Sample records for 16s rrna gene

  1. 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

  2. Greengenes: Chimera-checked 16S rRNA gene database and workbenchcompatible in ARB

    SciTech Connect (OSTI)

    DeSantis, T.Z.; Hugenholtz, P.; Larsen, N.; Rojas, M.; Brodie,E.L; Keller, K.; Huber, T.; Dalevi, D.; Hu, P.; Andersen, G.L.

    2006-02-01T23:59:59.000Z

    A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that incongruent taxonomic nomenclature exists among curators even at the phylum-level. Putative chimeras were identified in 3% of environmental sequences and 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages within the Archaea and Bacteria.

  3. Greengenes, a Chimera-checked 16S rRNA gene database and workbenchcompatible with ARB

    SciTech Connect (OSTI)

    DeSantis, Todd Z.; Hugenholtz, Philip; Larsen, Neils; Rojas,Mark; Brodie, Eoin L.; Keller, Keith; Huber, Thomas; Dalevi, Daniel; Hu,Ping; Andersen, Gary L.

    2006-04-10T23:59:59.000Z

    A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that in congruent taxonomic nomenclature exists among curators even at the phylum-level. Putative chimeras were identified in 3 percent of environmental sequences and 0.2 percent of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages within the Archaea and Bacteria.

  4. Direct Detection of 16S rRNA in Soil Extracts by Using Oligonucleotide Microarrays

    SciTech Connect (OSTI)

    Small, Jack A.; Call, Douglas R.; Brockman, Fred J.; Straub, Tim M.; Chandler, Darrell P.

    2001-10-01T23:59:59.000Z

    ABSTRACT-We report on the development and validation of simple microarray method for the direct detection of intact 16S rRNA from un-purified soil extracts. Total RNA from Geobacter chapellei and Desulfovibrio desulfuricans was hybridized to an oligonculeotide array consisting of universal and species-specific 16S rRNA probes...

  5. Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip and 16S rRNA gene clone library sequencing

    SciTech Connect (OSTI)

    Shankar Sagaram, U.; DeAngelis, K.M.; Trivedi, P.; Andersen, G.L.; Lu, S.-E.; Wang, N.

    2009-03-01T23:59:59.000Z

    The bacterial diversity associated with citrus leaf midribs was characterized 1 from citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rDNA microarray and 16S rDNA clone library sequencing to determine the microbial community composition of symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria from 15 phyla were present in the citrus leaf midribs while 20 orders from phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs compared to asymptomatic midribs. Candidatus Liberibacter asiaticus (Las) was detected at a very low level in asymptomatic plants, but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis was further verified by sequencing 16S rDNA clone libraries, which indicated the dominance of Las in symptomatic leaves. These data implicate Las as the pathogen responsible for HLB disease. Citrus is the most important commercial fruit crop in Florida. In recent years, citrus Huanglongbing (HLB), also called citrus greening, has severely affected Florida's citrus production and hence has drawn an enormous amount of attention. HLB is one of the most devastating diseases of citrus (6,13), characterized by blotchy mottling with green islands on leaves, as well as stunting, fruit decline, and small, lopsided fruits with poor coloration. The disease tends to be associated with a phloem-limited fastidious {alpha}-proteobacterium given a provisional Candidatus status (Candidatus Liberobacter spp. later changed to Candidatus Liberibacter spp.) in nomenclature (18,25,34). Previous studies indicate that HLB infection causes disorder in the phloem and severely impairs the translocation of assimilates in host plants (5,27,40). Tatineni and colleagues discovered that the HLB bacteria were unevenly distributed in phloem of bark tissue, vascular tissue of the leaf midrib, roots, and different floral and fruit parts (43). Unsuccessful attempts in culturing the pathogen are notably hampering efforts to understand its biology and pathogenesis mechanism. Using a modified Koch's Postulates approach, Jagoueix and colleagues were able to re-infect periwinkle plants from a mixed microbial community harvested from HLB diseased plants (25). Emergence of the disease in otherwise healthy plants led to the conclusion that HLB was associated with Candidatus Liberibacter sp. based on its 16S rDNA sequence (18,25). Currently, three species of the pathogen are recognized from trees with HLB disease based on 16S rDNA sequence: Ca. Liberibacter asiaticus (Las), Ca. Liberibacter africanus (Laf), and Ca. Liberibacter americanus (Lam); Las is the most prevalent species among HLB diseased trees (5,12,18,25,44). Las is naturally transmitted to citrus by the psyllid, Diaphorina citri Kuwayama, and can be artificially transmitted by grafting from citrus to citrus and dodder (Cuscuta campestris) to periwinkle (Catharanthus roseus) or tobacco (Nicotiana tabacum Xanthi) (5). Based on current research regarding the associations of Liberibacter in planta there is not enough evidence to implicate Liberibacter as the definitive causal agent of HLB disease due to its resistance to cultivation in vitro. It is possible that HLB disease may be the result of complex etiology where Liberibacter interacts with other endophytic bacteria. However, there is not enough evidence regarding its association(s) in planta to make this conclusion, nor is it known whether associated microbial communities play a role in expression of pathogenic traits. The main objective of the study was to test the hypothesis that other bacteria besides Ca. Liberibacter spp. are associated with citrus greening disease. The differences between the relative abundance, species richness and phylogenetic diversity of the microbial communitie

  6. Greengenes: 16S rRNA Database and Workbench Compatible with ARB

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

    DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.; Rojas, M.; Brodie, E.L.; Keller, K.; Huber, T.; Dalevi, D. Hu, P. Andersen, G. L.

    Greengenes was developed, as the abstract of an AEM reprint states, to "addresse limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria....Greengenes is also a functional workbench to assist in analysis of user-generated 16S rRNA gene sequences. Batches of sequencing reads can be uploaded for quality-based trimming and creation of multiple-sequence alignments (9). Three types of non-MSA similarity searches are also available, seed extension by BLAST (1), similarity based on shared 7-mers by a tool called Simrank, and a direct degenerative pattern match for probe/primer evaluation. Results are displayed using user-preferred taxonomic nomenclature and can be saved between sessions. [Taken from DeSantis, T. Z., P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Andersen. 2006. Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB. Appl Environ Microbiol 72:5069-72, pages 1 and 3] (Specialized Interface)

  7. Multi-site-specific 16S rRNA Methyltransferase RsmF from Thermus thermophilus

    SciTech Connect (OSTI)

    Demirci, H.; Larsen, L; Hansen, T; Rasmussen, A; Cadambi, A; Gregory, S; Kirpekar, F; Jogl, G

    2010-01-01T23:59:59.000Z

    Cells devote a significant effort toward the production of multiple modified nucleotides in rRNAs, which fine tune the ribosome function. Here, we report that two methyltransferases, RsmB and RsmF, are responsible for all four 5-methylcytidine (m{sup 5}C) modifications in 16S rRNA of Thermus thermophilus. Like Escherichia coli RsmB, T. thermophilus RsmB produces m{sup 5}C967. In contrast to E. coli RsmF, which introduces a single m{sup 5}C1407 modification, T. thermophilus RsmF modifies three positions, generating m{sup 5}C1400 and m{sup 5}C1404 in addition to m{sup 5}C1407. These three residues are clustered near the decoding site of the ribosome, but are situated in distinct structural contexts, suggesting a requirement for flexibility in the RsmF active site that is absent from the E. coli enzyme. Two of these residues, C1400 and C1404, are sufficiently buried in the mature ribosome structure so as to require extensive unfolding of the rRNA to be accessible to RsmF. In vitro, T. thermophilus RsmF methylates C1400, C1404, and C1407 in a 30S subunit substrate, but only C1400 and C1404 when naked 16S rRNA is the substrate. The multispecificity of T. thermophilus RsmF is potentially explained by three crystal structures of the enzyme in a complex with cofactor S-adenosyl-methionine at up to 1.3 {angstrom} resolution. In addition to confirming the overall structural similarity to E. coli RsmF, these structures also reveal that key segments in the active site are likely to be dynamic in solution, thereby expanding substrate recognition by T. thermophilus RsmF.

  8. Structure of ERA in complex with the 3? end of 16S rRNA: Implications for ribosome biogenesis

    SciTech Connect (OSTI)

    Tu, Chao; Zhou, Xiaomei; Tropea, Joseph E.; Austin, Brian P.; Waugh, David S.; Court, Donald L.; Ji, Xinhua; (NCI)

    2009-10-09T23:59:59.000Z

    ERA, composed of an N-terminal GTPase domain followed by an RNA-binding KH domain, is essential for bacterial cell viability. It binds to 16S rRNA and the 30S ribosomal subunit. However, its RNA-binding site, the functional relationship between the two domains, and its role in ribosome biogenesis remain unclear. We have determined two crystal structures of ERA, a binary complex with GDP and a ternary complex with a GTP-analog and the {sub 1531}AUCACCUCCUUA{sub 1542} sequence at the 3' end of 16S rRNA. In the ternary complex, the first nine of the 12 nucleotides are recognized by the protein. We show that GTP binding is a prerequisite for RNA recognition by ERA and that RNA recognition stimulates its GTP-hydrolyzing activity. Based on these and other data, we propose a functional cycle of ERA, suggesting that the protein serves as a chaperone for processing and maturation of 16S rRNA and a checkpoint for assembly of the 30S ribosomal subunit. The AUCA sequence is highly conserved among bacteria, archaea, and eukaryotes, whereas the CCUCC, known as the anti-Shine-Dalgarno sequence, is conserved in noneukaryotes only. Therefore, these data suggest a common mechanism for a highly conserved ERA function in all three kingdoms of life by recognizing the AUCA, with a 'twist' for noneukaryotic ERA proteins by also recognizing the CCUCC.

  9. Discrimination of Bacillus anthracis from closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microchips

    DOE Patents [OSTI]

    Bavykin, Sergei G. (Darien, IL); Mirzabekova, legal representative, Natalia V. (Westmont, IL); Mirzabekov, deceased, Andrei D. (Westmont, IL)

    2007-12-04T23:59:59.000Z

    The present invention relates to methods and compositions for using nucleotide sequence variations of 16S and 23S rRNA within the B. cereus group to discriminate a highly infectious bacterium B. anthracis from closely related microorganisms. Sequence variations in the 16S and 23S rRNA of the B. cereus subgroup including B. anthracis are utilized to construct an array that can detect these sequence variations through selective hybridizations and discriminate B. cereus group that includes B. anthracis. Discrimination of single base differences in rRNA was achieved with a microchip during analysis of B. cereus group isolates from both single and in mixed samples, as well as identification of polymorphic sites. Successful use of a microchip to determine the appropriate subgroup classification using eight reference microorganisms from the B. cereus group as a study set, was demonstrated.

  10. Discrimination of Bacillus anthracis from closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microchips

    DOE Patents [OSTI]

    Bavykin, Sergei G. (Darien, IL); Mirzabekov, Andrei D. (Moscow, RU)

    2007-10-30T23:59:59.000Z

    The present invention is directed to a novel method of discriminating a highly infectious bacterium Bacillus anthracis from a group of closely related microorganisms. Sequence variations in the 16S and 23S rRNA of the B. cereus subgroup including B. anthracis are utilized to construct an array that can detect these sequence variations through selective hybridizations. The identification and analysis of these sequence variations enables positive discrimination of isolates of the B. cereus group that includes B. anthracis. Discrimination of single base differences in rRNA was achieved with a microchip during analysis of B. cereus group isolates from both single and in mixed probes, as well as identification of polymorphic sites. Successful use of a microchip to determine the appropriate subgroup classification using eight reference microorganisms from the B. cereus group as a study set, was demonstrated.

  11. The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3; end of 16S rRNA

    SciTech Connect (OSTI)

    Tu, Chao; Zhou, Xiaomei; Tarasov, Sergey G.; Tropea, Joseph E.; Austin, Brian P.; Waugh, David S.; Court, Donald L.; Ji, Xinhua (NCI)

    2012-03-26T23:59:59.000Z

    Era, composed of a GTPase domain and a K homology domain, is essential for bacterial cell viability. It is required for the maturation of 16S rRNA and assembly of the 30S ribosomal subunit. We showed previously that the protein recognizes nine nucleotides (1531{sup AUCACCUCC}1539) near the 3{prime} end of 16S rRNA, and that this recognition stimulates GTP-hydrolyzing activity of Era. In all three kingdoms of life, the 1530{sup GAUCA}1534 sequence and helix 45 (h45) (nucleotides 1506-1529) are highly conserved. It has been shown that the 1530{sup GA}1531 to 1530{sup AG}1531 double mutation severely affects the viability of bacteria. However, whether Era interacts with G1530 and/or h45 and whether such interactions (if any) contribute to the stimulation of Era's GTPase activity were not known. Here, we report two RNA structures that contain nucleotides 1506-1542 (RNA301), one in complex with Era and GDPNP (GNP), a nonhydrolysable GTP-analogue, and the other in complex with Era, GNP, and the KsgA methyltransferase. The structures show that Era recognizes 10 nucleotides, including G1530, and that Era also binds h45. Moreover, GTPase assay experiments show that G1530 does not stimulate Era's GTPase activity. Rather, A1531 and A1534 are most important for stimulation and h45 further contributes to the stimulation. Although G1530 does not contribute to the intrinsic GTPase activity of Era, its interaction with Era is important for binding and is essential for the protein to function, leading to the discovery of a new cold-sensitive phenotype of Era.

