National Library of Energy BETA

Sample records for 16s rrna gene

  1. Complex Patterns of Plastid 16S rRNA Gene Evolution in Nonphotosynthetic Green Algae

    E-Print Network [OSTI]

    Nedelcu, Aurora M.

    Complex Patterns of Plastid 16S rRNA Gene Evolution in Nonphotosynthetic Green Algae Aurora M AT values are increased in nonphotosynthetic green algae compared to their closest photosynthetic relatives "green plants," both land plants and green algae, are known. Among such lineages are the parasitic

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

    E-Print Network [OSTI]

    Alvarez, Pedro J.

    Assessment of anaerobic benzene degradation potential using 16S rRNA gene-targeted real-time PCR University, MS 317, Houston, TX 77251-1892, USA. Summary Benzene is a common groundwater pollutant. Thus, determining the potential for anaerobic benzene deg- radation is important to assess

  3. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens

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

    Srinivasan, Ramya; Karaoz, Ulas; Volegova, Marina; MacKichan, Joanna; Kato-Maeda, Midori; Miller, Steve; Nadarajan, Rohan; Brodie, Eoin L.; Lynch, Susan V.; Heimesaat, Markus M.

    2015-02-06

    According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n =more »617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naďve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.« less

  4. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens

    SciTech Connect (OSTI)

    Srinivasan, Ramya; Karaoz, Ulas; Volegova, Marina; MacKichan, Joanna; Kato-Maeda, Midori; Miller, Steve; Nadarajan, Rohan; Brodie, Eoin L.; Lynch, Susan V.; Heimesaat, Markus M.

    2015-02-06

    According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naďve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.

  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.

    2009-03-01

    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

    2010-01-01

    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. Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema (OSTI)

    Tremblay, Julien [DOE JGI

    2013-01-25

    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.

  9. Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    SciTech Connect (OSTI)

    Tremblay, Julien [DOE JGI] [DOE JGI

    2012-06-01

    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.

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

    2007-12-04

    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.

  11. 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)

    2007-10-30

    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.

  12. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure

    SciTech Connect (OSTI)

    2014-12-01

    The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied.

  13. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure

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

    None

    2014-12-01

    The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illuminamore »16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied.« less

  14. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene

    E-Print Network [OSTI]

    the datasets to be as large as possible in order to limit stochastic variation in the proportions of sampled to be classified. Figure S1 shows the proportion of sequences in each tested sample that are within a given percent indicates the proportion of each sample that is within a given distance of any reference sequence. We see

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

    E-Print Network [OSTI]

    Lostak, Tracy Karon

    2009-05-15

    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...

  16. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression

    E-Print Network [OSTI]

    Har, Jia Y.

    We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant ...

  17. 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

  18. Kistimonas scapharcae sp. nov., isolated from a dead ark clam (Scapharca broughtonii), and

    E-Print Network [OSTI]

    Bae, Jin-Woo

    001T , with which it shared 98.2 % 16S rRNA gene sequence similarity. Strain A36T grew optimally at 30 related to K. asteriae KMD 001T (98.2 % 16S rRNA gene sequence similarity). The 16S rRNA gene sequences

  19. Databases for rRNA gene profiling of microbial communities

    DOE Patents [OSTI]

    Ashby, Matthew

    2013-07-02

    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.

  20. Natural bacterial communities serve as quantitative geochemical...

    Office of Scientific and Technical Information (OSTI)

    to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene...

  1. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 0099-2240/01/$04.00 0 DOI: 10.1128/AEM.67.9.43744376.2001

    E-Print Network [OSTI]

    Bruns, Tom

    ). Let X be a collection of sequences, such as a library of 16S rRNA genes. Define the "homologous Reserved. Quantitative Comparisons of 16S rRNA Gene Sequence Libraries from Environmental Samples DAVID R 11 June 2001 To determine the significance of differences between clonal libraries of environmental r

  2. Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

    SciTech Connect (OSTI)

    Lapidus, Alla; Kettler, Gregory C.; Martiny, Adam C.; Huang, Katherine; Zucker, Jeremy; Coleman, Maureen L.; Rodrigue, Sebastien; Chen, Feng; Lapidus, Alla; Ferriera, Steven; Johnson, Justin; Steglich, Claudia; Church, George M.; Richardson, Paul; Chisholm, Sallie W.

    2007-07-30

    Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolatesfrom diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3percent, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane synthesis and transport that dominate the flexible genome and set it apart from the core. Besides identifying islands and demonstrating their role throughout the history of Prochlorococcus, reconstruction of past gene gains and losses shows that much of the variability exists at the"leaves of the tree," between the most closely related strains. Finally, the identification of core and flexible genes from this 12-genome comparison is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between our understanding of these organisms in the lab and the wild.

  3. Development of a real-time PCR method for the detection of fossil 16S rDNA fragments of phototrophic sulfur bacteria

    E-Print Network [OSTI]

    Gilli, Adrian

    of phototrophic sulfur bacteria in the sediments of Lake Cadagno D. F. RAVASI,1 S. PEDUZZI,1 , 2 V. GUIDI,2 , 3 R sulfur bacteria in the chemocline has been monitored since 1994 with molecular methods such as 16S r sulfur bacteria populations from sediment samples. We detected fossil 16S rDNA of nine populations

  4. Adapting Polony Technology to Oligonucleotide Fingerprinting of Ribosomal rRNA Genes for Microbial Community Analysis

    E-Print Network [OSTI]

    Ruegger, Paul

    2011-01-01

    Fierer, and Rob Knight. 2010. Microbes and Health SacklerDesign 2.1 Introduction Microbes often exist in complex andFierer, and Rob Knight. 2010. Microbes and Health Sackler

  5. Search for: All records | DOE PAGES

    Office of Scientific and Technical Information (OSTI)

    contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich...

  6. The Skin Microbiome in Healthy and Allergic Dogs 

    E-Print Network [OSTI]

    Hoffmann, Aline Rodrigues; Patterson, Adam P.; Diesel, Alison; Lawhon, Sara D.; Ly, Hoai Jaclyn; Stephenson, Christine Elkins; Mansell, Joanne; Steiner, Jö rg M.; Dowd, Scot E.; Olivry, Thierry; Suchodolski, Jan S.

    2014-01-08

    Changes in the microbial populations on the skin of animals have traditionally been evaluated using conventional microbiology techniques. The sequencing of bacterial 16S rRNA genes has revealed that the human skin is inhabited by a highly diverse...

  7. 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 ...

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

    E-Print Network [OSTI]

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

    2013-01-01

    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 ...

  9. 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.

    2015-02-25

    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

  10. Fecal Microbiome in Dogs with Acute Diarrhea 

    E-Print Network [OSTI]

    Guard, Blake Crosby

    2013-11-07

    the functional gene content of the fecal microbiome. Fecal samples were collected from healthy dogs (n=13), dogs with NHD (n=5), and dogs with AHD (n=6). The fecal microbiota were analyzed by 454-pyrosequencing of 16S rRNA genes and qPCR assays. SCFAs were...

  11. Gene Concepts, Gene Talk, and Gene Patents

    E-Print Network [OSTI]

    Torrance, Andrew W.

    2010-01-01

    Since the existence of a discrete unit of heredity was first proposed by Gregor Mendel, scientific concepts of the “gene” have undergone rapid evolution. Beyond obvious epistemic and operational importance to the scientific community, changing gene...

  12. Intraspecific relationships among the stygobitic shrimp Typhlatya mitchelli, by analyzing sequence data from mitochondrial DNA 

    E-Print Network [OSTI]

    Webb, Michael Scott

    2004-09-30

    .40 W 87.33 Santa Maria SM 07/11/01 N 20.85 W 90.23 were included), within a single population of Penaeus notialis. They believe that this fragment of the large-subunit ribosomal RNA gene is a good marker... 1 Santa Maria/ SM 1 1 1 Total 33 18 23 PCR Reactions PCR primers (Table 3) for cytochrome b (Cyb), 16S rRNA (16S), and cytochrome oxidase I (CO) for mitochondrial DNA (mt...

  13. 23S rRNA base pair 20572611 determines ketolide susceptibility and fitness cost of the macrolide

    E-Print Network [OSTI]

    Yonath, Ada E.

    binding without evoking resistance mediated by inducible erm genes (reviewed in ref. 8). Additional modification may be the result of two different mechanisms: (i) modification in trans conferred by erm genes

  14. 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

  15. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, June 2009, p. 36733678 Vol. 75, No. 11 0099-2240/09/$08.00 0 doi:10.1128/AEM.02600-08

    E-Print Network [OSTI]

    into the cell and used for energy production. Cellulose is the most abundant biopolymer in the world addition of an exogenous mediator. Using a specially designed U-tube MFC, we enriched a consortium-to-extinction serial transfers of the consortium, 16S rRNA gene-based community analysis using denaturing gradient gel

  16. Diversity and heritability of the maize rhizosphere microbiome under field conditions

    E-Print Network [OSTI]

    Dangl, Jeff

    proportion of heritable variation in total bacterial diversity across fields, and substantially more, within a plant species, the impact of genetic variation on the composition of the microbiota is poorly conditions. Using pyrosequencing of bacterial 16S rRNA genes, we observed substantial variation in bacterial

  17. ORIGINAL PAPER Halolamina rubra sp. nov., a haloarchaeon isolated

    E-Print Network [OSTI]

    Bae, Jin-Woo

    extreme halophiles, designated CBA1107T and CBA1108, were isolated from non-purified solar salt. Based on the phylogenetic analysis, strains CBA1107T and CBA1108 were shown to belong to the genus Halolamina, with similarities for the 16S rRNA gene sequences between strains CBA1107T and Halolam- ina pelagica TBN21T

  18. Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments

    E-Print Network [OSTI]

    , targeting part of the ammonia monooxygenase (amoA), nitrous oxide reductase (nosZ), and 16S rRNA genes were practices on potential gross N mineralization and nitrifi- cation rates, as well as ammonia-term crop management practices that enhance agroecosystem services, such as, carbon (C) storage, N retention

  19. Vibrio litoralis sp. nov., isolated from a Yellow Sea tidal flat in Korea

    E-Print Network [OSTI]

    Bae, Jin-Woo

    Vibrio litoralis sp. nov., isolated from a Yellow Sea tidal flat in Korea Young-Do Nam,1,2 Ho-negative, facultatively anaerobic bacterial strains, MANO22DT and MANO22P, were isolated from a tidal flat area of Dae and energy sources. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains belong

  20. Host Plant Use by Insect Herbivores Mediated by Microorganisms 

    E-Print Network [OSTI]

    Antwi, Josephine Bema

    2015-08-10

    454 pyrosequencing of the 16S rRNA gene. There was no correlation between the two. Although CFH is widely distributed across cotton-growing regions in the U.S., it is considered a major cotton pest only in certain regions while in others it is rarely a...

