosis inhibitor in brown adipocytes 294 IV. How Significant Is Brown Adipose Tissue? 295 A. Parameters of...

  14. RESEARCH Open Access Gene expression and fractionation resistance

    E-Print Network [OSTI]

    Sankoff, David

    in Paramecium, Gout et al. [10] identify a clear relationship between high WGD duplicate gene retention rates for explaining variable resistance to fractionation. The Gout et al. paper [10] is the primary inspiration

  15. PI Control of Gene Expression in Tumorous Cell Lines

    E-Print Network [OSTI]

    Mendonca, Rouella J.

    2010-01-16T23:59:59.000Z

    cancer cell line genes behave more like their Human Embryonic Kidney cell line counterparts. Two methods of intervention were introduced. The first method was the simpler on-off control intervention while the second method used a more advanced...

  16. aldosterone synthase gene: Topics by E-print Network

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

    these genes in the CNS of male Wistar Kyoto (WKY) rats in response to systemic ACTH infusion, dexamethasone infusion, and to adrenalectomy. CYP11B1 and CYP11B2 mRNA levels were...

  17. RESEARCH Open Access In vivo gene transfer targeting in pancreatic

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    transfer of a bicistronic transgene bearing a luciferase gene and the herpes simplex virus thymidine kinase of the article © 2012 Lafitte et al.; licensee BioMed Central Ltd. This is an Open Access article distributed

  18. Hormonal interactions in progesterone regulation of gonadotropin gene expression

    E-Print Network [OSTI]

    Ghochani, Yasmin

    2009-01-01T23:59:59.000Z

    receptor (PR): PRA and PRB, both encoded by the same gene,thought to be involved in transactivational function in PRB,making PRB a specific transcriptional regulator of target

  19. Computational discovery of gene modules, regulatory networks and expression programs

    E-Print Network [OSTI]

    Gerber, Georg Kurt, 1970-

    2007-01-01T23:59:59.000Z

    High-throughput molecular data are revolutionizing biology by providing massive amounts of information about gene expression and regulation. Such information is applicable both to furthering our understanding of fundamental ...

  20. Gene Function Prediction Based on Sequence or Expression Data

    E-Print Network [OSTI]

    Horan, Kevin

    2011-01-01T23:59:59.000Z

    highly enriched in heat stress-related genes (GO:0009408, p-respond specifically to heat stress and to a much lessergene functions involved in heat stress response pathways.

  1. Intrinsic limits to gene regulation by global crosstalk

    E-Print Network [OSTI]

    Friedlander, Tamar; Guet, C?lin C; Barton, Nicholas H; Tka?ik, Gašper

    2015-01-01T23:59:59.000Z

    Gene regulation relies on the specificity of transcription factor (TF) - DNA interactions. In equilibrium, limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF-DNA interactions or remains erroneously inactive. We present a tractable biophysical model of global crosstalk, where many genes are simultaneously regulated by many TFs. We show that in the simplest regulatory scenario, a lower bound on crosstalk severity can be analytically derived solely from the number of (co)regulated genes and a suitable parameter that describes binding site similarity. Estimates show that crosstalk could present a significant challenge for organisms with low-specificity TFs, such as metazoans, unless they use appropriate regulation schemes. Strong cooperativity substantially decreases crosstalk, while joint regulation by activators and repressors, surprisingly, does not; moreover, certain microscopic details about promoter architecture emerge as global...

  2. adenosine receptor gene: Topics by E-print Network

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

    James A Zwiebel; Eli Gilboa; R Michael Blaese; Arthur Nienhuis; Richard J O& apos; reilly; W. French Anderson 1987-01-01 13 Recombinant AAV-Mediated Gene Transfer for the...

  3. adenosine deaminase gene: Topics by E-print Network

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

    James A Zwiebel; Eli Gilboa; R Michael Blaese; Arthur Nienhuis; Richard J O& apos; reilly; W. French Anderson 1987-01-01 4 High-Efficiency Gene Transfer into Normal and...

  4. Auxiliary metabolic genes in viruses infecting marine cyanobacteria

    E-Print Network [OSTI]

    Thompson, Luke Richard

    2010-01-01T23:59:59.000Z

    Marine viruses shape the diversity and biogeochemical role of their microbial hosts. Cyanophages that infect the cyanobacteria Prochlorococcus and Synechococcus often carry metabolic genes not found in other bacteriophages. ...

  5. MicroRNAs can generate thresholds in target gene expression

    E-Print Network [OSTI]

    Mukherji, Shankar

    MicroRNAs (miRNAs) are short, highly conserved noncoding RNA molecules that repress gene expression in a sequence-dependent manner. We performed single-cell measurements using quantitative fluorescence microscopy and flow ...

  6. Biological Cluster Validity Indices Based on the Gene Ontology

    E-Print Network [OSTI]

    Zell, Andreas

    Biological Cluster Validity Indices Based on the Gene Ontology Nora Speer, Christian Spieth 3646, pp. 429­439, 2005. c Springer-Verlag Berlin Heidelberg 2005 #12;430 N. Speer, C. Spieth, and A

  7. aneurysm susceptibility genes: Topics by E-print Network

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

    10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 The Dyslexia Susceptibility Genes and Neurodevelopment. Open Access Theses and Dissertations...

  8. atrophy susceptibility gene: Topics by E-print Network

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

    10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 The Dyslexia Susceptibility Genes and Neurodevelopment. Open Access Theses and Dissertations...

  9. Dynamics of gene expression and signal transduction in single cells

    E-Print Network [OSTI]

    Yang, Qiong, Ph. D. Massachusetts Institute of Technology

    2009-01-01T23:59:59.000Z

    Each individual cell is a highly dynamic and complex system. Characterizing dynamics of gene expression and signal transduction is essential to understand what underlie the behavior of the cell and has stimulated much ...

  10. astrocyte elevated gene-1: Topics by E-print Network

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

    Cardiomyopathy; Oliver Koeth; Uwe Zeymer; Rudolf Schiele; Ralf Zahn 2010-01-01 162 Graeber et al. 2013 -Roles of Lepidium Seed Dormancy Genes 1 Spatio-temporal Seed Development...

  11. antigen gene-1 induce: Topics by E-print Network

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

    of the immune system to attack foreign antigens, parasites Nowak, Martin A. 105 Graeber et al. 2013 -Roles of Lepidium Seed Dormancy Genes 1 Spatio-temporal Seed Development...

  12. abca3 gene leads: Topics by E-print Network

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

    (more) Schicker, Maresa 2014-01-01 2 A Practical Failure Prediction with Location and Lead Time for Blue GeneP Ziming Zheng Computer Technologies and Information Sciences...

  13. Effect of Nanoparticle Conjugation on Gene Silencing by RNA Interference

    E-Print Network [OSTI]

    Singh, Neetu

    RNA interference (RNAi) is a cellular process whereby the silencing of a particular gene is mediated by short RNAs (siRNAs). Although siRNAs have great therapeutic potential, cellular delivery has been a challenge. ...

  14. Contribution of gene duplications to the evolution of genetic networks

    E-Print Network [OSTI]

    Pando, Bernardo Fabián

    2010-01-01T23:59:59.000Z

    Exploring the forces that drive evolution at the gene network level and investigating underlying principles behind this process are fundamental questions in the context of understanding how evolution shapes transcriptional ...

  15. ; Evolution of genes and genomes on the Drosophila phylogeny

    E-Print Network [OSTI]

    Kellis, Manolis

    ARTICLES ; Evolution of genes and genomes on the Drosophila phylogeny Drosophila 12 Genomes Consortium* Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome

  16. Unique ER Cistromes Control Cell Type-Specific Gene Regulation

    E-Print Network [OSTI]

    Brown, Myles

    -specific E2 regulation of gene expression in MCF7 and U2OS- ER cells, we compared the ER binding sites on DNA a critical role in defining the ER cistrome in MCF7 cells, it is not expressed in U2OS-ER cells, and forkhead-specific effects, however, remains to be explained. We have compared the gene expres- sion profile of the MCF7

  17. Localization and cloning of the gene(s) of bacteriophage PM2 responsible for membrane morphogenesis

    SciTech Connect (OSTI)

    Armour, G.A.

    1988-01-01T23:59:59.000Z

    Proteins implicated in membrane morphogenesis (sp6.6 and sp13) have been previously identified by analysis of membrane proteins in the membrane of the purified phage. Analysis of a ts viral mutant that produces empty membrane vesicles also indicated the unique presence of viral structural protein sp6.6. In this work the gene for sp6.6 was localized on the PM2 genome by in vitro coupled transcription-translation directed by restriction endonuclease fragments of PM2 DNA. A Hind III fragment containing the sp6.6 gene among others was cloned into pBR322 in E. coli. Examination with the electron microscope revealed the production of new membrane vesicles whose size were similar to that of the natural membrane of PM2. Clones were then constructed in the pUC family of plasmids which uses the Lac promoter and pPL-lambda which uses the promoter left of lambda. pUC clones were unable to produce vesicles or detectable sp6.6. A pPL-lambda clone was produced 3.5 Kbp in size, that produced p6.6 as detected by SDS-PAGE of radiolabeled protein and immunoblotting.

  18. New mathematical methods in human gene mapping

    SciTech Connect (OSTI)

    Terwilliger, J.D.

    1993-01-01T23:59:59.000Z

    Three published papers are presented. The first paper consists of an analytical investigation of the effects of marker heterozygosity and intermarker distance on a linkage analysis with a disease gene. The goal of this paper was to determine optimal properties for a putative genome-spanning map of markers. The results showed, as expected, that the power is highest when marker heterozygosity is highest, and/or intermarker distance is smallest. However, the authors found that the expected length of the one-lod-unit support interval was almost exclusively dependent on intermarker distance. The second paper deals with a repeated subsampling strategy I developed based on the multisample bootstrap of Efron (1982). This technique allows the user to perform a normally computationally intensive simulation study in a dramatically shorter time. In the example discussed in the paper, determining the p-value of a maximized-over-models maximum lod score, the computer time required for the study was reduced from several weeks to a few hours. This statistical method has subsequently been applied to other problems by Maclean et al. (1992), Leal et al. (1993), and Kong et al. (1992), for example. In the final paper, a novel variation of the haplotype relative risk (HRR) statistic of Rubinstein et al. (1981) is presented. This method, like the original HRR allows one to construct a well-matched control sample from the non-transmitted alleles of the parents of an affected child. In the statistic, the two alleles transmitted to the child constitute two observations in the [open quotes]case[close quotes] sample, and the two alleles the parents did not transmit from the [open quotes]control[close quotes] sample. The relationship between the projects is outlined in the introduction to this thesis, as is the general scientific background which led to the implementation and development of this research.

  19. A Performance Counter Based Workload Characterization on Blue Gene/P

    E-Print Network [OSTI]

    John, Lizy Kurian

    A Performance Counter Based Workload Characterization on Blue Gene/P Karthik Ganesan Lizy John V--IBM's Blue Gene/P, the second generation of the Blue Gene supercomputer is designed with a Universal Perfor instrument applications and get a profound insight into its execution on the Blue Gene/P system which could

  20. Computational analysis of microarray gene expression profiles: clustering, classification, and beyond

    E-Print Network [OSTI]

    Dai, Yang

    Computational analysis of microarray gene expression profiles: clustering, classification) the discovery of gene clusters, and (3) the classification of biological samples. In addition, we discuss how inch, and a library of thousands of genes is placed on a single chip. To probe the global gene

  1. A phylogenetic mixture model for gene family loss in parasitic bacteria

    E-Print Network [OSTI]

    A phylogenetic mixture model for gene family loss in parasitic bacteria Submitted as a research words: gene families, mixture model, parasites, maximum likelihood,phylogenetics Running head: gene family gain and loss 1 #12;Abstract Gene families are frequently gained and lost from prokaryotic genomes

  2. The ``Domino Theory'' of Gene Death: Gradual and Mass Gene Extinction Events in Three Lineages of Obligate Symbiotic Bacterial Pathogens

    E-Print Network [OSTI]

    Graur, Dan

    between S. flexneri and Escherichia coli genomes revealed that at least 254 genes have become genome evolution is a very rare phenomenon and so far was only documented in the oxyphototrophic marine

  3. Rearrangement of Variable Region T Cell Receptor y Genes in Acute Lymphoblastic Leukemia Vy Gene Usage Differs in Mature and Immature T Cells

    E-Print Network [OSTI]

    Hara, Junichi; Benedict, Stephen H.; Yumura, Keiko; Ha-Kawa, Kyungsae; Gelfand, Erwin W.

    1989-04-01T23:59:59.000Z

    Using probes recognizing variable regions (V gamma) and joining regions (J gamma) of the T cell receptor (TCR) gamma gene, we have analyzed the usage of V gamma genes in 24 patients with T cell acute lymphoblastic leukemia ...

  4. Title: Subspace Clustering of Microarray Data based on Domain Transformation Keywords: gene expression, subspace clustering, inverted index, gene-gene rela-

    E-Print Network [OSTI]

    McLeod, Dennis

    of Southern California, Los Angeles, USA #12;Subspace Clustering of Microarray Data based on DomainTitle: Subspace Clustering of Microarray Data based on Domain Transformation Keywords: gene framework that supports the identi- fication of useful knowledge based on data clustering. With the recent

  5. Promoter sequence of 3-phosphoglycerate kinase gene 2 of lactic acid-producing fungus rhizopus oryzae and a method of expressing a gene of interest in fungal species

    DOE Patents [OSTI]

    Gao, Johnway [Richland, WA; Skeen, Rodney S [Pendleton, OR

    2003-03-04T23:59:59.000Z

    The present invention provides the promoter clone discovery of phosphoglycerate kinase gene 2 of a lactic acid-producing filamentous fungal strain, Rhizopus oryzae. The isolated promoter can constitutively regulate gene expression under various carbohydrate conditions. In addition, the present invention also provides a design of an integration vector for the transformation of a foreign gene in Rhizopus oryzae.

  6. Promoter sequence of 3-phosphoglycerate kinase gene 1 of lactic acid-producing fungus rhizopus oryzae and a method of expressing a gene of interest in fungal species

    DOE Patents [OSTI]

    Gao, Johnway [Richland, WA; Skeen, Rodney S [Pendleton, OR

    2002-10-15T23:59:59.000Z

    The present invention provides the promoter clone discovery of phosphoglycerate kinase gene 1 of a lactic acid-producing filamentous fungal strain, Rhizopus oryzae. The isolated promoter can constitutively regulate gene expression under various carbohydrate conditions. In addition, the present invention also provides a design of an integration vector for the transformation of a foreign gene in Rhizopus oryzae.

  7. Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters

    SciTech Connect (OSTI)

    Santini, Simona; Boore, Jeffrey L.; Meyer, Axel

    2003-12-31T23:59:59.000Z

    Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involved in the regulation of Hox genes, while several others are new elements that might have regulatory functions. The majority of these newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac). The conserved intergenic regions located between the most rostrally expressed genes in the developing embryo are longer and better retained through evolution. We document that presumed regulatory sequences are retained differentially in either A or A clusters resulting from a genome duplication in the fish lineage. This observation supports both the hypothesis that the conserved elements are involved in gene regulation and the Duplication-Deletion-Complementation model.

  8. Bitumen fume-induced gene expression profile in rat lung

    SciTech Connect (OSTI)

    Gate, Laurent [Institut National de Recherche et Securite, Avenue de Bourgogne, BP 27, 54501 Vandoeuvre Cedex (France)]. E-mail: laurent.gate@inrs.fr; Langlais, Cristina [Institut National de Recherche et Securite, Avenue de Bourgogne, BP 27, 54501 Vandoeuvre Cedex (France); Micillino, Jean-Claude [Institut National de Recherche et Securite, Avenue de Bourgogne, BP 27, 54501 Vandoeuvre Cedex (France); Nunge, Herve [Institut National de Recherche et Securite, Avenue de Bourgogne, BP 27, 54501 Vandoeuvre Cedex (France); Bottin, Marie-Claire [Institut National de Recherche et Securite, Avenue de Bourgogne, BP 27, 54501 Vandoeuvre Cedex (France); Wrobel, Richard [Institut National de Recherche et Securite, Avenue de Bourgogne, BP 27, 54501 Vandoeuvre Cedex (France); Binet, Stephane [Institut National de Recherche et Securite, Avenue de Bourgogne, BP 27, 54501 Vandoeuvre Cedex (France)

    2006-08-15T23:59:59.000Z

    Exposure to bitumen fumes during paving and roofing activities may represent an occupational health risk. To date, most of the studies performed on the biological effect of asphalt fumes have been done with regard to their content in carcinogenic polycyclic aromatic hydrocarbons (PAH). In order to gain an additional insight into the mechanisms of action of bitumen fumes, we studied their pulmonary effects in rodents following inhalation using the microarray technology. Fisher 344 rats were exposed for 5 days, 6 h/day to bitumen fumes generated at road paving temperature (170 {sup o}C) using a nose-only exposition device. With the intention of studying the early transcriptional events induced by asphalt fumes, lung tissues were collected immediately following exposure and gene expression profiles in control and exposed rats were determined by using oligonucleotide microarrays. Data analysis revealed that genes involved in lung inflammatory response as well as genes associated with PAH metabolization and detoxification were highly expressed in bitumen-exposed animals. In addition, the expression of genes related to elastase activity and its inhibition which are associated with emphysema was also modulated. More interestingly genes coding for monoamine oxidases A and B involved in the metabolism of neurotransmitters and xenobiotics were downregulated in exposed rats. Altogether, these data give additional information concerning the bitumen fumes biological effects and would allow to better review the health effects of occupational asphalt fumes exposure.

  9. Reliability of frequency- and amplitude-decoding in gene regulation

    E-Print Network [OSTI]

    Filipe Tostevin; Wiet de Ronde; Pieter Rein ten Wolde

    2012-02-07T23:59:59.000Z

    In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple model gene promoter in response to oscillating and constant transcription factor signals. We find that in biologically-relevant parameter regimes an oscillating input can produce a more constant protein level than a constant input. Our results suggest that oscillating signals may be used to minimize noise in gene regulation.

  10. Oscillations in probability distributions for stochastic gene expression

    SciTech Connect (OSTI)

    Petrosyan, K. G., E-mail: pkaren@phys.sinica.edu.tw; Hu, Chin-Kun, E-mail: huck@phys.sinica.edu.tw [Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan (China)

    2014-05-28T23:59:59.000Z

    The phenomenon of oscillations in probability distribution functions of number of components is found for a model of stochastic gene expression. It takes place in cases of low levels of molecules or strong intracellular noise. The oscillations distinguish between more probable even and less probable odd number of particles. The even-odd symmetry restores as the number of molecules increases with the probability distribution function tending to Poisson distribution. We discuss the possibility of observation of the phenomenon in gene, protein, and mRNA expression experiments.

  11. Divinyl ether synthase gene, and protein and uses thereof

    DOE Patents [OSTI]

    Howe, Gregg A.; Itoh, Aya

    2006-12-26T23:59:59.000Z

    The present invention relates to divinyl ether synthase genes, proteins, and methods of their use. The present invention encompasses both native and recombinant wild-type forms of the synthase, as well as mutants and variant forms, some of which possess altered characteristics relative to the wild-type synthase. The present invention also relates to methods of using divinyl ether synthase genes and proteins, including in their expression in transgenic organisms and in the production of divinyl ether fatty acids, and to methods of suing divinyl ether fatty acids, including in the protection of plants from pathogens.

  12. Divinyl ether synthase gene and protein, and uses thereof

    DOE Patents [OSTI]

    Howe, Gregg A. (East Lansing, MI); Itoh, Aya (Tsuruoka, JP)

    2011-09-13T23:59:59.000Z

    The present invention relates to divinyl ether synthase genes, proteins, and methods of their use. The present invention encompasses both native and recombinant wild-type forms of the synthase, as well as mutants and variant forms, some of which possess altered characteristics relative to the wild-type synthase. The present invention also relates to methods of using divinyl ether synthase genes and proteins, including in their expression in transgenic organisms and in the production of divinyl ether fatty acids, and to methods of suing divinyl ether fatty acids, including in the protection of plants from pathogens.

  13. LINGUISTIC ANALYSIS OF THE NUCLEOPROTEIN GENE OF INFLUENZA A VIRUS

    SciTech Connect (OSTI)

    A. SKOURIKHINE; T. BURR

    2000-05-01T23:59:59.000Z

    We applied linguistic analysis approach, specifically N-grams, to classify nucleotide and amino acids sequences of nucleoprotein (NP) gene of the Influenza A virus isolated from a range of hosts and geographic regions. We considered letter frequency (1-grams), letter pairs frequency (2-grams) and triplets' frequency (3-grams). Classification trees based on 1,2,3-grams variables were constructed for the same NP nucleotide and amino acids strains and their classification efficiency were compared with the clustering obtained using phylogenetic analysis. The results have shown that disregarding positional information for a NP gene can provide the same level of recognition accuracy like alternative more complex classification techniques.