  12. Genetic variation in the 16s mitochondrial rDNA gene from Texas and Oklahoma populations of Amblyomma maculatum

    E-Print Network [OSTI]

    Lostak, Tracy Karon

    2009-05-15T23:59:59.000Z

    Single-strand conformation polymorphism was used to detect different haplotypes of the 16S mitochondrial rDNA gene within samples of Gulf Coast ticks, Amblyomma maculatum Koch, collected from Payne County, Oklahoma and Brazos and Refugio Counties...

  13. 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.

  14. Assessment of anaerobic benzene degradation potential using 16S rRNA gene-targeted real-time PCR

    E-Print Network [OSTI]

    Alvarez, Pedro J.

    in the USA that are contaminated with gasoline leaks from underground storage tanks (UST) (USEPA, 2005 to remediate more than 50% of the existing gasoline-contaminated UST sites (USEPA, 2000). However

  15. ammonia oxidizer 16s: Topics by E-print Network

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

    16S ribosomal RNA (rRNA) is a central Walter, Nils G. 77 Energy Savings from Floating Head Pressure in Ammonia Refrigeration Systems Texas A&M University - TxSpace Summary:...

  16. Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip and 16S rRNA gene clone library sequencing

    E-Print Network [OSTI]

    Shankar Sagaram, U.

    2009-01-01T23:59:59.000Z

    citrus branches, the endophyte Curtobacterium flaccumfacienssimilarity between the endophytes of host plants and

  17. Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip and 16S rRNA gene clone library sequencing

    E-Print Network [OSTI]

    Shankar Sagaram, U.

    2009-01-01T23:59:59.000Z

    of armored scale insects (Hemiptera: Diaspididae) and theirwith scale insects (Hemiptera: Coccoidea), pp. 101- 116. In

  18. Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

    E-Print Network [OSTI]

    Chen, Ting

    clusters based on the natural organization of data without setting a hard cut-off threshold (3, University of Southern California, University Park, Los Angeles, CA 90089, USA and 2MOE Key Laboratory Windows. Contact: tingchen@usc.edu Supplementary information: Supplementary data are available

  19. Critical analysis of the topology and rooting of the parabasalian 16S rRNA treeq

    E-Print Network [OSTI]

    Flegr, Jaroslav

    of a double membrane bounded organelle named the hydrogeno- some, and cell division by semiopen pleuromitosis

  20. Structure of ERA in Complex with the 3 End of 16s rRNBA Implications for Ribosome Biogenesis

    SciTech Connect (OSTI)

    Tu, C.; Zhou, X; Tropea, J; Austin, B; Waugh, D; Court, D; Ji, X

    2009-01-01T23:59:59.000Z

    ERA, composed of an N-terminal GTPase domain followed by an RNA-binding KH domain, is essential for bacterial cell viability. It binds to 16S rRNA and the 30S ribosomal subunit. However, its RNA-binding site, the functional relationship between the two domains, and its role in ribosome biogenesis remain unclear. We have determined two crystal structures of ERA, a binary complex with GDP and a ternary complex with a GTP-analog and the 1531AUCACCUCCUUA1542 sequence at the 3? end of 16S rRNA. In the ternary complex, the first nine of the 12 nucleotides are recognized by the protein. We show that GTP binding is a prerequisite for RNA recognition by ERA and that RNA recognition stimulates its GTP-hydrolyzing activity. Based on these and other data, we propose a functional cycle of ERA, suggesting that the protein serves as a chaperone for processing and maturation of 16S rRNA and a checkpoint for assembly of the 30S ribosomal subunit. The AUCA sequence is highly conserved among bacteria, archaea, and eukaryotes, whereas the CCUCC, known as the anti-Shine-Dalgarno sequence, is conserved in noneukaryotes only. Therefore, these data suggest a common mechanism for a highly conserved ERA function in all three kingdoms of life by recognizing the AUCA, with a 'twist' for noneukaryotic ERA proteins by also recognizing the CCUCC.

  1. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

    E-Print Network [OSTI]

    Minnesota, University of

    Caporasoa , Christian L. Lauberb , William A. Waltersc , Donna Berg-Lyonsb , Catherine A. Lozuponea , Peter J. Turnbaughd , Noah Fiererb,e , and Rob Knighta,f,1 a Department of Chemistry and Biochemistry, b open up the possibility of con- ducting large-scale studies analyzing thousands of samples simul

  2. Mitochondrial DNA sequence variation of the 16s rRNA gene from five western Atlantic populations of the coral M?o?n?t?a?s?t?r?a?e?a? a?n?n?u?l?a?r?i?s?

    E-Print Network [OSTI]

    Holland, Brenden Stephen

    1991-01-01T23:59:59.000Z

    surface current velocities in the region of I Enmedio Reef are 0. 4 to 0. 5 kts, or about 0. 8 km per hour (Rannefeld 1972). A i competency period of 10 weeks gives a potential range of 1300 km for larvae coming from ~ the southwestern Gulf (Bright et... amplified products" (Innis et aL 1990). 28 PCR amplification was conducted using a Perkin-Elmer Cetus DNA Thermal Cycler~, Standard PCR protocols consisted of either 50 ttt or 100 td reactions in 0. 5 ml microfuge tubes (Innis et al. 1990), Reagents...

  3. Databases for rRNA gene profiling of microbial communities

    DOE Patents [OSTI]

    Ashby, Matthew

    2013-07-02T23:59:59.000Z

    The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

  4. Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen suppressive soil

    SciTech Connect (OSTI)

    Hjort, K.; Bergstrom, M.; Adesina, M.F.; Jansson, J.K.; Smalla, K.; Sjoling, S.

    2009-09-01T23:59:59.000Z

    Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal-restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal-restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF{sup 103} of the isolate, Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.

  5. Hunting the Monsters in the Database A critical review of computational tools for detecting chimeric 16S

    E-Print Network [OSTI]

    "The Chimera had the head of a lion and the tail of a serpent, while her chimera checking ... reduced diversity estimates based on pyrosequencing by a factor of 10." -Hass et al. Chimeric 16S detection using chimera slayer

  6. The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

    E-Print Network [OSTI]

    Tagmount, Abderrahmane

    2010-01-01T23:59:59.000Z

    and 28S ribosomal gene sequences [8]. PCAD: The Porcelain28S and 18S rRNA gene sequences to classify the arthropodsbased on the mtDNA 16S rDNA sequence: phylogeographic and

  7. Comparative analysis of dinoflagellate chloroplast genomes reveals rRNA and tRNA genes

    E-Print Network [OSTI]

    Barbrook, Adrian C; Santucci, Nicole; Plenderleith, Lindsey J; Hiller, Roger G; Howe, Christopher J

    2006-11-23T23:59:59.000Z

    GCAUCGGCUAA-CUCCGUGCCAGCAGCCGCGGUAAG-ACGGAGGAUGC Nephroselmis olivacea GCAUCGGCUAA-CUCCGUGCCAGCAGCCGCGGUAAG-ACGGAGGAUGC Chlorella vulgaris GCAUCGGCUAA-CUCUGUGCCAGCAGCCGCGGUAAG-ACAGAGGAUGC Pyrenomonas salina GCAUCGGCUAA...

  8. Evaluation of the Gastrointestinal Microbiota in Response to Dietary and Therapeutic Factors in Cats and Dogs Using Molecular Methods 

    E-Print Network [OSTI]

    Garcia-Mazcorro, Jose

    2012-02-14T23:59:59.000Z

    , and up to three weeks after discontinuation of the administration of the synbiotic. The fecal microbiota was analyzed using 454-pyrosequencing, denaturing gradient gel electrophoresis, quantitative real-time PCR, and 16S rRNA gene clone libraries...

  9. Microfluidic cell culture chambers with nanoporous walls for chemical communication

    E-Print Network [OSTI]

    Ge, Zhifei, S.M. Massachusetts Institute of Technology

    2013-01-01T23:59:59.000Z

    Reconstruction of phylogenetic trees based on 16S rRNA gene sequencing reveals that so far only a tiny fraction of microbial diversity has been cultured in the laboratory. One major reason behind this "unculturability" is ...

  10. Characterization of Corynebacterium Species in Macaques

    E-Print Network [OSTI]

    Venezia, Jaime

    Bacteria of the genus Corynebacterium are important primary and opportunistic pathogens. Many are zoonotic agents. In this report, phenotypic (API Coryne analysis), genetic (rpoB and 16S rRNA gene sequencing), and physical ...

  11. James S. Klaus Jorge Frias-Lopez George T. Bonheyo Jeffrey M. Heikoop

    E-Print Network [OSTI]

    Fouke, Bruce W.

    are extremely diverse. Estimates based on 14 different 16S rRNA gene sequence libraries suggest as many as 6 Department of Geology, University of Illinois, 1301, W. Green Street, Urbana, IL 61801, USA E-mail: jklaus

  12. Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater

    SciTech Connect (OSTI)

    Mouser, P.J.; N'Guessan, A.L.; Elifantz, H.; Holmes, D.E.; Williams, K.H.; Wilkins, M.J.; Long, P.E.; Lovley, D.R.

    2009-04-01T23:59:59.000Z

    The impact of ammonium availability on microbial community structure and the physiological status and activity of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by as much as two orders of magnitude (<4 to 400 {micro}M) across the study site. Analysis of 16S rRNA gene sequences suggested that ammonium influenced the composition of the microbial community prior to acetate addition with Rhodoferax species predominating over Geobacter species at the site with the highest ammonium, and Dechloromonas species dominating at sites with lowest ammonium. However, once acetate was added, and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms at all locations. Rates of U(VI) reduction appeared to be more related to the concentration of acetate that was delivered to each location rather than the amount of ammonium available in the groundwater. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium importer gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during in situ uranium reduction, and that the abundance of amtB transcripts was inversely correlated to ammonium levels across all sites examined. These results suggest that nifD and amtB expression by subsurface Geobacter species are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB expression appears to be a useful approach for monitoring the nitrogen-related physiological status of Geobacter species in subsurface environments during bioremediation. This study also emphasizes the need for more detailed analysis of geochemical/physiological interactions at the field scale, in order to adequately model subsurface microbial processes.

  13. Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater

    SciTech Connect (OSTI)

    Mouser, Paula; N'guessan, Lucie A.; Elifantz, H.; Holmes, Dawn; Williams, Kenneth H.; Wilkins, Michael J.; Long, Philip E.; Lovley, Derek R.

    2009-06-15T23:59:59.000Z

    The influence of ammonium availability on bacterial community structure and the physiological status of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by two orders of magnitude (<4 to 400 ?M) across the study site. Analysis of 16S rRNA sequences suggested that ammonium may have been one factor influencing the community composition prior to acetate amendment with Rhodoferax species predominating over Geobacter species with higher ammonium and Dechloromonas species dominating at the site with lowest ammonium. However, once acetate was added, and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms at all locations. Rates of U(VI)-reduction appeared to be more related to acetate concentrations rather than ammonium levels. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium transporter gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during uranium reduction. The abundance of amtB was inversely correlated to ammonium levels whereas nifD transcript levels were similar across all sites examined. These results suggest that nifD and amtB expression are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB transcript expression appears to be a useful approach for monitoring the nitrogen-related physiological status of subsurface Geobacter species and. This study also emphasizes the need for more detailed analysis of geochemical/physiological interactions at the field scale, in order to adequately model subsurface microbial processes during bioremediation.

  14. Phylogeny and Biogeography of a Cosmopolitan Frog Radiation: Late Cretaceous Diversification Resulted in Continent-Scale Endemism in the Family Ranidae

    E-Print Network [OSTI]

    Brown, Rafe M.

    2006-01-01T23:59:59.000Z

    of ranid frogs, using 104 representatives of all subfamilies and families, sampled from throughout their distribution. Analyses of ~1570 bp of nuclear gene fragments (Rag-1, rhod, Tyr) and ~2100 bp of the mitochondrial genome (12S rRNA, tRNAVAL, 16S r... of ~490 bp in exon 1 and 4 of the rhodopsin gene (Rhod). A fourth fragment covers -2100 bp of 12S rRNA, tRNAVAL, and 16S rRNA of the mitochondrial genome. Primers used in this study are given elsewhere (Bossuyt and Milinkovitch, 2000; Darst and Cannatella...

  15. Influence of ammonium availability on expression of nifD and amtB genes during biostimulation of a U(VI) contaminated aquifer: implications for U(VI) removal and monitoring the metabolic state of Geobacteraceae

    SciTech Connect (OSTI)

    Mouser, Paula J.; N'Guessan, A. Lucie; Elifantz, Hila; Holmes, Dawn E.; Williams, Kenneth H; Wilkins, Michael J.; Long, Philip E.; Lovley, Derek R.

    2009-03-25T23:59:59.000Z

    The influence of ammonium availability on bacterial community structure and the physiological status of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by 2 orders of magnitude (<4 to 400 ?M) across the study site. Analysis of 16S rRNA sequences suggested that ammonium may have been one factor influencing the community composition prior to acetate amendment with Rhodoferax species predominating over Geobacter species with higher ammonium and Dechloromonas species dominating at the site with lowest ammonium. However, once acetate was added and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms at all locations. Rates of U(VI) reduction appeared to be more related to acetate concentrations rather than ammonium levels. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium transporter gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during uranium reduction. The abundance of amtB was inversely correlated to ammonium levels, whereas nifD transcript levels were similar across all sites examined. These results suggest that nifD and amtB expression are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB transcript expression appears to be a useful approach for monitoring the nitrogen-related physiological status of subsurface Geobacter species. This study also emphasizes the need for more detailed analysis of geochemical and physiological interactions at the field scale in order to adequately model subsurface microbial processes during bioremediation.