  1. nature methods | VOL.9 NO.8 | AUGUST 2012 | 793 news and views

    E-Print Network [OSTI]

    Cai, Long

    set supports uses that 16S data can- not, which argues in favor of the shot- gun sequencing approach, thereby putting those genes in context. Reads or assemblies may run through automated annotation pipeS rRNA has serious draw- backs.First,sequencingrequiresPCRampli- fication of variable regions

  2. UNCORRECTEDPROOF Assessment of anaerobic benzene degradation

    E-Print Network [OSTI]

    Alvarez, Pedro J.

    UNCORRECTEDPROOF Assessment of anaerobic benzene degradation potential using 16S rRNA gene Engineering, Rice University, MS 317, Houston, TX 77251-1892, USA. Summary Benzene is a common groundwater-contaminated aquifers. Thus, determining the potential for anaerobic benzene deg- radation is important to assess

  3. Rea1, a Dynein-related Nuclear AAA-ATPase, Is Involved in Late rRNA Processing and Nuclear Export of 60 S Subunits*S

    E-Print Network [OSTI]

    Nissan, Tracy

    Rea1, a Dynein-related Nuclear AAA-ATPase, Is Involved in Late rRNA Processing and Nuclear Export we report that Rea1 is required for maturation and nuclear export of the pre-60 S subunit. Rea1. Using an in vivo 60 S subunit export assay, a strong accumulation of the large subunit reporter Rpl25

  4. Trichoderma genes

    DOE Patents [OSTI]

    Foreman, Pamela (Los Altos, CA); Goedegebuur, Frits (Vlaardingen, NL); Van Solingen, Pieter (Naaldwijk, NL); Ward, Michael (San Francisco, CA)

    2012-06-19

    Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

  5. 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)

    1991-12-31

    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.

  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. Human retinoblastoma gene

    SciTech Connect (OSTI)

    Bookstein, R.; Lee, E.Y.H.P.; Peccei, A.; Lee, W.H. (Dept. of Pathology M-012 and Center for Molecular Genetics, Univ. of California, San Diego, La Jolla, CA (US))

    1989-04-01

    Mutational inactivation of the retinoblastoma (RB) gene is considered a fundamental event in the formation of several types of human cancer. A substantial proportion of RB gene mutations are partial or complete deletions that extend an unknown distance beyond one or both ends of the gene. To provide a framework for measuring the extent of these deletions, the authors have constructed a long-range restriction map of SfiI sites spanning 850 kilobases around the RB gene. This map was applied in a molecular analysis of RB gene deletion in breast cancer cell line MB468. A previous study of this cell line demonstrated deletion of the entire RB gene except for exons 1 and 2. Genomic clones containing the deletion junction were isolated from a library made from MB468 DNA. A probe obtained from the far side of the deletion junction was used to localize and clone the unknown 3' endpoint, demonstrating that the chromosomal mutation in this case was a simple deletion spanning 200 kilobases. Sequence analysis of the deletion junction indicated a conservative deletion with no loss or gain of nucleotides. The deletion endpoints had no sequence homology to each other or to any repetitive sequence family, such as Alu, so the recombination event was illegitimate. Structural analysis of this and other RB gene deletions is important for understanding molecular mechanisms of recessive oncogenesis.

  8. Microfluidic gene synthesis

    E-Print Network [OSTI]

    Kong, David Sun, 1979-

    2008-01-01

    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 ...

  9. 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

  10. Gene expression heterogeneous

    E-Print Network [OSTI]

    Khaitovich, Philipp

    that phenotypic variation among individuals and among somatic cells increases with age [1­5]. However, no evidence for an age-dependent increase in variation in gene expression has yet been found [6­9]. Using eight published with this article online). We found that the proportion of probe sets showing a positive

  11. Intervention in gene regulatory networks 

    E-Print Network [OSTI]

    Choudhary, Ashish

    2006-10-30

    In recent years Boolean Networks (BN) and Probabilistic Boolean Networks (PBN) have become popular paradigms for modeling gene regulation. A PBN is a collection of BNs in which the gene state vector transitions according to the rules of one...

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

    DOE Patents [OSTI]

    Chen, Huei-Mei; Bissell, Mina

    2004-06-22

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

  13. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    SciTech Connect (OSTI)

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bćlum, Jacob; Ta?, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.

  14. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

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

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bćlum, Jacob; Ta?, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy numbermore »of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.« less

  15. Method of controlling gene expression

    DOE Patents [OSTI]

    Peters, Norman K. (Berkeley, CA); Frost, John W. (Menlo Park, CA); Long, Sharon R. (Palo Alto, CA)

    1991-12-03

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

  16. 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.

    2010-04-01

    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.

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

    SciTech Connect (OSTI)

    David Kirchman

    2011-12-31

    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.

  18. Gene-environment interactions in genetic epidemiology 

    E-Print Network [OSTI]

    Spinka, Christine Marie

    2005-02-17

    Gene-environment interactions are an area of increasing interest in complex hu- man diseases. The first step in any study of the interactions between genes and the environment involves identifying genes which influence ...

  19. Nonviral Vectors for Gene Delivery

    E-Print Network [OSTI]

    Baoum, Abdulgader Ahmed

    2011-04-26

    , two nonviral gene delivery systems using either biodegradable poly(D,L-lactide-co-glycolide) (PLG) nanoparticles or cell penetrating peptide (CPP) complexes have been designed and studied using A549 human lung epithelial cells. PLG nanoparticles were...

  20. Fusion genes in breast cancer

    E-Print Network [OSTI]

    Batty, Elizabeth

    2012-02-07

    Fusion genes in breast cancer Elizabeth M. Batty Clare College, University of Cambridge A dissertation submitted to the University of Cambridge in candidature for the degree of Doctor of Philosophy November 2010 ii... is the outcome of work done in collaboration except where specifically indicated in the text. It has not been submitted whole or in part for any other qualification at any other University. iii Summary Fusion genes in breast cancer Elizabeth Batty...

  1. Characterization of a unique embedded gene 

    E-Print Network [OSTI]

    Zhang, Ning

    1999-01-01

    The lysis gene region of bacteriophage [] consists of a cluster of three gene: S, R, and Rz. While the S and R genes are essential for [] lysis under all conditions, the Rz gene is required for [] lysis only under certain conditions. Transposon...

  2. 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.

    2008-10-01

    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.

  3. Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

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

    Moissl-Eichinger, Christine; Auerbach, Anna K.; Probst, Alexander J.; Mahnert, Alexander; Tom, Lauren; Piceno, Yvette; Andersen, Gary L.; Venkateswaran, Kasthuri; Rettberg, Petra; Barczyk, Simon; et al

    2015-03-17

    Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms weremore »mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.« less

  4. 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

    2007-09-15

    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.

  5. 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)

    2015-04-13

    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.

  6. 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

    2015-04-13

    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

  7. The Home Microbiome and Childhood Asthma

    E-Print Network [OSTI]

    Ciaccio, Christina Elizabeth

    2014-05-31

    . Innovative techniques have recently been developed that can more comprehensively characterize microbial communities. OBJECTIVE: To characterize the home microbiota of asthmatics and non-asthmatics utilizing 16S rRNA based phylogenetic analysis by microarray...

  8. 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 ...

  9. 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

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

    SciTech Connect (OSTI)

    Lee Kerkhof

    2013-01-01

    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.

  11. Gene encoding plant asparagine synthetase

    DOE Patents [OSTI]

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

    1993-10-26

    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. 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

  13. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2T) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010

    SciTech Connect (OSTI)

    Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [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; Chen, Feng [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; Han, Cliff [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Daum, Chris [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; Chang, Yun-Juan [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Pukall, Rudiger [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; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute

    2011-01-01

    Bacillus tusciae Bonjour & Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene sequencing was well established at the time of the initial description of the organism, 16S se- quence data were not available and the strain was placed into the genus Bacillus based on limited chemotaxonomic information. Despite the now obvious misplacement of strain T2T as a member of the genus Bacillus in 16S rRNA-based phylogenetic trees, the misclassification remained uncorrected for many years, which was likely due to the extremely difficult, analy- sis-hampering cultivation conditions and poor growth rate of the strain. Here we provide a taxonomic re-evaluation of strain T2T (= DSM 2912 = NBRC 15312) and propose its reclassi- fication as the type strain of a new species, Kyrpidia tusciae, and the type species of the new genus Kyrpidia, which is a sister-group of Alicyclobacillus. The family Alicyclobacillaceae da Costa and Rainey, 2010 is emended. The 3,384,766 bp genome with its 3,323 protein-coding and 78 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. Patching genes to fight disease

    SciTech Connect (OSTI)

    Holzman, D.