  14. Mutations of the tyrosinase gene produce autosomal recessive ocular albinism

    SciTech Connect (OSTI)

    King, R.A.; Summers, C.G.; Oetting, W.S. [Univ. of Minnesota, Minneapolis, MN (United States)] [and others

    1994-09-01T23:59:59.000Z

    Albinism has historically been divided into ocular (OA) and oculocutaneous (OCA) types based on the presence or absence of clinically apparent skin and hair involvement in an individual with the ocular features of albinism. The major genes for OCA include the tyrosinase gene in OCA1 and the P gene in OCA2. X-linked and autosomal recessive OA have been described and the responsible genes have not been identified. We now present six Caucasian individuals who have the phenotype of autosomal recessive OA but who have OCA1 as shown by the presence of mutations of the tyrosinase. They had white or very light hair and white skin at birth, and cutaneous pigment developed in the first decade of life. At ages ranging from 1.5-23 years, hair color was dark blond to light brown. The skin had generalized pigment and well developed tan was present on the exposed arm and face skin of four. Iris pigment was present and iris translucency varied. Molecular analysis of the tyrosinase gene, using PCR amplification and direct di-deoxy sequencing showed the following mutations: E398Z/E398Q, P406S/g346a, R402E/T373K, ?/D383N, and H211N/T373K. The homozygous individual was not from a known consanguineous mating. T373K is the most common tyrosinase gene mutation in our laboratory. Three of these mutations are associated with a total loss of tyrosinase activity (g346a splice-site, T373K, and D383N), while four are associated with residual enzyme activity (H211N, R402E, E398Q, and P406S). These studies show that mutations of the tyrosinase gene can produce the phenotype of autosomal recessive OA in an individual who has normal amounts of cutaneous pigment and the ability to tan after birth. This extends the phenotypic range of OCA1 to normal cutaneous pigment after early childhood, and suggest that mutations of the tyrosinase gene account for a significant number of individuals with autosomal recessive OA.

  15. Isolation and characterization of Agouti: a diabetes/obesity related gene

    DOE Patents [OSTI]

    Woychik, Richard P. (Knoxville, TN)

    2000-06-27T23:59:59.000Z

    The present invention relates to the cloning and expression of the Agouti gene and analogous genes in transformed, transfected and transgenic mice. The present invention provides an animal model for the study of diabetes, obesity and tumors for the testing of potential therapeutic agents. The present invention provides oligonucleotide probes for the detection of the Agouti gene and mutations in the gene. The present invention also relates to the isolation and recombinant production of the Agouti gene product, production of antibodies to the Agouti gene product and their use as diagnostic and therapeutic agents.

  16. Isolation and characterization of Agouti: a diabetes/obesity related gene

    DOE Patents [OSTI]

    Woychik, Richard P. (Knoxville, TN)

    1998-01-01T23:59:59.000Z

    The present invention relates to the cloning and expression of the Agouti gene and analogous genes in transformed, transfected and transgenic mice. The present invention provides an animal model for the study of diabetes, obesity and tumors for the testing of potential therapeutic agents. The present invention provides oligonucleotide probes for the detection of the Agouti gene and mutations in the gene. The present invention also relates to the isolation and recombinant production of the Agouti gene product, production of antibodies to the Agouti gene product and their use as diagnostic and therapeutic agents.

  17. BIOINFORMATICS Inferring Gene Regulatory Networks from Time Series

    E-Print Network [OSTI]

    Babu, M. Madan

    model regulatory relations in terms of Boolean relationships and combinatorial logic circuits (Kauffman the model (Shmulevich et al., 2002), the immediate extension of PBNs to any finite quantization (also. As opposed to PBNs, where gene interactions are modeled explicitly in terms of binary or multi-valued logical

  18. Heterocyst Morphogenesis and Gene Expression in Anabaena sp. PCC 7120 

    E-Print Network [OSTI]

    Mella Herrera, Rodrigo Andres

    2010-10-12T23:59:59.000Z

    , diazotrophic grow, and heterocyst morphogenesis. In our studies we characterized the expression of sigma factors genes in Anabaena PCC 7120 during heterocyst differentiation, and we found that the expression of sigC, sigG and sigE is localized primarily...

  19. Green genes: bioinformatics and systems biology innovations drive algal biotechnology

    E-Print Network [OSTI]

    Reijnders, Maarten J. M. F.; van Heck, Ruben; Lam, Carolyn M. C.; Scaife, Mark A.; Martins dos Santos, Vitor A. P.; Smith, Alison G.; Schaap, Peter J.

    2014-10-21T23:59:59.000Z

    by carbon dioxide and the CO2-concentrating mechanism regulator 2 CIA5/CCM1. Plant Cell 24, 1876-1893 3 78 Rasala, B.A., et al. (2012) Robust expression and secretion of xylanase 1 in Chlamydomonas 4 reinhardtii by fusion to a selection gene...

  20. RESEARCH Open Access Mutations in human lipoyltransferase gene LIPT1

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    in genes involved in the specific process of attachment of lipoic acid to apoenzymes pyruvate dehydrogenase with secondary deficiency for pyruvate and alpha-ketoglutarate dehydrogenase Yohan Soreze1 , Audrey Boutron2 de Lonlay1* Abstract Background: Synthesis and apoenzyme attachment of lipoic acid have emerged

  1. Inflammatory Gene Expression in Goats in Response to Transport

    E-Print Network [OSTI]

    Carter, Mark

    2012-10-19T23:59:59.000Z

    was to determine whether expression of immune-related genes changes in goats that are exposed to transport stress. In this study, 15 Spanish-Boer goats ranging from 3 to 4 yrs of age were transported for 12 h. Goats were divided into 5 groups of 3 and placed in 1...

  2. Signal Transduction Pathways that Regulate CAB Gene Expression

    SciTech Connect (OSTI)

    Chory, Joanne

    2006-01-16T23:59:59.000Z

    The process of chloroplast differentiation, involves the coordinate regulation of many nuclear and chloroplast genes. The cues for the initiation of this developmental program are both extrinsic (e.g., light) and intrinsic (cell-type and plastid signals). During this project period, we utilized a molecular genetic approach to select for Arabidopsis mutants that did not respond properly to environmental light conditions, as well as mutants that were unable to perceive plastid damage. These latter mutants, called gun mutants, define two retrograde signaling pathways that regulate nuclear gene expression in response to chloroplasts. A major finding was to identify a signal from chloroplasts that regulates nuclear gene transcription. This signal is the build-up of Mg-Protoporphyrin IX, a key intermediate of the chlorophyll biosynthetic pathway. The signaling pathways downstream of this signal are currently being studied. Completion of this project has provided an increased understanding of the input signals and retrograde signaling pathways that control nuclear gene expression in response to the functional state of chloroplasts. These studies should ultimately influence our abilities to manipulate plant growth and development, and will aid in the understanding of the developmental control of photosynthesis.

  3. Signal Transduction Pathways that Regulate CAB Gene Expression

    SciTech Connect (OSTI)

    Chory, Joanne

    2004-12-31T23:59:59.000Z

    The process of chloroplast differentiation, involves the coordinate regulation of many nuclear and chloroplast genes. The cues for the initiation of this developmental program are both extrinsic (e.g., light) and intrinsic (cell-type and plastid signals). During this project period, we utilized a molecular genetic approach to select for Arabidopsis mutants that did not respond properly to environmental light conditions, as well as mutants that were unable to perceive plastid damage. These latter mutants, called gun mutants, define two retrograde signaling pathways that regulate nuclear gene expression in response to chloroplasts. A major finding was to identify a signal from chloroplasts that regulates nuclear gene transcription. This signal is the build-up of Mg-Protoporphyrin IX, a key intermediate of the chlorophyll biosynthetic pathway. The signaling pathways downstream of this signal are currently being studied. Completion of this project has provided an increased understanding of the input signals and retrograde signaling pathways that control nuclear gene expression in response to the functional state of chloroplasts. These studies should ultimately influence our abilities to manipulate plant growth and development, and will aid in the understanding of the developmental control of photosynthesis.

  4. Symbolic Discriminant Analysis for Mining Gene Expression Patterns Jason Moore

    E-Print Network [OSTI]

    Fernandez, Thomas

    multivariate statistical approach for classification of observations into groups because the theory is wellSymbolic Discriminant Analysis for Mining Gene Expression Patterns Jason Moore Vanderbilt: Leukemia Jason H. Moore, Joel S. Parker, Lance W. Hahn Linear discriminant analysis is a popular

  5. Clustering of Unevenly Sampled Gene Expression Time-Series Data

    E-Print Network [OSTI]

    Rostock, Universität

    -means, k-means, average linkage hierarchical algorithm and random clustering are compared to the proposed the genes which define the model profiles in [2]. The fuzzy c-means, k- means, average linkage hierarchical as follows: The effects of the temporal information in the comparison of shapes are discussed first, followed

  6. ORIGINAL PAPER Expression of genes involved in energy mobilization

    E-Print Network [OSTI]

    Lee Jr., Richard E.

    ORIGINAL PAPER Expression of genes involved in energy mobilization and osmoprotectant synthesis, mobilizing carbohydrate energy reserves to promote synthesis of low-molecular-mass osmoprotectants Department of Entomology, Ohio State University, Columbus, OH 43210, USA e-mail: teets.23@osu.edu Y

  7. Noise-based switches and amplifiers for gene expression

    E-Print Network [OSTI]

    Hasty, Jeff

    controlled at the level of gene transcription. Such genetic regulation usually consists of interacting and manipulation of such networks lies within the constraints of current technology. Here we develop a model can be used to regulate expression. In the additive case, we demonstrate the utility of such control

  8. Retinoblastoma-like RRB gene of arabidopsis thaliana

    DOE Patents [OSTI]

    Durfee, Tim; Feiler, Heidi; Gruissem, Wilhelm; Jenkins, Susan; Roe, Judith; Zambryski, Patricia

    2004-02-24T23:59:59.000Z

    This invention provides methods and compositions for altering the growth, organization, and differentiation of plant tissues. The invention is based on the discovery that, in plants, genetically altering the levels of Retinoblastoma-related gene (RRB) activity produces dramatic effects on the growth, proliferation, organization, and differentiation of plant meristem.

  9. Transcriptional Targeting for Ovarian Cancer Gene Therapy E. Casado,*,

    E-Print Network [OSTI]

    Hemminki, Akseli

    ; gene therapy. INTRODUCTION Ovarian cancer afflicts more than 25,000 women annually in the United States Paz, Madrid, Spain Received November 10, 2000 Ovarian carcinoma is a leading cause of cancer death in women. Though advances in conventional therapies have been achieved, long-term survival rates for most

  10. Revealing strengths and weaknesses of methods for gene network inference

    E-Print Network [OSTI]

    Floreano, Dario

    -performing method failed to accu- rately infer multiple regulatory inputs (combinatorial regulation) of genes MDM2, its key regulator (1). Indeed, the map- ping of biological interactions in the intracellular realm remains the bottleneck in the pipeline to produce biological knowledge from high-throughput data

  11. Diet, nutrients, phytochemicals, and cancer metastasis suppressor genes

    E-Print Network [OSTI]

    Collins, Gary S.

    studied are the ways that major components of the diet such as protein, fat, and lifestyle issues impactDiet, nutrients, phytochemicals, and cancer metastasis suppressor genes Gary G. Meadows # Springer and mortality of cancer patients is metastasis. There exists a relative lack of specific therapeutic approaches

  12. Tracking the Performance Evolution of Blue Gene Systems

    SciTech Connect (OSTI)

    Kerbyson, Darren J.; Barker, Kevin J.; Gallo, Diego S.; Chen, Dong; Brunheroto, Jose R.; Ryu, Kyung D.; Chiu, George L.; Hoisie, Adolfy

    2013-06-17T23:59:59.000Z

    — IBM’s Blue Gene supercomputer has evolved through three generations from the original Blue Gene/L to P to Q. A higher level of integration has enabled greater single-core performance, and a larger concurrency per compute node. Although these changes have brought with them a higher overall system peak-performance, no study has examined in detail the evolution of perfor-mance across system generations. In this work we make two significant contri-butions – that of providing a comparative performance analysis across Blue Gene generations using a consistent set of tests, and also in providing a validat-ed performance model of the NEK-Bone proxy application. The combination of empirical analysis and the predictive performance model enable us to not only directly compare measured performance but also allow for a comparison of sys-tem configurations that cannot currently be measured. We provide insights into how the changing characteristics of Blue Gene have impacted on the application performance, as well as what future systems may be able to achieve.

  13. evolution genetics lab GENE 4230L: MECHANISMSAND INFERENCES

    E-Print Network [OSTI]

    Arnold, Jonathan

    evolution genetics lab GENE 4230L: MECHANISMSAND INFERENCES OFEVOLUTIONARYPROCESSES Fall2006, 12 Selection 1. Aug. 28 Lab 4. Measuring Natural Selection 2. Aug. 30 LABOR DAY Sep. 4 Lab 5. Evolution. 30 Lab 20. Phylogenetics part 2 Nov. 1 Lab 21. Evolution of Development Nov. 6 Lab 22. Catch

  14. Lower Oil Prices: A Reason to Give Thanks GENE EPSTEIN

    E-Print Network [OSTI]

    California at Davis, University of

    Lower Oil Prices: A Reason to Give Thanks By GENE EPSTEIN Nov. 29, 2014 1:31 a.m. ET I give thanks thanks for an oil price that fell below $70 a barrel Friday, mainly because it bodes well for general early this year ("Here Comes $75 Oil," March 31). Amy Jaffe, executive director of energy

  15. MICROFLUIDIC DEVICES FOR GENENTIC ANAYLSIS AND GENE EXPRESSION STUDIES

    E-Print Network [OSTI]

    Quake, Stephen R.

    MICROFLUIDIC DEVICES FOR GENENTIC ANAYLSIS AND GENE EXPRESSION STUDIES Thesis by Jian Liu field of microfluidics. His advice has helped me out many times when I was struggling in my research, Ziyang Ma, Emil Kartalov, and many other colleagues. I thank Dr. Jessica Melin and the microfluidic

  16. NUCLEOTIDE SUBSTITUTIONS AND THE EVOLUTION OF DUPLICATE GENES

    E-Print Network [OSTI]

    Oregon, University of

    167 NUCLEOTIDE SUBSTITUTIONS AND THE EVOLUTION OF DUPLICATE GENES JOHN S. CONERY Computational to gener- ate a corresponding alignment of the underlying nucleotide sequences and perform a codon by codon comparison of the nucleotides. Observed numbers of nucleotide substitutions can be used to make inferences

  17. Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes

    E-Print Network [OSTI]

    Jordan, King

    for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894. Makarova,1,2,3 John L. Spouge,1 Yuri I. Wolf,1,3 and Eugene V. Koonin1,4 1 National Center. Ohno's particular model of evolution by gene du- plication and, specifically, the role of natural

  18. Plasticity of opsin gene expression in cichlids from Lake Malawi

    E-Print Network [OSTI]

    Carleton, Karen L.

    Plasticity of opsin gene expression in cichlids from Lake Malawi CHRISTOPHER M. HOFMANN, KELLY E. O plasticity has important evolutionary implications. In this study, we examined retinal plasticity in five found that the magnitude of plasticity varied across species. These findings have important implications

  19. Genes order and phylogenetic reconstruction: application to #Proteobacteria

    E-Print Network [OSTI]

    Fertin, Guillaume

    @lacim.uqam.ca Abstract. We study the problem of phylogenetic reconstruction based on gene order for whole genomes. We define three genomic distances between whole genomes represented by signed sequences, based­ logeny for a group of 12 complete genomes of #­Proteobacteria. Keywords: Phylogenetic reconstruction

  20. Genes order and phylogenetic reconstruction: application to -Proteobacteria

    E-Print Network [OSTI]

    Fertin, Guillaume

    @lacim.uqam.ca Abstract. We study the problem of phylogenetic reconstruction based on gene order for whole genomes. We define three genomic distances between whole genomes represented by signed sequences, based- logeny for a group of 12 complete genomes of -Proteobacteria. Keywords: Phylogenetic reconstruction

  1. Genome Organization and Gene Expression Shape the Transposable Element Distribution

    E-Print Network [OSTI]

    Alvarez, Nadir

    Genome Organization and Gene Expression Shape the Transposable Element Distribution The distribution of transposable elements (TEs) in a genome reflects a balance between insertion rate and selection shaping the organization of genomes. Past research has shown that TEs tend to accumulate in genomic

  2. Effects of Acute and Chronic Stress on Immune- and Inflammatory-response Gene Expression in Beef Calves

    E-Print Network [OSTI]

    Terrill, Cooper

    2012-02-14T23:59:59.000Z

    . ........................... 56 18 Amplification plot of gene expression for primer IL-10RB ....................... 57 19 Amplification plot of gene expression for primer IL-12B .......................... 58 20 Amplification plot of gene expression for primer LBP...

  3. MODELING GENE EXPRESSION WITH DIFFERENTIAL Department of Genetics, Harvard Medical School

    E-Print Network [OSTI]

    Church, George M.

    MODELING GENE EXPRESSION WITH DIFFERENTIAL EQUATIONSa TING CHEN Department of Genetics, Harvard for gene expression and provide two methods to constructthe model from a set of temporaldata. We model both tran- scriptionand translationby kinetic equationswith feedbackloops from translation products

  4. Linking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression

    E-Print Network [OSTI]

    Xie, Xiaoliang Sunney

    expression. (a) Kinetic schLinking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression propagation in a simple genetic network. This model allows for the extraction of kinetic parameters of gene

  5. ORIGINAL ARTICLE Retroviral vector insertions in T-lymphocytes used for suicide gene therapy

    E-Print Network [OSTI]

    Granada, Universidad de

    ORIGINAL ARTICLE Retroviral vector insertions in T-lymphocytes used for suicide gene therapy occur­ prodrug combination is the herpes simplex virus thymidine kinase (HSV-TK) gene and ganciclovir (GCV

  6. Microbial metatranscriptomics : towards understanding microbial gene expression and regulation in natural habitats

    E-Print Network [OSTI]

    Shi, Yanmei, Ph. D. Massachusetts Institute of Technology

    2011-01-01T23:59:59.000Z

    Metagenomic research has paved the way for a comprehensive understanding of the microbial gene parts list in nature, but a full understanding of microbial gene expression, regulation, and ecology remains a challenge. In ...

  7. Mining large collections of gene expression data to elucidate transcriptional regulation of biological processes 

    E-Print Network [OSTI]

    Curry, Edward William James

    2011-06-27T23:59:59.000Z

    A vast amount of gene expression data is available to biological researchers. As of October 2010, the GEO database has 45,777 chips of publicly available gene expression pro ling data from the Affymetrix (HGU133v2) ...

  8. Neurophysiological Defects and Neuronal Gene Deregulation in Drosophila mir-124 Mutants

    E-Print Network [OSTI]

    Oregon, University of

    Neurophysiological Defects and Neuronal Gene Deregulation in Drosophila mir-124 Mutants Kailiang and Neuronal Gene Deregulation in Drosophila mir-124 Mutants. PLoS Genet 8(2): e1002515. doi:10.1371/journal

  9. Tissue-engineered liver microreactor as an in vitro surrogate assay for gene delivery

    E-Print Network [OSTI]

    Kalezi, Artemis

    2007-01-01T23:59:59.000Z

    The lack of correlation between in vitro and in vivo gene delivery experiments presents a significant obstacle in the progress of gene therapy studies by preventing the extrapolation of successful cell culture results into ...

  10. A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory

    E-Print Network [OSTI]

    Song, Joe

    Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast Mingzhou (Joe) Song1 significantly expressed genes in response to bioethanol conversion inhibitor 5-hydroxymethylfurfural in detoxification for bioethanol conversion by yeast. 1 Introduction Computational modeling of gene regulatory

  11. Genetic analyses of the Rb and p53 genes in murine development and tumorigenesis

    E-Print Network [OSTI]

    MacPherson, David (David P.)

    2005-01-01T23:59:59.000Z

    The RB and p53 genes play central roles in cell cycle and checkpoint control, apoptosis and many other biological processes. These are central tumor suppressor genes that are each inactivated in many human cancers. Mouse ...

  12. Gene silencing in cancer cells using siRNA : genetic and functional studies 

    E-Print Network [OSTI]

    Abdel Rahim, Ma'en Ahmad

    2004-09-30T23:59:59.000Z

    Sequence-specific small interfering RNA (siRNA) duplexes can be used for gene silencing in mammalian cells and as mechanistic probes for determining gene function. Transfection of siRNA for specificity protein 1 (Sp1) in ...

  13. Genomic neighbourhood and the regulation of gene expression Genomic neighbourhood and transcriptional regulation

    E-Print Network [OSTI]

    Babu, M. Madan

    Genomic neighbourhood and the regulation of gene expression Genomic neighbourhood and transcriptional regulation Subhajyoti De and M. Madan Babu MRC Laboratory of Molecular Biology, Hills Road..................................................................................................................................................................................1 2. Genomic neighbourhood and its influence on gene regulation

  14. HOPEGM REPORT Primate Origins of Human Evolution: From Genes to Mind

    E-Print Network [OSTI]

    Takada, Shoji

    HOPEGM REPORT Primate Origins of Human Evolution: From Genes to Mind Japan Society of Human Evolution: From Genes to Mind" (HOPE GM) , is a program funded by the Japan Society

  15. Extensive and Continuous Duplication Facilitates Rapid Evolution and Diversification of Gene Families

    E-Print Network [OSTI]

    Dean, Matthew D.

    in Escherichia coli (Yamanaka et al. 1998). Gene duplication is also associated with many types of spec, we investigated the evolutionary history of the A-superfamily of conotoxin genes of predatory marine

  16. Cloning and sequencing of the alcohol dehydrogenase II gene from Zymomonas mobilis

    DOE Patents [OSTI]

    Ingram, Lonnie O. (Gainesville, FL); Conway, Tyrrell (Gainesville, FL)

    1992-01-01T23:59:59.000Z

    The alcohol dehydrogenase II gene from Zymomonas mobilis has been cloned and sequenced. This gene can be expressed at high levels in other organisms to produce acetaldehyde or to convert acetaldehyde to ethanol.