  16. SPINE: SParse eIgengene NEtwork Linking Gene Expression Clusters in Dehalococcoides mccartyi to Perturbations in Experimental Conditions

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

    Mansfeldt, Cresten B.; Logsdon, Benjamin A.; Debs, Garrett E.; Richardson, Ruth E.; Mande, Shekhar C.

    2015-02-25T23:59:59.000Z

    We present a statistical model designed to identify the effect of experimental perturbations on the aggregate behavior of the transcriptome expressed by the bacterium Dehalococcoides mccartyi strain 195. Strains of Dehalococcoides are used in sub-surface bioremediation applications because they organohalorespire tetrachloroethene and trichloroethene (common chlorinated solvents that contaminate the environment) to non-toxic ethene. However, the biochemical mechanism of this process remains incompletely described. Additionally, the response of Dehalococcoides to stress-inducing conditions that may be encountered at field-sites is not well understood. The constructed statistical model captured the aggregate behavior of gene expression phenotypes by modeling the distinct eigengenes of 100more »transcript clusters, determining stable relationships among these clusters of gene transcripts with a sparse network-inference algorithm, and directly modeling the effect of changes in experimental conditions by constructing networks conditioned on the experimental state. Based on the model predictions, we discovered new response mechanisms for DMC, notably when the bacterium is exposed to solvent toxicity. The network identified a cluster containing thirteen gene transcripts directly connected to the solvent toxicity condition. Transcripts in this cluster include an iron-dependent regulator (DET0096-97) and a methylglyoxal synthase (DET0137). To validate these predictions, additional experiments were performed. Continuously fed cultures were exposed to saturating levels of tetrachloethene, thereby causing solvent toxicity, and transcripts that were predicted to be linked to solvent toxicity were monitored by quantitative reverse-transcription polymerase chain reaction. Twelve hours after being shocked with saturating levels of tetrachloroethene, the control transcripts (encoding for a key hydrogenase and the 16S rRNA) did not significantly change. By contrast, transcripts for DET0137 and DET0097 displayed a 46.8±11.5 and 14.6±9.3 fold up-regulation, respectively, supporting the model. This is the first study to identify transcripts in Dehalococcoides that potentially respond to tetrachloroethene solvent-toxicity conditions that may be encountered near contamination source zones in sub-surface environments.« less

  17. 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...

  18. Phylogeography of pipistrelle-like bats within the Canary Islands, based on mtDNA sequences

    E-Print Network [OSTI]

    Brown, Richard

    Phylogeography of pipistrelle-like bats within the Canary Islands, based on mtDNA sequences J January 2002; received in revised form 7 July 2002 Abstract Evolution of three Canary Island by comparison of 1 kbp of mtDNA (from cytochrome b and 16S rRNA genes) between islands. mtDNA reveals that both

  19. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Sept. 2003, p. 55035511 Vol. 69, No. 9 0099-2240/03/$08.00 0 DOI: 10.1128/AEM.69.9.55035511.2003

    E-Print Network [OSTI]

    Bennett, Philip

    aquifers, typically associated with geothermal regions and oil-field ba- sins, which play an important role on the phy- logeny of bacterial community 16S rRNA genes characterized filamentous microbial mats from libraries, most clones were affiliated with un- characterized environmental groups within the "Epsilonpro

  20. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Oct. 2002, p. 50645081 Vol. 68, No. 10 0099-2240/02/$04.00 0 DOI: 10.1128/AEM.68.10.50645081.2002

    E-Print Network [OSTI]

    Stamatakis, Alexandros

    Rights Reserved. Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages the chemocline of a hypersaline cyanobacterial mat from Solar Lake (Sinai, Egypt). Consistent with previous- not perform anaerobic sulfate reduction for energy generation hamper cultivation-independent detection

  1. Phylogeny of the Asian spiny frog tribe Paini (Family Dicroglossidae) sensu Dubois Jing Che a,1

    E-Print Network [OSTI]

    Murphy, Bob

    , tyrosinase) and mitochondrial (12S, 16S rRNA) DNA sequence data to infer the phylogenetic relationships

  2. Carbon dioxide, hydrographic, and chemical data obtained in the Central South Pacific Ocean (WOCE sections P17S and P16S) during the tunes-2-expedition of the R/V Thomas Washington, July--August 1991

    SciTech Connect (OSTI)

    NONE

    1991-12-31T23:59:59.000Z

    This data documentation discusses the procedures and methods used to measure total carbon dioxide (TCO{sub 2}), discrete partial pressure of TCO{sub 2} (pCO{sub 2}), and total alkalinity (TALK), during the Research Vessel (R/V) Thomas Washington TUNES Leg 2 Expedition in the central South Pacific Ocean. Conducted as part of the World Ocean Circulation Experiment (WOCE), the cruise began in Papeete, Tahiti, French Polynesia, on July 16, 1991, and returned to Papeete on August 25, 1991. WOCE Meridional Sections P17S along 135{degrees} W and P16S along 150{degrees} W were completed during the 40-day expedition. A total of 97 hydrographic stations were occupied. Hydrographic and chemical measurements made along WOCE Sections P17S and P16S included pressure, temperature, salinity, and oxygen measured by conductivity, temperature and depth sensor; bottle salinity; oxygen; phosphate; nitrate; nitrite; silicate; CFC-12; CFC- 11; TCO{sub 2}; TALK; and pCO{sub 2} measured at 20{degrees}C. The TCO{sub 2} concentration in 1000 seawater samples was determined with a coulometric analysis system, the pCO{sub 2} in 940 water samples was determined with an equilibrator/gas chromatograph system, while the TALK concentration in 139 samples was determined on shore at the laboratory of C. Goyet of Woods Hole Oceanographic Institution with an alkalinity titration system. In addition, 156 coulometric measurements for the Certified Reference Material (Batch {number_sign}6) were made and yielded a mean value of 2303.2 {plus_minus} 1.5 {mu}mol/kg. This mean value agrees within a standard deviation of the 2304.6 {plus_minus} 1.6 {mu}mol/kg (N=9) value determined with the manometer of C. D. Keeling at Scripps Institution of Oceanography (SIO). Replicate samples from 11 Niskin bottles at 4 stations were also collected for later shore-based reference analyses of TCO{sub 2} and TALK by vacuum extraction and manometry in the laboratory of C. D. Keeling of SIO.

  3. Effect of Post-extraction Algal Residue Supplementation on the Therumen Microbiome of Steers Consuming Low-quality Forage

    E-Print Network [OSTI]

    McCann, Joshua C

    2013-06-07T23:59:59.000Z

    and Hughes, 2003). Because Chao1 is only based on observed OTUs, it does not account for unobserved OTUs and therefore can underestimate diversity. It is also subject to bias from varying abundance of PCR-amplified genes (multiple copies of 16S rRNA gene..., or other models. However, drawbacks include an unclear choice of the appropriate abundance model and necessary assumptions of the estimated total specie number and most abundant OTU (Bohannan and Hughes, 2003). Recent advancements in this area...

  4. Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules

    E-Print Network [OSTI]

    Gillespie, Joseph James

    2005-11-01T23:59:59.000Z

    sequence conservation and less length variation. The eukaryotic rDNA occurs as a multi-gene family of tandemly-repeated units of the 23S-like, 16S-like and 5.8S rRNA transcripts that evolve concertedly (Arnheim et al., 1980; Dover, 1982; Arnheim, 1983... over and gene conversion keep the many copies of NORs conserved within species (Dover, 1982). The three functional rRNA transcripts are separated by internally transcribed spacers (ITSs) that are spliced out of the transcripts after NOR expression...

  5. Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments

    SciTech Connect (OSTI)

    Holmes, Dawn; O'Neil, Regina; Vrionis, Helen A.; N'guessan, Lucie A.; Ortiz-Bernad, Irene; Larrahondo, Maria J.; Adams, Lorrie A.; Ward, Joy A.; Nicoll, Julie S.; Nevin, Kelly P.; Chavan, Milind A.; Johnson, Jessica P.; Long, Philip E.; Lovely, Derek R.

    2007-12-01T23:59:59.000Z

    There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants

  6. Ribosomal Database Project II

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

    The Ribosomal Database Project (RDP) provides ribosome related data and services to the scientific community, including online data analysis and aligned and annotated Bacterial small-subunit 16S rRNA sequences. As of March 2008, RDP Release 10 is available and currently (August 2009) contains 1,074,075 aligned 16S rRNA sequences. Data that can be downloaded include zipped GenBank and FASTA alignment files, a histogram (in Excel) of the number of RDP sequences spanning each base position, data in the Functional Gene Pipeline Repository, and various user submitted data. The RDP-II website also provides numerous analysis tools.[From the RDP-II home page at http://rdp.cme.msu.edu/index.jsp

  7. Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer

    SciTech Connect (OSTI)

    Lin, Xueju; McKinley, James P.; Resch, Charles T.; Kaluzny, Rachael M.; Lauber, C.; Fredrickson, Jim K.; Knight, Robbie C.; Konopka, Allan

    2012-03-29T23:59:59.000Z

    Pyrosequencing analysis of 16S rRNA genes was used to study temporal dynamics of groundwater Bacteria and Archaea over 10 months within 3 well clusters separated by ~30 m and located 250 m from the Columbia River on the Hanford Site, WA. Each cluster contained 3 wells screened at different depths ranging from 10 to 17 m that differed in hydraulic conductivities. Representative samples were selected for analyses of prokaryotic 16S and eukaryotic 18S rRNA gene copy numbers. Temporal changes in community composition occurred in all 9 wells over the 10 month sampling period. However, there were particularly strong effects near the top of the water table when the seasonal rise in the Columbia River caused river water intrusion at the top of the aquifer. The occurrence and disappearance of some microbial assemblages (such as Actinobacteria ACK-M1) were correlated to river water intrusion. This seasonal impact on microbial community structure was greater in the shallow saturated zone than deeper in the aquifer. Spatial and temporal patterns for several 16S rRNA gene operational taxonomic units associated with particular physiological functions (e.g.methane oxidizers and metal reducers) suggests dynamic changes in fluxes of electron donors and acceptors over an annual cycle. In addition, temporal dynamics in eukaryotic 18S rRNA gene copies and the dominance of protozoa in 18S clone libraries suggest that bacterial community dynamics could be affected not only by the physical and chemical environment, but also by top-down biological control.

  8. 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...

  9. A16S (SAVE 5) Smethie & McCartney R/V Melville 1989 1. Cruise Narrative: A16S

    E-Print Network [OSTI]

    Ship R/V MELVILLE Ports of call Cape Town, South Africa to Montevideo, Uruguay Number of stations 73 Cape Town, South Africa to Montevideo, Uruguay 23 January 1989 - 8 March 1989 Stations 236 through 308 1989 Cape Town, South Africa to Montevideo, Uruguay Data Report Prepared by: Oceanographic Data

  10. 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 ...

  11. Microbiological and Geochemical Heterogeneity in an In Situ

    E-Print Network [OSTI]

    Uranium Bioremediation; Field Site; Helen A. Vrionis; Robert T. Anderson; Irene Ortiz-bernad; Kathleen R. O’neill; Philip E. Long; Derek R. Lovley

    2005-01-01T23:59:59.000Z

    The geochemistry and microbiology of a uranium-contaminated subsurface environment that had undergone two seasons of acetate addition to stimulate microbial U(VI) reduction was examined. There were distinct horizontal and vertical geochemical gradients that could be attributed in large part to the manner in which acetate was distributed in the aquifer, with more reduction of Fe(III) and sulfate occurring at greater depths and closer to the point of acetate injection. Clone libraries of 16S rRNA genes derived from sediments and groundwater indicated an enrichment of sulfate-reducing bacteria in the order Desulfobacterales in sediment and groundwater samples. These samples were collected nearest the injection gallery where microbially reducible Fe(III) oxides were highly depleted, groundwater sulfate concentrations were low, and increases in acid volatile sulfide were observed in the sediment. Further down-gradient, metal-reducing conditions were present as indicated by intermediate Fe(II)/Fe(total) ratios, lower acid volatile sulfide values, and increased abundance of 16S rRNA gene sequences belonging to the dissimilatory Fe(III)- and U(VI)-reducing family Geobacteraceae. Maximal Fe(III) and U(VI) reduction correlated with maximal recovery of Geobacteraceae 16S rRNA gene sequences in both groundwater and sediment; however, the sites at which these maxima occurred were spatially separated within the aquifer. The substantial microbial and geochemical heterogeneity at this site demonstrates that attempts should be made to deliver acetate in a more uniform manner and that closely

  12. 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

  13. 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

  14. Characterization of Methane Degradation and Methane-Degrading Microbes in Alaska Coastal Water

    SciTech Connect (OSTI)

    David Kirchman

    2011-12-31T23:59:59.000Z

    The net flux of methane from methane hydrates and other sources to the atmosphere depends on methane degradation as well as methane production and release from geological sources. The goal of this project was to examine methane-degrading archaea and organic carbon oxidizing bacteria in methane-rich and methane-poor sediments of the Beaufort Sea, Alaska. The Beaufort Sea system was sampled as part of a multi-disciplinary expedition (â??Methane in the Arctic Shelfâ?ť or MIDAS) in September 2009. Microbial communities were examined by quantitative PCR analyses of 16S rRNA genes and key methane degradation genes (pmoA and mcrA involved in aerobic and anaerobic methane degradation, respectively), tag pyrosequencing of 16S rRNA genes to determine the taxonomic make up of microbes in these sediments, and sequencing of all microbial genes (â??metagenomesâ?ť). The taxonomic and functional make-up of the microbial communities varied with methane concentrations, with some data suggesting higher abundances of potential methane-oxidizing archaea in methane-rich sediments. Sequence analysis of PCR amplicons revealed that most of the mcrA genes were from the ANME-2 group of methane oxidizers. According to metagenomic data, genes involved in methane degradation and other degradation pathways changed with sediment depth along with sulfate and methane concentrations. Most importantly, sulfate reduction genes decreased with depth while the anaerobic methane degradation gene (mcrA) increased along with methane concentrations. The number of potential methane degradation genes (mcrA) was low and inconsistent with other data indicating the large impact of methane on these sediments. The data can be reconciled if a small number of potential methane-oxidizing archaea mediates a large flux of carbon in these sediments. Our study is the first to report metagenomic data from sediments dominated by ANME-2 archaea and is one of the few to examine the entire microbial assemblage potentially involved in anaerobic methane oxidation.