    1990-09-03

    The National Institutes of Health has approved the first gene therapy experiments, one of which will try to cure cancer by bolstering the immune system. The applications of such therapy are limited, but the potential aid to people with genetic diseases is great.

  15. Eukaryotic Gene Prediction Kelli Davies

    E-Print Network [OSTI]

    -scale genome sequencing has revolutionized the field of genetics and biology. Sequencing projects require sophisticated computational analysis to manage vast collections of data. Scientists first sequenced a genome, coding genes comprise 95% of the genome.1 Since then, numerous prokaryotic and eukaryotic genomes have

  16. Gene Expression in the Stallion Testes 

    E-Print Network [OSTI]

    Laughlin, Andy M.

    2011-08-08

    Understanding the genes that regulate spermatogenesis and steroidogenesis in the testis is critical for enhancement of stallion fertility. Stallion testicular samples were used to identify candidate genes by cDNA microarrays ...

  17. Enhanced polymeric nanoparticles for gene delivery

    E-Print Network [OSTI]

    Green, Jordan Jamieson

    2007-01-01

    The potential of gene therapy to treat disease and improve human health is tremendous. The failure of viral gene therapy clinical trials due to toxicity, immunogenicity, and carcinogenicity has been tragic and strongly ...

  18. 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)

    2001-01-01

    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

  19. Uses of antimicrobial genes from microbial genome

    DOE Patents [OSTI]

    Sorek, Rotem; Rubin, Edward M.

    2013-08-20

    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.

  20. Does evolution in body patterning genes drive

    E-Print Network [OSTI]

    Monteiro, Antónia

    to the adult form of a metazoan has, in particular, led to a relatively common and distinctive view of how the effects one might expect it to have on adult phenotype.(3) Whereas mutations in downstream genes (and low-level Hox genes) might cause subtle shifts in morphology, Hox gene mutations can also cause wholesale

  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. Environmental Microbiology (2006) 8(1), 100113 doi:10.1111/j.1462-2920.2005.00873.x 2005 Society for Applied Microbiology and Blackwell Publishing Ltd

    E-Print Network [OSTI]

    Roden, Eric E.

    2006-01-01

    M) medium with a small quantity (1% v/v) of wetland sediment, and resulted in the transient accumulation reaction- amplified 16S rRNA, as well as by construction of 16S rDNA clone libraries for four different. Introduction Iron (Fe)-bearing minerals are abundant in soil and sedi- mentary environments, where they exist

  4. Neural Networks Approaches for Discovering the Learnable Correlation between Gene Function and Gene

    E-Print Network [OSTI]

    Bonner, Anthony

    Neural Networks Approaches for Discovering the Learnable Correlation between Gene Function and Gene novel clustering and Neural Network (NN) approaches for predicting mouse gene functions from gene. Our results show that neural networks can be extremely useful in this area. We present the improved

  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.

    2006-06-08

    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. Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park

    SciTech Connect (OSTI)

    Mead, David [University of Wisconsin, Madison; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Zhang, Xiaojing [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Brumm, Catherine [United States Department of Energy Joint Genome Institute; Hochstein, Rebecca [Lucigen Corporation, Middleton, Wisconsin; Schoenfeld, Thomas [Lucigen Corporation, Middleton, Wisconsin; Brumm, Phillip [University of Wisconsin, Madison

    2012-01-01

    Paenibacillus speciesY412MC10 was one of a number of organisms initially isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA. The isolate Y412MC10 was initially classified as a Geobacillus sp. based on its isolation conditions and similarity to other organisms isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered with Paenibacillus species and not Geobacillus; the 16S rRNA analysis indicated the organism was a strain of Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome of Paenibacillus lautus strain Y412MC10 consists of one circular chromosome of 7,121,665 bp with an average G+C content of 51.2%. The Paenibacillus sp.Y412MC10 genome sequence was deposited at the NCBI in October 2009 (NC{_}013406). Comparison to other Paenibacillus species shows the organism lacks nitrogen fixation, antibiotic production and social interaction genes reported in other Paenibacilli. Over 25% of the proteins predicted by the Y412MC10 genome share no identity with the closest sequenced Paenibacillus species; most of these are predicted hypothetical proteins and their specific function in the environment is unknown.

  7. Method for determining gene knockouts

    DOE Patents [OSTI]

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

    2013-06-04

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

    2011-09-27

    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. Gene prioritization aims to identify the most promising genes (or proteins) among a larger pool of candidates

    E-Print Network [OSTI]

    initially developed to help to identify the disease-causing potential candidate genes for asthma, and a sub- sequent association study of 91SNPs in these genes found-onset asthma23 . Beyond positional disease gene identification, gene

  10. Apolipoprotein gene involved in lipid metabolism

    DOE Patents [OSTI]

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

    2007-07-03

    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.

  11. Application of multidisciplinary analysis to gene expression.

    SciTech Connect (OSTI)

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

    2004-01-01

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

  12. Methods for monitoring multiple gene expression

    DOE Patents [OSTI]

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

    2012-05-01

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

  13. Methods for monitoring multiple gene expression

    DOE Patents [OSTI]

    Berka, Randy; Bachkirova, Elena; Rey, Michael

    2013-10-01

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

  14. Gene expression abnormalities in the autistic brain

    E-Print Network [OSTI]

    Chow, Maggie Lok Mun

    2011-01-01

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

  15. Exploring candidate genes for human brain diseases from a brain-specific gene network

    E-Print Network [OSTI]

    Jiang,Tianzi

    identifying multiple candidate genes for genetic human brain diseases from a brain-specific gene network; Candidate genes Many common human brain diseases, such as schizo- phrenia, Alzheimer's disease, Parkinson's disease, depres- sion, etc., have prominent genetic components [1,2]. Most researchers think that large

  16. Finding Predictive Gene Groups from Microarray Data

    E-Print Network [OSTI]

    Buehlmann, Peter

    ur Statistik, ETH Zurich, CH-8092 Zurich, Switzerland Abstract Microarray experiments generate large datasets with expression values for thousands of genes, but not more than a few dozens of samples. A challenging task the genes. We present Pelora, an algorithm based on penalized logistic regression analysis, that combines

  17. Finding Predictive Gene Groups from Microarray Data

    E-Print Network [OSTI]

    Buehlmann, Peter

    ¨ur Statistik, ETH Z¨urich, CH-8092 Z¨urich, Switzerland Abstract Microarray experiments generate large datasets with expression values for thousands of genes, but not more than a few dozens of samples. A challenging task the genes. We present Pelora, an algorithm based on penalized logistic regression analysis, that combines

  18. Posttranscriptional gene silencing in nuclei Paul Hoffera

    E-Print Network [OSTI]

    Pikaard, Craig

    (1). RNAi can be divided into two major categories: transcriptional gene silencing (TGS) and posttranscriptional gene silencing (PTGS). Both TGS and PTGS depend on small interfering RNAs (siRNA) or microRNAs (miRNA) that are produced from double-stranded RNA (dsRNA) precursors. TGS occurs in nuclei via DNA methylation and histone

  19. Gene coding for the E1 endoglucanase

    DOE Patents [OSTI]

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

    1996-07-16

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

  20. HMM-Based Gene Annotation Methods

    SciTech Connect (OSTI)

    Haussler, David; Hughey, Richard; Karplus, Keven

    1999-09-20

    Development of new statistical methods and computational tools to identify genes in human genomic DNA, and to provide clues to their functions by identifying features such as transcription factor binding sites, tissue, specific expression and splicing patterns, and remove homologies at the protein level with genes of known function.

  1. Genes Regulated by Learning in the Hippocampus

    E-Print Network [OSTI]

    Smith, Desmond J.

    Richard M. Leahy,2 and Desmond J. Smith1* 1 Department of Molecular and Medical Pharmacology and Crump hippocampal gene expression in mice undergoing training in the Morris water maze and control mice forced words: DNA microarrays; gene expression; hip- pocampus; mice; Morris water maze The hippocampus

  2. 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

  3. 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 ...

  4. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca

    E-Print Network [OSTI]

    Zhao, Dehua

    Bacterial genes associated with a single trait are often grouped in a contiguous unit of the genome known as a gene cluster. It is difficult to genetically manipulate many gene clusters because of complex, redundant, and ...

  5. Tissue-Specific Gene Delivery via Nanoparticle Coating

    E-Print Network [OSTI]

    Harris, Todd J.

    The use of biomaterials for gene delivery can potentially avoid many of the safety concerns with viral gene delivery. However, the efficacy of polymeric gene delivery methods is low, particularly in vivo. One significant ...

  6. Research Articles Combining Drug and Gene Similarity Measures

    E-Print Network [OSTI]

    Sharan, Roded

    of drug-drug and gene-gene similarity measures, combined with a logistic regression component to detection problems due to multiple gene and compound names. Additional attempts were based on reverse

  7. Uses of antimicrobial genes from microbial genome Sorek, Rotem...

    Office of Scientific and Technical Information (OSTI)

    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...

  8. Single, Key Gene Discovery Could Streamline Production of Biofuels...

    Energy Savers [EERE]

    Single, Key Gene Discovery Could Streamline Production of Biofuels Single, Key Gene Discovery Could Streamline Production of Biofuels August 11, 2011 - 3:51pm Addthis WASHINGTON,...

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

    Office of Scientific and Technical Information (OSTI)

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

  10. The specificity and evolution of gene regulatory elements

    E-Print Network [OSTI]

    Friedman, Robin Carl

    2010-01-01

    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 ...

  11. Radiation-induced gene responses

    SciTech Connect (OSTI)

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

    1996-12-31

    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.

  12. Dynamics Modelling of Biolistic Gene Guns

    SciTech Connect (OSTI)

    Zhang, M.; Tao, W.; Pianetta, P.A.