  17. Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress

    E-Print Network [OSTI]

    Palva, Tapio

    approaches, as in e.g. k-means clustering (3,5). Regard- less of the chosen clustering approach, however- nections to defense-related gene clusters. Thus, in comparison to analyses of manually selected gene lists

  18. Multimodality imaging of reporter gene expression using a novel fusion vector in living cells and animals

    DOE Patents [OSTI]

    Gambhir; Sanjiv (Portola Valley, CA), Pritha; Ray (Mountain View, CA)

    2009-04-28T23:59:59.000Z

    Novel double and triple fusion reporter gene constructs harboring distinct imageable reporter genes are provided, as well as applications for the use of such double and triple fusion constructs in living cells and in living animals using distinct imaging technologies.

  19. Multimodality imaging of reporter gene expression using a novel fusion vector in living cells and animals

    DOE Patents [OSTI]

    Gambhir, Sanjiv (Portola Valley, CA); Pritha, Ray (Mountain View, CA)

    2011-06-07T23:59:59.000Z

    Novel double and triple fusion reporter gene constructs harboring distinct imagable reporter genes are provided, as well as applications for the use of such double and triple fusion constructs in living cells and in living animals using distinct imaging technologies.

  20. Immunological genomics of Brugia malayi: filarial genes implicated in immune evasion and protective immunity 

    E-Print Network [OSTI]

    Maizels, Rick; Blaxter, Mark; Scott, Alan

    2001-01-01T23:59:59.000Z

    Filarial nematodes are metazoan parasites with genome sizes of > 100 million base pairs, probably encoding 15 000-20 000 genes. Within this considerable gene complement, it seems likely that filariae have evolved ...

  1. Downstream genes of Pax6 revealed by comprehensive transcriptome profiling in the developing rat hindbrain

    E-Print Network [OSTI]

    2010-01-01T23:59:59.000Z

    C: A screen for downstream effectors of Neurogenin2 in theNumayama-Tsuruta et al. : Downstream genes of Pax6 revealedARTICLE Open Access Downstream genes of Pax6 revealed by

  2. The chosen genes : Jews, genetics, and the future of ethnic medicine

    E-Print Network [OSTI]

    Anthes, Emily Kennedy

    2006-01-01T23:59:59.000Z

    All humans have certain genes that cause or predispose them to various diseases. In the ideal medical future, scientists will have hyperfast gene analyzers able to sequence anyone's DNA in a matter of minutes. In that ...

  3. Discovery of Candidate Genes for Stallion Fertility from the Horse Y Chromosome

    E-Print Network [OSTI]

    Paria, Nandina

    2012-02-14T23:59:59.000Z

    significant differential expression in testis of normal fertile stallions and stallions with impaired fertility. Gene copy number analysis showed that the average copy number of 4 such genes was decreased in subfertile/infertile stallions compared to normal...

  4. Identification of endometrial genes important for conceptus survival and development in sheep

    E-Print Network [OSTI]

    Gray, Catherine Allison

    2005-08-29T23:59:59.000Z

    from Day 14 cyclic, pregnant, and bred UGKO ewes, as well as ewes treated with interferon tau (IFN??) and progesterone, to identify genes important for conceptus development. A number of novel and previously known IFN??-stimulated genes, as well...

  5. Analysis of genomic Regions of IncreaseD Gene Expression (RIDGE)s in immune activation 

    E-Print Network [OSTI]

    Hansson, Lena

    2009-01-01T23:59:59.000Z

    A RIDGE (Region of IncreaseD Gene Expression), as defined by previous studies, is a consecutive set of active genes on a chromosome that span a region around 110 kbp long. This study investigated RIDGE formation by ...

  6. A tree-decomposed transfer matrix for computing exact Potts model partition functions for arbitrary

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    graphs, with applications to planar graph colourings Andrea Bedini1,2 and Jesper Lykke Jacobsen3 1-mail: andrea.bedini@mi.infn.it, jesper.jacobsen@ens.fr Abstract. Combining tree decomposition and transfer

  7. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    SciTech Connect (OSTI)

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10T23:59:59.000Z

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  8. Genes encoding p-coumarate 3-hydroxylase (C3H) and methods of use

    DOE Patents [OSTI]

    Chapple, Clinton C. S.; Franke, Rochus; Ruegger, Max O.

    2006-07-04T23:59:59.000Z

    The present invention is directed to a method for altering secondary metabolism in plants, specifically phenylpropanoid metabolism. The present invention is further directed to a mutant p-coumarate 3-hydroxylase gene, referred to herein as the ref8 gene, its protein product which can be used to prepare gene constructs and transgenic plants. The gene constructs and transgenic plants are further aspects of the present invention.

  9. Gene mapping of bovine phosphoribosylglycinamide synthetase (PRGS) and phosphoribosylaminoimidazole synthetase (PAIS) in hybrid somatic cells

    E-Print Network [OSTI]

    McAvin, James Charles

    1986-01-01T23:59:59.000Z

    independent lines and displayed equally vigorous segregation of other cattle gene products. The data support a syntenic relationship of bovine PRGS, PAIS, SOD1 and IFREC, and a linkage conservation with human chromosome 21. PRGS, PAIS, and SOD1 also... of their linkage relationships to marker genes. A genetic map is a zepresentation of the physical and recombinational zelationships of genes on chromosomes. Markers used for mapping may be the actual DNA sequences, expressed. gene products, functions...

  10. The effect of PKG II deficiency on osteoblast-specific gene expression in mice

    E-Print Network [OSTI]

    Alwood, Amanda Raquel

    2011-01-01T23:59:59.000Z

    mice develop osteoporosis and arterial calcification. GenesOPG -/- mice suffer osteoporosis, a hollowing of the bone

  11. Gynoecium patterning in Arabidopsis thaliana : control of transmitting tract development by the HECATE genes

    E-Print Network [OSTI]

    Gremski, Kristina

    2006-01-01T23:59:59.000Z

    generated overexpression lines driving HEC gene expressionan overexpression line, by driving At3g59060 expression from

  12. Visualizing the Gene Ontology-Annotated Clusters of Co-expressed Genes: A Two-Design Study

    E-Print Network [OSTI]

    Hong,Seokhee

    of bioprocesses is largely driven by the co-ordinated expression of genes [3]. HTP-GOMinerTM [4] and Exploratory-child relationship between GO terms. The cluster map presented in HTP- GOMinerTM is a form of color matrix designed

  13. A portal to gene-centered information from different sources http://www.ncbi.nlm.nih.gov/gene/

    E-Print Network [OSTI]

    Levin, Judith G.

    .nlm.nih.gov/feed/rss.cgi?ChanKey=genenews Searching Gene Searching is as simple as entering a set of query terms and clicking the Search button (A). The search interface auto- matically flags and corrects the misspelling in the input term (B). Selecting Details" portlet (D) in the right column displays the actual terms used in the search. Retrieved records

  14. Genome-wide analysis of the chalcone synthase superfamily genes of Physcomitrella patens

    E-Print Network [OSTI]

    Suh, Dae-Yeon

    manipulation make Physcomitrella a highly suitable model system for studying expansion and functional for their differential regulation. Observed diversity within the moss CHS superfamily and amenability to gene superfamily Á Multigene family Á Enzyme evolution Á Gene duplication Á Retrotransposition Á Gene regulation Á

  15. Identifying the promoter features governing differential kinetics of co-regulated genes using fuzzy expressions

    E-Print Network [OSTI]

    Granada, Universidad de

    of the biggest challenges in genomics is the elucidation of the design principles controlling gene expression features used by a transcriptional regulator to differentially control genes that display distinctIdentifying the promoter features governing differential kinetics of co-regulated genes using fuzzy

  16. Mycological Society of America A Gene Genealogical Approach to Recognize Phylogenetic Species Boundaries in the Lichenized

    E-Print Network [OSTI]

    California at Berkeley, University of

    Mycological Society of America A Gene Genealogical Approach to Recognize Phylogenetic Species-8897 A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungus, was investigated as a model system in which to recognize species boundaries. Gene genealogies of 6 and 12 loci were

  17. The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case

    E-Print Network [OSTI]

    2007-08-16T23:59:59.000Z

    analysis of his gene fusions in available genomes to understand the role of gene fusions in shaping this pathway. Results The analysis of HisA structures revealed that several gene elongation events are at the root of this protein family: internal...

  18. Isolated gene encoding an enzyme with UDP-glucose pyrophosphorylase and phosphoglucomutase activities from Cyclotella cryptica

    DOE Patents [OSTI]

    Jarvis, E.E.; Roessler, P.G.

    1999-07-27T23:59:59.000Z

    The present invention relates to a cloned gene which encodes an enzyme, the purified enzyme, and the applications and products resulting from the use of the gene and enzyme. The gene, isolated from Cyclotella cryptica, encodes a multifunctional enzyme that has both UDP-glucose pyrophosphorylase and phosphoglucomutase activities. 8 figs.

  19. Red Algae Lose Key Mitochondrial Genes in Response to Becoming Parasitic

    E-Print Network [OSTI]

    Lane, Chris

    Red Algae Lose Key Mitochondrial Genes in Response to Becoming Parasitic Lillian Hancock1 , Lynda independently evolved hundreds of times among the floridiophyte red algae. Much is known about the life history class of red algae, Plocamiocolax puvinata, has lost the atp8 gene entirely, indicating that this gene

  20. Gene- or region-based association study via kernel principal component analysis

    E-Print Network [OSTI]

    Gao, Qingsong; He, Yungang; Yuan, Zhongshang; Zhao, Jinghua; Zhang, Bingbing; Xue, Fuzhong

    2011-08-26T23:59:59.000Z

    . The American Journal of Human Genetics 2005, 77(4):567-581. 43. Källberg H, Padyukov L, Plenge R, Rnnelid J, Gregersen P, van der Helm-van Mil A, Toes R, Huizinga T, Klareskog L, Alfredsson L: Gene-gene and gene- environment interactions involving HLA-DRB1...

  1. PCA-based bootstrap confidence interval tests for gene-disease association involving multiple SNPs

    E-Print Network [OSTI]

    Peng, Qianqian; Zhao, Jinghua; Xue, Fuzhong

    2010-01-26T23:59:59.000Z

    2005, 77:567-581. 23. Kallberg H, Padyukov L, Plenge RM, Ronnelid J, Gregersen PK, Helm-van Mil van der AHM, Toes REM, Huizinga TW, Klareskog L, Alfredsson L, et al: Gene-gene and gene-environment interactions involving HLA-DRB1, PTPN22, and smoking...

  2. A Gene Necessary for Normal Male Courtship, yellow, Acts Downstream of fruitless in the

    E-Print Network [OSTI]

    Gruber, Jonathan

    A Gene Necessary for Normal Male Courtship, yellow, Acts Downstream of fruitless in the Drosophila- ship behavior, genes acting downstream of fru have not yet been identified. Here we demonstrate that the yellow (y) gene is genetically downstream of fru in the 3rd -instar larval brain. Yellow protein

  3. Carotenoid Gene Nucleotide Diversity Reflects Carrot History and J. Clotault1

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Carotenoid Gene Nucleotide Diversity Reflects Carrot History and Selection J. Clotault1 , Emmanuel. The purpose of our work was to study the nucleotide diversity of carotenoid biosynthesis genes. A sample of 48). Compared to other species, a quite high single nucleotide (SNP) frequency was found for these genes (1

  4. A Model of Gene Expression and Regulation in an Artificial Cellular Organism

    E-Print Network [OSTI]

    Fernandez, Thomas

    expression and regulation based on the operon model of Jacob and Monod. Operons are groups of genes regulated and complexity of gene expression in real cells and it should also bear close relationships to EC so that it can, Jacob and Monod developed the operon model of gene expression and regulation [1, 5, 7] to explain

  5. Neural Network Classifiers and Gene Selection Methods for Microarray Data on Human Lung Adenocarcinoma

    E-Print Network [OSTI]

    Narasimhan, Giri

    Neural Network Classifiers and Gene Selection Methods for Microarray Data on Human Lung with lung cancer gene expression data sets available from the CAMDA website. Many different classification several new methods for classifying gene expression data from lung cancer patients. Our approach uses

  6. Effect of metallothionein 2A gene polymorphism on allele-specific gene expression and metal content in prostate cancer

    SciTech Connect (OSTI)

    Krze?lak, Anna; Forma, Ewa [Department of Cytobiochemistry, University of ?ód?, Pomorska 141/143, 90-236 ?ód? (Poland); Chwatko, Gra?yna [Department of Environmental Chemistry, University of ?ód?, Pomorska 163, 90-236 ?ód? (Poland); Jó?wiak, Pawe?; Szymczyk, Agnieszka [Department of Cytobiochemistry, University of ?ód?, Pomorska 141/143, 90-236 ?ód? (Poland); Wilkosz, Jacek; Ró?a?ski, Waldemar [2nd Department of Urology, Medical University of ?ód?, Pabianicka 62, 93-513 ?ód? (Poland); Bry?, Magdalena, E-mail: zreg@biol.uni.lodz.pl [Department of Cytobiochemistry, University of ?ód?, Pomorska 141/143, 90-236 ?ód? (Poland)

    2013-05-01T23:59:59.000Z

    Metallothioneins (MTs) are highly conserved, small molecular weight, cysteine rich proteins. The major physiological functions of metallothioneins include homeostasis of essential metals Zn and Cu and protection against cytotoxicity of heavy metals. The aim of this study was to determine whether there is an association between the ? 5 A/G single nucleotide polymorphism (SNP; rs28366003) in core promoter region and expression of metallothionein 2A (MT2A) gene and metal concentration in prostate cancer tissues. MT2A polymorphism was determined by the polymerase chain reaction–restriction fragment length polymorphism technique (PCR–RFLP) using 412 prostate cancer tissue samples. MT2A gene expression analysis was performed by real-time RT-PCR method. A significant association between rs28366003 genotype and MT2A expression level was found. The average mRNA level was found to be lower among minor allele carriers (the risk allele) than average expression among homozygotes for the major allele. Metal levels were analyzed by flamed atomic absorption spectrometer system. Highly statistically significant associations were detected between the SNP and Cd, Zn, Cu and Pb levels. The results of Spearman's rank correlation showed that the expressions of MT2A and Cu, Pb and Ni concentrations were negatively correlated. On the basis of the results obtained in this study, we suggest that SNP polymorphism may affect the MT2A gene expression in prostate and this is associated with some metal accumulation. - Highlights: • MT2A gene expression and metal content in prostate cancer tissues • Association between SNP (rs28366003) and expression of MT2A • Significant associations between the SNP and Cd, Zn, Cu and Pb levels • Negative correlation between MT2A gene expression and Cu, Pb and Ni levels.

  7. COHERENCE IN ZOOPLANKTON OF A LARGE NORTHWEST ATLANTIC ECOSYSTEM1

    E-Print Network [OSTI]

    declines in fish stocks (Glover 1957; Glover etaL 1961; Williamson 1961; Jacobsen 1980). Although it has

  8. Italo calvino Les villes invisibles

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    (Manifestations of Identity: The Lived Reality of Palestinian Refugees in Lebanon), Muhammad Ali Khalidi (Ed . . - - . . . .16 Karen Jacobsen :17

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

    DOE Patents [OSTI]

    Meagher, Richard B. (Athens, GA); Balish, Rebecca S. (Oxford, OH); Tehryung, Kim (Athens, GA); McKinney, Elizabeth C. (Athens, GA)

    2009-02-17T23:59:59.000Z

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

  10. GENE E. LIKENS FOUNDING DIRECTOR AND PRESIDENT EMERITUS

    E-Print Network [OSTI]

    Canham, Charles D.

    . Likens. 2012. Acid rain, in Encyclopedia of Environmetrics Second Edition. In: A.-H. El-Shaarawi and W Butler, T. J. and G.E. Likens. 2012. Acid rain, in Encyclopædia Britannica. Encyclopædia Britannica://www.britannica.com/EBchecked/topic/3761/acid-rain> #12;2012-13 Annual Report -- Dr. Gene E. Likens 2 D'Elia, C. F and G. E. Likens. 2012

  11. Heterocyst Morphogenesis and Gene Expression in Anabaena sp. PCC 7120

    E-Print Network [OSTI]

    Mella Herrera, Rodrigo Andres

    2010-10-12T23:59:59.000Z

    RT-PCR) ....................... 104 Results ..................................................................................................... 105 NtcA interacts with the promoter region of sigE in vitro. .................... 105 nifH expression is delayed and reduced... in controlling heterocyst development (96). NtcA, a transcriptional regulator belonging to the CRP (cyclic AMP receptor protein) family of proteins, senses 2-oxoglutarate levels. The protein is conserved in all cyanobacteria and regulates a number of genes...

  12. Methods for identifying an essential gene in a prokaryotic microorganism

    DOE Patents [OSTI]

    Shizuya, Hiroaki

    2006-01-31T23:59:59.000Z

    Methods are provided for the rapid identification of essential or conditionally essential DNA segments in any species of haploid cell (one copy chromosome per cell) that is capable of being transformed by artificial means and is capable of undergoing DNA recombination. This system offers an enhanced means of identifying essential function genes in diploid pathogens, such as gram-negative and gram-positive bacteria.

  13. Pnp gene modification for improved xylose utilization in Zymomonas

    DOE Patents [OSTI]

    Caimi, Perry G G; Qi, Min; Tao, Luan; Viitanen, Paul V; Yang, Jianjun

    2014-12-16T23:59:59.000Z

    The endogenous pnp gene encoding polynucleotide phosphorylase in the Zymomonas genome was identified as a target for modification to provide improved xylose utilizing cells for ethanol production. The cells are in addition genetically modified to have increased expression of ribose-5-phosphate isomerase (RPI) activity, as compared to cells without this genetic modification, and are not limited in xylose isomerase activity in the absence of the pnp modification.

  14. Plant isoflavone and isoflavanone O-methyltransferase genes

    DOE Patents [OSTI]

    Broeckling, Bettina E.; Liu, Chang-Jun; Dixon, Richard A.

    2014-08-19T23:59:59.000Z

    The invention provides enzymes that encode O-methyltransferases (OMTs) from Medicago truncatula that allow modification to plant (iso)flavonoid biosynthetic pathways. In certain aspects of the invention, the genes encoding these enzymes are provided. The invention therefore allows the modification of plants for isoflavonoid content. Transgenic plants comprising such enzymes are also provided, as well as methods for improving disease resistance in plants. Methods for producing food and nutraceuticals, and the resulting compositions, are also provided.

  15. Operon Formation is Driven by Co-Regulation and Not by Horizontal Gene Transfer

    SciTech Connect (OSTI)

    Price, Morgan N.; Huang, Katherine H.; Arkin, Adam P.; Alm, Eric J.

    2005-04-12T23:59:59.000Z

    Although operons are often subject to horizontal gene transfer (HGT), non-HGT genes are particularly likely to be in operons. To resolve this apparent discrepancy and to determine whether HGT is involved in operon formation, we examined the evolutionary history of the genes and operons in Escherichia coli K12. We show that genes that have homologs in distantly related bacteria but not in close relatives of E. coli (indicating HGTi) form new operons at about the same rates as native genes. Furthermore, genes in new operons are no more likely than other genes to have phylogenetic trees that are inconsistent with the species tree. In contrast, essential genes and ubiquitous genes without paralogs (genes believed to undergo HGT rarely) often form new operons. We conclude that HGT is not associated with operon formation, but instead promotes the prevalence of pre-existing operons. To explain operon formation, we propose that new operons reduce the amount of regulatory information required to specify optimal expression patterns. Consistent with this hypothesis, operons have greater amounts of conserved regulatory sequences than do individually transcribed genes.

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

    DOE Patents [OSTI]

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

    2014-09-16T23:59:59.000Z

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

  17. Identification of genes from pattern formation, tyrosine kinase, and potassium channel families by DNA amplification

    SciTech Connect (OSTI)

    Kamb, A.; Weir, M.; Rudy, B.; Varmus, H.; Kenyon, C. (Univ. of California, San Francisco (USA))

    1989-06-01T23:59:59.000Z

    The study of gene family members has been aided by the isolation of related genes on the basis of DNA homology. The authors have adapted the polymerase chain reaction to screen animal genomes very rapidly and reliably for likely gene family members. Using conserved amino acid sequences to design degenerate oligonucleotide primers, they have shown that the genome of the nematode Caenorhabditis elegans contains sequences homologous to many Drosophila genes involved in pattern formation, including the segment polarity gene wingless (vertebrate int-1), and homeobox sequences characteristic of the Antennapedia, engrailed, and paired families. In addition, they have used this method to show that C. elegans contains at least five different sequences homologous to genes in the tyrosine kinase family. Lastly, they have isolated six potassium channel sequences from humans, a result that validates the utility of the method with large genomes and suggests that human potassium channel gene diversity may be extensive.

  18. Transcriptional regulation of the Arabidopsis thaliana chalcone synthase gene

    SciTech Connect (OSTI)

    Feinbaum, R.L.; Ausubel, F.M.