  15. 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.

  16. Selective progressive response of soil microbial community to wild oat roots

    SciTech Connect (OSTI)

    DeAngelis, K.M.; Brodie, E.L.; DeSantis, T.Z.; Andersen, G.L.; Lindow, S.E.; Firestone, M.K.

    2008-10-01T23:59:59.000Z

    Roots moving through soil enact physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. Use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies previously reported compositional changes, including increases in chitinase and protease specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change in 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA T-RFLP analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared to bulk soil, but then increased in older root zones. Quantitative PCR revealed {beta}-Proteobacteria and Actinobacteria present at about 10{sup 8} copies of 16S rRNA genes g{sup -1} soil, with Nitrospira having about 10{sup 5} copies g{sup -1} soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in function in progressively more mature rhizosphere zones.

  17. 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;

  18. Spatial distribution of an uranium-respiring betaproteobacterium at the rifle, CO field research site

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

    Koribanics, Nicole M.; Tuorto, Steven J.; Lopez-Chiaffarelli, Nora; McGuinness, Lora R.; Häggblom, Max M.; Williams, Kenneth H.; Long, Philip E.; Kerkhof, Lee J.; Morais, Paula V

    2015-04-13T23:59:59.000Z

    The Department of Energy’s Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminalmore »electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.« less

  19. Experimental factors affecting PCR-based estimates of microbial species richness and evenness

    SciTech Connect (OSTI)

    Engelbrektson, Anna; Kunin, Victor; Wrighton, Kelly C.; Zvenigorodsky, Natasha; Chen, Feng; Ochman, Howard; Hugenholtz, Philip

    2009-12-01T23:59:59.000Z

    Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield greater than two orders of magnitude more sensitivity than traditional PCR-cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCRbased community structure profiling methods. We tested the effect of amplicon length and primer pair on estimates of species richness number of species and evenness relative abundance of species by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1-V2 or V8 regions, using amplicons ranging n length from 352 to 1443 bp. Our results demonstrate that both amplicon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities.

  20. Spatial distribution of an uranium-respiring betaproteobacterium at the rifle, CO field research site

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

    Koribanics, Nicole M. [Rutgers Univ., New Brunswick, NJ (United States); Tuorto, Steven J. [Rutgers Univ., New Brunswick, NJ (United States); Lopez-Chiaffarelli, Nora [Rutgers Univ., New Brunswick, NJ (United States); McGuinness, Lora R. [Rutgers Univ., New Brunswick, NJ (United States); Häggblom, Max M. [Rutgers Univ., New Brunswick, NJ (United States); Williams, Kenneth H. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Long, Philip E. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kerkhof, Lee J. [Rutgers Univ., New Brunswick, NJ (United States); Morais, Paula V [Univ. of Coimbra (Portugal)

    2015-04-13T23:59:59.000Z

    The Department of Energy’s Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminal electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.

  1. Degradative capacities and bioaugmentation potential of an anaerobic benzene-degrading bacterium strain DN11

    SciTech Connect (OSTI)

    Yuki Kasai; Yumiko Kodama; Yoh Takahata; Toshihiro Hoaki; Kazuya Watanabe [Marine Biotechnology Institute, Kamaishi (Japan)

    2007-09-15T23:59:59.000Z

    Azoarcus sp. strain DN11 is a denitrifying bacterium capable of benzene degradation under anaerobic conditions. The present study evaluated strain DN11 for its application to bioaugmentation of benzene-contaminated underground aquifers. Strain DN11 could grow on benzene, toluene, m-xylene, and benzoate as the sole carbon and energy sources under nitrate-reducing conditions, although o- and p-xylenes were transformed in the presence of toluene. Phenol was not utilized under anaerobic conditions. Kinetic analysis of anaerobic benzene degradation estimated its apparent affinity and inhibition constants to be 0.82 and 11 {mu}M, respectively. Benzene-contaminated groundwater taken from a former coal-distillation plant site in Aichi, Japan was anaerobically incubated in laboratory bottles and supplemented with either inorganic nutrients (nitrogen, phosphorus, and nitrate) alone, or the nutrients plus strain DN11, showing that benzene was significantly degraded only when DN11 was introduced. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments, and quantitative PCR revealed that DN11 decreased after benzene was degraded. Following the decrease in DN11 16S rRNA gene fragments corresponding to bacteria related to Owenweeksia hongkongensis and Pelotomaculum isophthalicum, appeared as strong bands, suggesting possible metabolic interactions in anaerobic benzene degradation. Results suggest that DN11 is potentially useful for degrading benzene that contaminates underground aquifers at relatively low concentrations. 50 refs., 6 figs., 1 tab.

  2. Multiple Syntrophic Interactions in a Terephthalate-Degrading Methanogenic Consortium

    E-Print Network [OSTI]

    Lykidis, Athanasios

    2012-01-01T23:59:59.000Z

    of the TA-degrading bioreactor as revealed by 16S rRNA clonethermophilic), TA-degrading bioreactor. We identified geneslaboratory-scale hybrid bioreactor (Fig. 1a) as described

  3. Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit

    E-Print Network [OSTI]

    Preheim, Sarah Pacocha

    16S rRNA sequencing, commonly used to survey microbial communities, begins by grouping individual reads into operational taxonomic units (OTUs). There are two major challenges in calling OTUs: identifying bacterial population ...

  4. 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.

  5. Final Technical Report: DOE-Biological Ocean Margins Program. Microbial Ecology of Denitrifying Bacteria in the Coastal Ocean.

    SciTech Connect (OSTI)

    Lee Kerkhof

    2013-01-01T23:59:59.000Z

    The focus of our research was to provide a comprehensive study of the bacterioplankton populations off the coast of New Jersey near the Rutgers University marine field station using terminal restriction fragment polymorphism analysis (TRFLP) coupled to 16S rRNA genes for large data set studies. Our three revised objectives to this study became: (1) to describe bacterioplankton population dynamics in the Mid Atlantic Bight using TRFLP analysis of 16S rRNA genes. (2) to determine whether spatial and temporal factors are driving bacterioplankton community dynamics in the MAB using monthly samping along our transect line over a 2-year period. (3) to identify dominant members of a coastal bacterioplankton population by clonal library analysis of 16S rDNA genes and sequencing of PCR product corresponding to specific TRFLP peaks in the data set. Although open ocean time-series sites have been areas of microbial research for years, relatively little was known about the population dynamics of bacterioplankton communities in the coastal ocean on kilometer spatial and seasonal temporal scales. To gain a better understanding of microbial community variability, monthly samples of bacterial biomass were collected in 1995-1996 along a 34-km transect near the Long-Term Ecosystem Observatory (LEO-15) off the New Jersey coast. Surface and bottom sampling was performed at seven stations along a transect line with depths ranging from 1 to 35m (n=178). The data revealed distinct temporal patterns among the bacterioplankton communities in the Mid-Atlantic Bight rather than grouping by sample location or depth (figure 2-next page). Principal components analysis models supported the temporal patterns. In addition, partial least squares regression modeling could not discern a significant correlation from traditional oceanographic physical and phytoplankton nutrient parameters on overall bacterial community variability patterns at LEO-15. These results suggest factors not traditionally measured during oceanographic studies are structuring coastal microbial communities.

  6. 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...

  7. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods

    SciTech Connect (OSTI)

    Wu, Liyou; Yi, T. Y.; Van Nostrand, Joy; Zhou, Jizhong

    2010-05-17T23:59:59.000Z

    Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site [Hanford Reach of the Columbia River (HRCR), 11 strains], Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.

  8. 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 ...

  9. 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...

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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...

  15. 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...

  16. 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...

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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 ...

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts

    SciTech Connect (OSTI)

    Mason, Olivia U.; Di Meo-Savoie, Carol A.; Van Nostrand, Joy D.; Zhou, Jizhong; Fisk, Martin R.; Giovannoni, Stephen J.

    2008-09-30T23:59:59.000Z

    We used molecular techniques to analyze basalts of varying ages that were collected from the East Pacific Rise, 9 oN, from the rift axis of the Juan de Fuca Ridge, and from neighboring seamounts. Cluster analysis of 16S rDNA Terminal Restriction Fragment Polymorphism data revealed that basalt endoliths are distinct from seawater and that communities clustered, to some degree, based on the age of the host rock. This age-based clustering suggests that alteration processes may affect community structure. Cloning and sequencing of bacterial and archaeal 16S rRNA genes revealed twelve different phyla and sub-phyla associated with basalts. These include the Gemmatimonadetes, Nitrospirae, the candidate phylum SBR1093 in the c, andin the Archaea Marine Benthic Group B, none of which have been previously reported in basalts. We delineated novel ocean crust clades in the gamma-Proteobacteria, Planctomycetes, and Actinobacteria that are composed entirely of basalt associated microflora, and may represent basalt ecotypes. Finally, microarray analysis of functional genes in basalt revealed that genes coding for previously unreported processes such as carbon fixation, methane-oxidation, methanogenesis, and nitrogen fixation are present, suggesting that basalts harbor previously unrecognized metabolic diversity. These novel processes could exert a profound influence on ocean chemistry.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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

  18. Dissecting Biological Dark Matter: Single Cell Genetic Analysis of TM7, a Rare and Uncultivated Microbe from the Human Mouth

    SciTech Connect (OSTI)

    Fenner, Marsha W; Marcy, Yann; Ouverney, Cleber; Bik, Elisabeth M.; Losekann, Tina; Ivanova, Natalia; Martin, H. Garcia; Szeto, E.; Platt, Darren; Hugenholtz, Philip; Relman, David A.; Quake, Stephen R.

    2007-07-01T23:59:59.000Z

    We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community.

  19. Atmospheric cloud water contains a diverse bacterial community

    SciTech Connect (OSTI)

    Kourtev, P. S.; Hill, Kimberly A.; Shepson, Paul B.; Konopka, Allan

    2011-06-15T23:59:59.000Z

    Atmospheric cloud water contains an active microbial community which can impact climate, human health and ecosystem processes in terrestrial and aquatic systems. Most studies on the composition of microbial communities in clouds have been performed with orographic clouds that are typically in direct contact with the ground. We collected water samples from cumulus clouds above the upper U.S. Midwest. The cloud water was analyzed for the diversity of bacterial phylotypes by denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene amplicons. DGGE analyses of bacterial communities detected 17e21 bands per sample. Sequencing confirmed the presence of a diverse bacterial community; sequences from seven bacterial phyla were retrieved. Cloud water bacterial communities appeared to be dominated by members of the cyanobacteria, proteobacteria, actinobacteria and firmicutes.

  20. Role of Pam16's degenerate J domain in protein import across the mitochondrial inner membrane

    E-Print Network [OSTI]

    Craig, Elizabeth A

    Patrick R. D'Silva*, Brenda Schilke*, William Walter, and Elizabeth A. Craig Department of Biochemistry domain to stim- ulate Ssc1's ATPase domain, and (iii) the innately lower stimulatory activity of the Pam-terminal regions. In addition, the C-terminal region of Pam16 has significant sequence similarity to Pam18's C

  1. 20 Cd4In16S35 14-Supertetrahedral T4 Clusters as

    E-Print Network [OSTI]

    Yaghi, Omar M.