    2009-06-04

    The gene transfer process using biolistic gene guns is a highly dynamic process. To achieve good performance, the process needs to be well understood and controlled. Unfortunately, no dynamic model is available in the open literature for analysing and controlling the process. This paper proposes such a model. Relationships of the penetration depth with the helium pressure, the penetration depth with the acceleration distance, and the penetration depth with the micro-carrier radius are presented. Simulations have also been conducted. The results agree well with experimental results in the open literature. The contribution of this paper includes a dynamic model for improving and manipulating performance of the biolistic gene gun.

  13. Characterization of the Bovine Cathelicidin Gene Family 

    E-Print Network [OSTI]

    Flores, Erin Gillenwaters

    2012-10-19

    and Methods Primer Design Based on available sequence data from the Baylor College of Medicine Bovine Genome Project Btau_4.0 genome assembly, primers were designed for as many unique CATHL loci as possible using Primer3 online (http... pseudogene and one duplicated gene in the CATHL region. The currently annotated CATHL genes, the pseudogene, the duplicated gene, and three STS markers (UniSTS277967, UniSTS 268269, and UniSTS255316) were included in the analysis. Primers for CATHLs 1, 2...

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

    E-Print Network [OSTI]

    Otto Pulkkinen; Ralf Metzler

    2013-05-13

    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.

  15. 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 ...

  16. Control of gene expression by cell size

    E-Print Network [OSTI]

    Wu, Chia-Yung

    2010-01-01

    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 ...

  17. Noise and multistability in gene regulatory networks

    E-Print Network [OSTI]

    Ozbudak, Ertugrul M. (Ertugrul Mustafa), 1976-

    2004-01-01

    Proteins are the functional machinery in living cells. Proteins interact with each other and bind to DNA to form so-called gene regulatory networks and in this way regulate the level, location and timing of expression of ...

  18. Improved Gene Targeting through Cell Cycle Synchronization

    E-Print Network [OSTI]

    Tsakraklides, Vasiliki

    Gene targeting is a challenge in organisms where non-homologous end-joining is the predominant form of recombination. We show that cell division cycle synchronization can be applied to significantly increase the rate of ...

  19. Adhesion gene regulation in mammary cell proliferation

    E-Print Network [OSTI]

    Lau, Eric HonYui

    2011-01-01

    A. , et al. , Nectin: an adhesion molecule involved in OF CALIFORNIA, MERCED Adhesion Gene Regulation in Mammary1 1.2 Role of Adhesion Molecules in Development and

  20. Changes in gene expression following EMF exposure

    SciTech Connect (OSTI)

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

    1997-10-01

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

  1. Gene expression profiles in irradiated cancer cells

    SciTech Connect (OSTI)

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

    2013-07-26

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

  2. The Ribosomal DNA Genes Influence Genome-Wide Gene Expression in Drosophila melanogaster 

    E-Print Network [OSTI]

    Paredes Martinez, Lida Silvana

    2012-07-16

    used to address the effect of rDNA deletions on gene expression using reporter genes sensitive to Position Effect Variegation (PEV). In addition, the effect of the deletions in nucleolus size and structure as well as the effect of spontaneous r.... Muller discovered a phenomenon known as Position Effect Variegation (PEV) that changed the view of chromosome structure (48). He created a series of X-ray induced Drosophila mutants that affected the 8 expression of the white+ gene (which confers...

  3. Interferon-Stimulated Genes in the Pregnant Mouse Uterus 

    E-Print Network [OSTI]

    Tilford, Sarah

    2008-08-24

    (7034):772-777. 44. Colina R, Costa-Mattioli M, Dowling RJO, Jaramillo M, Tai L-H, Breitbach CJ, Martineau Y, Larsson O, Rong L, Svitkin YV et al: Translational control of the innate immune response through IRF-7. Nature 2008. 45. Bratton DL, Fadok VA, Richter DA... in the maintenance of pregnancy [23]. 11 2'-5' oligoadenylate synthetase 2 (Oas2) Oas2 has an important role in viral RNA degradation, namely OAS2 cleaves viral mRNA from rRNA [55]. Other cellular roles include apoptosis induction and growth...

  4. 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.

    2007-07-01

    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.

  5. Doug Brutlag 2015 Your Genes and Your Health

    E-Print Network [OSTI]

    Brutlag, Doug

    =252 #12;© Doug Brutlag 2015 Variations in -Amylase Gene Tandem Repeat Arrays Sharp, Cheng & Eichler

  6. Clustering of Pathogenic Genes in Human Co-regulatory Network

    E-Print Network [OSTI]

    Poonen, Bjorn

    Multiple Sclerosis ­ Psoriasis · More connections between similarly classified genes than expected #12

  7. 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 for each core ­ No tree to help here: not fast within one I/O node! ­ The bottleneck of IBM Blue Gene /P

  8. Stress-induced changes in gene interactions in human cells

    E-Print Network [OSTI]

    Ives, Zachary G.

    Stress-induced changes in gene interactions in human cells Renuka R. Nayak1 , William E. Bernal2 environments by changing gene expression and gene interactions. To study how human cells response to stress, we endo- plasmic reticulum stress and exposure to ionizing radiation. We identified thousands of genes

  9. 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.

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

    DOE Patents [OSTI]

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

    1995-03-07

    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.

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

    DOE Patents [OSTI]

    Murnane, John P. (San Francisco, CA); Painter, Robert B. (Burlingame, CA); Kapp, Leon N. (San Rafael, CA); Yu, Loh-Chung (Redwood City, CA)

    1995-03-07

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

  12. Gene Conversion and DNA Sequence Polymorphism in the Sex-Determination Gene fog-2 and Its Paralog ftr-1

    E-Print Network [OSTI]

    Bergthorsson, Ulfar

    Gene Conversion and DNA Sequence Polymorphism in the Sex-Determination Gene fog-2 and Its Paralog to duplication events. fog-2, a sex-determination gene unique to Caenorhabditis elegans and implicated of unknown function. Synonymous sequence divergence in regions of fog-2 and ftr-1 (excluding recent gene

  13. Measuring semantic similarities by combining gene ontology annotations and gene co-function networks

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

    Peng, Jiajie; Uygun, Sahra; Kim, Taehyong; Wang, Yadong; Rhee, Seung Y.; Chen, Jin

    2015-02-14

    Background: Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the limited proportion of genes that are annotated to GO in most organisms. Results: We introduce a novel approach called NETSIM (network-based similarity measure) that incorporates information from gene co-function networks in addition to using the GO structure and annotations. Using metabolic reaction maps of yeast, Arabidopsis, and human, we demonstrate that NETSIM can improve the accuracy of GO term similarities. We also demonstratemore »that NETSIM works well even for genomes with sparser gene annotation data. We applied NETSIM on large Arabidopsis gene families such as cytochrome P450 monooxygenases to group the members functionally and show that this grouping could facilitate functional characterization of genes in these families. Conclusions: Using NETSIM as an example, we demonstrated that the performance of a semantic similarity measure could be significantly improved after incorporating genome-specific information. NETSIM incorporates both GO annotations and gene co-function network data as a priori knowledge in the model. Therefore, functional similarities of GO terms that are not explicitly encoded in GO but are relevant in a taxon-specific manner become measurable when GO annotations are limited.« less

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

    E-Print Network [OSTI]

    Hemminki, Akseli

    , FIN-70211 Kuopio, Finland 2 Cancer Gene Therapy Group, Rational Drug Design Program, Biomedicum, University of Helsinki, FIN-00140 Helsinki, Finland 3 Department of Oncology, Helsinki University Central Hospital, FIN-00290 Helsinki, Finland 4 Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland

  15. Key gene regulating cell wall biosynthesis and recalcitrance in Populus, gene Y

    DOE Patents [OSTI]

    Chen, Jay; Engle, Nancy; Gunter, Lee E.; Jawdy, Sara; Tschaplinski, Timothy J.; Tuskan, Gerald A.

    2015-12-08

    This disclosure provides methods and transgenic plants for improved production of renewable biofuels and other plant-derived biomaterials by altering the expression and/or activity of Gene Y, an O-acetyltransferase. This disclosure also provides expression vectors containing a nucleic acid (Gene Y) which encodes the polypeptide of SEQ ID NO: 1 and is operably linked to a heterologous promoter.

  16. Single gene and gene interaction effects on fertilization and embryonic survival rates in cattle

    E-Print Network [OSTI]

    Yandell, Brian S.

    Single gene and gene interaction effects on fertilization and embryonic survival rates in cattle H as an entire pathway can be used in selection programs to improve reproduction performance in dairy cattle. Key to genotypes in dairy cattle that are suboptimal for reproductive competence (Royal et al., 2000; Lucy, 2001

  17. Towards an informative mutant phenotype for every bacterial gene

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

    Deutschbauer, Adam; Price, Morgan N.; Wetmore, Kelly M.; Tarjan, Daniel R.; Xu, Zhuchen; Shao, Wenjen; Leon, Dacia; Arkin, Adam P.; Skerker, Jeffrey M.

    2014-08-11

    Mutant phenotypes provide strong clues to the functions of the underlying genes and could allow annotation of the millions of sequenced yet uncharacterized bacterial genes. However, it is not known how many genes have a phenotype under laboratory conditions, how many phenotypes are biologically interpretable for predicting gene function, and what experimental conditions are optimal to maximize the number of genes with a phenotype. To address these issues, we measured the mutant fitness of 1,586 genes of the ethanol-producing bacterium Zymomonas mobilis ZM4 across 492 diverse experiments and found statistically significant phenotypes for 89% of all assayed genes. Thus, inmore »Z. mobilis, most genes have a functional consequence under laboratory conditions. We demonstrate that 41% of Z. mobilis genes have both a strong phenotype and a similar fitness pattern (cofitness) to another gene, and are therefore good candidates for functional annotation using mutant fitness. Among 502 poorly characterized Z. mobilis genes, we identified a significant cofitness relationship for 174. For 57 of these genes without a specific functional annotation, we found additional evidence to support the biological significance of these gene-gene associations, and in 33 instances, we were able to predict specific physiological or biochemical roles for the poorly characterized genes. Last, we identified a set of 79 diverse mutant fitness experiments in Z. mobilis that are nearly as biologically informative as the entire set of 492 experiments. Therefore, our work provides a blueprint for the functional annotation of diverse bacteria using mutant fitness.« less

  18. Pathogenicity island mobility and gene content.

    SciTech Connect (OSTI)

    Williams, Kelly Porter

    2013-10-01

    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.