    1988-05-01T23:59:59.000Z

    The authors cloned an Arabiodpsis thaliana chalcone synthase (CHS) gene on the basis of cross-hybridization with a Petroselinum hortense CHS cDNA clone. The protein sequence deduced from the A. thaliana CHS DNA sequence is at least 85% homologous to the CHS sequences from P. hortense, Antirrhinum majus, and Petunia hybrida. Southern blot analysis indicated that CHS is a single-copy gene in A. thaliana. High-intensity light treatment of A. thaliana plants for 24 h caused a 50-fold increase in CHS enzyme activity and an accumulation of visibly detectable levels of anthocyanin pigments in the vegetative structures of these plants. A corresponding increase in the steady-state level of CHS mRNA was detected after high-intensity light treatment for the same period of time. The accumulation of CHS mRNA in response to high-intensity light was due, at least in part, to an increased rate of transcription of the CHS gene as demonstrated by nuclear runoff experiment.

  19. Listening to the noise: random fluctuations reveal gene network parameters

    SciTech Connect (OSTI)

    Munsky, Brian [Los Alamos National Laboratory; Khammash, Mustafa [UCSB

    2009-01-01T23:59:59.000Z

    The cellular environment is abuzz with noise. The origin of this noise is attributed to the inherent random motion of reacting molecules that take part in gene expression and post expression interactions. In this noisy environment, clonal populations of cells exhibit cell-to-cell variability that frequently manifests as significant phenotypic differences within the cellular population. The stochastic fluctuations in cellular constituents induced by noise can be measured and their statistics quantified. We show that these random fluctuations carry within them valuable information about the underlying genetic network. Far from being a nuisance, the ever-present cellular noise acts as a rich source of excitation that, when processed through a gene network, carries its distinctive fingerprint that encodes a wealth of information about that network. We demonstrate that in some cases the analysis of these random fluctuations enables the full identification of network parameters, including those that may otherwise be difficult to measure. This establishes a potentially powerful approach for the identification of gene networks and offers a new window into the workings of these networks.

  20. Compositions and methods for detecting gene rearrangements and translocations

    DOE Patents [OSTI]

    Rowley, Janet D. (Chicago, IL); Diaz, Manuel O. (Chicago, IL)

    2000-01-01T23:59:59.000Z

    Disclosed is a series of nucleic acid probes for use in diagnosing and monitoring certain types of leukemia using, e.g., Southern and Northern blot analyses and fluorescence in situ hybridization (FISH). These probes detect rearrangements, such as translocations involving chromosome band 11q23 with other chromosomes bands, including 4q21, 6q27, 9p22, 19p13.3, in both dividing leukemic cells and interphase nuclei. The breakpoints in all such translocations are clustered within an 8.3 kb BamHI genomic region of the MLL gene. A novel 0.7 kb BamH1 cDNA fragment derived from this gene detects rearrangements on Southern blot analysis with a single BamHI restriction digest in all patients with the common 11q23 translocations and in patients with other 11q23 anomalies. Northern blot analyses are presented demonstrating that the MLL gene has multiple transcripts and that transcript size differentiates leukemic cells from normal cells. Also disclosed are MLL fusion proteins, MLL protein domains and anti-MLL antibodies.

  1. Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes

    E-Print Network [OSTI]

    Gent, Universiteit

    -finned fishes (Actinopterygii) seem to have two copies of many tetrapod (Sarcopterygii) genes. The origin of these duplicate fish genes is the subject of some controversy. One explanation for the existence of these extra fish genes could be an increase in the rate of independent gene duplications in fishes. Alternatively

  2. ARTIFICIAL GENE-CLUSTERS ENGINEERED INTO PLANTS USING A VECTOR SYSTEM BASED ON INTRON-AND INTEIN-ENCODED ENDONUCLEASES

    E-Print Network [OSTI]

    Parrott, Wayne

    ARTIFICIAL GENE-CLUSTERS ENGINEERED INTO PLANTS USING A VECTOR SYSTEM BASED ON INTRON- AND INTEIN; accepted 13 May 2002; editor K. D'Halluin) Summary The ability to create artificial gene, or with traits which result from the expression of multiple genes. A simple method to assemble artificial gene

  3. Chitosan-based therapeutic nanoparticles for combination gene therapy and gene silencing of in vitro cell lines relevant to type 2 diabetes

    E-Print Network [OSTI]

    Buschmann, Michael

    Chitosan-based therapeutic nanoparticles for combination gene therapy and gene silencing found chitosans to form spherical nanocomplexes with these nucleic acids, generating two distinct non-cell function declines, efficacies of current treatments diminish (Turner et al., 1999). Recently, the discovery

  4. Effects of alien and intraspecies cytoplasms on manifestation of nuclear genes for wheat resistance to brown rust: II. Specificity of cytoplasm influence on different Lr genes

    SciTech Connect (OSTI)

    Voluevich, E.A.; Buloichik, A.A.; Palilova, A.N. [Institute of Genetics and Cytology, Minsk (Belarus)

    1995-04-01T23:59:59.000Z

    Specificity of expression of the major nuclear genes Lr to two brown rust clones in hybrids with the same maternal cytoplasm was analyzed. It was evaluated by a resistant: susceptible ratio in the F{sub 2}. Reciprocal hybrids were obtained from the cross between the progeny of homozygous susceptible plants of the cultivar Penjamo 62 and its alloplasmatic lines carrying cytoplasms of Triticum dicoccoides var. fulvovillosum, Aegilops squarrosa var. typical, Agropyron trichophorum, and isogenic lines of the cultivar Thatcher (Th) with the Lr1, Lr9, Lr15, and Lr19 genes. It was shown that the effect of the Lr1 gene in the cytoplasm of cultivar Thatcher and in eu-, and alloplasmatic forms of Penjamo 62 was less expressed than that of other Lr genes. Cytoplasm of the alloplasmatic line (dicoccoides)-Penjamo 62 was the only exception: in the F{sub 2}, hybrids with Th (Lr1) had a higher yield of resistant forms than those with Th (Lr15). In the hybrid combinations studied, expression and/or transmission of the Lr19 gene was more significant than that of other genes. This gene had no advantages over Lr15 and Lr19 only in cytoplasm of the alloplasmatic line (squarrosa)-Penjamo 62. In certain hybrid cytoplasms, the display of the Lr1, Lr15, and Lr19 genes, in contrast to Lr9, varied with the virulence of the pathogen clones. 15 refs., 5 tabs.

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

    SciTech Connect (OSTI)

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

    2004-02-25T23:59:59.000Z

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

  6. Prolactin receptor and signal transduction to milk protein genes

    SciTech Connect (OSTI)

    Djiane, J.; Daniel, N.; Bignon, C. [Unite d`Endocrinologie Moleculaire, Jouy en Josas (France)] [and others

    1994-06-01T23:59:59.000Z

    After cloning of the mammary gland prolactin (PRL) receptor cDNA, a functional assay was established using co-transfection of PRL receptor cDNA together with a milk protein promoter/chloramphenicol acetyl transferase (CAT) construct in Chinese hamster ovary (CHO) cells. Different mutants of the PRL receptor were tested in this CAT assay to delimit the domains in the receptor necessary for signal transduction to milk protein genes. In CHO cells stably transfected with PRL receptor cDNA, high numbers of PRL receptor are expressed. By metabolic labeling and immunoprecipitation, expressed PRL receptor was identified as a single species of 100 kDa. Using these cells, we analyzed the effects of PRL on intracellular free Ca{sup ++} concentration. PRL stimulates Ca{sup ++} entry and induces secondary Ca{sup ++} mobilization. The entry of Ca{sup ++} is a result of an increase in K{sup +} conductance that hyperpolarizes the membranes. We have also analyzed tyrosine phosphorylation induced by PRL. In CHO cells stably transfected with PRL receptor cDNA, PRL induced a very rapid and transient tyrosine phosphorylation of a 100-kDa protein which is most probably the PRL receptor. The same finding was obtained in mammary membranes after PRL injection to lactating rabbits. Whereas tyrosine kinase inhibitors genistein and lavendustin were without effect, PRL stimulation of milk protein gene promoters was partially inhibited by 2 {mu}M herbimycin in CHO cells co-transfected with PRL receptor cDNA and the {Beta} lactoglobulin CAT construct. Taken together these observations indicate that the cytoplasmic domain of the PRL receptor interacts with one or several tyrosine kinases, which may represent early postreceptor events necessary for PRL signal transduction to milk protein genes. 14 refs., 4 figs.

  7. A genetic and molecular analysis of the Drosophila dachs gene

    E-Print Network [OSTI]

    Hu, Wei-Li

    1999-01-01T23:59:59.000Z

    -kerosine kinase, containing well conserved SH3, SH2, and kinase catalytic domains. Much of the interest in this gene originally stemmed from its proto-oncogenic properties in Philadelphia chromosome-positive chronic myelogenous leukemia (CML) and acute... lymphocytic leukemia (ALL) in humans, and in the pre-B-cell leukemia caused by Abelson murine leukemia virus in mice. Abl is widely expressed and thought to be involved in the development of a variety of tissues (Hoffmann, 1991). In addition to its tyrosine...

  8. Imaging gene expression in real-time using aptamers

    SciTech Connect (OSTI)

    Shin, Il Chung [Ames Laboratory

    2012-11-02T23:59:59.000Z

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

  9. Analysis of sunflower 2S seed storage protein genes

    E-Print Network [OSTI]

    Cohen, Elizabeth Anne

    1986-01-01T23:59:59.000Z

    classes of proteins: 11S legumin-like proteins and 2S albumins. Sunflower 2S seed proteins resolved by SDS-Polyacrlamide gel electrophoresis run as a diffuse band about 19 kd. Embryo specific cDNA clones were selected from Agtll library prepared from... and appears to represent a single copy gene. A full length Ha5 was obtained by matching the AHa5 cDNA clone nucleotide sequence with that of a Ha5 genomic clone. This full length sequence encodes a 37 kd protein with a estimated pl of 11. 52 and it appears...

  10. Imaging gene expression in real-time using aptamers

    SciTech Connect (OSTI)

    Shin, Il Chung

    2011-12-13T23:59:59.000Z

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

  11. From genes to folds: a review of cortical gyrification theory

    E-Print Network [OSTI]

    Ronan, Lisa; Fletcher, Paul C

    2014-12-16T23:59:59.000Z

    REVIEW From genes to folds: a review of cortical gyrification theory Lisa Ronan • Paul C. Fletcher Received: 5 September 2014 / Accepted: 6 December 2014 #2; The Author(s) 2014. This article is published with open access at Springerlink.com Abstract... microcephaly. Curr Opin Neurol 14:151 Nonaka-Kinoshita M, Reillo I, Artegiani B, Martinez-Martinez MA, Nelson M, Borrell V, Calegari F (2013) Regulation of cerebral cortex size and folding by expansion of basal progenitors. EMBO J 32:1817–1828 O’Leary DDM, Chou...

  12. Gene Geracao Eolica Do Nordeste | Open Energy Information

    Open Energy Info (EERE)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page onYou are now leaving Energy.gov You are now leaving Energy.gov You are being directedAnnual Siteof Energy 2,AUDIT REPORTEnergyFarms A SUK Place: Newport,Gate SolarGroupsGenDriveGene

  13. Gene Controls Flowering Time in Corn - Energy Innovation Portal

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField8,Dist.Newof EnergyFundingGene Controls Flowering Time in Corn Great

  14. Genes for Xylose Fermentation, Enhanced Biofuel Production in Yeast -

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField8,Dist.Newof EnergyFundingGene ControlsCounselGeneral- EnergyEnergy

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

    SciTech Connect (OSTI)

    Schneider, J.S., E-mail: jay.schneider@jefferson.edu; Anderson, D.W.; Sonnenahalli, H.; Vadigepalli, R.

    2011-10-15T23:59:59.000Z

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

  16. Massively-parallel electrical-conductivity imaging of hydrocarbons using the Blue Gene/L supercomputer

    E-Print Network [OSTI]

    2008-01-01T23:59:59.000Z

    CONDUCTIVITY IMAGING OF HYDROCARBONS USING THE BLUE GENE/Lidentification of hydrocarbon filled layers in deepwater,”Remote sensing of hydrocarbon layers by seabed logging (

  17. Functional gene screening in embryonic stem cell implicates Wnt antagonism in neural differentiation. 

    E-Print Network [OSTI]

    Aubert, Jerome; Dunstan, Hannah; Chambers, Ian; Smith, Austin G

    2002-01-01T23:59:59.000Z

    The multilineage differentiation capacity of mouse embryonic stem (ES) cells offers a potential testing platform for gene products that mediate mammalian lineage determination and cellular specialization. Identification ...

  18. Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

    E-Print Network [OSTI]

    Pignatta, Daniela

    Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could ...

  19. Cytochrome b5 gene and protein of Candida tropicalis and methods relating thereto

    DOE Patents [OSTI]

    Craft, David L. (Fort Thomas, KY); Madduri, Krishna M. (Westfield, IN); Loper, John C. (Cincinnati, OH)

    2003-01-01T23:59:59.000Z

    A novel gene has been isolated which encodes cytochrome b5 (CYTb5) protein of the .omega.-hydroxylase complex of C. tropicalis 20336. Vectors including this gene, and transformed host cells are provided. Methods of increasing the production of a CYTb5 protein are also provided which involve transforming a host cell with a gene encoding this protein and culturing the cells. Methods of increasing the production of a dicarboxylic acid are also provided which involve increasing in the host cell the number of genes encoding this protein.

  20. Identification of ubiad1 as a gene involved in cardiovascular homeostasis and development

    E-Print Network [OSTI]

    Hegarty, Jeffrey Miles

    2011-01-01T23:59:59.000Z

    gene causes defects of bioenergetics and de novo pyrimidineparticipate in cardiac bioenergetics (Kumar et al. , 2009),defects affecting bioenergetics (López- Martín et al. ,

  1. Transcript levels and synthesis of photosystem II components in cyanobacterial mutants with inactivated photosystem II genes

    SciTech Connect (OSTI)

    Jiujiang Yu; Vermaas, W.F.J. (Arizona State Univ., Tempe (United States))

    1990-04-01T23:59:59.000Z

    After interruption or deletion of the photosystem II genes psbB, psbC, and psbD in the cyanobacterium Synechocystis sp. PCC 6803, thylakoids from such mutants were found to be depleted in a number of photosystem II proteins in addition to those for which the gene(s) had been inactivated. Transcript levels of photosystem II genes were measured and protein pulse-labeling was carried out to determine the reason for this effect. Transcripts of all photosystem II genes except the inactivated one(s) were found to be present in the various mutants. In certain cases, inactivation of one photosystem II gene led to overexpression of another. Protein pulse-labeling experiments using {sup 35}S-methionine, in which not only the rapidly turing over D1 protein but also D2, CP43, and CP47 appear to be preferentially labeled, showed that the mutants studied synthesize the D1 protein as well as other photosystem II proteins whose genes were not inactivated. The fact that, in the various mutants, photosystem II proteins for which the gene is not inactivated are synthesized but do not accumulate in the thylakoid indicates that the psbB, psbC, and psbD gene products are all required for a stable assembly of the photosystem II complex.

  2. Id-1 and Id-2 genes and products as markers of epithelial cancer

    SciTech Connect (OSTI)

    Desprez, Pierre-Yves (El Cerrito, CA); Campisi, Judith (Berkeley, CA)

    2011-10-04T23:59:59.000Z

    A method for detection and prognosis of breast cancer and other types of cancer. The method comprises detecting expression, if any, for both an Id-1 and an Id-2 genes, or the ratio thereof, of gene products in samples of breast tissue obtained from a patient. When expressed, Id-1 gene is a prognostic indicator that breast cancer cells are invasive and metastatic, whereas Id-2 gene is a prognostic indicator that breast cancer cells are localized and noninvasive in the breast tissue.

  3. Id-1 and Id-2 genes and products as markers of epithelial cancer

    DOE Patents [OSTI]

    Desprez, Pierre-Yves (El Cerrito, CA); Campisi, Judith (Berkeley, CA)

    2008-09-30T23:59:59.000Z

    A method for detection and prognosis of breast cancer and other types of cancer. The method comprises detecting expression, if any, for both an Id-1 and an Id-2 genes, or the ratio thereof, of gene products in samples of breast tissue obtained from a patient. When expressed, Id-1 gene is a prognostic indicator that breast cancer cells are invasive and metastatic, whereas Id-2 gene is a prognostic indicator that breast cancer cells are localized and noninvasive in the breast tissue.

  4. ai-ciii-aiv gene cluster: Topics by E-print Network

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

    the application of a novel clustering algorithm, Super-Paramagnetic Clustering (SPC) to analysis of gene expression profiles that were generated recently during a study of...

  5. apoa1-c3-a4-a5 gene cluster: Topics by E-print Network

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

    the application of a novel clustering algorithm, Super-Paramagnetic Clustering (SPC) to analysis of gene expression profiles that were generated recently during a study of...

  6. Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease

    E-Print Network [OSTI]

    2014-01-01T23:59:59.000Z

    Integrative Genomics Reveals Novel Molecular Pathways and7 | e1004502 Integrative Genomics of Coronary Artery Disease2012) Use of functional genomics to identify candidate genes

  7. arabidopsis ycf20-like genes: Topics by E-print Network

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

    Babu, M. Madan 4 Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling Biology and Medicine Websites Summary: VIB MicroArray Facility,...

  8. E-Print Network 3.0 - activator inhibitor-1 gene Sample Search...

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

    activator inhibitor-1 gene Page: << < 1 2 3 4 5 > >> 1 EdinburghStanford TREC 2003 Genomics Track: Notebook Paper Summary: -dependent kinase inhibitor 1a'' ''dna synthesis...

  9. E-Print Network 3.0 - assembly protein gene Sample Search Results

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

    >> 1 Specialist Review 99. Contextual inference of protein Summary: -scale functional genomics experiments such as gene expression, transcriptional interaction, and protein...

  10. SciTech Connect: Uses of antimicrobial genes from microbial genome

    Office of Scientific and Technical Information (OSTI)

    Information Service, Springfield, VA at www.ntis.gov. We describe a method for mining microbial genomes to discover antimicrobial genes and proteins having broad spectrum...

  11. A Systematic Analysis of Epigenetic Genes across Different Stages of Lung Adenocarcinoma Akshay Desai1

    E-Print Network [OSTI]

    Zhou, Yaoqi

    A Systematic Analysis of Epigenetic Genes across Different Stages of Lung Adenocarcinoma Akshay across different stages of lung adenocarcinoma (LUAD). Method: An integrative system biology approach

  12. Clock-controlled output gene Dbp is a regulator of Arnt/Hif-1? gene expression in pancreatic islet ?-cells

    SciTech Connect (OSTI)

    Nakabayashi, Hiroko; Ohta, Yasuharu, E-mail: yohta@yamaguchi-u.ac.jp; Yamamoto, Masayoshi; Susuki, Yosuke; Taguchi, Akihiko; Tanabe, Katsuya; Kondo, Manabu; Hatanaka, Masayuki; Nagao, Yuko; Tanizawa, Yukio, E-mail: tanizawa@yamaguchi-u.ac.jp

    2013-05-03T23:59:59.000Z

    Highlights: •Arnt mRNA expressed in a circadian manner in mouse pancreatic islets. •Expressions of Dbp and Arnt damped in the islets of a diabetic model mouse. •DBP and E4BP4 regulate Arnt promoter activity by direct binding. •Arnt may have a role in connecting circadian rhythm and metabolism. -- Abstract: Aryl hydrocarbon receptor nuclear translocator (ARNT)/hypoxia inducible factor-1? (HIF-1?) has emerged as a potential determinant of pancreatic ?-cell dysfunction and type 2 diabetes in humans. An 82% reduction in Arnt expression was observed in islets from type 2 diabetic donors as compared to non-diabetic donors. However, few regulators of Arnt expression have been identified. Meanwhile, disruption of the clock components CLOCK and BMAL1 is known to result in hypoinsulinemia and diabetes, but the molecular details remain unclear. In this study, we identified a novel molecular connection between Arnt and two clock-controlled output genes, albumin D-element binding protein (Dbp) and E4 binding protein 4 (E4bp4). By conducting gene expression studies using the islets of Wfs1{sup ?/?} A{sup y}/a mice that develop severe diabetes due to ?-cell apoptosis, we demonstrated clock-related gene expressions to be altered in the diabetic mice. Dbp mRNA decreased by 50%, E4bp4 mRNA increased by 50%, and Arnt mRNA decreased by 30% at Zeitgever Time (ZT) 12. Mouse pancreatic islets exhibited oscillations of clock gene expressions. E4BP4, a D-box negative regulator, oscillated anti-phase to DBP, a D-box positive regulator. We also found low-amplitude circadian expression of Arnt mRNA, which peaked at ZT4. Over-expression of DBP raised both mRNA and protein levels of ARNT in HEK293 and MIN6 cell lines. Arnt promoter-driven luciferase reporter assay in MIN6 cells revealed that DBP increased Arnt promoter activity by 2.5-fold and that E4BP4 competitively inhibited its activation. In addition, on ChIP assay, DBP and E4BP4 directly bound to D-box elements within the Arnt promoter in MIN6 cells. These results suggest that in mouse pancreatic islets mRNA expression of Arnt fluctuates significantly in a circadian manner and that the down-regulation of Dbp and up-regulation E4bp4 contribute to direct suppression of Arnt expression in diabetes.