    -287. (c) Cahill, C. L.; Parise, J. B. Chem. Mater. 1997, 9, 807-811. (3) (a) Hammerschmidt, A.; zum Hebel.; Parise, J. B. Chem. Mater. 1998

  2. FAMeS: Fidelity of Analysis of Metagenomic Samples

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

    Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods currently used to process metagenomic sequences, simulated datasets of varying complexity were constructed by combining sequencing reads randomly selected from 113 isolate genomes. These datasets were designed to model real metagenomes in terms of complexity and phylogenetic composition. Assembly, gene prediction and binning, employing methods commonly used for the analysis of metagenomic datasets at the DOE JGI, were performed. This site provides access to the simulated datasets, and aims to facilitate standardized benchmarking of tools for metagenomic analysis. FAMeS now hosts data coming from a comprehensive study of methodologies used to create OTUs from 16S rRNA targeted studies of microbial communities. Studies of phylogenetic markers at the molecular level have revealed a vast biodiversity of microorganisms living in the sea, land, and even within the human body. Microbial diversity studies of uncharacterized environments typically seek to estimate the richness and diversity of endemic microflora using a 16S rRNA gene sequencing approach. When most of the species in an environment are unknown and cannot be classified through a database search, researchers cluster 16S sequences into operational taxonomic units (OTUs) or phylotypes, thereby providing an estimate of population structure. Using real 16S sequence data, we have performed a critical analysis of OTU clustering methodologies to assess the potential variability in OTU quality. FAMeS provides the sequence data, taxonomic information, multiple sequence alignments, and distance matrices used and described in the core paper, as well as compiled results of more than 700 unique OTU methods. [The above was copied from the FAMeS home page at http://fames.jgi-psf.org/] The core paper behind FAMeS is: Konstantinos Mavromatis, Natalia Ivanova, Kerrie Barry, Harris Shapiro, Eugene Goltsman, Alice C McHardy, Isidore Rigoutsos, Asaf Salamov, Frank Korzeniewski, Miriam Land, Alla Lapidus, Igor Grigoriev, Paul Richardson, Philip Hugenholtz, Nikos C Kyrpides, Nature Methods 2007 Jun;4(6):495-500.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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 ...

  9. 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

  10. Extremophilic iron-reducing bacteria: Their implications for possible life in extraterrestrial environments

    SciTech Connect (OSTI)

    Zhou, J.; Liu, S.V.; Zhang, C.; Palumbo, A.V.; Phelps, T.J.

    1998-06-01T23:59:59.000Z

    Iron reduction is believed to be an early form of respiration and iron-reducing bacteria might have evolved very early on Earth. To support this hypothesis, the authors began to search for both thermophilic and psychrophilic iron-reducing bacteria because iron-reducing capacity may be a widely distributed trait if ancestral microorganisms include extremophilic iron-reducing bacteria. To date, they have obtained thermophilic Fe(III)-reducing and magnetite-forming enrichment cultures from geologically and hydrologically isolated, millions of years-old deep terrestrial subsurface samples. Three dominant bacteria were identified based on 16S ribosomal RNA gene sequences. Phylogenetical analysis indicated that these bacteria were closely related to Thermoanaerobacter ethanoliticus. Two pure thermophilic iron-reducing bacteria have been isolated and characterized from these enrichments, they also are able to degrade cellulose and xylan. Geological evidence indicated that these bacteria were separated from modern organisms for about 200 million years, and they are the oldest isolated bacteria available now. Evolutionary sequence analysis showed that the 16S rRNA genes evolved extremely slowly in these bacteria. In addition, the authors have obtained about 30 psychrophilic iron-reducing bacteria in samples from Siberia and Alaska permafrost soils, Pacific marine sediments and Hawaii deep sea water. These bacteria were also able to reduce other heavy metals. The isolation of both thermophilic and psychrophilic iron-reducing bacteria from surface and subsurface environments has significant implications for microbial evolution and for studying the origin of life in extraterrestrial environments.

  11. Endosymbiosis In Statu Nascendi: Close Phylogenetic RelationshipBetween Obligately Endosymbiotic and Obligately Free-LivingPolynucleobacter Strains (Betaproteobacteria)

    SciTech Connect (OSTI)

    Vannini, Claudia; Pockl, Matthias; Petroni, Giulio; Wu, Qinglong; Lang, Elke; Stackebrandt, Erko; Schrallhammer, Martina; Richardson, PaulM.; Hahn, Martin W.

    2006-07-21T23:59:59.000Z

    Bacterial strains affiliated to the phylogenetically shallowsubcluster C (PnecC) of the 28 Polynucleobacter cluster, which ischaracterized by a minimal 16S rRNA gene sequence similarity of approx.98.5 percent, have been reported to occur as obligate endosymbionts of 30ciliates (Euplotes spp.), as well as to occur as free-living cells in thepelagic zone of freshwater habitats. We investigated if these two groupsof closely related bacteria represent 32 strains fundamentally differingin lifestyle, or if they simply represent different stages of afacultative endosymbiotic lifestyle. The phylogenetic analysis of 16SrRNA gene and 16S34 23S ITS sequences of five endosymbiont strains fromtwo different Euplotes species and 40 pure culture strains demonstratedhost-species-specific clustering of the endosymbiont 36 sequences withinthe PnecC subcluster. The sequences of the endosymbionts showedcharacteristics indicating an obligate endosymbiotic lifestyle.Cultivation experiments 38 revealed fundamental differences inphysiological adaptations, and determination of the genome sizesindicated a slight size reduction in endosymbiotic strains. We concludethat the 40 two groups of PnecC bacteria represent obligately free-livingand obligately endosymbiotic strains, respectively, and do not representdifferent stages of the same complex lifecycle. 42 These closely relatedstrains occupy completely separated ecological niches. To our bestknowledge, this is the closest phylogenetic relationship between obligateendosymbionts and 44 obligately free-living bacteria everrevealed.

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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.

  19. 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 ...

  20. 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...

  1. 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...

  2. 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.

  3. 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.

  4. Gene expression profiles in irradiated cancer cells

    SciTech Connect (OSTI)

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

  5. 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 ...

  6. 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 ...

  7. 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...

  8. 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 ...

  9. 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

  10. 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...

  11. 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...

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. Molecular and in vitro characterization of a Babesia divergens-like agent from eastern cottontail rabbits (Sylvilagus floridanus) on Nantucket Island

    E-Print Network [OSTI]

    Spencer, Angela M

    2006-10-30T23:59:59.000Z

    related to the European parasite, Babesia divergens. The ribosomal RNA (rRNA) internal transcribed spacer regions (ITS1 and ITS2) and the 5.8S rRNA genes of Babesia isolates were sequenced and analyzed. The rRNA ITS region sequences of three isolates, one...

  3. adjacent rrna nucleotide: Topics by E-print Network

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

    eScholarship Repository Summary: Archaeological Test Excavation at Prehis- toric Site CA-TRI-327, Trinity County, Cali- fornia. ReportArchaeological Test Excavation of the Fay...

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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...

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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 ...

  17. 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 ...

  18. 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

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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 ...

  8. 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.

  9. 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...

  10. 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...

  11. 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

  12. 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

  13. 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

  14. 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...

  15. 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

  16. 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

  17. PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema (OSTI)

    Lukjancenko, Oksana [Technical University of Denmark

    2013-01-25T23:59:59.000Z

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  18. A Large-scale Benchmark Study of Existing Algorithms for Taxonomy-Independent

    E-Print Network [OSTI]

    Slatton, Clint

    A Large-scale Benchmark Study of Existing Algorithms for Taxonomy-Independent Microbial Community sequencing technology have created new op- portunities to probe the hidden world of microbes. Taxonomy: pyrosequencing, 16S rRNA, taxonomy independent analysis, massive data, clustering, microbial diversity estimation

  19. The Highly Conserved Bacterial RNase YbeY Is Essential in Vibrio cholerae, Playing a Critical Role in Virulence, Stress Regulation, and RNA Processing

    E-Print Network [OSTI]

    Vercruysse, Maarten

    YbeY, a highly conserved protein, is an RNase in E. coli and plays key roles in both processing of the critical 3? end of 16 S rRNA and in 70 S ribosome quality control under stress. These central roles account for YbeY's ...

  20. Algal Research1 Screening and selection of growth-promoting bacteria for Dunaliella cultures2

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    and potential applications for microalgae, which include food,44 animal feed, healthcare, energy microalgae species and identified using 16S rRNA phylogenetic analysis. The recovered bacteria were27 found38 accumulation in Dunaliella sp. cells.39 Keywords: Microalgae, Dunaliella, bacteria, interaction

  1. Integrated Ecogenomics Study for Bioremediation of Cr(VI) at Hanford 100H Area

    SciTech Connect (OSTI)

    Chakraborty, Romy; Chakraborty, Romy

    2008-08-12T23:59:59.000Z

    Hexavalent chromium is a widespread contaminant found in groundwater. In order to stimulate microbially mediated Cr(VI)-reduction, a poly-lactate compound was injected into Cr(VI)-contaminated aquifers at site 100H at Hanford. Investigation of bacterial community composition using high-density DNA microarray analysis of 16S rRNA gene products revealed a stimulation of Pseudomonas, Desulfovibrio and Geobacter species amongst others. Enrichment of these organisms coincided with continued Cr(VI) depletion. Functional gene-array analysis of DNA from monitoring well indicated high abundance of genes involved in nitrate-reduction, sulfate-reduction, iron-reduction, methanogenesis, chromium tolerance/reduction. Clone-library data revealed Psedomonas was the dominant genus in these samples. Based on above results, we conducted lab investigations to study the dominant anaerobic culturable microbial populations present at this site and their role in Cr(VI)-reduction. Enrichments using defined anaerobic media resulted in isolation of an iron-reducing, a sulfate-reducing and a nitrate-reducing isolate among several others. Preliminary 16S rDNA sequence analysis identified the isolates as Geobacter metallireducens, Pseudomonas stutzeri and Desulfovibrio vulgaris species respectively. The Pseudomonas isolate utilized acetate, lactate, glycerol and pyruvate as alternative carbon sources, and reduced Cr(VI). Anaerobic washed cell suspension of strain HLN reduced almost 95?M Cr(VI) within 4 hr. Further, with 100?M Cr(VI) as sole electron-acceptor, cells grew to 4.05 x 107 /ml over 24 h after an initial lag, demonstrating direct enzymatic Cr(VI) reduction coupled to growth. These results demonstrate that Cr(VI)-immobilization at Hanford 100H site could be mediated by direct microbial metabolism in addition to indirect chemical reduction of Cr(VI) by end-products of microbial activity.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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.

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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

  19. 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...

  20. 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...

  1. 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

  2. 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.

  3. 16S rRNA-Based Tag Pyrosequencing of Complex Food and Wastewater Environments: Microbial Diversity and Dynamics

    E-Print Network [OSTI]

    McElhany, Katherine

    2012-02-14T23:59:59.000Z

    pyrosequencing and traditional culture-based techniques to investigate the diversity and dynamics of bacterial populations within milk and untreated sewage sludge samples. Pasteurized and raw milk samples were collected from grocery stores and dairies within...

  4. Nuclear Engineering Courses No. Course Title F14 S15 F15 S16 F16 S17

    E-Print Network [OSTI]

    Wisconsin at Madison, University of

    JB x x 405 Nuc. Reactor Theory GAM x x 406 Nuc. Reactor Analysis x 408 Ionizing Radiation DLH x x 411 Lab ?? x 427 Nuclear Instr. Lab RJF RJF x x x x 428 Nuclear Reactor Lab RA RA x x x x 506 Monte Carlo Analysis JPB x 602 Reactor Safety x x 602 Seminar JPB 705 Adv. Reactor Theory x x 724 Waves & Inst. in Pl

  5. 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.

  6. 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.

  7. The use of microarrays in microbial ecology

    SciTech Connect (OSTI)

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15T23:59:59.000Z

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer oligonucleotide probes and covers more than 10,000 gene sequences in 150 gene categories involved in carbon, nitrogen, sulfur, and phosphorus cycling, metal resistance and reduction, and organic contaminant degradation. GeoChip can be used as a generic tool for microbial community analysis, and also link microbial community structure to ecosystem functioning. Examples of the application of both arrays in different environmental samples will be described in the two subsequent sections.

  8. 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...

  9. 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 , NĂşria 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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...

  1. 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

  2. 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

  3. 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

  4. 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...

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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...

  13. 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

  14. 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...

  15. 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

  16. Deduction and Analysis of the Interacting Stress Response Pathways of Metal/Radionuclide-reducing Bacteria

    SciTech Connect (OSTI)

    Zhou, Jizhong [University of Oklahoma; He, Zhili [University of Oklahoma

    2010-02-28T23:59:59.000Z

    Project Title: Deduction and Analysis of the Interacting Stress Response Pathways of Metal/Radionuclide-reducing Bacteria DOE Grant Number: DE-FG02-06ER64205 Principal Investigator: Jizhong (Joe) Zhou (University of Oklahoma) Key members: Zhili He, Aifen Zhou, Christopher Hemme, Joy Van Nostrand, Ye Deng, and Qichao Tu Collaborators: Terry Hazen, Judy Wall, Adam Arkin, Matthew Fields, Aindrila Mukhopadhyay, and David Stahl Summary Three major objectives have been conducted in the Zhou group at the University of Oklahoma (OU): (i) understanding of gene function, regulation, network and evolution of Desulfovibrio vugaris Hildenborough in response to environmental stresses, (ii) development of metagenomics technologies for microbial community analysis, and (iii) functional characterization of microbial communities with metagenomic approaches. In the past a few years, we characterized four CRP/FNR regulators, sequenced ancestor and evolved D. vulgaris strains, and functionally analyzed those mutated genes identified in salt-adapted strains. Also, a new version of GeoChip 4.0 has been developed, which also includes stress response genes (StressChip), and a random matrix theory-based conceptual framework for identifying functional molecular ecological networks has been developed with the high throughput functional gene array hybridization data as well as pyrosequencing data from 16S rRNA genes. In addition, GeoChip and sequencing technologies as well as network analysis approaches have been used to analyze microbial communities from different habitats. Those studies provide a comprehensive understanding of gene function, regulation, network, and evolution in D. vulgaris, and microbial community diversity, composition and structure as well as their linkages with environmental factors and ecosystem functioning, which has resulted in more than 60 publications.