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

    DOE Patents [OSTI]

    Desprez, Pierre-Yves; Campisi, Judith

    2014-08-19

    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.

  20. Aridlands Ecology Lab Protocol Modified: 2010.02.16, S.Castle

    E-Print Network [OSTI]

    Barger, Nichole

    24 inch section of tygon tubing with needle fitting 1000 mL volumetric flask with armhole is not over pressurized. 4. Take time zero (t0) readings: Pump the air in the jar gently with a syringe to mix

  1. Contribution of glacier runoff to water resources of La Paz city, Bolivia (16 S)

    E-Print Network [OSTI]

    Rabatel, Antoine

    accelerated in recent decades in response to climate change and, in particular, increasing temperatures mass balance is a valuable indicator of climate change over the past century (Stocker and others, 2013). Tropical glaciers are very sensitive and respond rapidly to climate fluctuations, mainly due

  2. 16. S. E. Burns, J. P. Hassett, M. V. Rossi, Environ. Sci. Technol. 30, 2934 (1996).

    E-Print Network [OSTI]

    Born, Andreas

    1996-01-01

    , T. Mill, Photochem. Photobiol. 45, 317 (1987). 34. P. B. Merkel, R. Nilsson, D. R. Kearns, J. Am Daniel R. Muhs,4 Richard B. Alley,5 Jeffrey T. Kiehl2 Sea-level rise from melting of polar ice sheets

  3. Universal light-switchable gene promoter system

    DOE Patents [OSTI]

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

    2005-02-22

    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.

  4. Current trends in mapping human genes

    SciTech Connect (OSTI)

    Mckusick, V.A. )

    1991-01-01

    The human is estimated to have at least 50,000 expressed genes (gene loci). Some information is available concerning about 5,000 of these gene loci and about 1,900 have been mapped, i.e., assigned to specific chromosomes (and in most instances particular chromosome regions). Progress has been achieved by a combination of physical mapping (e.g., study of somatic cell hybrids and chromosomal in situ hybridization) and genetic mapping (e.g., genetic linkage studies). New methods for both physical and genetic mapping are expanding the armamentarium. The usefulness of the mapping information is already evident; the spin-off from the Human Genome Project (HGP) begins immediately. the complete nucleotide sequence is the ultimate map of the human genome. Sequencing, although already under way for limited segments of the genome, will await further progress in gene mapping, and in particular creation of contig maps for each chromosome. Meanwhile the technology of sequencing and sequence information handling will be developed.

  5. Differential gene expression Anja von Heydebreck

    E-Print Network [OSTI]

    Spang, Rainer

    on ANOVA/linear models r continuous response variable: linear models; censored survival times: e.g. Cox proportional hazards models #12;Example Golub data, 27 ALL vs. 11 AML samples, 3,051 genes. Histogram). The FDR (Benjamini & Hochberg 1995) is the expected proportion of Type I errors among the rejected

  6. Designing Neural Networks Using Gene Expression Programming

    E-Print Network [OSTI]

    Fernandez, Thomas

    1 Designing Neural Networks Using Gene Expression Programming CândidaFerreira Gepsoft, 73 Elmtree aspects of neural networks, such as the weights, the thresholds, and the network architec- ture. Indeed neural network, including the architecture, the weights and thresholds, could be totally encoded

  7. Gene encoding acetyl-coenzyme A carboxylase

    DOE Patents [OSTI]

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

    1996-09-24

    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.

  8. SHORT REVIEW Ecological genomics: understanding gene and

    E-Print Network [OSTI]

    Herman, Mike

    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

  9. ISSUE 55 JULY 2008 Genes and disease

    E-Print Network [OSTI]

    Rambaut, Andrew

    ISSUE 55 JULY 2008 FUNDING Genes and disease In this issue... FUNDING AND UPDATES 2­5 Project building, in Kenya, South Africa, Uganda and elsewhere in Africa (see page 5). The largest ever study. The Institute will devote a large part of its high-throughput genotyping pipeline, headed by Dr Panos Deloukas

  10. Mechanisms of radiation-induced gene responses

    SciTech Connect (OSTI)

    Woloschak, G.E.; Paunesku, T.

    1996-10-01

    In the process of identifying genes differentially expressed in cells exposed ultraviolet radiation, we have identified a transcript having a 26-bp region that is highly conserved in a variety of species including Bacillus circulans, yeast, pumpkin, Drosophila, mouse, and man. When the 5` region (flanking region or UTR) of a gene, the sequence is predominantly in +/+ orientation with respect to the coding DNA strand; while in the coding region and the 3` region (UTR), the sequence is most frequently in the +/-orientation with respect to the coding DNA strand. In two genes, the element is split into two parts; however, in most cases, it is found only once but with a minimum of 11 consecutive nucleotides precisely depicting the original sequence. The element is found in a large number of different genes with diverse functions (from human ras p21 to B. circulans chitonase). Gel shift assays demonstrated the presence of a protein in HeLa cell extracts that binds to the sense and antisense single-stranded consensus oligomers, as well as to the double- stranded oligonucleotide. When double-stranded oligomer was used, the size shift demonstrated as additional protein-oligomer complex larger than the one bound to either sense or antisense single-stranded consensus oligomers alone. It is speculated either that this element binds to protein(s) important in maintaining DNA is a single-stranded orientation for transcription or, alternatively that this element is important in the transcription-coupled DNA repair process.

  11. 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.

    2009-01-01

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

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

    E-Print Network [OSTI]

    Bolliet, Catherine

    2007-01-01

    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 ...

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

    E-Print Network [OSTI]

    Palle, Sreenath Reddy

    2011-10-21

    Gene expression analyses using native populations can provide information on the genetic and molecular mechanisms that determine intraspecific variation and contribute to the understanding of plant development and adaptation ...

  14. Characterization of genes in the sterigmatocystin gene cluster and their role in fitness of Aspergillus nidulans 

    E-Print Network [OSTI]

    Sim, Sung Chur

    2001-01-01

    Sterigmatocystin (ST) is the penulitmate precursor of aflatoxin (AF) and a carcinogenic mycotoxin produced by A. nidulans, a fungus well established as a genetic model system. Previously, a 60 kb ST gene cluster in A. ...

  15. THE JOURNAL OF GENE MEDICINE RESEARCH ARTICLE J Gene Med 2011; 13: 253261.

    E-Print Network [OSTI]

    Hemminki, Akseli

    , Helsinki, Finland 2HUSLAB, Helsinki University Central Hospital, Helsinki, Finland 3Department of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland 4International Comprehensive Cancer Center Docrates, Helsinki, Finland Correspondence to: Akseli Hemminki, Cancer Gene Therapy

  16. Evidence of efficient stop codon readthrough in four mammalian genes

    E-Print Network [OSTI]

    Loughran, Gary

    Stop codon readthrough is used extensively by viruses to expand their gene expression. Until recent discoveries in Drosophila, only a very limited number of readthrough cases in chromosomal genes had been reported. Analysis ...

  17. Diametric gene-dosage effects as windows into neurogenetic architecture

    E-Print Network [OSTI]

    Crespi, Bernard J.

    Diametric gene-dosage effects as windows into neurogenetic architecture Bernard Crespi Gene, which provide unique insights into neurodevelopmental architecture. These convergent studies of perturbations. One-to-one dosage-phenotype mappings also reveal neurodevelop- mental architecture: what

  18. Rhizobium common nod genes are required for biofilm formation.

    E-Print Network [OSTI]

    Fujishige, Nancy A; Lum, Michelle R; De Hoff, Peter L; Whitelegge, Julian P; Faull, Kym F; Hirsch, Ann M

    2008-01-01

    E. , and Bisseling, T. (2005) Nod factor signaling genes andLegume symbioses: absence of nod genes in photosyntheticactivity of Rhizobium sp. NGR234 Nod-factors on Macroptilium

  19. Rhizobium common nod genes are required for biofilm formation

    E-Print Network [OSTI]

    Fujishige, Nancy A; Lum, Michelle R; De Hoff, Peter L; Whitelegge, Julian P; Faull, Kym F; Hirsch, Ann M

    2008-01-01

    E. , and Bisseling, T. (2005) Nod factor signaling genes andLegume symbioses: absence of nod genes in photosyntheticactivity of Rhizobium sp. NGR234 Nod-factors on Macroptilium

  20. PI Control of Gene Expression in Tumorous Cell Lines 

    E-Print Network [OSTI]

    Mendonca, Rouella J.

    2010-01-16

    Recent experiments are bringing to the fore more and more information about the effects of different treatments on the gene expression of different genes. The results obtained from these experiments show that some definite trends are observed...

  1. Copy Number and Gene Expression: Stochastic Modeling and Therapeutic Application 

    E-Print Network [OSTI]

    Hsu, Fang-Han

    2013-05-01

    (CNAs), which are known to be common mutations in genetic diseases, on steady- state gene expression values, time-course expression activities, and the e?ectiveness of targeted therapy. Assuming DNA copies operate as independent subsystems producing gene...

  2. 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 ...