  13. Isolated fungal promoters and gene transcription terminators and methods of protein and chemical production in a fungus

    DOE Patents [OSTI]

    Dai, Ziyu; Lasure, Linda L; Magnuson, Jon K

    2014-05-27T23:59:59.000Z

    The present invention encompasses isolated gene regulatory elements and gene transcription terminators that are differentially expressed in a native fungus exhibiting a first morphology relative to the native fungus exhibiting a second morphology. The invention also encompasses a method of utilizing a fungus for protein or chemical production. A transformed fungus is produced by transforming a fungus with a recombinant polynucleotide molecule. The recombinant polynucleotide molecule contains an isolated polynucleotide sequence linked operably to another molecule comprising a coding region of a gene of interest. The gene regulatory element and gene transcription terminator may temporally and spatially regulate expression of particular genes for optimum production of compounds of interest in a transgenic fungus.

  14. Wide-cross whole-genome radiation hybrid (WWRH) mapping and identification of cold-responsive genes using oligo-gene microarray analysis in cotton

    E-Print Network [OSTI]

    Gao, Wenxiang

    2005-02-17T23:59:59.000Z

    that the WWRH mapping method can be used to map the cotton genome, and that this method complements traditional linkage mapping approaches. The second part of this research focused on the identification of cold-responsive genes using spotted oligo...

  15. Human KZNF Gene Catalog - A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors

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

    Huntley, S; Baggott, D. M.; Hamilton, A. T.; Tran-Gyamfi, M.; Yang, S.; Kim, J.; Gordon, L.; Branscomb, E.; Stubbs, L.

    Kruppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached to a tandem array of DNA-binding zinc-finger motifs, are specific to tetrapod vertebrates and represent the largest class of ZNF proteins in mammals. To define the full repertoire of human KRAB-ZNF proteins, we searched the genome sequence for key motifs and then constructed and manually curated gene models incorporating those sequences. The resulting gene catalog contains 423 KRAB-ZNF protein-coding loci, yielding alternative transcripts that altogether predict at least 742 structurally distinct proteins. Active rounds of segmental duplication, involving single genes or larger regions and including both tandem and distributed duplication events, have driven the expansion of this mammalian gene family. Comparisons between the human genes and ZNF loci mined from the draft mouse, dog, and chimpanzee genomes not only identified 103 KRAB-ZNF genes that are conserved in mammals but also highlighted a substantial level of lineage-specific change; at least 136 KRAB-ZNF coding genes are primate specific, including many recent duplicates. KRAB-ZNF genes are widely expressed and clustered genes are typically not coregulated, indicating that paralogs have evolved to fill roles in many different biological processes. To facilitate further study, we have developed a Web-based public resource with access to gene models, sequences, and other data, including visualization tools to provide genomic context and interaction with other public data sets. [This abstract was copied from: S Huntley, DM Baggott, AT Hamilton, M Tran-Gyamfi, S Yang, J Kim, L Gordon, E Branscomb, and L Stubbs. 2006. A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors, Genome Research 16(5):669 - 677] The website provides the ability to search the online catalog by genomic coordinates, name, locus type, and motifs, to utilize a graphical browser and to download data files.

  16. RESEARCH ARTICLE Open Access Bridging the gap between gene expression and

    E-Print Network [OSTI]

    , and metabolome data using kinetic models to create a mechanistic link between gene expression and metabolism expression, Kinetic models, Metabolic networks, S. cerevisiae, Transcriptomics, Fluxomics, MetabolomicsRESEARCH ARTICLE Open Access Bridging the gap between gene expression and metabolic phenotype via

  17. Modeling the segment polarity gene network First: System is biologically defined; known expression patterns

    E-Print Network [OSTI]

    Albert, Réka

    are assumed to be not expressed. · Generate a set of kinetic parameters from the biologically relevant rangeModeling the segment polarity gene network First: System is biologically defined; known expression Boolean model: mRNA and protein activity is switch-like Validation: reproduces known gene expression

  18. Tissue-specific gene delivery via nanoparticle coating Todd J. Harris a,1

    E-Print Network [OSTI]

    Bhatia, Sangeeta

    Tissue-specific gene delivery via nanoparticle coating Todd J. Harris a,1 , Jordan J. Green b,1 delivery to the spleen and bone marrow. Thus, vari- ations in nanoparticle peptide coating density can Accepted 5 October 2009 Available online 21 October 2009 Keywords: Nanoparticle Targeting Gene delivery

  19. Nuclear and Mitochondrial Genes Contain Similar Phylogenetic Signal for Pigeons and Doves (Aves: Columbiformes)

    E-Print Network [OSTI]

    Clayton, Dale H.

    Nuclear and Mitochondrial Genes Contain Similar Phylogenetic Signal for Pigeons and Doves (Aves of this assumption in the pigeons and doves (Aves: Columbiformes) by comparing phylog- enies derived from nuclear incongruence between trees derived from the two genes; so, we combined nuclear and mitochondrial data

  20. Exclusion of Angiotensinogen Gene in Molecular Basis of Human Hypertension: Sibpair Linkage and

    E-Print Network [OSTI]

    Nyholt, Dale R.

    Exclusion of Angiotensinogen Gene in Molecular Basis of Human Hypertension: Sibpair Linkage. Benjafield,1 Dale R. Nyholt,2 and Brian J. Morris1 * 1 Hypertension Gene Laboratory, Department of Physiology Research Centre, Griffith University, Gold Coast, Queensland, Australia Linkage with essential hypertension

  1. Prokupek 2008 THE ANALYSIS OF GENES EXPRESSED IN THE SPERM STORAGE

    E-Print Network [OSTI]

    Moriyama, Etsuko

    Prokupek 2008 THE ANALYSIS OF GENES EXPRESSED IN THE SPERM STORAGE ORGANS OF DROSOPHILA and Learning Company. #12;Prokupek 2008 THE ANALYSIS OF GENES EXPRESSED IN THE SPERM STORAGE ORGANS reproductive system. Sperm storage organs are important to the reproductive success of both males and females

  2. Enhanced Hydrogen Production in Escherichia coli Through Chemical Mutagenesis, Gene Deletion, and Transposon Mutagenesis

    E-Print Network [OSTI]

    Garzon Sanabria, Andrea Juliana

    2011-08-08T23:59:59.000Z

    ENHANCED HYDROGEN PRODUCTION IN ESCHERICHIA COLI THROUGH CHEMICAL MUTAGENESIS, GENE DELETION, AND TRANSPOSON MUTAGENESIS A Thesis by ANDREA JULIANA GARZON SANABRIA Submitted to the Office of Graduate Studies of Texas A...&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE May 2010 Major Subject: Chemical Engineering ENHANCED HYDROGEN PRODUCTION IN ESCHERICHIA COLI THROUGH CHEMICAL MUTAGENESIS, GENE DELETION...

  3. Biodegradable branched poly(ethylenimine sulfide) for gene delivery Heebeom Koo 1

    E-Print Network [OSTI]

    Park, Jong-Sang

    Biodegradable branched poly(ethylenimine sulfide) for gene delivery Heebeom Koo 1 , Geun-woo Jin 1 , Hyunseo Kang, Yan Lee, Kihoon Nam, Cheng Zhe Bai, Jong-Sang Park* School of Chemistry & Molecular October 2009 Keywords: Gene transfer Biodegradation Cytotoxicity Cell viability Biocompatibility a b s t r

  4. NHR-23 dependent collagen and hedgehog-related genes required for molting

    SciTech Connect (OSTI)

    Kouns, Nathaniel A.; Nakielna, Johana; Behensky, Frantisek [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic)] [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic); Krause, Michael W. [Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (United States)] [Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (United States); Kostrouch, Zdenek [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic)] [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic); Kostrouchova, Marta, E-mail: marta.kostrouchova@lf1.cuni.cz [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic)] [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic)

    2011-10-07T23:59:59.000Z

    Highlights: {yields} NHR-23 is a critical regulator of nematode development and molting. {yields} The manuscript characterizes the loss-of-function phenotype of an nhr-23 mutant. {yields} Whole genome expression analysis identifies new potential targets of NHR-23. {yields} Hedgehog-related genes are identified as NHR-23 dependent genes. {yields} New link between sterol mediated signaling and regulation by NHR-23 is found. -- Abstract: NHR-23, a conserved member of the nuclear receptor family of transcription factors, is required for normal development in Caenorhabditis elegans where it plays a critical role in growth and molting. In a search for NHR-23 dependent genes, we performed whole genome comparative expression microarrays on both control and nhr-23 inhibited synchronized larvae. Genes that decreased in response to nhr-23 RNAi included several collagen genes. Unexpectedly, several hedgehog-related genes were also down-regulated after nhr-23 RNAi. A homozygous nhr-23 deletion allele was used to confirm the RNAi knockdown phenotypes and the changes in gene expression. Our results indicate that NHR-23 is a critical co-regulator of functionally linked genes involved in growth and molting and reveal evolutionary parallels among the ecdysozoa.

  5. Regulation of E2F-1 gene expression in human breast cancer cells 

    E-Print Network [OSTI]

    Ngwenya, Sharon Khethiwe

    2005-08-29T23:59:59.000Z

    17?-Estradiol induces E2F-1 gene expression in ZR-75 and MCF-7 human breast cancer cells. Analysis of the E2F-1 gene promoter in MCF-7 cells previously showed that hormone-induced transactivation required interactions between ...

  6. Transcriptional networks: reverse-engineering gene regulation on a global scale

    E-Print Network [OSTI]

    Babu, M. Madan

    understand the transcriptional control of each gene and the targets of each transcription factor. In yeast, cis regulatory elements, and transcription factor DNA binding sites in vivo. Methods for modeling). This provides a mechanism to control specific aspects of phy- siology; it also enables the use of gene co

  7. Towards Automatic Detecting of Overlapping Genes -Clustered BLAST Analysis of Viral

    E-Print Network [OSTI]

    Reiterer, Harald

    overlaps. In case of short, trivial overlaps, the #12;2 Neuhaus et al. Fig. 1. A double strand of DNA overlapping genes has been modeled by mutational events, which displace the start or stop codons [3­9]. The focus of this project, however, is on embedded genes which encode two completely different functional

  8. Irradiated Esophageal Cells are Protected from Radiation-Induced Recombination by MnSOD Gene Therapy

    E-Print Network [OSTI]

    Engelward, Bevin

    Irradiated Esophageal Cells are Protected from Radiation-Induced Recombination by MnSOD Gene. Irradiated Esophageal Cells are Protected from Radiation- Induced Recombination by MnSOD Gene Therapy. Radiat,a Bevin Engelward,b Michael Epperlya and Joel S. Greenbergera,1 a Departments of Radiation Oncology

  9. ASIAN: a web server for inferring a regulatory network framework from gene expression profiles

    E-Print Network [OSTI]

    Babu, M. Madan

    ASIAN: a web server for inferring a regulatory network framework from gene expression profiles developed to deduce the gene regulatory network. Here, we describe our web server for inferring a framework matrix between variables, and therefore, our server can analyze a wide variety of data within

  10. The Role of the Bcl-X Gene as a Tumor Supressor

    E-Print Network [OSTI]

    McCorvey, Farah

    2007-09-17T23:59:59.000Z

    as a tumor suppressor in certain types of cancers (e.g. breast cancer) is the gene Bcl-x. I seek to determine if Bcl-x is an effective tumor suppressor in hopes that it may be used in gene targeting for treating breast cancer. The methods of my...

  11. Cryptic Speciation and Recombination in the Fungus Paracoccidioides brasiliensis as Revealed by Gene Genealogies

    E-Print Network [OSTI]

    by Gene Genealogies Daniel R. Matute,* 1 Juan G. McEwen,*à1 Rosana Puccia,§ Beatriz A. Montes,* Gioconda and possible recombination using concordance and nondiscordance of gene genealogies with respect to phylogenies with six isolates), and PS3 (phylogenetic species 3 with 21 isolates). Genealogies of four of the regions

  12. On Transition Bias in Mitochondrial Genes of Pocket Gophers Xuhua Xia,1

    E-Print Network [OSTI]

    Xia, Xuhua

    On Transition Bias in Mitochondrial Genes of Pocket Gophers Xuhua Xia,1 Mark S. Hafner,1,2 Philip D selection to transition bias has not been quan- titatively assessed in mitochondrial protein genes. The observed transition/transversion (s/v) ratio is ( s Ps)/( v Pv), where s and v denote mutation rate

  13. Gene Feature Extraction Using T-Test Statistics and Kernel Partial Least Squares

    E-Print Network [OSTI]

    Kwok, James Tin-Yau

    Gene Feature Extraction Using T-Test Statistics and Kernel Partial Least Squares Shutao Li1 , Chen Clear Water Bay, Hong Kong shutao li@yahoo.com.cn, lc337199@sina.com, jamesk@cs.ust.hk Abstract. In this paper, we propose a gene extraction method by us- ing two standard feature extraction methods, namely

  14. GAD2 on Chromosome 10p12 Is a Candidate Gene for Human Obesity

    E-Print Network [OSTI]

    Boyer, Edmond

    GAD2 on Chromosome 10p12 Is a Candidate Gene for Human Obesity Philippe Boutin1[ , Christian Dina1 encoding the glutamic acid decarboxylase enzyme (GAD65) is a positional candidate gene for obesity on Chromosome 10p11­12, a susceptibility locus for morbid obesity in four independent ethnic populations. GAD65

  15. Horizontal gene transfer and the evolution of transcriptionalregulation in Escherichia coli

    SciTech Connect (OSTI)

    Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.

    2007-12-20T23:59:59.000Z

    Background: Most bacterial genes were acquired by horizontalgene transfer from other bacteria instead of being inherited bycontinuous vertical descent from an ancient ancestor}. To understand howthe regulation of these {acquired} genes evolved, we examined theevolutionary histories of transcription factors and of regulatoryinteractions from the model bacterium Escherichia coli K12. Results:Although most transcription factors have paralogs, these usually arose byhorizontal gene transfer rather than by duplication within the E. colilineage, as previously believed. In general, most neighbor regulators --regulators that are adjacent to genes that they regulate -- were acquiredby horizontal gene transfer, while most global regulators evolvedvertically within the gamma-Proteobacteria. Neighbor regulators wereoften acquired together with the adjacent operon that they regulate, sothe proximity might be maintained by repeated transfers (like "selfishoperons"). Many of the as-yet-uncharacterized (putative) regulators havealso been acquired together with adjacent genes, so we predict that theseare neighbor regulators as well. When we analyzed the histories ofregulatory interactions, we found that the evolution of regulation byduplication was rare, and surprisingly, many of the regulatoryinteractions that are shared between paralogs result from convergentevolution. Another surprise was that horizontally transferred genes aremore likely than other genes to be regulated by multiple regulators, andmost of this complex regulation probably evolved after the transfer.Conclusions: Our results highlight the rapid evolution of niche-specificgene regulation in bacteria.

  16. A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks

    E-Print Network [OSTI]

    Diggavi, Suhas

    A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks that this cross-platform pipeline characterizes known and uncovers many novel TF­DNA interactions. In addition, we an excellent model organism for studying metazoan gene regulation, especially mamma- lian-specific complex

  17. TP53 gene mutations of lung cancer patients in upper northern Thailand and environmental risk factors

    E-Print Network [OSTI]

    TP53 gene mutations of lung cancer patients in upper northern Thailand and environmental risk mutations are observed in about 40e70% of lung cancer tissues, and the hot spot codon mu- tations factors that influence TP53 gene mutation in lung cancer patients residing areas with high lung cancer

  18. Genome-wide patterns of divergence and gene flow across a butterfly radiation

    E-Print Network [OSTI]

    Mallet, James

    Genome-wide patterns of divergence and gene flow across a butterfly radiation NICOLA J. NADEAU, Panama City, Naos Island, Causeway Amador, Panama, Facultad de Ciencias Naturales y Matema butterflies are a diverse recent radiation comprising multiple levels of divergence with ongoing gene flow

  19. FUNCTIONAL ANNOTATION OF OIL PALM GENES USING AN AUTOMATED BIOINFORMATICS APPROACH FUNCTIONAL ANNOTATION OF OIL PALM

    E-Print Network [OSTI]

    Sinskey, Anthony J.

    FUNCTIONAL ANNOTATION OF OIL PALM GENES USING AN AUTOMATED BIOINFORMATICS APPROACH 35 FUNCTIONAL ANNOTATION OF OIL PALM GENES USING AN AUTOMATED BIOINFORMATICS APPROACH LAURA B WILLIS*; PHILIP A LESSARDBank, and duplicate entries were eliminated by pairwise BLAST searches, resulting in a collection of unique oil palm

  20. Genetic analyses of bovine CARD15, a putative disease resistance gene 

    E-Print Network [OSTI]

    Taylor, Kristen Hawkins

    2004-09-30T23:59:59.000Z

    Through a binding partner the CARD15 gene activates NF-kB, a molecule with a role in the initiation of the inflammatory immune response. The gene is highly conserved in both structure and function in human and mouse and ...

  1. Genetic analyses of bovine CARD15, a putative disease resistance gene

    E-Print Network [OSTI]

    Taylor, Kristen Hawkins

    2004-09-30T23:59:59.000Z

    Through a binding partner the CARD15 gene activates NF-kB, a molecule with a role in the initiation of the inflammatory immune response. The gene is highly conserved in both structure and function in human and mouse and has recently been implicated...

  2. Gene expression divergence and nucleotide differentiation between males of different color morphs and mating

    E-Print Network [OSTI]

    Gene expression divergence and nucleotide differentiation between males of different color morphs sequencing, it is possible to obtain data on both nucleotide sequence variation and gene expression. We have between males, but many genetic markers showed nucleotide differentiation between different color morphs

  3. Pigment-cell-specific genes from fibroblasts are transactivated after chromosomal transfer into melanoma cells

    SciTech Connect (OSTI)

    Powers, T.P.; Davidson, R.L. [Univ. of Illinois College of Medicine, Chicago, IL (United States); Shows, T.B. [Roswell Park Memorial Inst., Buffalo, NY (United States)

    1994-02-01T23:59:59.000Z

    Human and mouse fibroblast chromosomes carrying tyrosinase or b-locus genes were introduced, by microcell hybridization, into pigmented Syrian hamster melanoma cells, and the microcell hybrids were tested for transactivation of the fibroblast tyrosinase and b-locus genes. By using species-specific PCR amplification to distinguish fibroblast and melanoma cDNAs, it was demonstrated that the previously silent fibroblast tyrosinase and b-locus genes were transactivated following chromosomal transfer into pigmented melanoma cells. However, transactivation of the mouse fibroblast tyrosinase gene was unstable in microcell hybrid subclones and possibly dependent on a second fibroblast locus that could have segregated in the subclones. This second locus was not necessary for transactivation of the fibroblast b-locus gene, thus demonstrating noncoordinate transactivation of fibroblast tyrosinase and b-locus genes. Transactivation of the fibroblast tyrosinase gene in microcell hybrids apparently is dependent on the absence of a putative fibroblast extinguisher locus for tyrosinase gene expression, which presumably is responsible for the extinction of pigmentation in hybrids between karyotypically complete fibroblasts and melanoma cells. 46 refs., 5 figs., 2 tabs.

  4. Evolutionary Conservation of Expression Profiles Between Human and Mouse Orthologous Genes

    E-Print Network [OSTI]

    Zhang, Jianzhi

    ­array-based observations from many individual genes and imply the uselessness of mouse models for studying human genes­profiling technologies became available (Cavalieri, Townsend, and Hartl 2000; Enard et al. 2002; Oleksiak, Churchill all the technologies for producing transcriptome data, the DNA (oligonucleotide or cDNA) microarray

  5. Gene galaxies in the maize genome Virginia Walbot* and Dmitri A. Petrov

    E-Print Network [OSTI]

    Petrov, Dmitri

    Commentary Gene galaxies in the maize genome Virginia Walbot* and Dmitri A. Petrov Department of higher eukary- otic genomes yielded the surprise that despite hundreds of millions of years in gene number, eukaryotic genome size varies over 5 orders of magnitude (4), a paradoxical feature

  6. Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes

    E-Print Network [OSTI]

    Frey, Brendan J.

    Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes provided information regarding the dynamics of gene expression during development of the mouse lung a global survey of protein expression during mouse lung organogenesis from embryonic day E13.5 until

  7. Promoter Analysis of Co-regulated Genes in the Yeast Genome Michael Q. Zhang

    E-Print Network [OSTI]

    of large-scale expression data. It is well-known that complex gene expression patterns result from dynamic exploration of various initial experimental data. We will use cell-cycle regulated gene expression to develop computational tools which would allow us or bench scientists to make efficient use of the new

  8. TECHNICAL ADVANCE The ethanol switch: a tool for tissue-specic gene induction

    E-Print Network [OSTI]

    Murray, J.A.H.

    TECHNICAL ADVANCE The ethanol switch: a tool for tissue-speci®c gene induction during plant is a powerful tool for the analysis of gene function during plant development. Here, we report ethanol inducible of an ethanol-regulated transcription factor, ALCR, is restricted to precise domains using speci®c promoters

  9. New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched

    E-Print Network [OSTI]

    New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones required during embryogenesis. These studies have demonstrated that the ovary is enriched for transcripts selected to represent ovary-enriched genes not associated with an embryonic phenotype. We discovered 155

  10. New Markov Model Approaches to Deciphering Microbial Genome Function and Evolution: Comparative Genomics of Laterally Transferred Genes

    SciTech Connect (OSTI)

    Borodovsky, M.