  17. Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T)

    SciTech Connect (OSTI)

    Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Mwirichia, Romano [Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

    2011-01-01T23:59:59.000Z

    Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262 T forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na + ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na + ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. Environmental Shortcourse Final report [Joint US-EC Short Course on Environmental Biotechnology: Microbial Catalysts for the Environment

    SciTech Connect (OSTI)

    Zylstra, Gerben; van der Meer, Jan Roelof

    2013-03-05T23:59:59.000Z

    The Joint US-EC Short Course on Environmental Biotechnology is designed for several purposes. One of the central tenets is to bring together young scientists (at the late Ph.D. or early postdoctoral stages of their careers) in a forum that will set the groundwork for future overseas collaborative interactions. The course is also designed to give the scientists hands-on experience in modern, up-to-date biotechnological methods for the analysis of microbes and their activities pertinent to the remediation of pollutants in the environment. The 2011 course covered multiple theoretical and practical topics in environmental biotechnology. The practical part was centered around a full concise experiment to demonstrate the possibility for targeted remediation of contaminated soil. Experiments included chemical, microbiological, and molecular analyses of sediments and/or waters, contaminant bioavailability assessment, seeded bioremediation, gene probing, PCR amplification, microbial community analysis based on 16S rRNA gene diversity, and microarray analyses. Each of these topics is explained in detail. The practical part of the course was complemented with two lectures per day, given by distinguished scientists from the US and from Europe, covering a research area related to what the students are doing in the course.

  19. 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...

  20. 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...

  1. 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.

  2. 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.

  3. 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...

  4. 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

  5. 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:...

  6. 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:...

  7. 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:...

  8. 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:...

  9. 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

  10. 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...

  11. 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

  12. 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...

  13. 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...

  14. 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

  15. 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

  16. 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 ...

  17. 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.

  18. 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...

  19. 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...

  20. 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...

  1. 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. ...

  2. 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 ...

  3. 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

  4. 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...

  5. 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...

  6. 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 ...

  7. 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...

  8. 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...

  9. 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...

  10. 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. ...

  11. 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 ...

  12. ; 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

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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 ...

  1. 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

  2. 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.

  3. 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.

  4. The Epsomitic Phototrophic Microbial Mat of Hot Lake, Washington: Community Structural Responses to Seasonal Cycling

    SciTech Connect (OSTI)

    Lindemann, Stephen R.; Moran, James J.; Stegen, James C.; Renslow, Ryan S.; Hutchison, Janine R.; Cole, Jessica K.; Dohnalkova, Alice; Tremblay, Julien; Singh, Kanwar; Malfatti, Stephanie; Chen, Feng; Tringe, Susannah; Beyenal, Haluk; Fredrickson, Jim K.

    2013-11-13T23:59:59.000Z

    Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring, disassembles each fall, and is subject to greater than tenfold variation in salinity (primarily Mg2+ and SO2?4) and irradiation over the annual cycle. We examined spatiotemporal variation in the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by amplicon sequencing of the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya), and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus). Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium) and Deltaproteobacteria (e.g., Desulfofustis) that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function.

  5. Characterization of the bacterial metagenome in an industrial algae bioenergy production system

    SciTech Connect (OSTI)

    Huang, Shi [Chinese Academy of Sciences; Fulbright, Scott P [Colorado State University; Zeng, Xiaowei [Chinese Academy of Sciences; Yates, Tracy [Solix Biofuels; Wardle, Greg [Solix Biofuels; Chisholm, Stephen T [Colorado State University; Xu, Jian [Chinese Academy of Sciences; Lammers, Peter [New Mexico State University

    2011-03-16T23:59:59.000Z

    Cultivation of oleaginous microalgae for fuel generally requires growth of the intended species to the maximum extent supported by available light. The presence of undesired competitors, pathogens and grazers in cultivation systems will create competition for nitrate, phosphate, sulfate, iron and other micronutrients in the growth medium and potentially decrease microalgal triglyceride production by limiting microalgal health or cell density. Pathogenic bacteria may also directly impact the metabolism or survival of individual microalgal cells. Conversely, symbiotic bacteria that enhance microalgal growth may also be present in the system. Finally, the use of agricultural and municipal wastes as nutrient inputs for microalgal production systems may lead to the introduction and proliferation of human pathogens or interfere with the growth of bacteria with beneficial effects on system performance. These considerations underscore the need to understand bacterial community dynamics in microalgal production systems in order to assess microbiome effects on microalgal productivity and pathogen risks. Here we focus on the bacterial component of microalgal production systems and describe a pipeline for metagenomic characterization of bacterial diversity in industrial cultures of an oleaginous alga, Nannochloropsis salina. Environmental DNA was isolated from 12 marine algal cultures grown at Solix Biofuels, a region of the 16S rRNA gene was amplified by PCR, and 16S amplicons were sequenced using a 454 automated pyrosequencer. The approximately 70,000 sequences that passed quality control clustered into 53,950 unique sequences. The majority of sequences belonged to thirteen phyla. At the genus level, sequences from all samples represented 169 different genera. About 52.94% of all sequences could not be identified at the genus level and were classified at the next highest possible resolution level. Of all sequences, 79.92% corresponded to 169 genera and 70 other taxa. We apply a principal component analysis across the initial sample set to draw correlations between sample variables and changes in microbiome populations.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Joint United States-European Union Theoretical and Practical Course on Molecular Approaches for In Situ Biogradation

    SciTech Connect (OSTI)

    Suflita, Joseph M.; Duncan, Kathleen E.

    2010-08-14T23:59:59.000Z

    The Joint United States - European Union Theoretical and Practical Course on Molecular Approaches for in situ Biodegradation was held May 24 through June 7 at The University of Oklahoma. Twenty-four graduate and postgraduate students from both the United States and the European Union attended the course. Nine states and ten European countries were represented. Students were assigned living quarters and laboratory partners to maximize interactions between US and EU participants as well as to mix people with different technical backgrounds together. The students used the latest methods in molecular biology to characterize beneficial microorganisms and genes involved in the biodegradation of pollutants at a nearby landfill as well as an active hydrocarbon-producing site, part of which is undergoing bioremediation. Seminars by distinguished scientists were organized to expose the students to the breadth of the environmental field, including field assay and engineering applications, laboratory scale bioreactors, microbiology, genetics, regulation, pathway analysis, design of recombinant bacteria, and application of the associated techniques to the field. Lectures were given by various OU faculty on the principles behind the techniques to be used in the laboratory. These lectures included troubleshooting hints and encouraged questions and comments from the audience. The laboratory experiments covered chemical, microbiological, and molecular genetic analyses of soils; bioavailability of contaminants; enrichment cultures; gene probing; PCR amplification of known genes and gene families; identification of microbes based traditional and nontraditional approaches, nutritional capabilities, and 16S rRNA sequence; mRNA detection; and enzyme assays. Field trips were made to the USGS landfill field sampling site, and to the Tall Grass Prairie Preserve, a Nature Conservancy site which also featured long-term studies of bioremediation of crude oil and brine spills by one of the Principal Investigators in collaboration with University of Tulsa faculty. The students are expected to bring the methods that they learned back to their laboratories to enrich their own and their colleagues' ability to perform state of the art environmental biotechnology research.

  17. Molecular comparisons of Babesia odocoilei using the internal transcribed spacers of ribosomal RNA

    E-Print Network [OSTI]

    Schoelkopf, Lorien

    2005-11-01T23:59:59.000Z

    and host range continue to extend as new incidence of infection is detected. A genomic DNA region spanning the internal transcribed spacer 1 (ITS1), 5.8S rRNA gene, and ITS2 of ribosomal RNA (rRNA) from 18 B. odocoilei isolates (speciation confirmed...

  18. 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

  19. 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...

  20. 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...

  1. 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

  2. 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...

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  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. 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

  2. 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

  3. Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S°-reducing bacteria in a sulfate-rich environment

    SciTech Connect (OSTI)

    Kovacik, William P.; Takai, Ken; Mormile, Melanie R.; McKinley, James P.; Brockman, Fred J.; Fredrickson, Jim K.; Holben, William E.

    2006-01-01T23:59:59.000Z

    A multi-level sampler (MLS) was emplaced in a borehole straddling anaerobic, sulfate-rich Cretaceous-era shale and sandstone rock formations {approx}200 m below ground surface at Cerro Negro, New Mexico. Sterile quartzite sand contained in chambers in the sampler allowed in situ colonization and recovery of nucleic acids for molecular analyses. DGGE and 16S rRNA gene cloning results indicated a homogeneously distributed bacterial community across the shale/sandstone interface. ?-Proteobacteria sequences were common at all depths, and were dominated by members of the Geobacteraceae family (Pelobacter, Desulfuromonas, and Geobacter). Other members of this group are capable of dissimilatory Fe(III) and/or S0 reduction, but not sulfate reduction. RNA hybridization data also suggested that Fe(III)/S0 reducing bacteria were predominant. These findings are striking considering the lack of significant concentrations of these electron acceptors in this environment. The next most abundant bacterial group indicated was the sulfate reducers, including Desulfobacterium, Desulfocapsa and Desulfobulbus. Sequences related to fermenters, denitrifiers and acetogens were also recovered. The presence of a phylogenetically and functionally diverse microbial community in this deep subsurface environment likely reflects the complex nature of the primary energy and carbon sources, kerogen associated with the shale.

  4. Microbial Community Changes in Response to Ethanol or Methanol Amendments for U(VI) Reduction

    SciTech Connect (OSTI)

    Vishnivetskaya, Tatiana A [ORNL; Brandt, Craig C [ORNL; Madden, Andrew [University of Oklahoma, Norman; Drake, Meghan M [ORNL; Kostka, Joel [Florida State University; Akob, Denise M. [Florida State University; Kusel, Kirsten [Friedrich Schiller University Jena, Jena Germany; Palumbo, Anthony Vito [ORNL

    2010-01-01T23:59:59.000Z

    Microbial community responses to ethanol, methanol and methanol + humics amendments in relationship to uranium bioremediation were studied in laboratory microcosm experiments using sediments and ground water from a uranium-contaminated site in Oak Ridge, Tennessee. Ethanol addition always resulted in uranium reduction at rate of 0.8-1.0 mol l-1 d-1 while methanol addition did so occasionally at rate 0.95 mol l-1 d-1. The type of carbon source added, the duration of incubation, and the sampling site influenced the bacterial community structure upon incubation. Analysis of 16S rRNA gene clone libraries indicated (1) bacterial communities found in ethanol- and methanol-amended samples with U(VI) reduction were similar due to presence of -Proteobacteria, and -Proteobacteria (members of the families Burkholderiaceae, Comamonadaceae, Oxalobacteraceae, and Rhodocyclaceae); (2) methanol-amended samples without U(VI) reduction exhibited the lowest diversity and the bacterial community contained 69.2-92.8% of the family Methylophilaceae; and (3) the addition of humics resulted in an increase of phylogenetic diversity of -Proteobacteria (Rodoferax, Polaromonas, Janthinobacterium, Methylophilales, unclassified) and Firmicutes (Desulfosporosinus, Clostridium).

  5. Genotypic and phenotypic characterization of aerosolized bacteria collected from African dust events

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

    Brigmon, Robin L.; Wilson, Christina A.; Yeager, Chris; Smith, Garriet W.; Polson, Shawn W.

    2013-07-31T23:59:59.000Z

    Twenty-one bacteria were isolated and characterized from air samples collected in Africa and the Caribbean by the United States Geological Survey (USGS). Isolates were selected based on preliminary characterization as possible pathogens. Identification of the bacterial isolates was 25 achieved using 16S rRNA gene sequence analysis, fatty acid methyl esters (FAMEs) profiling, the BIOLOG Microlog® System (carbon substrate assay), and repetitive extragenic palindromic (REP)-PCR analysis. The majority of isolates (18/21) were identified as species of the genus Bacillus. Three isolates were classified within the Bacillus cereus senso lato group, which includes Bacillus anthracis, Bacillus thuringiensis, and Bacillus cereus strains. Onemore »isolate was identified as a Staphylococcus sp., 30 most closely related to species (i.e Staphylococcus kloosii, Staphylococcus warneri) that are commonly associated with human or animal skin, but can also act as opportunistic pathogen. Another isolate was tentatively identified as Tsukamurella inchonensis, a known respiratory pathogen, and was resistant to the ten antibiotics tested including vancomycin.« less

  6. Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)

    SciTech Connect (OSTI)

    Han, Cliff [Los Alamos National Laboratory (LANL); Mwirichia, Romano [Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya; Chertkov, Olga [Los Alamos National Laboratory (LANL); Held, Brittany [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute

    2011-01-01T23:59:59.000Z

    Syntrophobotulus glycolicus Friedrich et al. 1996 is currently the only member of the genus Syntrophobotulus within the family Peptococcaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of tree of life. When grown in pure culture with glyoxylate as carbon source the organism utilizes glyoxylate through fermentative oxidation, whereas, when grown in syntrophic co-culture with homoacetogenic or methanogenic bacteria, it is able to oxidize glycolate to carbon dioxide and hydrogen. No other organic or inorganic carbon source is utilized by S. glycolicus. The subdivision of the family Peptococcaceae into genera does not reflect the natural relationships, particularly re- garding the genera most closely related to Syntrophobotulus. Both Desulfotomaculum and Pelotomaculum are paraphyletic assemblages, and the taxonomic classification is in signifi- cant conflict with the 16S rRNA data. S. glycolicus is already the ninth member of the family Peptococcaceae with a completely sequenced and publicly available genome. The 3,406,739 bp long genome with its 3,370 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  7. An Electrode-based approach for monitoring in situ microbial activity during subsurface bioremediation

    SciTech Connect (OSTI)

    Williams, K.H.; Nevin, K.P.; Franks, A.; Englert, A.; Long, P.E.; Lovley, D.R.