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

    Office of Scientific and Technical Information (OSTI)

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

  4. Environmental Scientists Find Antibiotics, Bacteria, Resistance Genes in Feedlot Dust

    E-Print Network [OSTI]

    Rock, Chris

    Environmental Scientists Find Antibiotics, Bacteria, Resistance Genes in Feedlot Dust :: Texas Tech Today http://today.ttu.edu/2015/01/environmental-scientists-find-antibiotics Print Email + Font - Font Environmental Scientists Find Antibiotics, Bacteria, Resistance Genes

  5. Analysis of the Arabidopsis NAC gene superfamily in plant development 

    E-Print Network [OSTI]

    Alvarado Chavez, Veria Ysabel

    2009-05-15

    There are a vast number of transcription factors that regulate plant growth and development. The NAC gene superfamily is one of the largest families of transcription factors in the plant kingdom. NAC gene expression profiles using Affymetrix ATH1...

  6. SVM-RFE With MRMR Filter for Gene Selection

    E-Print Network [OSTI]

    Mundra, Piyushkumar A.

    We enhance the support vector machine recursive feature elimination (SVM-RFE) method for gene selection by incorporating a minimum-redundancy maximum-relevancy (MRMR) filter. The relevancy of a set of genes are measured ...

  7. Effects of Pinealectomy on Hypothalamic Metabolic and Clock Gene Rhythms 

    E-Print Network [OSTI]

    Clauson, Amanda

    2006-07-11

    the validity of the neuroendocrine loop model by suggesting that although melatonin administration affects overt clock function, (Lu and Cassone, 1993) it has no effect on the transcription of clock genes (Yasuo et al., 2002). Thus, expression of these genes...

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

    E-Print Network [OSTI]

    Lässig, Michael

    , that it is not the only mode of gene interactions. Especially in eukaryotes, additional regulation mechanims involving

  9. QB1 - Stochastic Gene Regulation Munsky, Brian [Los Alamos National

    Office of Scientific and Technical Information (OSTI)

    FACILITIES; FLUCTUATIONS; GENE REGULATION; KINETICS; QUANTIZATION; SIMULATION; SWITCHES Summaries of this presentation are: (1) Stochastic fluctuations or 'noise' is present...

  10. Estimation and Detection of Multivariate Gene Regulatory Relationships 

    E-Print Network [OSTI]

    Chen, Ting

    2013-09-18

    and canalyzing genes like p53 and DUSP1 from real data sets, respectively. This indicates that our methodology could serve as a promising tool for the detection of potential gene regulatory relationships and canalyzing genes. In one word, this dissertation...

  11. Evolution by gene duplication: an update Jianzhi Zhang

    E-Print Network [OSTI]

    Zhang, Jianzhi

    Evolution by gene duplication: an update Jianzhi Zhang Department of Ecology and Evolutionary The importance of gene duplication in supplying raw genetic material to biological evolution has been recog- tions, and what role does gene duplication play in the evolution of genomes and organisms? Detailed

  12. Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T

    SciTech Connect (OSTI)

    Oosterkamp, Margreet J.; Veuskens, Teun; Saia, Flavia Talarico; Weelink, Sander A.B.; Goodwin, Lynne A.; Daligault, Hajnalka E.; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Land, Miriam L; Hauser, Loren John; Langenhoff, A. M.; Gerritse, Jan; Van Berkel, Willem J. H.; Pieper, Dietmar; Junca, Howard; Smidt, Hauke; Schraa, Gosse; Davids, Mark; Schaap, Peter J; Plugge, Caroline M.; Stams, Alfons J. M.

    2013-01-01

    The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.

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

    E-Print Network [OSTI]

    Noor, Amina

    2013-12-10

    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...

  14. Towards an informative mutant phenotype for every bacterial gene

    SciTech Connect (OSTI)

    Deutschbauer, Adam; Price, Morgan N.; Wetmore, Kelly M.; Tarjan, Daniel R.; Xu, Zhuchen; Shao, Wenjen; Leon, Dacia; Arkin, Adam P.; Skerker, Jeffrey M.

    2014-08-11

    Mutant phenotypes provide strong clues to the functions of the underlying genes and could allow annotation of the millions of sequenced yet uncharacterized bacterial genes. However, it is not known how many genes have a phenotype under laboratory conditions, how many phenotypes are biologically interpretable for predicting gene function, and what experimental conditions are optimal to maximize the number of genes with a phenotype. To address these issues, we measured the mutant fitness of 1,586 genes of the ethanol-producing bacterium Zymomonas mobilis ZM4 across 492 diverse experiments and found statistically significant phenotypes for 89% of all assayed genes. Thus, in Z. mobilis, most genes have a functional consequence under laboratory conditions. We demonstrate that 41% of Z. mobilis genes have both a strong phenotype and a similar fitness pattern (cofitness) to another gene, and are therefore good candidates for functional annotation using mutant fitness. Among 502 poorly characterized Z. mobilis genes, we identified a significant cofitness relationship for 174. For 57 of these genes without a specific functional annotation, we found additional evidence to support the biological significance of these gene-gene associations, and in 33 instances, we were able to predict specific physiological or biochemical roles for the poorly characterized genes. Last, we identified a set of 79 diverse mutant fitness experiments in Z. mobilis that are nearly as biologically informative as the entire set of 492 experiments. Therefore, our work provides a blueprint for the functional annotation of diverse bacteria using mutant fitness.

  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. Repression of the interleukin 6 gene promoter by p53 and the retinoblastoma susceptibility gene product

    SciTech Connect (OSTI)

    Santhanam, U.; Ray, A.; Sehgal, P.B. (Rockefeller Univ., New York, NY (United States))

    1991-09-01

    The aberrant overexpression of interleukin 6 (IL-6) is implicated as an autocrine mechanism in the enhanced proliferation of the neoplastic cell elements in various B- and T-cell malignancies and in some carcinomas and sarcomas; many of these neoplasms have been shown to be associated with a mutated p53 gene. The possibility that wild-type (wt) p53, a nuclear tumor-suppressor protein, but not its transforming mutants might serve to repress IL-6 gene expression was investigated in HeLa cells. The authors transiently cotransfected these cells with constitutive cytomegalovirus (CMV) enhancer/promoter expression plasmids overproducing wt or mutant human or murine p53 and with appropriate chloramphenicol acetyltransferase (CAT) reporter plasmids containing the promoter elements of human IL-6, c-fos, or {beta}-actin genes or of porcine major histocompatibility complex (MHC) class I gene in pN-38 to evaluate the effect of the various p53 species on these promoters. These observations identify transcriptional repression as a property of p53 and suggest that p53 and RB may be involved as transcriptional repressors in modulating IL-6 gene expression during cellular differentiation and oncogenesis.

  17. Gene Calling Standards (GSC8 Meeting)

    ScienceCinema (OSTI)

    Kyrpides, Nikos [Genome Biology Program, DOE JGI

    2011-04-28

    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.

  18. Algorithms for Gene Clustering Analysis on Genomes 

    E-Print Network [OSTI]

    Yi, Gang Man

    2012-07-16

    CLUSTERING ANALYSIS ON GENOMES A Dissertation by GANG MAN YI Submitted to the O ce of Graduate Studies of Texas A&M University in partial ful llment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2011 Major Subject: Computer Science... ALGORITHMS FOR GENE CLUSTERING ANALYSIS ON GENOMES A Dissertation by GANG MAN YI Submitted to the O ce of Graduate Studies of Texas A&M University in partial ful llment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair...

  19. Hemicellulolytic organisms in the particle-associated microbiota of the hoatzin crop

    SciTech Connect (OSTI)

    Godoy-Vitorino, Filipa; Malfatti, Stephanie; Garcia-Amado, Maria A.; Dominguez-Bello, Maria Gloria; Hugenholtz, Phillip; Tringe, Susannah

    2011-05-31

    The hoatzin (Opisthocomus hoazin) is a South American herbivorous bird, that has an enlarged crop analogous to the rumen, where foregut microbes degrade the otherwise indigestible plant materials, providing energy to the host. The crop harbors an impressive array of microorganisms with potentially novel cellulolytic enzymes. Thie study describes the composition ofthe particle-associated microbiota in the hoatzin crop, combining a survey of 16S rRNA genes in 7 adult birds and metagenome sequencing of two animals. The pyrotag survey demonstrates that Prevotellaceae, are the most abundant and ubiquitous taxa, suggesting that the degradation of hemicellulose is an important activity in the crop. Nonetheless, preliminary results from the metagnome of the particle-associated microbiota of two adult birds show that the crop microbiome contains a high number of genes encoding cellulases (such as GH5) more abundant than those of the termite gut, as well as genes encoding hemicellulases. These preliminary results show that the carbohydate-active enzyme genes in the cropmetagenome could be a source of biochemical catalysts able to deconstruct plant biomass.

  20. Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments

    SciTech Connect (OSTI)

    Edlund, A.; Jansson, J.

    2008-05-01

    The aim of this study was to enrich and identify psychrotolerant phenanthrenedegrading bacteria from polluted Baltic Sea sediments. Polyaromatic hydrocarbon (PAH)-contaminated sediments were spiked with phenanthrene and incubated for 2 months in the presence of bromodeoxyuridine that is incorporated into the DNA of replicating cells. The bromodeoxyuridine-incorporated DNA was extracted by immunocapture and analyzed by terminal-restriction fragment length polymorphism and 16S rRNA gene cloning and sequencing to identify bacterial populations that were growing. In addition, degradation genes were quantified in the bromodeoxyuridine-incorporated DNA by real-time PCR. Phenanthrene concentrations decreased after 2 months of incubation in the phenanthrene-enriched sediments and this reduction correlated to increases in copy numbers of xylE and phnAc dioxygenase genes. Representatives of Exiguobacterium, Schewanella,Methylomonas, Pseudomonas, Bacteroides and an uncultured Deltaproteobacterium and a Gammaproteobacterium dominated the growing community in the phenanthrene spiked sediments. Isolates that were closely related to three of these bacteria (two pseudomonads and an Exiguobacterium sp.) could reduce phenanthrene concentrations in pure cultures and they all harbored phnAc dioxygenase genes. These results confirm that this combination of culture-based and molecular approaches was useful for identification of actively growing bacterial species with a high potential for phenanthrene degradation.