    2013-04-11T23:59:59.000Z

    Algorithmic methods for gene prediction have been developed and successfully applied to many different prokaryotic genome sequences. As the set of genes in a particular genome is not homogeneous with respect to DNA sequence composition features, the GeneMark.hmm program utilizes two Markov models representing distinct classes of protein coding genes denoted "typical" and "atypical". Atypical genes are those whose DNA features deviate significantly from those classified as typical and they represent approximately 10% of any given genome. In addition to the inherent interest of more accurately predicting genes, the atypical status of these genes may also reflect their separate evolutionary ancestry from other genes in that genome. We hypothesize that atypical genes are largely comprised of those genes that have been relatively recently acquired through lateral gene transfer (LGT). If so, what fraction of atypical genes are such bona fide LGTs? We have made atypical gene predictions for all fully completed prokaryotic genomes; we have been able to compare these results to other "surrogate" methods of LGT prediction.

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

    DOE Patents [OSTI]

    Ingram, Lonnie O. (Gainesville, FL); Ohta, Kazuyoshi (Gainesville, FL); Wood, Brent E. (Gainesville, FL)

    2000-08-22T23:59:59.000Z

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

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

    DOE Patents [OSTI]

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

    1998-10-13T23:59:59.000Z

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

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

    DOE Patents [OSTI]

    Ingram, Lonnie O. (Gainesville, FL); Ohta, Kazuyoshi (Gainesville, FL); Wood, Brent E. (Gainesville, FL)

    1998-01-01T23:59:59.000Z

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

  14. Use of NAP gene to manipulate leaf senescence in plants

    DOE Patents [OSTI]

    Gan, Susheng; Guo, Yongfeng

    2013-04-16T23:59:59.000Z

    The present invention discloses transgenic plants having an altered level of NAP protein compared to that of a non-transgenic plant, where the transgenic plants display an altered leaf senescence phenotype relative to a non-transgenic plant, as well as mutant plants comprising an inactivated NAP gene, where mutant plants display a delayed leaf senescence phenotype compared to that of a non-mutant plant. The present invention also discloses methods for delaying leaf senescence in a plant, as well as methods of making a mutant plant having a decreased level of NAP protein compared to that of a non-mutant plant, where the mutant plant displays a delayed leaf senescence phenotype relative to a non-mutant plant. Methods for causing precocious leaf senescence or promoting leaf senescence in a plant are also disclosed. Also disclosed are methods of identifying a candidate plant suitable for breeding that displays a delayed leaf senescence and/or enhanced yield phenotype.

  15. LAMMPS strong scaling performance optimization on Blue Gene/Q

    SciTech Connect (OSTI)

    Coffman, Paul; Jiang, Wei; Romero, Nichols A.

    2014-11-12T23:59:59.000Z

    LAMMPS "Large-scale Atomic/Molecular Massively Parallel Simulator" is an open-source molecular dynamics package from Sandia National Laboratories. Significant performance improvements in strong-scaling and time-to-solution for this application on IBM's Blue Gene/Q have been achieved through computational optimizations of the OpenMP versions of the short-range Lennard-Jones term of the CHARMM force field and the long-range Coulombic interaction implemented with the PPPM (particle-particle-particle mesh) algorithm, enhanced by runtime parameter settings controlling thread utilization. Additionally, MPI communication performance improvements were made to the PPPM calculation by re-engineering the parallel 3D FFT to use MPICH collectives instead of point-to-point. Performance testing was done using an 8.4-million atom simulation scaling up to 16 racks on the Mira system at Argonne Leadership Computing Facility (ALCF). Speedups resulting from this effort were in some cases over 2x.

  16. Studies on gene expression profiling in JB6 cells susceptible and resistant to tumor promoter induced neoplastic transformation and regulation of gene expression at the AP-1 DNA binding site 

    E-Print Network [OSTI]

    Samuel, Shaija

    2005-11-01T23:59:59.000Z

    Gene expression underlies all important biological processes in a cell and mis-regulated gene expression plays a causal or contributory role in several diseases including cancers. Towards identifying molecular determinants ...

  17. Technology development for gene discovery and full-length sequencing

    SciTech Connect (OSTI)

    Marcelo Bento Soares

    2004-07-19T23:59:59.000Z

    In previous years, with support from the U.S. Department of Energy, we developed methods for construction of normalized and subtracted cDNA libraries, and constructed hundreds of high-quality libraries for production of Expressed Sequence Tags (ESTs). Our clones were made widely available to the scientific community through the IMAGE Consortium, and millions of ESTs were produced from our libraries either by collaborators or by our own sequencing laboratory at the University of Iowa. During this grant period, we focused on (1) the development of a method for preferential cloning of tissue-specific and/or rare transcripts, (2) its utilization to expedite EST-based gene discovery for the NIH Mouse Brain Molecular Anatomy Project, (3) further development and optimization of a method for construction of full-length-enriched cDNA libraries, and (4) modification of a plasmid vector to maximize efficiency of full-length cDNA sequencing by the transposon-mediated approach. It is noteworthy that the technology developed for preferential cloning of rare mRNAs enabled identification of over 2,000 mouse transcripts differentially expressed in the hippocampus. In addition, the method that we optimized for construction of full-length-enriched cDNA libraries was successfully utilized for the production of approximately fifty libraries from the developing mouse nervous system, from which over 2,500 full-ORF-containing cDNAs have been identified and accurately sequenced in their entirety either by our group or by the NIH-Mammalian Gene Collection Program Sequencing Team.

  18. Effect of Amino Acid Subsititution in Set1 on Histone H3 Methylation and Gene Silencing in Saaccharomyces Cerevisiae

    E-Print Network [OSTI]

    Chateau, Morgan

    2008-08-24T23:59:59.000Z

    silencing is necessary for normal cell development and regulation. Incorrect or missing histone modifications can cause the loss of gene silencing and uncontrolled gene expression similar to the situation in cells of patients with cancer or leukemia. My...

  19. Study Finds that Children with Autism and Gastrointestinal Symptoms Have Altered Expression of Genes Involved in Digestion

    E-Print Network [OSTI]

    Salzman, Daniel

    of Genes Involved in Digestion These changes may also affect the mix of bacteria present in the digestive disturbances have altered expression of genes involved in digestion. These variations may contribute to changes

  20. The comparative genomics of salinispora and the distribution and abundance of secondary metabolite genes in marine plankton

    E-Print Network [OSTI]

    Penn, Kevin Matthew

    2012-01-01T23:59:59.000Z

    rplB smpB Comparative genomics Gene gain Gene loss Totalbiology and comparative genomics. BMC Bioinformatics 10(1):Intersection of Evolution and Genomics. Science 300(5626):

  1. Characterizing cell-cycle as a global regulator of stochastic transcription and noisy gene expression in S. cerevisiae

    E-Print Network [OSTI]

    Quinn, Katie J. (Katie Julia)

    2014-01-01T23:59:59.000Z

    Even in the same environment, genetically identical cells can exhibit remarkable variability, or noise, in gene expression. This expression noise impacts the function of gene regulatory networks, depending on its origins. ...

  2. Feasibility of a predictive model of Hsp70b-activated gene therapy protein expression during ultrasound hyperthermia

    E-Print Network [OSTI]

    Silcox, Christina Elise

    2014-01-01T23:59:59.000Z

    Gene therapy has been heralded as a possible approach to a variety of diseases and conditions, ranging from cancer and heart disease to blindness and neurodegenerative diseases. However, progress in gene therapy requires ...

  3. Gene Expression Profile of Mesenchymal Stem Cells from Paired Umbilical Cord Units: Cord is Different from Blood

    E-Print Network [OSTI]

    2009-01-01T23:59:59.000Z

    2002). Gene expression profile of human bone marrow stromal2003). Gene expression profile of mouse bone marrow stromalRNA (ncRNA) expression profiles of MSC from match-paired UC

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

    E-Print Network [OSTI]

    Gordan, Raluca

    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 ...

  5. Functional Identification of Tumor Suppressor Genes Through an in vivo RNA Interference Screen in a Mouse Lymphoma Model

    E-Print Network [OSTI]

    Bric, Anka

    Short hairpin RNAs (shRNAs) capable of stably suppressing gene function by RNA interference (RNAi) can mimic tumor-suppressor-gene loss in mice. By selecting for shRNAs capable of accelerating lymphomagenesis in a ...

  6. Mechanisms of hormonal regulation of CAD gene expression and inhibition by Aryl hydrocarbon receptor agonist in human breast cancer cells 

    E-Print Network [OSTI]

    Khan, Shaheen Munawar Ali

    2007-04-25T23:59:59.000Z

    The CAD gene is trifunctional and expresses carbamoylphosphate synthetase/aspartate carbamyltransferase/dihydroorotase, which are required for pyrimidine biosynthesis. CAD gene activities are induced in MCF-7 human breast ...

  7. Stability and Electronic Properties of TiO2 Nanostructures With and Without B and D. J. Mowbray,* J. I. Martinez, J. M. Garcia Lastra, K. S. Thygesen, and K. W. Jacobsen

    E-Print Network [OSTI]

    Thygesen, Kristian

    Ved: January 8, 2009 We address one of the main challenges to TiO2 photocatalysis, namely band gap narrowing photocatalysis has been intensely researched as a possible candidate for addressing these issues. Since the first

  8. 6 Gerlai, R. (2001) Gene targeting: technical confounds and potential solutions in behavioral brain research. Behav. Brain Res. 125,

    E-Print Network [OSTI]

    Zhang, ZhaoLei

    at different alternative splice donor sites of the tyrosinase gene in murine albinism. Genomics 37, 245­248 17

  9. redD as a Reporter for Transcriptional Activity 551 Application of redD, the Transcriptional Activator Gene

    E-Print Network [OSTI]

    Bibb, Mervyn

    glaucescens, which encodes tyrosinase (Paget et al., 1994), and the EGFP gene for green-fluorescent protein

  10. New screening software shows most recent large 16S rRNA gene clone libraries1 contain chimeras.2

    E-Print Network [OSTI]

    Jones, Antonia J.

    1 New screening software shows most recent large 16S rRNA gene clone libraries1 contain chimeras.2 3 Running title4 Detecting chimeras within 16S rRNA gene libraries.5 6 Authors7 Kevin E. Ashelford for screening entire 16S rRNA gene2 libraries, of up to 1,000 sequences, for chimeras and other artifacts

  11. A Continuous-State Coalescent and the Impact of Weak Selection on the Structure of Gene Genealogies

    E-Print Network [OSTI]

    Adler, Fred

    A Continuous-State Coalescent and the Impact of Weak Selection on the Structure of Gene Genealogies for understanding the shape of gene genealogies and resulting patterns of genetic diversity. However, the coalescent words: coalescent, weak selection, gene genealogies, interference,multisite selection. Researcharticle

  12. The CER3 wax biosynthetic gene from Arabidopsis thaliana is allelic to WAX2/YRE/FLP1

    E-Print Network [OSTI]

    Kunst, Ljerka

    The CER3 wax biosynthetic gene from Arabidopsis thaliana is allelic to WAX2/YRE/FLP1 Owen Rowlanda with waxes. The Arabidopsis CER3 gene is important for cuticular wax biosynthesis and was reported and instead corresponds to WAX2/ YRE/FLP1 (At5g57800), a gene of unknown function required for wax

  13. Nucleotide sequence of the 2 matrix protein genes (M1 and M2) of hirame rhabdovirus (HRV),

    E-Print Network [OSTI]

    Boyer, Edmond

    Nucleotide sequence of the 2 matrix protein genes (M1 and M2) of hirame rhabdovirus (HRV), a fish of hirame rhabdovirus (HRV). The M1 protein gene was 684 nucleotides long, encoding 227 amino acids.8% at the nucleotide level and 81.1 and 44.8% at the amino acid level. The M2 protein gene was 582 nucleotides long

  14. Supplementary material Setting the weight cut-off in the labelling of gene families with GOslim annotation

    E-Print Network [OSTI]

    Gent, Universiteit

    Supplementary material Setting the weight cut-off in the labelling of gene families with GOslim cut-off values in the abscis. The plots show how many gene labels were appointed to the family S1 shows that if the cut-off value increases, the amount of gene families with many GOslim labels

  15. An accurate prostate cancer prognosticator using a seven-gene signature plus Gleason score and taking cell type heterogeneity into account.

    E-Print Network [OSTI]

    2012-01-01T23:59:59.000Z

    in low risk group defined by the seven-gene prognosticin the high risk group defined by the seven-gene with post

  16. Self-assembled pentablock copolymers for selective and sustained gene delivery

    SciTech Connect (OSTI)

    Zhang, Bingqi

    2011-05-15T23:59:59.000Z

    The poly(diethylaminoethyl methacrylate) (PDEAEM) - Pluronic F127 - PDEAEM pentablock copolymer (PB) gene delivery vector system has been found to possess an inherent selectivity in transfecting cancer cells over non-cancer cells in vitro, without attaching any targeting ligands. In order to understand the mechanism of this selective transfection, three possible intracellular barriers to transfection were investigated in both cancer and non-cancer cells. We concluded that escape from the endocytic pathway served as the primary intracellular barrier for PB-mediated transfection. Most likely, PB vectors were entrapped and rendered non-functional in acidic lysosomes of non-cancer cells, but survived in less acidic lysosomes of cancer cells. The work highlights the importance of identifying intracellular barriers for different gene delivery systems and provides a new paradigm for designing targeting vectors based on intracellular differences between cell types, rather than through the use of targeting ligands. The PB vector was further developed to simultaneously deliver anticancer drugs and genes, which showed a synergistic effect demonstrated by significantly enhanced gene expression in vitro. Due to the thermosensitive gelation behavior, the PB vector packaging both drug and gene was also investigated for its in vitro sustained release properties by using polyethylene glycol diacrylate as a barrier gel to mimic the tumor matrix in vivo. Overall, this work resulted in the development of a gene delivery vector for sustained and selective gene delivery to tumor cells for cancer therapy.

  17. Molecular dissection of the roles of the SOD genes in mammalian response to low dose irradiation

    SciTech Connect (OSTI)

    Eric Y. Chuang

    2006-08-31T23:59:59.000Z

    It has been long recognized that a significant fraction of the radiation-induced genetic damage to cells are caused by secondary oxidative species. Internal cellular defense systems against oxidative stress play significant roles in countering genetic damage induced by ionizing radiation. The role of the detoxifying enzymes may be even more prominent in the case of low-dose, low-LET irradiation, as the majority of genetic damage may be caused by secondary oxidative species. In this study we have attempted to decipher the roles of the superoxide dismutase (SOD) genes, which are responsible for detoxifying the superoxide anions. We used adenovirus vectors to deliver RNA interference (RNAi or siRNA) technology to down-regulate the expression levels of the SOD genes. We have also over-expressed the SOD genes by use of recombinant adenovirus vectors. Cells infected with the vectors were then subjected to low dose ?-irradiation. Total RNA were extracted from the exposed cells and the expression of 9000 genes were profiled by use of cDNA microarrays. The result showed that low dose radiation had clear effects on gene expression in HCT116 cells. Both over-expression and down-regulation of the SOD1 gene can change the expression profiles of sub-groups of genes. Close to 200 of the 9000 genes examined showed over two-fold difference in expression under various conditions. Genes with changed expression pattern belong to many categories that include: early growth response, DNA-repair, ion transport, apoptosis, and cytokine response.

  18. Coregulation of terpenoid pathway genes and prediction of isoprene production in Bacillus subtilis using transcriptomics

    SciTech Connect (OSTI)

    Hess, Becky M.; Xue, Junfeng; Markillie, Lye Meng; Taylor, Ronald C.; Wiley, H. S.; Ahring, Birgitte K.; Linggi, Bryan E.

    2013-06-19T23:59:59.000Z

    The isoprenoid pathway converts pyruvate to isoprene and related isoprenoid compounds in plants and some bacteria. Currently, this pathway is of great interest because of the critical role that isoprenoids play in basic cellular processes as well as the industrial value of metabolites such as isoprene. Although the regulation of several pathway genes has been described, there is a paucity of information regarding the system level regulation and control of the pathway. To address this limitation, we examined Bacillus subtilis grown under multiple conditions and then determined the relationship between altered isoprene production and the pattern of gene expression. We found that terpenoid genes appeared to fall into two distinct subsets with opposing correlations with respect to the amount of isoprene produced. The group whose expression levels positively correlated with isoprene production included dxs, the gene responsible for the commitment step in the pathway, as well as ispD, and two genes that participate in the mevalonate pathway, yhfS and pksG. The subset of terpenoid genes that inversely correlated with isoprene production included ispH, ispF, hepS, uppS, ispE, and dxr. A genome wide partial least squares regression model was created to identify other genes or pathways that contribute to isoprene production. This analysis showed that a subset of 213 regulated genes was sufficient to create a predictive model of isoprene production under different conditions and showed correlations at the transcriptional level. We conclude that gene expression levels alone are sufficiently informative about the metabolic state of a cell that produces increased isoprene and can be used to build a model which accurately predicts production of this secondary metabolite across many simulated environmental conditions.

  19. System and method for introduction and stabilization of genes in Thermus sp.

    DOE Patents [OSTI]

    Kayser, Kevin J.; Park, Ho-Shin; Kilbane, II, John J.

    2005-03-01T23:59:59.000Z

    A method for introducing and stabilizing heterologous and recombinant genes in a thermophilic host in which a characteristic gene defining a detectable host characteristic is inactivated or deleted from the thermophilic host, resulting in a modified thermophilic host expressing an absence of the detectable host characteristic. A DNA fragment of interest is inserted into the modified thermophilic host together with an intact characteristic gene, whereby the detectable host characteristic is restored to the thermophilic host, thereby enabling detection and confirmation of successful transformation using plasmid vectors and integration of the DNA fragment into the chromosome of the thermophilic host.

  20. Studies on the chalcone synthase gene of two higher plants: petroselinum hortense and matthiola incana

    SciTech Connect (OSTI)

    Hemleben, V.; Frey, M.; Rall, S.; Koch, M.; Kittel, M.; Kreuzaler, F.; Ragg, H.; Fautz, E.; Hahlbrock, K.

    1982-01-01T23:59:59.000Z

    Two higher plant systems are presented which allow to study coordinated gene expression of the light-induced metabolic pathway of flavonoid biosynthesis: tissue culture cells of Petroselinum hortense (Apiaceae) and different developmental stages of various genotypes of Matthiola incana (Brassicaceae). The gene structure of the chalcone synthase is mainly studied. A cDNA clone (pLF56) of parsley has been constructed and characterized conferring the chalcone synthase gene sequence. Strong cross hybridization between the parsley cDNA and Matthiola DNA allowed to identify a HindIII fragment (6000 bp) identical in size for parsley and different Matthiola wild type lines and a mutant line.

  1. Expression and rearrangement of the ROS1 gene in human glioblastoma cells

    SciTech Connect (OSTI)

    Birchmeier, C.; Sharma, S.; Wigler, M.

    1987-12-01T23:59:59.000Z

    The human ROS1 gene, which possibly encodes a growth factor receptor, was found to be expressed in human tumor cell lines. In a survey of 45 different human cell lines, the authors found ROS1 to be expressed in glioblastoma-derived cell lines at high levels and not to be expressed at all, or expressed at very low levels, in the remaining cell lines. The ROS1 gene was present in normal copy numbers in all cell lines that expressed the gene. However, in one particular glioblastoma line, they detected a potentially activating mutation at the ROS1 locus.

  2. Mutations of the tyrosinase gene in Indo-Pakistani patients with type I (tyrosinase-deficient) oculocutaneous albinsm (OCA)

    SciTech Connect (OSTI)

    Tripathi, R.K.; Droetto, S.; Strunk, K.M.; Holmes, S.A.; Spritz, R.A. (Univ. of Wisconsin, Madison, WI (United States)); Bundey, S.; Musarella, M.A.

    1993-12-01T23:59:59.000Z

    Oculocutaneous albinism (OCA) is a group of autosomal recessive disorders characterized by deficient synthesis of melanin pigment. Type I (tyrosinase-deficient) OCA results from mutations of the tyrosinase gene (TYR gene) encoding tyrosinase, the enzyme that catalyzes the first two steps of melanin biosynthesis. Mutations of the TYR gene have been identified in a large number of patients, most of Caucasian ethnic origin, with various forms of type I OCA. The authors present an analysis of the TYR gene in eight Indo-Pakistani patients with type I OCA. The authors describe four novel TYR gene mutations and a fifth mutation previously observed in a Caucasian patient. 16 refs., 6 figs.

  3. Mapping our genes: The genome projects: How big, how fast

    SciTech Connect (OSTI)

    none,

    1988-04-01T23:59:59.000Z

    For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for /open quotes/writing the rules/close quotes/ of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. OTA prepared this report with the assistance of several hundred experts throughout the world. 342 refs., 26 figs., 11 tabs.