    2009-11-15T23:59:59.000Z

    Current production by microorganisms colonizing subsurface electrodes and its relationship to substrate availability and microbial activity was evaluated in an aquifer undergoing bioremediation. Borehole graphite anodes were installed downgradient from a region of acetate injection designed to stimulate bioreduction of U(VI); cathodes consisted of graphite electrodes embedded at the ground surface. Significant increases in current density ({<=}50 mA/m{sup 2}) tracked delivery of acetate to the electrodes, dropping rapidly when acetate inputs were discontinued. An upgradient control electrode not exposed to acetate produced low, steady currents ({<=}0.2 mA/m{sup 2}). Elevated current was strongly correlated with uranium removal but minimal correlation existed with elevated Fe(II). Confocal laser scanning microscopy of electrodes revealed firmly attached biofilms, and analysis of 16S rRNA gene sequences indicated the electrode surfaces were dominated (67-80%) by Geobacter species. This is the first demonstration that electrodes can produce readily detectable currents despite long-range (6 m) separation of anode and cathode, and these results suggest that oxidation of acetate coupled to electron transfer to electrodes by Geobacter species was the primary source of current. Thus it is expected that current production may serve as an effective proxy for monitoring in situ microbial activity in a variety of subsurface anoxic environments.

  8. Genotypic and phenotypic characterization of aerosolized bacteria collected from African dust events

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

    Brigmon, Robin L. [Savannah River National Lab. (SRNL), Aiken, SC (United States); Wilson, Christina A. [Univ. of South Carolina, Aiken, SC (United States); Yeager, Chris [Savannah River National Lab. (SRNL), Aiken, SC (United States); Smith, Garriet W. [Univ. of South Carolina, Aiken, SC (United States); Polson, Shawn W. [Medical Univ. of South Carolina, Charleston, SC (United States). Hollings Marine Lab.

    2013-07-31T23:59:59.000Z

    Twenty-one bacteria were isolated and characterized from air samples collected in Africa and the Caribbean by the United States Geological Survey (USGS). Isolates were selected based on preliminary characterization as possible pathogens. Identification of the bacterial isolates was 25 achieved using 16S rRNA gene sequence analysis, fatty acid methyl esters (FAMEs) profiling, the BIOLOG Microlog® System (carbon substrate assay), and repetitive extragenic palindromic (REP)-PCR analysis. The majority of isolates (18/21) were identified as species of the genus Bacillus. Three isolates were classified within the Bacillus cereus senso lato group, which includes Bacillus anthracis, Bacillus thuringiensis, and Bacillus cereus strains. One isolate was identified as a Staphylococcus sp., 30 most closely related to species (i.e Staphylococcus kloosii, Staphylococcus warneri) that are commonly associated with human or animal skin, but can also act as opportunistic pathogen. Another isolate was tentatively identified as Tsukamurella inchonensis, a known respiratory pathogen, and was resistant to the ten antibiotics tested including vancomycin.

  9. Field Evidence for Co-Metabolism of Trichloroethene Stimulated by Addition of Electron Donor to Groundwater

    SciTech Connect (OSTI)

    Conrad, Mark E.; Brodie, Eoin L.; Radtke, Corey W.; Bill, Markus; Delwiche, Mark E.; Lee, M. Hope; Swift, Dana L.; Colwell, Frederick S.

    2010-05-17T23:59:59.000Z

    For more than 10 years, electron donor has been injected into the Snake River aquifer beneath the Test Area North site of the Idaho National Laboratory for the purpose of stimulating microbial reductive dechlorination of trichloroethene (TCE) in groundwater. This has resulted in significant TCE removal from the source area of the contaminant plume and elevated dissolved CH4 in the groundwater extending 250 m from the injection well. The delta13C of the CH4 increases from 56o/oo in the source area to -13 o/oo with distance from the injection well, whereas the delta13C of dissolved inorganic carbon decreases from 8 o/oo to -13 o/oo, indicating a shift from methanogenesis to methane oxidation. This change in microbial activity along the plume axis is confirmed by PhyloChip microarray analyses of 16S rRNA genes obtained from groundwater microbial communities, which indicate decreasing abundances of reductive dechlorinating microorganisms (e.g., Dehalococcoides ethenogenes) and increasing CH4-oxidizing microorganisms capable of aerobic co-metabolism of TCE (e.g., Methylosinus trichosporium). Incubation experiments with 13C-labeled TCE introduced into microcosms containing basalt and groundwater from the aquifer confirm that TCE co-metabolism is possible. The results of these studies indicate that electron donor amendment designed to stimulate reductive dechlorination of TCE may also stimulate co-metabolism of TCE.

  10. Microbial Community Changes in Hydraulic Fracturing Fluids and Produced Water from Shale Gas Extraction

    SciTech Connect (OSTI)

    Mohan, Arvind Murali; Hartsock, Angela; Bibby, Kyle J.; Hammack, Richard W.; Vidic, Radisav D.; Gregory, Kelvin B.

    2013-11-19T23:59:59.000Z

    Microbial communities associated with produced water from hydraulic fracturing are not well understood, and their deleterious activity can lead to significant increases in production costs and adverse environmental impacts. In this study, we compared the microbial ecology in prefracturing fluids (fracturing source water and fracturing fluid) and produced water at multiple time points from a natural gas well in southwestern Pennsylvania using 16S rRNA gene-based clone libraries, pyrosequencing, and quantitative PCR. The majority of the bacterial community in prefracturing fluids constituted aerobic species affiliated with the class Alphaproteobacteria. However, their relative abundance decreased in produced water with an increase in halotolerant, anaerobic/facultative anaerobic species affiliated with the classes Clostridia, Bacilli, Gammaproteobacteria, Epsilonproteobacteria, Bacteroidia, and Fusobacteria. Produced water collected at the last time point (day 187) consisted almost entirely of sequences similar to Clostridia and showed a decrease in bacterial abundance by 3 orders of magnitude compared to the prefracturing fluids and produced water samplesfrom earlier time points. Geochemical analysis showed that produced water contained higher concentrations of salts and total radioactivity compared to prefracturing fluids. This study provides evidence of long-term subsurface selection of the microbial community introduced through hydraulic fracturing, which may include significant implications for disinfection as well as reuse of produced water in future fracturing operations.

  11. Electrode-based approach for monitoring in situ microbial activity during subsurface bioremediation

    SciTech Connect (OSTI)

    Williams, Kenneth H.; Nevin, Kelly P.; Franks, Ashley; Englert, Andreas L.; Long, Philip E.; Lovley, Derek R.

    2010-01-01T23:59:59.000Z

    Current production by microorganisms colonizing subsurface electrodes and its relationship to substrate availability and microbial activity was evaluated in an aquifer undergoing bioremediation. Borehole graphite anodes were installed downgradient from a region of acetate injection designed to stimulate bioreduction of U(VI); cathodes consisted of graphite electrodes embedded at the ground surface. Significant increases in current density (?50 mA/m2) tracked delivery of acetate to the electrodes, dropping rapidly when acetate inputs were discontinued. An upgradient control produced low, steady currents (?0.2 mA/m2). Elevated current was strongly correlated with uranium removal but minimal correlation existed with elevated Fe(II). Confocal laser scanning microscopy of electrodes revealed firmly attached biofilms, and analysis of 16S rRNA gene sequences indicated the electrode surfaces were dominated (67-80%) by Geobacter species. These results suggest that oxidation of acetate coupled to electron transfer to electrodes by Geobacter species was the primary source of current. This is the first demonstration that electrodes can produce readily detectable currents despite long-range (6 m) separation of anode and cathode and that current levels are likely related to rates of subsurface metabolism. It is expected that current production may serve as an effective proxy for monitoring in situ microbial activity in a variety of subsurface anoxic environments.

  12. Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas

    SciTech Connect (OSTI)

    Mohan, Arvind Murali; Hartsock, Angela; Hammack, Richard W.; Vidic, Radisav D; Gregory, Kelvin B.

    2013-12-01T23:59:59.000Z

    Hydraulic fracturing for natural gas extraction from shale produces waste brine known as flowback that is impounded at the surface prior to reuse and/or disposal. During impoundment, microbial activity can alter the fate of metals including radionuclides, give rise to odorous compounds, and result in biocorrosion that complicates water and waste management and increases production costs. Here, we describe the microbial ecology at multiple depths of three flowback impoundments from the Marcellus shale that were managed differently. 16S rRNA gene clone libraries revealed that bacterial communities in the untreated and biocide-amended impoundments were depth dependent, diverse, and most similar to species within the taxa [gamma]-proteobacteria, [alpha]-proteobacteria, ?-proteobacteria, Clostridia, Synergistetes, Thermotogae, Spirochetes, and Bacteroidetes. The bacterial community in the pretreated and aerated impoundment was uniform with depth, less diverse, and most similar to known iodide-oxidizing bacteria in the [alpha]-proteobacteria. Archaea were identified only in the untreated and biocide-amended impoundments and were affiliated to the Methanomicrobia class. This is the first study of microbial communities in flowback water impoundments from hydraulic fracturing. The findings expand our knowledge of microbial diversity of an emergent and unexplored environment and may guide the management of flowback impoundments.

  13. 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...

  14. 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

  15. 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

  16. 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

  17. 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 ...

  18. 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) ...

  19. 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

  20. 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 ...

  1. 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

  2. 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 ...

  3. 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 ...

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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 ...

  12. 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

  13. 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 ...

  14. 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...

  15. 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...

  16. 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 ...

  17. 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.

  18. 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.

  19. 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...

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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...

  8. 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.

  9. 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

  10. 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...

  11. 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...

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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...

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Hexavalent Chromium Reduction under Fermentative Conditions with Lactate Stimulated Native Microbial Communities

    SciTech Connect (OSTI)

    Somenahally, Anil C [ORNL] [ORNL; Mosher, Jennifer J [ORNL] [ORNL; Yuan, Tong [University of Oklahoma] [University of Oklahoma; Phelps, Tommy Joe [ORNL] [ORNL; Brown, Steven D [ORNL] [ORNL; Yang, Zamin Koo [ORNL] [ORNL; Hazen, Terry C [ORNL] [ORNL; Arkin, Adam [Lawrence Berkeley National Laboratory (LBNL)] [Lawrence Berkeley National Laboratory (LBNL); Palumbo, Anthony Vito [ORNL] [ORNL; Van Nostrand, Dr. Joy D. [Oklahoma University; Zhou, Jizhong [University of Oklahoma] [University of Oklahoma; Elias, Dwayne A [ORNL] [ORNL

    2013-01-01T23:59:59.000Z

    Microbial reduction of toxic hexavalent chromium (Cr(VI)) in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. However, higher [Cr(VI)] may impose stress on syntrophic communities and impact community structure and function. The study objectives were to understand the impacts of Cr(VI) concentrations on community structure and on the Cr(VI)-reduction potential of groundwater communities at Hanford, WA. Steady state continuous flow bioreactors were used to grow native communities enriched with lactate (30 mM) and continuously amended with Cr(VI) at 0.0 (No-Cr), 0.1 (Low-Cr) and 3.0 (High-Cr) mg/L. Microbial growth, metabolites, Cr(VI), 16S rRNA gene sequences and GeoChip based functional gene composition were monitored for 15 weeks. Temporal trends and differences in growth, metabolite profiles, and community composition were observed, largely between Low-Cr and High-Cr bioreactors. In both High-Cr and Low-Cr bioreactors, Cr(VI) levels were below detection from week 1 until week 15. With lactate enrichment, native bacterial diversity substantially decreased as Pelosinus spp., and Sporotalea spp., became the dominant groups, but did not significantly differ between Cr concentrations. The Archaea diversity also substantially decreased after lactate enrichment from Methanosaeta (35%), Methanosarcina (17%) and others, to mostly Methanosarcina spp. (95%). Methane production was lower in High-Cr reactors suggesting some inhibition of methanogens. Several key functional genes were distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant microbes, Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result 3.0 mg/L Cr(VI) did not impact the overall bacterial community structure.