  1. Surface enhanced Raman gene probe and methods thereof

    DOE Patents [OSTI]

    Vo-Dinh, T.

    1998-02-24

    The subject invention disclosed is a new gene probe biosensor and methods based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed thereon. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays. 18 figs.

  2. Surface enhanced Raman gene probe and methods thereof

    DOE Patents [OSTI]

    Vo-Dinh, T.

    1998-09-29

    The subject invention disclosed herein is a new gene probe biosensor and methods based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed thereon. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means supporting the SERS active substrate includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays. 18 figs.

  3. Surface enhanced Raman gene probe and methods thereof

    DOE Patents [OSTI]

    Vo-Dinh, T.

    1998-07-21

    The subject invention disclosed is a new gene probe biosensor and methods based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means supporting the SERS active substrate includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays. 18 figs.

  4. Gene clustering pattern, promoter architecture, and gene expression stability in eukaryotic genomes

    E-Print Network [OSTI]

    Zhang, Jianzhi

    . We hypothe- sized that upstream distance and orientation (head-to-head or head-to-tail) are important upstream distance tend to have low gene expression variability, and their promoter is flanked by strongly positioned nucleosomes and tends to have low nucleosome occupancy. These observations suggest that in vivo

  5. 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

  6. ORIGINAL RESEARCH ARTICLE published: 22 April 2013

    E-Print Network [OSTI]

    evidence for sulfur lithotrophy by Epsilonproteobacteria as the major energy source for primary was the most abundant chemical energy source. Small subunit ribosomal RNA (SSU rRNA) gene sequence data showed). The free energy, SSU rRNA gene and quantitative functional gene data are all consistent with the hypothesis

  7. Engineering disease resistance with pectate lyase-like genes

    DOE Patents [OSTI]

    Vogel, John; Somerville, Shauna

    2005-03-08

    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.

  8. Measuring semantic similarities by combining gene ontology annotations...

    Office of Scientific and Technical Information (OSTI)

    the members functionally and show that this grouping could facilitate functional characterization of genes in these families. Conclusions: Using NETSIM as an example, we...

  9. Measuring semantic similarities by combining gene ontology annotations...

    Office of Scientific and Technical Information (OSTI)

    the members functionally and show that this grouping could facilitate functional characterization of genes in these families. Conclusions: Using NETSIM as an example, we...

  10. Modulation of histone methylation and MLH1 gene silencing by...

    Office of Scientific and Technical Information (OSTI)

    LIFE SCIENCES; ARGININE; CARCINOGENS; CHROMIUM; DNA DAMAGES; GENES; HUMAN POPULATIONS; LUNGS; LYSINE; METHYLATION; NEOPLASMS; OCCUPATIONAL EXPOSURE; PROMOTERS Word Cloud More Like...

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

    E-Print Network [OSTI]

    2012-01-01

    5096–5108. 36. Macnab RM: How bacteria assemble. Annu Revgene fitness among related bacteria. BMC Genomics 2012 13:gene fitness among related bacteria Rocio Canals 1 , Xiao-

  12. Gibbs Sampling for Gene Cis-Regulatory Elements

    E-Print Network [OSTI]

    Newberg, Heidi

    : "Bayesian computational approaches for gene regulation studies of bioethanol and biohydrogen production ... for the understanding of cell function, differentiation, and pathology ... because the elements affect both the products

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

    E-Print Network [OSTI]

    Posada-Buitrago, Martha Lucia

    2005-01-01

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

  14. Functional Ecological Gene Networks to Reveal the Changes Among...

    Office of Scientific and Technical Information (OSTI)

    network structure among different microbial speciespopulations. Here, a novel random matrix theory (RMT)-based conceptual framework for identifying functional ecological gene...

  15. MAVTgsa: An R Package for Gene Set (Enrichment) Analysis

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

    Chien, Chih-Yi; Chang, Ching-Wei; Tsai, Chen-An; Chen, James J.

    2014-01-01

    Gene set analysis methods aim to determine whether an a priori defined set of genes shows statistically significant difference in expression on either categorical or continuous outcomes. Although many methods for gene set analysis have been proposed, a systematic analysis tool for identification of different types of gene set significance modules has not been developed previously. This work presents an R package, called MAVTgsa, which includes three different methods for integrated gene set enrichment analysis. (1) The one-sided OLS (ordinary least squares) test detects coordinated changes of genes in gene set in one direction, either up- or downregulation. (2)more »The two-sided MANOVA (multivariate analysis variance) detects changes both up- and downregulation for studying two or more experimental conditions. (3) A random forests-based procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes. MAVTgsa computes the P values and FDR (false discovery rate) q -value for all gene sets in the study. Furthermore, MAVTgsa provides several visualization outputs to support and interpret the enrichment results. This package is available online. « less

  16. 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)

    2008-02-05

    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.

  17. Designer gene circuits for basic science, engineering, and medicine /

    E-Print Network [OSTI]

    Prindle, Arthur

    2014-01-01

    Programmable Probiotics . . . . . . . . . . .Chapter 5 Programmable Probiotics: Gene circuit chaperonesFigure 5.1: PROP-Z probiotics for noninvasive cancer

  18. Listening to the noise: random fluctuations reveal gene network...

    Office of Scientific and Technical Information (OSTI)

    Title: Listening to the noise: random fluctuations reveal gene network parameters The cellular environment is abuzz with noise. The origin of this noise is attributed to the...

  19. ARIMA Models versus Gene Expression Programming In Precipitation Modeling

    E-Print Network [OSTI]

    Fernandez, Thomas

    ARIMA Models versus Gene Expression Programming In Precipitation Modeling ALINA BRBULESCU and ELENA, Precipitation 1 Introduction Time series are ubiquitous in the real world. They are usually generated

  20. 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))

    1989-04-01

    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.

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

    SciTech Connect (OSTI)

    Daniel J. Arp

    2005-05-25

    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.

  2. EXCAVATOR: A Computer Program for Efficiently Mining Gene-Expression Data

    E-Print Network [OSTI]

    EXCAVATOR: A Computer Program for Efficiently Mining Gene-Expression Data Dong Xu 1,* , Victor: gene expression, gene regulation, biological data mining, clustering, minimum spanning tree, Java GUI@ornl.gov. #12;ABSTRACT Massive gene-expression data are generated using microarrays, and clustering gene

  3. 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

  4. Toehold Switches: De-Novo-Designed Regulators of Gene Expression

    E-Print Network [OSTI]

    Polz, Martin

    Resource Toehold Switches: De-Novo-Designed Regulators of Gene Expression Alexander A. Green,1. Here, we report a class of de-novo-designed prokaryotic riboregulators called toehold switches that activate gene expression in response to cognate RNAs with arbitrary sequences. Toehold switches provide

  5. Time-synchronized Clustering of Gene Expression Trajectories

    E-Print Network [OSTI]

    MĂĽller, Hans-Georg

    Time-synchronized Clustering of Gene Expression Trajectories RONG TANG Division of Biostatistics, USA ABSTRACT Current clustering methods are routinely applied to gene expression time course data at different rates, successful clustering in this context requires dealing with varying time and shape patterns

  6. 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

  7. Analysis of Antibiotic Resistant Genes in Aquacultural Bacteria

    E-Print Network [OSTI]

    Kane, Andrew S.

    1 Analysis of Antibiotic Resistant Genes in Aquacultural Bacteria JY Wang* YJ Geng RX Wang J Feng in the selection pressure, retained the resistant strains, spread among the same or different species of bacteria also increased #12;3 2.Potential Hazards of Resistant Bacteria · Resistant bacteria · Resistant gene

  8. Innovation and robustness in complex regulatory gene networks

    E-Print Network [OSTI]

    Wagner, Andreas

    Innovation and robustness in complex regulatory gene networks S. Ciliberti*, O. C. Martin* , and A involves countless evolutionary innovations, a steady stream of ingenuity that has been flowing for more such innovation. Here, we examine these principles for evolutionary innovation in gene expression patterns

  9. Non-random gene flow: an underappreciated force in evolution

    E-Print Network [OSTI]

    Bolnick, Daniel I.

    , adaptation to climate change, biological invasion, and speciation. Giv- en the possible ubiquity and impacts-random gene flow and to more fully incorporate its effects into theory. Rethinking the homogenizing effect of gene flow Theory suggests that evolutionary change depends on the action of a limited number

  10. Visualizing Conserved Gene Location across Microbe Chris D Shaw

    E-Print Network [OSTI]

    Shaw, Chris

    Visualizing Conserved Gene Location across Microbe Genomes Chris D Shaw School of Interactive Arts of microbes. The purpose of this visualizatiuon is to enable a biologist to examine the layout of genes help a biologist better confirm the structure and function of newly analyzed microbe DNA sequences. We

  11. Mining gene sets for measuring similarities CHRISTINE NARDINI1

    E-Print Network [OSTI]

    Nardini, Christine

    Mining gene sets for measuring similarities CHRISTINE NARDINI1 , DANIELE MASOTTI2 , SUNGROH YOON3 and data mining of these new, large types of data. The proliferation of devices able to process in paral of number of genes under different environmental conditions. Data mining algorithms demanded to the analysis

  12. GenePRIMP: A software quality control tool

    ScienceCinema (OSTI)

    Amrita Pati

    2010-09-01

    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.

  13. GenePRIMP: A software quality control tool

    SciTech Connect (OSTI)

    Amrita Pati

    2010-05-05

    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.