  4. Tyrosinase-positive oculocutaneous albinism in Southern African blacks: P gene-associated haplotypes suggest a major mutation in the 5{prime} region of the gene

    SciTech Connect (OSTI)

    Ramsay, M.; Stevens, G.; Beukering, J. van [Univ. of the Witwatersrand, Johannesburg (South Africa)] [and others

    1994-09-01T23:59:59.000Z

    Tyrosinase-positive oculocutaneous albinism (ty-pos OCA) occurs with a prevalence of 1 in 3900 among Southern African (SA) blacks. The major contributors to morbidity and mortality are skin cancer and decreased visual acuity. Two distinct phenotypes occur, namely individuals with ephelides (darkly pigmented patches) and those without. There is complete concordance with regard to ephelus status among siblings. The disorder is linked to markers on chromosome 15q11.2-q12, and no obligatory cross-overs were observed with polymophic markers at the human homolog, P, of the mouse pink eyed dilute gene, p. Contrary to what has been shown for Caucasoid ty-pos OCA, this condition shows locus homogeneity among SA blacks. The P gene is an excellent candidate for ty-pos OCA and mutations in this gene will confirm its role in causing the common form of albinism in SA. Numerous P gene mutations have been described in other populations. In an attempt to detect mutations, the P gene cDNA was used to search for structural rearrangements or polymorphisms. Six polymorphisms (plR10/Scal, 912/Xbal, 912/HincII, 912/TaqI, 1412/TaqI [two systems] and 1412/HindIII) were detected with subclones of the P cDNA and haplotypes were determined in each family. None were clearly associated with an albinism-related rearrangement. However, strong linkage disequilibrium was observed with alleles at loci toward the 5{prime} region of the gene ({triangle}=0.65, 0.57 and 0.80 for the three polymorphisms detected with the 912 subclone), suggesting a major ty-pos OCA mutation in this region. Haplotype analysis provides evidence for a major mutation associated with the same haplotype in individuals with ephelides (8/12 OCA chromosomes) and those without ephelides (24:30). The presence of other ty-pos OCA associated haplotypes indicates several other less common mutations.

  5. Genomic analysis of 12-oxo-phytodienoic acid reductase genes of Zea mays

    E-Print Network [OSTI]

    Zhang, Jinglan

    2006-04-12T23:59:59.000Z

    because they are transiently induced by salicylic acid (SA), chitooligosaccharides and by infection with Cochliobolus carbonum, Bipolaris maydis and Fusarium verticillioides and not by wounding. In contrast to these two genes, ZmOPR6 and ZmOPR7...

  6. Hairpin RNAs and Retrotransposon LTRs Effect RNAi and Chromatin-Based Gene Silencing 

    E-Print Network [OSTI]

    Schramke, Vera; Allshire, Robin C

    2003-01-01T23:59:59.000Z

    The expression of short hairpin RNAs in several organisms silences gene expression by targeted mRNA degradation. This RNA interference (RNAi) pathway can also affect the genome, as DNA methylation arises at loci homologous ...

  7. ORIGINAL ARTICLE Gene Transfer to Mouse Heart and Skeletal Muscles Using

    E-Print Network [OSTI]

    Kay, Mark A.

    ORIGINAL ARTICLE Gene Transfer to Mouse Heart and Skeletal Muscles Using a Minicircle Expressing-globin polyA. It also contains a translation initiation signal and an untranslated herpes simplex virus

  8. A Novel Approach to Determine Normal Variation in Gene Expression Data

    E-Print Network [OSTI]

    Zaki, Mohammed Javeed

    among identical mice, thus enabling a comprehensive database of normal variations in gene expression EIA-0103708 under-appreciated problem in microarray analysis is the in- cidence of microarrays

  9. Interactogeneous: Disease Gene Prioritization Using Heterogeneous Networks and Full Topology Scores

    E-Print Network [OSTI]

    and associations from the STRING database, was used to prioritize genes for Parkinson's disease. This method/2007 to JPG; and project contract PTDC/EIA-EIA/111239/2009 to Neuroclinomics. The funders had no role in study

  10. Gene expression profiling in the lungs of pigs with different susceptibilities to Glasser's disease

    E-Print Network [OSTI]

    Wilkinson, Jamie M; Sargent, Carole A; Galina-Pantoja, Lucina; Tucker, Alexander W

    2010-07-29T23:59:59.000Z

    microarray to identify genes that were differentially expressed (DE) in the lungs of colostrum-deprived animals previously characterized as being either 'Fully Resistant' (FR) or 'Susceptible' to infection by H. parasuis in a bacterial challenge experiment...

  11. Mysteries of the Deep: What happens inside of MPI on Blue Gene...

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

    Mysteries of the Deep: What happens inside of MPI on Blue GeneQ and why it matters Jeff Hammond Leadership Computing Facility Argonne National Laboratory March 5, 2013 Jeff...

  12. Analysis of metazoan DNA replication initiation using Drosophila gene amplification as a model system

    E-Print Network [OSTI]

    Kim, Jane Christina

    2011-01-01T23:59:59.000Z

    Gene amplification in Drosophila follicle cells is an excellent model to study origin specification and developmental regulation of DNA replication in vivo. We mapped all follicle cell amplicons using a comparative genomic ...

  13. Applying Machine Learning Methods to Suggest Network Involvement and Functionality of Genes in Saccharomyces cerevisiae

    E-Print Network [OSTI]

    Amthauer, Heather A.

    2008-10-10T23:59:59.000Z

    Elucidating genetic networks provides the foundation for the development of new treatments or cures for diseased pathways, and determining novel gene functionality is critical for bringing a better understanding on how an ...

  14. Heterogeneity of tumor-induced gene expression changes in the human metabolic network

    E-Print Network [OSTI]

    Hu, Jie

    Reprogramming of cellular metabolism is an emerging hallmark of neoplastic transformation. However, it is not known how the expression of metabolic genes in tumors differs from that in normal tissues, or whether different ...

  15. Gene expression and deletion analysis of mechanisms for electron transfer from electrodes to Geobacter sulfurreducens

    E-Print Network [OSTI]

    Lovley, Derek

    transfer to electrodes. Keywords: microbial fuel cell, Geobacter sulfurreducens, cathode, electron donor. Surprisingly, genes for putative cell-electrode connections, such as outer-surface cytochromes and pili, which emerging area in microbe-electrode interactio

  16. Defining a new vision for the retinoblastoma gene: report from the 3rd International Rb Meeting

    E-Print Network [OSTI]

    Rubin, Seth M; Sage, Julien

    2013-01-01T23:59:59.000Z

    and chromatin structure by pRB: here, there and everywhere.screen links LATS2 and the pRB tumor suppressor. Genes DevMV: Combined inactivation of pRB and hippo pathways induces

  17. Proceedings of the Sudden Oak Death Third Science Symposium Global Gene Expression Profiles of

    E-Print Network [OSTI]

    Standiford, Richard B.

    , United States Department of Agriculture, Corvallis, OR. #12;Proceedings of the Sudden Oak Death Third Science Symposium 435 Global Gene Expression Profiles types if they were statistically significant P=0.05 after false discovery rate correction and resulted

  18. p63 and p73 Transcriptionally Regulate Genes Involved in DNA Repair

    E-Print Network [OSTI]

    Lin, Yu-Li

    The p53 family activates many of the same genes in response to DNA damage. Because p63 and p73 have structural differences from p53 and play distinct biological functions in development and metastasis, it is likely that ...

  19. Distinct Cyclin D Genes Show Mitotic Accumulation or Constant Levels of Transcripts in Tobacco

    E-Print Network [OSTI]

    Murray, J.A.H.

    Distinct Cyclin D Genes Show Mitotic Accumulation or Constant Levels of Transcripts in Tobacco-type cyclins accumulate peri- odically during the S, G2, and early M phases (A types) or G2 and early M phases

  20. Characterization in cochlea of KCTD12/PFET1, an intronless gene with predominant fetal expression

    E-Print Network [OSTI]

    Kuo, Sharon Fan

    2006-01-01T23:59:59.000Z

    The prevalence of severe to profound bilateral congenital hearing loss is estimated at 1 in 1000 births, at least half of which can be attributed to a genetic cause. To date, mutations in at least 67 genes have been ...

  1. Novel enabling technologies of gene isolation and plant transformation for improved crop protection

    SciTech Connect (OSTI)

    Torok, Tamas

    2013-02-04T23:59:59.000Z

    Meeting the needs of agricultural producers requires the continued development of improved transgenic crop protection products. The completed project focused on developing novel enabling technologies of gene discovery and plant transformation to facilitate the generation of such products.

  2. Genes: Philosophical Analyses Put to the Test Karola Stotz1 and Paul Griffiths2

    E-Print Network [OSTI]

    Stotz, Karola

    of the concept of the gene were operationalized and tested against questionnaire data obtained from working of science ­ a case study of conceptual change and its role in science. Empirical science is a powerhouse

  3. Tumor suppressor gene Rb is required for self-renewal of spermatogonial stem cells in mice

    E-Print Network [OSTI]

    Hu, Yueh-Chiang

    The retinoblastoma tumor suppressor gene Rb is essential for maintaining the quiescence and for regulating the differentiation of somatic stem cells. Inactivation of Rb in somatic stem cells typically leads to their ...

  4. A role for the Spemann organizer gene, Goosecoid, in tumor metastasis

    E-Print Network [OSTI]

    Hartwell, Kimberly A. (Kimberly Ann)

    2007-01-01T23:59:59.000Z

    The process of invasion and metastasis during tumor progression is often reminiscent of cell migration events occurring during embryonic development. I hypothesized that genes controlling cellular changes in the Spemann ...

  5. Effects of Alcohol on the Regulation of Imprinted Genes in Mouse Stem Cells

    E-Print Network [OSTI]

    Crocker, Alyssa

    2013-02-04T23:59:59.000Z

    ABSTRACT Effects of Alcohol on the Regulation of Imprinted Genes in Mouse Stem Cells. (December 2013) Alyssa Crocker Department of Animal Science Texas A&M University Research Advisor: Dr. Michael Golding Department of Veterinary Physiology...

  6. Spatial patterning of gene expression using surface-immobilized recombinant adenovirus

    E-Print Network [OSTI]

    Chen, Christopher S.

    organization of cells but also control of their gene expression patterns. We report a method to generate (Serls et al. 2005). By controlling which and how much mRNA and protein is produced, one can regulate

  7. Molecular cloning and characterization of important stress and redox regulatory genes from Hydra vulgaris

    E-Print Network [OSTI]

    Dash, Bhagirathi

    2007-04-25T23:59:59.000Z

    In this research, important stress and redox regulatory genes present in Hydra vulgaris were isolated and characterized to facilitate our understanding of the evolution and mechanisms of stress response. H. vulgaris heat shock protein 70 (HvHSP70...

  8. Genes related to xylose fermentation and methods of using same for enhanced biofuel production

    DOE Patents [OSTI]

    Wohlbach, Dana J.; Gasch, Audrey P.

    2014-08-05T23:59:59.000Z

    The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

  9. THE ROLE OF THE MURINE HOMEOBOX GENE CUX-1 IN KIDNEY DEVELOPMENT AND POLYCYSTIC KIDNEY DISEASE

    E-Print Network [OSTI]

    Alcalay, Neal

    2008-02-25T23:59:59.000Z

    The murine homeobox gene cux-1 is evolutionarily conserved in drosophila, mice and humans. Cux-1 contains four DNA binding domains (3 cut repeat domains and a homeodomain) and functions as a transcription factor that ...

  10. Molecular studies of longevity-associated genes in yeast and mammalian cells

    E-Print Network [OSTI]

    Liszt, Gregory (Gregory Birjandi)

    2006-01-01T23:59:59.000Z

    Aging is a complex process affecting diverse organisms from bacteria to humans. Despite strong evolutionary arguments against the conservation of a single mechanism of aging, a variety of conserved single gene mutations ...

  11. Regulation of horizontal gene transfer by intercellular peptide signaling in Bacillus subtilis

    E-Print Network [OSTI]

    Auchtung, Jennifer M

    2006-01-01T23:59:59.000Z

    Horizontal gene transfer plays an important role in bacterial evolution. Although acquisition of foreign DNA can be beneficial to cells, it can also be detrimental. Therefore, cells that possess mechanisms to regulate ...

  12. Combinatorial control of temporal gene expression in the Drosophila wing by enhancers and core promoters

    E-Print Network [OSTI]

    O’Keefe, David D; Thomas, Sean R; Bolin, Kelsey; Griggs, Ellen; Edgar, Bruce A; Buttitta, Laura A

    2012-01-01T23:59:59.000Z

    program to per- form k-means clustering, imposing values ofof expression for each k-means cluster and Supple- mentalthe genes within each k-means cluster, and ordered the

  13. EXCAVATOR: A Computer Program for Efficiently Mining Gene-Expression Data

    E-Print Network [OSTI]

    demonstrated on several experimental data sets. Its performance also compares favorably against the popular K-means-specified seed genes, (iv) cluster identification from a noisy background, and (v) automated comparison between

  14. Modified cellulose synthase gene from Arabidopsis thaliana confers herbicide resistance to plants

    DOE Patents [OSTI]

    Somerville, Chris R. (Portola Valley, CA); Scheible, Wolf (Golm, DE)

    2007-07-10T23:59:59.000Z

    Cellulose synthase ("CS"), a key enzyme in the biosynthesis of cellulose in plants is inhibited by herbicides comprising thiazolidinones such as 5-tert-butyl-carbamoyloxy-3-(3-trifluromethyl)phenyl-4-thiazolidinone (TZ), isoxaben and 2,6-dichlorobenzonitrile (DCB). Two mutant genes encoding isoxaben and TZ-resistant cellulose synthase have been isolated from isoxaben and TZ-resistant Arabidopsis thaliana mutants. When compared with the gene coding for isoxaben or TZ-sensitive cellulose synthase, one of the resistant CS genes contains a point mutation, wherein glycine residue 998 is replaced by an aspartic acid. The other resistant mutation is due to a threonine to isoleucine change at amino acid residue 942. The mutant CS gene can be used to impart herbicide resistance to a plant; thereby permitting the utilization of the herbicide as a single application at a concentration which ensures the complete or substantially complete killing of weeds, while leaving the transgenic crop plant essentially undamaged.

  15. RESEARCH ARTICLES Evolutionary Origins of a Novel Host Plant Detoxification Gene in Butterflies

    E-Print Network [OSTI]

    Wheat, Christopher

    RESEARCH ARTICLES Evolutionary Origins of a Novel Host Plant Detoxification Gene in Butterflies of Biological Sciences, Pennsylvania State University Chemical interactions between plants and their insect as a coevolutionary key innovation. By generating and sequencing expressed sequence tags, genomic libraries

  16. Modeling the Fitness Consequences of a Cyanophage-Encoded Photosynthesis Gene

    E-Print Network [OSTI]

    Chisholm, Sallie (Penny)

    Background: Phages infecting marine picocyanobacteria often carry a psbA gene, which encodes a homolog to the photosynthetic reaction center protein, D1. Host encoded D1 decays during phage infection in the light. Phage ...

  17. Whole-Exome Sequencing and Homozygosity Analysis Implicate Depolarization-Regulated Neuronal Genes in Autism

    E-Print Network [OSTI]

    Schubert, Christian R.

    Although autism has a clear genetic component, the high genetic heterogeneity of the disorder has been a challenge for the identification of causative genes. We used homozygosity analysis to identify probands from ...

  18. Induction of murine CYP1A2 gene expression by acenaphthylene

    E-Print Network [OSTI]

    Miggins, John Wesley

    1996-01-01T23:59:59.000Z

    Acenaphthylene and related polynuclear aromatic hydrocarbons (PAH) are industrial combustion by-products which are also found in cooked foods. Recent studies in this laboratory have shown that acenaphthylene induces Cypla2 gene expression in mice...

  19. Sam Wang, Princeton Genes, Brain Circuits, and the Mind: From Optical Imaging to Genomics

    E-Print Network [OSTI]

    Glashausser, Charles

    Sam Wang, Princeton WANG 12-4 Genes, Brain Circuits, and the Mind: From Optical Imaging to Genomics information, my laboratory uses multiphoton optical methods to image activity in the cerebellum, a structure

  20. Identification of NF-kappaB responsive elements in follistatin related gene (FLRG) promoter

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    : electrophoresis mobility-shift assay FLRG: follistatin related gene FSRP: follistatin-related protein FSTL3 lymphocytic leukemia (B-CLL). FLRG (alternative names: follistatin- related protein, FSRP / follistatin-like-3

  1. Kiss1 Gene Expression and the Effects of Kisspeptin During Pubertal Development in the Ewe Lamb

    E-Print Network [OSTI]

    Redmond, Jeremy Scott

    2012-02-14T23:59:59.000Z

    Increased pulsatile release of gonadotropin-releasing hormone (GnRH) and luteinizing hormone (LH) is critical for pubertal initiation of ovarian cycles in female mammals. Kisspeptin, a peptide product of the Kiss1 gene, is required for normal...

  2. Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Rubin, Eddy

    2011-04-25T23:59:59.000Z

    Director Eddy Rubin on "Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  3. Phylogenetic diversity of gram-positive bacteria and their secondary metabolite genes

    E-Print Network [OSTI]

    Gontang, Erin Ann

    2008-01-01T23:59:59.000Z

    in Oceanography by Erin Ann Gontang Committee in charge:The Dissertation of Erin Ann Gontang is approved, and it isMetabolite Genes by Erin Ann Gontang Doctor of Philosophy in

  4. Mechanisms of transcriptional activation of estrogen responsive genes in breast cancer cells 

    E-Print Network [OSTI]

    Chen, Chien-Cheng

    2009-06-02T23:59:59.000Z

    Estrogen receptor (ER) acts as a ligand-activated transcription factor that regulates the expression of genes. The genomic mechanisms of ER action include ligand-induced dimerization of ER which binds estrogen responsive elements (EREs...

  5. Mechanisms of transcriptional activation of estrogen responsive genes in breast cancer cells

    E-Print Network [OSTI]

    Chen, Chien-Cheng

    2009-06-02T23:59:59.000Z

    Estrogen receptor (ER) acts as a ligand-activated transcription factor that regulates the expression of genes. The genomic mechanisms of ER action include ligand-induced dimerization of ER which binds estrogen responsive elements (EREs...

  6. Genomic Insights into Sexual Selection and the Evolution of Reproductive Genes in Teleost Fishes

    E-Print Network [OSTI]

    Small, Clayton

    2012-10-19T23:59:59.000Z

    that genes associated with reproductive biology evolve especially rapidly planted this notion, but many details about the genomics of sex remain elusive. Numerous studies have characterized rapid sequence and expression divergence of sex-related molecules...

  7. Gene Transfer into the Lung by Nanoparticle Dextran-Spermine/Plasmid DNA Complexes

    E-Print Network [OSTI]

    Abdullah, Syahril

    2010-01-01T23:59:59.000Z

    A novel cationic polymer, dextran-spermine (D-SPM), has been found to mediate gene expression in a wide variety of cell lines and in vivo through systemic delivery. Here, we extended the observations by determining the ...

  8. Mutational heterogeneity in cancer and the search for new cancer genes

    E-Print Network [OSTI]

    Helman, Elena

    Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched ...

  9. Variability in the Stability and Productivity of Transfected Genes in Chinese Hamster Ovary (CHO) cells

    E-Print Network [OSTI]

    Ng, Say Kong

    In the field of biologics production, productivity and stability of the transfected gene of interest are two very important attributes that dictate if a production process is viable. To further understand and improve these ...

  10. Massively-parallel electrical-conductivity imaging of hydrocarbons using the Blue Gene/L supercomputer

    E-Print Network [OSTI]

    2008-01-01T23:59:59.000Z

    OF HYDROCARBONS USING THE BLUE GENE/L SUPERCOMPUTER M.of the sail lines (red and blue) and 23 detector locations (detector arrays marked in blue. Figure 3. Six selected plots

  11. Identifying genes that are required for the maintenance of pancreatic ductal adenocarcinoma

    E-Print Network [OSTI]

    Jenq, Harry

    2012-01-01T23:59:59.000Z

    We searched for genes that are potentially important for the maintenance of Pancreatic Ductal Adenocarcinoma (PDAC). PDAC is the 4th leading cause for cancer-related deaths and exhibits a 5-year survival rate of less than ...

  12. Effects of Pinealectomy on Metabolic Activity and Clock Gene Expression in Passer domesticus

    E-Print Network [OSTI]

    McCormick, Ryan

    2008-08-19T23:59:59.000Z

    coupled oscillatory mechanisms. To this end, we utilized activity-monitoring equipment to measure locomotor activity; 2DG uptake was measured via autoradiography and scintillation counts in the brain and peripheral tissues, respectively; and clock gene...

  13. Quantitative analysis of non-viral gene therapy in primary liver culture systems

    E-Print Network [OSTI]

    Tedford, Nathan C

    2007-01-01T23:59:59.000Z

    Gene therapy has the potential to cure thousands of diseases caused by genetic abnormalities, provide novel combination therapies for cancers and viral infections, and offer a new and effective platform for next generation ...

  14. Endogenous control of stochastic gene expression in the development of Caenorhabditis elegans

    E-Print Network [OSTI]

    Ji, Ni, Ph. D. Massachusetts Institute of Technology

    2013-01-01T23:59:59.000Z

    Studies in the past decade have established gene expression as an inherently variable process. Accompanying this exciting finding is a fundamental question: how do physiological events, such as cell fate specification, ...