  10. Influence of hexavalent chromium on lactate-enriched Hanford groundwater microbial communities.

    SciTech Connect (OSTI)

    Somenahally, Anil C [ORNL] [ORNL; Mosher, Jennifer J [ORNL] [ORNL; Yuan, Tong [University of Oklahoma] [University of Oklahoma; Podar, Mircea [ORNL] [ORNL; Phelps, Tommy Joe [ORNL] [ORNL; Brown, Steven D [ORNL] [ORNL; Yang, Zamin Koo [ORNL] [ORNL; Hazen, Terry C [ORNL] [ORNL; Arkin, Adam [Lawrence Berkeley National Laboratory (LBNL)] [Lawrence Berkeley National Laboratory (LBNL); Palumbo, Anthony Vito [ORNL] [ORNL; Zhou, Jizhong [University of Oklahoma] [University of Oklahoma; Elias, Dwayne A [ORNL] [ORNL

    2013-01-01T23:59:59.000Z

    Microbial reduction and immobilization of chromate (Cr(VI)) is a plausible bioremediation strategy. However, higher Cr(VI) concentrations may impose stress on native Cr-reducing communities. We sought to determine if Cr(VI) would influence the lactate enriched native microbial community structure and function in groundwater from the Cr contaminated site at Hanford, WA. Steady state continuous flow bioreactors were amended with lactate and Cr(VI) (0.0, 0.1 and 3.0 mg/L). Microbial growth, metabolites, Cr(VI) concentrations, 16S rRNA gene sequences and GeoChip based functional gene composition in bioreactors were monitored for 15 weeks. Temporal trends and some differences in growth, metabolite profiles, and community composition were observed, largely between Low-Cr and High-Cr bioreactors. In both High-Cr and Low-Cr bioreactors, Cr(VI) was reduced in the bioreactors. With lactate enrichment, the native communities did not significantly differ between Cr concentrations. Native bacterial communities were diverse, whereas after lactate enrichment, Pelosinus spp., and Sporotalea spp., were the most predominant groups in all bioreactors. Similarly, the Archaea diversity significantly decreased from Methanosaeta (35%), Methanosarcina (17%), Halobacteriales (12%), Methanoregula (8%) and others, to mostly Methanosarcina spp. (95%) after lactate enrichment. Composition of several key functional genes was distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant probes (chrA), Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result the 3.0 mg/L Cr(VI) did not appear to give chromate reducing strains a competitive advantage for proliferation or for increasing Cr-reduction.

  11. 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

  12. 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

  13. Evaluating bacterial activity from cell-specific ribosomal RNA content measured with oligonucleotide probes

    SciTech Connect (OSTI)

    Kemp, P.F.; Lee, S.; LaRoche, J.

    1992-01-01T23:59:59.000Z

    We describe a procedure for measuring the cell-specific quantity of ribosomal RNA (rRNA) and DNA in order to evaluate the frequency distribution of activity among cells. The procedure is inherently quantitative, does not require sample incubation and potentially can be taxon-specific. Fluorescently-labelled oligonucleotide probes are hybridized to the complementary 16S rRNA sequences in preserved, intact cells. The resulting cell fluorescence is proportional to cellular rRNA content and can be measured with a microscope-mounted photometer system, by image analysis, or by flow cytometry. Similarly, DNA content is measured as fluorescence of cells stained with the DNA specific fluorochrome DAPI. These are either prepared as separate samples for purposes of enumeration and DNA measurements, or are dual-labelled cells which are also hybridized with oligonucleotide probes.

  14. Evaluating bacterial activity from cell-specific ribosomal RNA content measured with oligonucleotide probes

    SciTech Connect (OSTI)

    Kemp, P.F.; Lee, S.; LaRoche, J.

    1992-10-01T23:59:59.000Z

    We describe a procedure for measuring the cell-specific quantity of ribosomal RNA (rRNA) and DNA in order to evaluate the frequency distribution of activity among cells. The procedure is inherently quantitative, does not require sample incubation and potentially can be taxon-specific. Fluorescently-labelled oligonucleotide probes are hybridized to the complementary 16S rRNA sequences in preserved, intact cells. The resulting cell fluorescence is proportional to cellular rRNA content and can be measured with a microscope-mounted photometer system, by image analysis, or by flow cytometry. Similarly, DNA content is measured as fluorescence of cells stained with the DNA specific fluorochrome DAPI. These are either prepared as separate samples for purposes of enumeration and DNA measurements, or are dual-labelled cells which are also hybridized with oligonucleotide probes.

  15. 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

  16. 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.

  17. Discovery of a free-living chlorophyll d-producing cyanobacterium with a hybrid proteobacterial

    E-Print Network [OSTI]

    Oregon, University of

    of the SSU rRNA gene (V1) (Escherichia coli nucleotide positions 61­106) in A. marina strain MBIC-11017 focus of photosyn- thesis research, previously known only from marine environments in symbiosis

  18. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, May 2006, p. 36853695 Vol. 72, No. 5 0099-2240/06/$08.00 0 doi:10.1128/AEM.72.5.36853695.2006

    E-Print Network [OSTI]

    Negro, Baja California Sur, Mexico. To identify the constituents of the mat, small-subunit rRNA genes and biological diversity. Microbial mats are benthic aquatic ecosystems fueled by light energy and composed

  19. arbuscular mycorrhizal populations: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  20. arbuscular mycorrhizal symbiosis: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  1. arbuscular mycorrhizal hyphae: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  2. arbuscular mycorrhizal status: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  3. arbuscular mycorrhizal symbiosis1woa: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  4. arbuscular mycorrhizal fungus: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  5. arbuscular mycorrhizal fungal: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  6. arbuscular mycorrhiza cultures1: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  7. arbuscular mycorrhizae improves: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  8. arbuscular mycorrhiza enhanced: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  9. 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.

  10. Integrated omics opportunity | EMSL

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

    microbial community to a pH decrease caused by the addition of acid to the bioreactor containing microbes. 16S rDNA gene pyrosequencing, proteomics and metabolomics were...

  11. 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.

  12. 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...

  13. 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.

  14. 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...

  15. 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.

  16. 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...

  17. 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

  18. 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

  19. 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

  20. 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.

  1. a1555g 12s rrna: Topics by E-print Network

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

    Masaru 47 Scaling properties of two-dimensional turbulence in wakes behind bluff bodies B. Protas,1,2,* S. Goujon-Durand,2,3, Mathematics Websites Summary: Scaling properties of...

  2. 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 (

  3. 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 ...

  4. 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 ...

  5. 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.

  6. 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. ,

  7. 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.

  8. 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.

  9. 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.

  10. 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...

  11. 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...

  12. 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

  13. 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,...

  14. 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...

  15. 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...

  16. 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...

  17. 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

  18. 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.

  19. International Journal of Greenhouse Gas Control 16S (2013) S203S215 Contents lists available at SciVerse ScienceDirect

    E-Print Network [OSTI]

    Elkhoury, Jean

    integrity (Shukla et al., 2010). When combined with enhanced oil recovery (EOR) operations, water and CO2.elsevier.com/locate/ijggc Dissolution and deformation in fractured carbonates caused by flow of CO2-rich brine under reservoir 2013 Keywords: Weyburn Fracture Deformation Dissolution Supercritical CO2-rich brine CO2 sequestration

  20. ./. Mol. Riol. (1988) 200, 65-87 Positions of S2, S13, S16, S17, S19 and S21 in the

    E-Print Network [OSTI]

    1988-01-01T23:59:59.000Z

    2 June 1987, and in revised form 28 September 1987) Neutron scat,tering distance data are presented the mapping of its proteins by neutron scattering. Comparisons with other data suggest that, the neutron map can be measured by neutron t Present address: Biology Department. Brookhaven Xational Laboratory

  1. A chronology of the Little Ice Age in the tropical Andes of Bolivia (16S) and its implications for climate reconstruction

    E-Print Network [OSTI]

    Rabatel, Antoine

    c IRD, Great Ice (UR032 IRD), Apartado postal 17 12 857 - Whymper 442 y Coruńa, Quito, Ecuador d coincides with the Maunder minimum of solar irradiance. By reconstructing the equilibrium-line altitude

  2. 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.

  3. 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...

  4. Whole-genorne analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1

    SciTech Connect (OSTI)

    Kane, Staci R. [Lawrence Livermore National Laboratory (LLNL); Chakicherla, Anu Y. [Lawrence Livermore National Laboratory (LLNL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Schmidt, Radomir [University of California, Davis; Shin, M [U.S. Department of Energy, Joint Genome Institute; Legler, Tina C. [Lawrence Livermore National Laboratory (LLNL); Scow, Kate M. [University of California, Davis; Larimer, Frank W [ORNL; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Hristova, Krassimira R. [University of California, Davis

    2007-03-01T23:59:59.000Z

    Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (C, to C,,) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an similar to 4-Mb circular chromosome and an similar to 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (similar to 99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.

  5. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome

    SciTech Connect (OSTI)

    Jakobsson, H.; Jernberg, C.; Andersson, A.F.; Sjolund-Karlsson, M.; Jansson, J.K.; Engstrand, L.

    2010-01-15T23:59:59.000Z

    Antibiotic administration is the standard treatment for the bacterium Helicobacter pylori, the main causative agent of peptic ulcer disease and gastric cancer. However, the long-term consequences of this treatment on the human indigenous microbiota are relatively unexplored. Here we studied short- and long-term effects of clarithromycin and metronidazole treatment, a commonly used therapy regimen against H. pylori, on the indigenous microbiota in the throat and in the lower intestine. The bacterial compositions in samples collected over a four year period were monitored by analyzing the 16S rRNA gene using 454-based pyrosequencing and terminal-restriction fragment length polymorphism (T-RFLP). While the microbial communities of untreated control subjects were relatively stable over time, dramatic shifts were observed one week after antibiotic treatment with reduced bacterial diversity in all treated subjects in both locations. While the microbiota of the different subjects responded uniquely to the antibiotic treatment some general trends could be observed; such as a dramatic decline in Actinobacteria in both throat and feces immediately after treatment. Although the diversity of the microbiota subsequently recovered to resemble the pre treatment states, the microbiota remained perturbed in some cases for up to four years post treatment. In addition, four years after treatment high levels of the macrolide resistance gene erm(B) were found, indicating that antibiotic resistance, once selected for, can persist for longer periods of time than previously recognized. This highlights the importance of a restrictive antibiotic usage in order to prevent subsequent treatment failure and potential spread of antibiotic resistance.

  6. The Exiguobacterium genus: biodiversity and biogeography

    SciTech Connect (OSTI)

    Vishnivetskaya, Tatiana A [ORNL; Kathariou, Sophia [North Carolina State University; Tiedje, James M. [Michigan State University, East Lansing

    2009-01-01T23:59:59.000Z

    Abstract. Bacteria of the genus Exiguobacterium are low G + C, Gram-positive facultative anaerobes that have been repeatedly isolated from ancient Siberian permafrost. In addition, Exiguobacterium spp. have been isolated from markedly diverse sources, including Greenland Glacial ice, hot springs at Yellowstone National Park, the rhizosphere of plants, and the environment of food processing plants. Strains of this hereto little known bacterium that have been retrieved from such different (and often extreme) environments are worthy of attention as they are likely to be specifically adapted to such environments and to carry variations in the genome which may correspond to psychrophilic and thermophilic adaptations. However, comparative genomic investigations of Exiguobacterium spp. from different sources have been limited. In this study, we employed different molecular approaches for the comparative analysis of 24 isolates from markedly diverse environments including ancient Siberian permafrost and hot springs at Yellowstone National Park. Pulsed-field gel electrophoresis (PFGE) with I-CeuI (an intron-encoded endonuclease), AscI and NotI were optimized for the determination of genomic fingerprints of nuclease-producing isolates. The application of a DNA macroarray for 82 putative stress-response genes yielded strain-specific hybridization profiles. Cluster analyses of 16S rRNA gene sequence data, PFGE I-CeuI restriction patterns and hybridization profiles suggested that Exiguobacterium strains formed two distinct divisions that generally agreed with temperature ranges for growth. With few exceptions (e.g., Greenland ice isolate GIC31), psychrotrophic and thermophilic isolates belonged to different divisions.

  7. Fe-phyllosilicate redox cycling organisms from a redox transition zone in Hanford 300 Area sediments

    SciTech Connect (OSTI)

    Benzine, Jason; Shelobolina, Evgenya S.; Xiong, Mai Yia; Kennedy, David W.; McKinley, James P.; Lin, Xueju; Roden, Eric E.

    2013-01-01T23:59:59.000Z

    Microorganisms capable of reducing or oxidizing structural iron (Fe) in Fe-bearing phyllosilicate minerals were enriched and isolated from a subsurface redox transition zone at the Hanford 300 Area site in eastern Washington, USA. Both conventional and in situ "i-chip" enrichment strategies were employed. One Fe(III)-reducing Geobacter (G. bremensis strain R1, Deltaproteobacteria) and six Fe(II) phyllosilicate-oxidizing isolates from the Alphaproteobacteria (Bradyrhizobium japonicum strains 22, is5, and in8p8), Betaproteobacteria (Cupriavidus necator strain A5-1, Dechloromonas agitata strain is5), and Actinobacteria (Nocardioides sp. strain in31) were recovered. The G. bremensis isolate grew by oxidizing acetate with the oxidized form of NAu-2 smectite as the electron acceptor. The Fe(II)-oxidizers grew by oxidation of chemically reduced smectite as the energy source with nitrate as the electron acceptor. The Bradyrhizobium isolates could also carry out aerobic oxidation of biotite. This is the first report of the recovery of a Fe(II)-oxidizing Nocardioides, and to date only one other Fe(II)-oxidizing Bradyrhizobium is known. The 16S rRNA gene sequences of the isolates were similar to ones found in clone libraries from Hanford 300 sediments and groundwater, suggesting that such organisms may be present and active in situ. Whole genome sequencing of the isolates is underway, the results of which will enable comparative genomic analysis of mechanisms of extracellular phyllosilicate Fe redox metabolism, and facilitate development of techniques to detect the presence and expression of genes associated with microbial phyllosilicate Fe redox cycling in sediments.

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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...

  16. 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

  17. 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.

  18. 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 ...

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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...

  4. 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,*ŕ1 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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 ...

  14. 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...

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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 ...

  10. 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.

  11. 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...

  12. 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

  13. 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):

  14. 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. ...

  15. 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 ...

  16. 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

  17. 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 ...

  18. 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 ...

  19. 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 ...

  20. 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