  15. Land clearing reduces gene flow in the granite outcrop-dwelling lizard, Ctenophorus ornatus

    E-Print Network [OSTI]

    Tomkins, Joseph L.

    not provide adequate resources or protection from predation (Stow et al. 2001; Berry et al. 2005; Hoehn et al genetic variation as an indicator of levels of gene flow (e.g. Driscoll & Hardy 2005; Hoehn et al. 2007

  16. Nucleotide diversity and neutrality testing in genes involved in adaptation in Douglas-fir

    E-Print Network [OSTI]

    Nucleotide diversity and neutrality testing in genes involved in adaptation in Douglas-fir B. Pande-Oregon region, and 684 SNPs were identified in total. We report the estimation of nucleotide diversity and tests

  17. Differential Gene Expression Pre-processing: from CEL files to ExpressionSet

    E-Print Network [OSTI]

    Qiu, Weigang

    different between mutants and wild types Install Libraries and Load Data > source-processing: from CEL files to ExpressionSet Gene Annotation Visualize Expression Profile using Heatmap Produce

  18. Gene Expression and Association Analyses of Stress Responses in Loblolly Pine (Pinus taeda L.)

    E-Print Network [OSTI]

    Seeve, Candace Marie

    2012-02-14T23:59:59.000Z

    The molecular mechanisms underlying disease-resistance and drought-resistance in forest trees are not well understood. Linking variation in gene expression with genetic polymorphisms and with variations in disease- and drought-resistance phenotypes...

  19. Moral obligation and the human germ-line gene therapy debate

    E-Print Network [OSTI]

    Clark, Alan B

    1998-01-01T23:59:59.000Z

    genetic engineering, there are few arguments made for a positive moral obligation to genetic intervention. This is especially so with respect to human germ-line gene therapy. Burke. K. Zimmerman makes one of the few arguments that society...

  20. The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants

    SciTech Connect (OSTI)

    Grigoriev, Igor V.; Banks, Jo Ann; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Bowman, John L.; Gribskov, Michael; dePamphilis, Claude; Albert, Victor A.; Aono, Naoki; Aoyama, Tsuyoshi; Ambrose, Barbara A.; Ashton, Neil W.; Axtell, Michael J.; Barker, Elizabeth; Barker, Michael S.; Bennetzen, Jeffrey L.; Bonawitz, Nicholas D.; Chapple, Clint; Cheng, Chaoyang; Correa, Luiz Gustavo Guedes; Dacre, Michael; DeBarry, Jeremy; Dreyer, Ingo; Elias, Marek; Engstrom, Eric M.; Estelle, Mark; Feng, Liang; Finet, Cedric; Floyd, Sandra K.; Frommer, Wolf B.; Fujita, Tomomichi; Gramzow, Lydia; Gutensohn, Michael; Harholt, Jesper; Hattori, Mitsuru; Heyl, Alexander; Hirai, Tadayoshi; Hiwatashi, Yuji; Ishikawa, Masaki; Iwata, Mineko; Karol, Kenneth G.; Koehler, Barbara; Kolukisaoglu, Uener; Kubo, Minoru; Kurata, Tetsuya; Lalonde, Sylvie; Li, Kejie; Li, Ying; Litt, Amy; Lyons, Eric; Manning, Gerard; Maruyama, Takeshi; Michael, Todd P.; Mikami, Koji; Miyazaki, Saori; Morinaga, Shin-ichi; Murata, Takashi; Mueller-Roeber, Bernd; Nelson, David R.; Obara, Mari; Oguri, Yasuko; Olmstead, Richard G.; Onodera, Naoko; Petersen, Bent Larsen; Pils, Birgit; Prigge, Michael; Rensing, Stefan A.; Riano-Pachon, Diego Mauricio; Roberts, Alison W.; Sato, Yoshikatsu; Scheller, Henrik Vibe; Schulz, Burkhard; Schulz, Christian; Shakirov, Eugene V.; Shibagaki, Nakako; Shinohara, Naoki; Shippen, Dorothy E.; Sorensen, Iben; Sotooka, Ryo; Sugimoto, Nagisa; Sugita, Mamoru; Sumikawa, Naomi; Tanurdzic, Milos; Theilsen, Gunter; Ulvskov, Peter; Wakazuki, Sachiko; Weng, Jing-Ke; Willats, William W.G.T.; Wipf, Daniel; Wolf, Paul G.; Yang, Lixing; Zimmer, Andreas D.; Zhu, Qihui; Mitros, Therese; Hellsten, Uffe; Loque, Dominique; Otillar, Robert; Salamov, Asaf; Schmutz, Jeremy; Shapiro, Harris; Lindquist, Erika; Lucas, Susan; Rokhsar, Daniel

    2011-04-28T23:59:59.000Z

    We report the genome sequence of the nonseed vascular plant, Selaginella moellendorffii, and by comparative genomics identify genes that likely played important roles in the early evolution of vascular plants and their subsequent evolution

  1. Computational evolutionary genomics : phylogenomic models spanning domains, genes, individuals, and species

    E-Print Network [OSTI]

    Wu, Yi-Chieh, Ph. D. Massachusetts Institute of Technology

    2014-01-01T23:59:59.000Z

    Computational techniques have long been applied to biological data to address a wide range of evolutionary questions. In phylogenetics, methods for reconstructing gene histories from sequence data have enabled researchers ...

  2. Palindromes on the human X chromosome : testis-biased transcription, gene conversion and evolution

    E-Print Network [OSTI]

    Saionz, Jennifer R., 1976-

    2005-01-01T23:59:59.000Z

    Recent genomic studies of the Y chromosome revealed massive, testis-specific palindromes that span 30% of the chromosome and are subject to gene conversion. We conducted studies to determine whether similar palindromes ...

  3. E-Print Network 3.0 - adenylate cyclase gene Sample Search Results

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

    for: adenylate cyclase gene Page: << < 1 2 3 4 5 > >> 1 Comparative and Functional Genomics Comp Funct Genom 2004; 5: 1738. Summary: Cue et al., 2000) and recently at least two...

  4. BMP7 Gene Transfer via Gold Nanoparticles into Stroma Inhibits Corneal Fibrosis In Vivo

    E-Print Network [OSTI]

    Tandon, Ashish

    This study examined the effects of BMP7 gene transfer on corneal wound healing and fibrosis inhibition in vivo using a rabbit model. Corneal haze in rabbits was produced with the excimer laser performing -9 diopters ...

  5. Genomic studies of motif enrichment and conservation in the regulation of gene expression in the brain

    E-Print Network [OSTI]

    Harmin, David Alan, 1954-

    2008-01-01T23:59:59.000Z

    Several bioinformatic tools will be brought to bear in this thesis to identify specific genomic loci that serve as regulatory gateways of gene expression in brain. These "motifs" are short nucleotide patterns that occur ...

  6. Engineering a software tool for gene structure prediction in higher organisms Gordon Gremme a

    E-Print Network [OSTI]

    Brendel, Volker

    called `bioinformatics' has brought together biologists, computer scientists, statisticians, and scientists of many other fields of expertise to work on computational solutions to biological problems.V. All rights reserved. Keywords: Computational biology; Genome annotation; Similarity-based gene

  7. Gene silencing in cancer cells using siRNA : genetic and functional studies

    E-Print Network [OSTI]

    Abdel Rahim, Ma'en Ahmad

    2004-09-30T23:59:59.000Z

    modulators??????. 73 VI Different phenotypes in ERs knockout mice??????????. 78 VII Regulatory factors of VEGF gene expression?????????.. 106 VIII Single chemotherapy used to treat pancreatic cancer?????? 109 IX Combination... analysis a possibility (89). For example targeting of essential and non-essential genes resulted in cellular phenotypes that were identical to phenotypes previously observed in cells derived from transgenic knockout mice (89), illustrating the value...

  8. Genetic evaluation of the ovine and bovine prion protein genes (PRNP)

    E-Print Network [OSTI]

    Seabury, Christopher Mark

    2006-04-12T23:59:59.000Z

    for the degree of DOCTOR OF PHILOSOPHY December 2004 Major Subject: Genetics GENETIC EVALUATION OF THE OVINE AND BOVINE PRION PROTEIN GENES (PRNP) A Dissertation by CHRISTOPHER MARK SEABURY Submitted to Texas A... of Department) December 2004 Major Subject: Genetics iii ABSTRACT Genetic Evaluation of the Ovine and Bovine Prion Protein Genes (PRNP). (December 2004) Christopher Mark Seabury, B.S.; M.S., Sul Ross State University Chair of Advisory...

  9. Physiological Ageing as it is Related to Gene Function in the Lone Star Tick, Amblyomma americanum

    E-Print Network [OSTI]

    Catena, Amanda M.

    2010-07-14T23:59:59.000Z

    ..................... 12 Figure 2 Electrophoresis gel results for the expression of the ATP synthase gene in Amblyomma americanum subdivided by the mortality percentile to the right of the result, the sample number over the top of the result, and the group... ............................ 15 Figure 4 Electrophoresis gel results for the expression of the 16S gene in Amblyomma americanum subdivided by the mortality percentile to the right of the result, the sample number over the top of the result, and the group...

  10. Viability of mammalian embryos subjected to liposome interaction or centrifugation for gene transfer

    E-Print Network [OSTI]

    Loskutoff, Nadia Mikhail

    1985-01-01T23:59:59.000Z

    VIABILITY OF MAMMALIAN EMBRYOS SUBJECTED TO LIPOSOME INTERACTION OR CENTRIFUGATION FOR GENE TRANSFER A Thesis by NADIA MIKHAIL LOSKUTOFF Submitted to the Graduate College of Texas AAM University in partial fulfillment of the requirements... for the degree of MASTER OF SCIENCE December 1985 Major Subject: Veterinary Physiology VIABILITY OF MAMMALIAN EMBRYOS SUBJECTED TO LIPOSOME INTERACTION OR CENTRIFUGATION FOR GENE TRANSFER A Thesis by Nadia Mikhail Loskutoff Approved as to style...

  11. Snapshot of iron response in Shewanella oneidensis by gene network reconstruction

    SciTech Connect (OSTI)

    Yang, Yunfeng; Harris, Daniel P.; Luo, Feng; Xiong, Wenlu; Joachimiak, Marcin; Wu, Liyou; Dehal, Paramvir; Jacobsen, Janet; Yang, Zamin; Palumbo, Anthony V.; Arkin, Adam P.; Zhou, Jizhong

    2008-10-09T23:59:59.000Z

    Background: Iron homeostasis of Shewanella oneidensis, a gamma-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, we integrate physiological, transcriptomics and genetic approaches to delineate the iron response of S. oneidensis. Results: We show that the iron response in S. oneidensis is a rapid process. Temporal gene expression profiles were examined for iron depletion and repletion, and a gene co-expression network was reconstructed. Modules of iron acquisition systems, anaerobic energy metabolism and protein degradation were the most noteworthy in the gene network. Bioinformatics analyses suggested that genes in each of the modules might be regulated by DNA-binding proteins Fur, CRP and RpoH, respectively. Closer inspection of these modules revealed a transcriptional regulator (SO2426) involved in iron acquisition and ten transcriptional factors involved in anaerobic energy metabolism. Selected genes in the network were analyzed by genetic studies. Disruption of genes encoding a putative alcaligin biosynthesis protein (SO3032) and a gene previously implicated in protein degradation (SO2017) led to severe growth deficiency under iron depletion conditions. Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways. Conclusions: Using a reconstructed gene network, we identified major biological pathways that were differentially expressed during iron depletion and repletion. Genetic studies not only demonstrated the importance of iron acquisition and protein degradation for iron depletion, but also characterized a novel transcriptional factor (SO1415) with a role in anaerobic energy metabolism.

  12. Bayesian Semiparametric Models for Heterogeneous Cross-platform Differential Gene Expression

    E-Print Network [OSTI]

    Dhavala, Soma Sekhar

    2012-02-14T23:59:59.000Z

    BAYESIAN SEMIPARAMETRIC MODELS FOR HETEROGENEOUS CROSS-PLATFORM DIFFERENTIAL GENE EXPRESSION A Dissertation by SOMA SEKHAR DHAVALA Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements... for the degree of DOCTOR OF PHILOSOPHY December 2010 Major Subject: Statistics BAYESIAN SEMIPARAMETRIC MODELS FOR HETEROGENEOUS CROSS-PLATFORM DIFFERENTIAL GENE EXPRESSION A Dissertation by SOMA SEKHAR DHAVALA Submitted to the Office of Graduate Studies...

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

    SciTech Connect (OSTI)

    William Grundy; Manuel Ares, Jr.; David Haussler

    2001-06-18T23:59:59.000Z

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

  14. DALTONFULLPAPER DOI: 10.1039/b005612j J. Chem. Soc., Dalton Trans., 2000, 41874191 4187

    E-Print Network [OSTI]

    Gao, Song

    )] (pyz = pyrazine)7 which contains two interpenetrating -Po-like networks, therefore [MII (apo)(N(CN)2-dimensional co-ordination polymers constructed by dimer subunits Bai-Wang Sun, Song Gao,* Bao-Qing Ma, De-ordination polymers have been reported, for example 3-D for MII [N(CN)2]2 (M = Cu, Co, Ni or Mn),2,3 2-D for Zn[N(CN)2

  15. Gene expression profiling in Ishikawa cells: A fingerprint for estrogen active compounds

    SciTech Connect (OSTI)

    Boehme, Kathleen; Simon, Stephanie [Merck KGaA, Merck Serono, NCD/Toxicology, Early and Explanatory Toxicology, 64271 Darmstadt (Germany); Mueller, Stefan O. [Merck KGaA, Merck Serono, NCD/Toxicology, Early and Explanatory Toxicology, 64271 Darmstadt (Germany)], E-mail: stefan.o.mueller@merck.de

    2009-04-01T23:59:59.000Z

    Several anthropogenous and naturally occurring substances, referred to as estrogen active compounds (EACs), are able to interfere with hormone and in particular estrogen receptor signaling. EACs can either cause adverse health effects in humans and wildlife populations or have beneficial effects on estrogen-dependent diseases. The aim of this study was to examine global gene expression profiles in estrogen receptor (ER)-proficient Ishikawa plus and ER-deficient Ishikawa minus endometrial cancer cells treated with selected well-known EACs (Diethylstilbestrol, Genistein, Zearalenone, Resveratrol, Bisphenol A and o,p'-DDT). We also investigated the effect of the pure antiestrogen ICI 182,780 (ICI) on the expression patterns caused by these compounds. Transcript levels were quantified 24 h after compound treatment using Illumina BeadChip Arrays. We identified 87 genes with similar expression changes in response to all EAC treatments in Ishikawa plus. ICI lowered the magnitude or reversed the expression of these genes, indicating ER dependent regulation. Apart from estrogenic gene regulation, Bisphenol A, o,p'-DDT, Zearalenone, Genistein and Resveratrol displayed similarities to ICI in their expression patterns, suggesting mixed estrogenic/antiestrogenic properties. In particular, the predominant antiestrogenic expression response of Resveratrol could be clearly distinguished from the other test compounds, indicating a distinct mechanism of action. Divergent gene expression patterns of the phytoestrogens, as well as weaker estrogenic gene expression regulation determined for the anthropogenous chemicals Bisphenol A and o,p'-DDT, warrants a careful assessment of potential detrimental and/or beneficial effects of EACs. The characteristic expression fingerprints and the identified subset of putative marker genes can be used for screening chemicals with an unknown mode of action and for predicting their potential to exert endocrine disrupting effects.

  16. Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus

    SciTech Connect (OSTI)

    Burke-Agueero, D.H.

    1992-08-01T23:59:59.000Z

    Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight ``bch`` genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

  17. Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus

    SciTech Connect (OSTI)

    Burke-Agueero, D.H.

    1992-08-01T23:59:59.000Z

    Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight bch'' genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

  18. DNA rearrangement in human follicular lymphoma can involve the 5' or the 3' region of the bcl-2 gene

    SciTech Connect (OSTI)

    Tsujimoto, Y.; Bashir, M.M.; Givol, I.; Cossman, J.; Jaffe, E.; Croce, C.M.

    1987-03-01T23:59:59.000Z

    In most human lymphomas, the chromosome translocation t(14;18) occurs within two breakpoint clustering regions on chromosome 18, the major one at the 3' untranslated region of the bcl-2 gene and the minor one at 3' of the gene. Analysis of a panel of follicular lymphoma DNAs using probes for the first exon of the bcl-2 gene indicates that DNA rearrangements may also occur 5' to the involved bcl-2 gene. In this case the IgH locus and the bcl-2 gene are found in an order suggesting that an inversion also occurred during the translocation process. The coding region of the bcl-2 gene, however, are left intact in all cases of follicular lymphoma studied to date.

  19. A novel strategy to activate cytoprotective genes in the injured brain

    SciTech Connect (OSTI)

    Zhao, Jing, E-mail: Jing.Zhao@uth.tmc.edu [Department of Neurobiology and Anatomy, The University of Texas Medical School, P.O. Box 20708, Houston, TX 77225 (United States)] [Department of Neurobiology and Anatomy, The University of Texas Medical School, P.O. Box 20708, Houston, TX 77225 (United States); Redell, John B., E-mail: John.B.Redell@uth.tmc.edu [Department of Neurobiology and Anatomy, The University of Texas Medical School, P.O. Box 20708, Houston, TX 77225 (United States); Moore, Anthony N., E-mail: Anthony.N.Moore@uth.tmc.edu [Department of Neurobiology and Anatomy, The University of Texas Medical School, P.O. Box 20708, Houston, TX 77225 (United States); Dash, Pramod K., E-mail: p.dash@uth.tmc.edu [Department of Neurobiology and Anatomy, The University of Texas Medical School, P.O. Box 20708, Houston, TX 77225 (United States)

    2011-04-15T23:59:59.000Z

    Highlights: {yields} A strategy to increase cytoprotective gene expression in injured tissue is outlined. {yields} A peptide containing a DEETGE motif can increase Nrf2 responsive genes in vivo. {yields} Gene expression in injured brains requires a calpain cleavage site. {yields} This peptide decreases BBB compromise when infused pre- or post-brain injury. {yields} Cleavage sites for disease-specific proteases could be used to treat that condition. -- Abstract: The transcription factor nuclear factor E2-related factor 2 (Nrf2) regulates the expression of multiple cytoprotective genes that have been shown to offer protection in response to a number of insults. The present study describes a novel strategy to increase expression of Nrf2-responsive genes in brain injured mice. Under normal conditions, the adapter protein Kelch-like ECH-associated protein 1 (Keap1) binds to Nrf2 and promotes its proteosomal degradation in the cytoplasm. The amino acid sequence DEETGE, located at amino acid 77-82 of Nrf2, is critical for Nrf2-Keap1 interaction, and synthetic peptides containing this sequence can be used to disrupt the complex in vitro. We observed that intracerebroventricular (i.c.v.) infusion of a peptide containing the DEETGE sequence along with the cell transduction domain of the HIV-TAT protein (TAT-DEETGE) into brain-injured mice did not increase the mRNA levels for Nrf2-driven genes. However, when a calpain cleavage sequence was introduced between the TAT sequence and the DEETGE sequence, the new peptide (TAT-CAL-DEETGE) increased the mRNA levels of these genes. Increased gene expression was not observed when the TAT-CAL-DEETGE peptide was injected into uninjured animals. Furthermore, injection of TAT-CAL-DEETGE peptides before or after brain injury reduced blood-brain barrier compromise, a prominent secondary pathology that negatively influences outcome. The present strategy to increase Nrf2-responsive gene expression can be adapted to treat other insults or diseases based on their underlying mechanism(s) of cellular damage.

  20. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria

    SciTech Connect (OSTI)

    Field, K.G.; Gordon, D.; Wright, T. [Oregon State Univ., Corvallis, OR (United States)] [and others

    1997-01-01T23:59:59.000Z

    Small-subunit (SSU) ribosomal DNA (rDNA) gene clusters are phylogenetically related sets of SSU rRNA genes, commonly encountered in genes amplified from natural populations. Genetic variability in gene clusters could result form artifacts (polymerase error or PCR chimera formation), microevolution (variation among rrn copies within strains), or macroevolution (genetic divergence correlated with long-term evolutionary divergence). To better understand gene clusters, this study assessed genetic diversity and distribution of a single environmental SSU rDNA gene cluster, the SAR11 cluster. SAR11 cluster genes, from an uncultured group of the {alpha} subclass of the class Proteobacteria, have been recovered from coastal and midoceanic waters of the North Atlantic and Pacific. We cloned and bidirectionally sequenced 23 new SAR11 cluster 16S rRNA genes, from 80 and 250 m im the Sargasso Sea and from surface coastal waters of the Atlantic and Pacific, and analyzed them with previously published sequences. Two SAR11 genes were obviously PCR chimeras, but the biological (nonchimeric) origins of most subgroups within the cluster were confirmed by independent recovery from separate gene libraries. Using group-specific oligonucleotide probes, we analyzed depth profiles of nucleic acids, targeting both amplified rDNAs and bulk RNAs. Two subgroups within the SAR11 cluster showed different highly depth-specific distributions. We conclude that some of the genetic diversity within the SAR11 gene cluster represents macroevolutionary divergence correlated with niche specialization. Furthermore, we demonstrate the utility for marine microbial ecology of oligonucleotide probes based on gene sequences amplified from natural populations and show that a detailed knowledge of sequence variability may be needed to effectively design these probes. 48 refs., 7 figs., 3 tabs.