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

    E-Print Network [OSTI]

    supplement at http://www.genome.org.] As the Human Genome Project enters its large-scale sequencing phaseIdentification 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

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

    E-Print Network [OSTI]

    Shvartsman, Stanislav "Stas"

    Kinetics of gene derepression by ERK signaling Bomyi Lima , 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

  16. 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

  17. 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

  18. 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

  19. 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

    2010-05-04

    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.

  20. 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

    2013-01-25

    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.

  1. UNCORRECTEDPROOF Assessment of anaerobic benzene degradation

    E-Print Network [OSTI]

    Alvarez, Pedro J.

    the feasibility of intrin- sic bioremediation. In this work we developed a 16S rRNA biomarker to estimate). Such widespread contamination of potential drinking water sources is a major concern because benzene is a known on intrinsic anaerobic bioremediation processes that proceed without human intervention, and has been selected

  2. Influence of Dietary Starch Inclusion on Cecal Environment and Microbial Populations in Horses 

    E-Print Network [OSTI]

    Warzecha, Christine Marie

    2013-08-07

    Project 16S rRNA dataset. Data were analyzed using PROC MIXED procedure of SAS. Bacterial phyla were largely unaffected by dietary treatment for the first 12 h after the initial concentrate meal except for Verrucomicrobia which was greater in LS horses (P...

  3. Novel Microbial Diversity Retrieved by Autonomous Robotic Exploration of the World's Deepest

    E-Print Network [OSTI]

    Novel Microbial Diversity Retrieved by Autonomous Robotic Exploration of the World's Deepest environment. Key Words: Autonomous--Robotics--Microbial diversity--16S rRNA. Astrobiology 10, 201­213. 1 of exploratory autonomous robotics (Diaz-Calderon et al., 2007). To search for microbial life on planetary bodies

  4. 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

  5. Water Resources Center Annual Technical Report

    E-Print Network [OSTI]

    Publication #12;Basic Information Title: Origin and Transport of Radioactive Ra-226 in Coal-Mine Effluent Category: Waste Water, Treatment, None Descriptors: 16S rRNA, biofouling, membrane bioreactor, wastewater Category: Focus Category: Radioactive Substances, Surface Water, Geomorpological and Geochemical Processes

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

    SciTech Connect (OSTI)

    Lukjancenko, Oksana [Technical University of Denmark] [Technical University of Denmark

    2012-06-01

    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.

  7. ORIGINAL RESEARCH ARTICLE published: 20 May 2014

    E-Print Network [OSTI]

    Widder, Stefanie

    microbial interactions and detecting keystone species with co-occurrence networks David Berry1 features associated with keystone species in co-occurrence networks. This study provides a substantiated cooperation, 16S rRNA sequencing surveys, Lotka-Volterra models, keystone species, habitat filtering

  8. 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

    2015-02-10

    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.

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

    SciTech Connect (OSTI)

    Hunsperger, Heather M. [Univ. of Washington, Seattle, WA (United States); Randhawa, Tejinder [Univ. of Washington, Seattle, WA (United States); Cattolico, Rose Ann [Univ. of Washington, Seattle, WA (United States)

    2015-01-01

    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.

  10. Review: Gene amplification--a cellular response to genotoxic stress

    SciTech Connect (OSTI)

    Lueke-Huhle, C. (Kernforschungszentrum Karlsruhe, Institut fuer Genetik und Toxikologie (West Germany))

    1989-10-01

    Recent years of cancer research have defined the role of key regulatory genes in oncogenesis. Oncogenes and suppressor genes are affected in the process of carcinogenesis either by mutations within the coding region, promoter mutations, or gene amplification. This review describes the authors studies on gene amplification in mammalian cells, with emphasis on the initiating events induced by carcinogenic chemicals and various types of radiation. The influence of genomic instability, cell dedifferentiation, and the malignant potential of a cell on their capacity to amplify genes is demonstrated by molecular biologic and cytogenetic studies on human and rodent cells. Cells that contain amplified DNA are at risk for chromosomal aberrations, sister chromatid exchanges, and rearrangements. Surviving cells show such cancer-prone genetic consequences. 52 references.

  11. Domestication of the neotropical tree Chrysophyllum cainito from a geographically limited yet genetically diverse gene pool in Panama

    E-Print Network [OSTI]

    Parker, Ingrid M.

    2014-01-01

    genetically diverse gene pool in Panama Jennifer J. Petersenincorporating a diverse gene pool. These results refute theof human influences on gene pools through selection and

  12. Genomic analyses of bacterial porin-cytochrome gene clusters

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

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

    2014-11-26

    In this study, 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 bacteriamore »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.« less

  13. Identification of DNA marker for root-knot nematode resistance gene and characterization of disease resistance gene candidates in cotton 

    E-Print Network [OSTI]

    He, Limei

    2000-01-01

    , bacteria, viruses and nematodes, in cotton, resistance gene candidates were cloned by PCR using a pair of degenerate primers designed from the conserved sequences of disease resistance genes cloned from a variety of plant taxa. From a 96-clone sample, 23...

  14. 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

    2015-01-01

    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

  15. B and C class MADS-box genes and the developmental genetics of maize flower development

    E-Print Network [OSTI]

    Whipple, Clinton J.

    2006-01-01

    diversification of the two C-Class MADS box genes OSMADS32004). Conservation of B-class floral homeotic gene function2004). Conservation of B-class floral homeotic gene function

  16. A CRTC2 Repressor Role Regulates DNA Damage Response Genes in Germinal Center B-cells

    E-Print Network [OSTI]

    Schontzler, Olivia Tersa

    2012-01-01

    as DNA damage response (DDR) genes throughout this proposal.binding to and repression of DDR genes. Secondly, repressorcontextual repressor role on DDR genes as part of an ATM

  17. The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome

    E-Print Network [OSTI]

    The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus September 2006 Abstract Metazoan genomes contain large numbers of genes that participate in responses families thought to protect against chemical stressors; these genes collectively comprise the `chemical

  18. Application of Logic Synthesis Toward the Inference and Control of Gene Regulatory Networks 

    E-Print Network [OSTI]

    Lin, Pey Chang K

    2013-06-27

    effort of modeling cell behavior, inferring biological networks, and controlling genetic diseases. Genes interact with other genes in a Gene Regulatory Network (GRN) and can be modeled as a Boolean Network (BN) or equivalently as a Finite State Machine...

  19. Modeling Gene Regulatory Networks from Time Series Data using Particle Filtering 

    E-Print Network [OSTI]

    Noor, Amina

    2012-10-19

    This thesis considers the problem of learning the structure of gene regulatory networks using gene expression time series data. A more realistic scenario where the state space model representing a gene network evolves nonlinearly is considered while...

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

    E-Print Network [OSTI]

    Paria, Nandina

    2012-02-14

    of selected body tissues showed that some ECAY genes are expressed exclusively in testes while others show ubiquitous or intermediate expression. Quantitative Real-Time PCR using primers for 9 testis-specific multicopy genes revealed 5 genes with statistically...

  1. 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

  2. Polymorphic nuclear gene sequences indicate a novel genome donor in the polyploid genus Thinopyrum

    E-Print Network [OSTI]

    Pappu, Hanu R.

    of the granule-bound starch synthase (GBSSI) gene and intron III of the beta-amylase gene (Bmy1) were isolated

  3. Characterization of BoLA class II genes 

    E-Print Network [OSTI]

    Sherwood, Sidney James

    1989-01-01

    or growth of the tumors was attributed to a genetically inherited system of about fifteen dominant genes. The last major step leading to Borer defining of the mouse MHC was the work done on human blood groups by Landsteiner (1901) and others... antigen. Second an Ir gene mutation that affects Ir gene control also carries amino acid 10 substitutions in the class II but in no other molecule. Third, immune response in vitro and in vivo can be manipulated by class II specific antibodies. Last...

  4. LATERAL GENE TRANSFER AND THE HISTORY OF BACTERIAL GENOMES

    SciTech Connect (OSTI)

    Howard Ochman

    2006-02-22

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

  5. New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes for Methanosarcina species

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

    Guss, Adam M.; Rother, Michael; Zhang, Jun Kai; Kulkkarni, Gargi; Metcalf, William W.

    2008-01-01

    A highly efficient method for chromosomal integration of cloned DNA into Methanosarcina spp. was developed utilizing the site-specific recombination system from the Streptomyces phage ?C31. Host strains expressing the ?C31 integrase gene and carrying an appropriate recombination site can be transformed with non-replicating plasmids carrying the complementary recombination site at efficiencies similar to those obtained with self-replicating vectors. We have also constructed a series of hybrid promoters that combine the highly expressed M. barkeri P mcrB promoter with binding sites for the tetracycline-responsive, bacterial TetR protein. These promoters are tightly regulated by the presence or absence of tetracycline inmore »strains that express the tetR gene. The hybrid promoters can be used in genetic experiments to test gene essentiality by placing a gene of interest under their control. Thus, growth of strains with tetR -regulated essential genes becomes tetracycline-dependent. A series of plasmid vectors that utilize the site-specific recombination system for construction of reporter gene fusions and for tetracycline regulated expression of cloned genes are reported. These vectors were used to test the efficiency of translation at a variety of start codons. Fusions using an ATG start site were the most active, whereas those using GTG and TTG were approximately one half or one fourth as active, respectively. The CTG fusion was 95% less active than the ATG fusion. « less

  6. 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. ...

  7. Auxiliary metabolic genes in viruses infecting marine cyanobacteria

    E-Print Network [OSTI]

    Thompson, Luke Richard

    2010-01-01

    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. ...

  8. Genes with internal repeats require the THO complex for transcription

    E-Print Network [OSTI]

    Voynov, Vladimir

    2006-01-01

    A genome-wide screen for promoter-independent regulators of the Saccharomyces cerevisiae adhesin FLOII identified 37 novel regulators. Among the mutants with the strongest phenotype were the deletions of genes encoding ...

  9. Low-Rank Regularization for Learning Gene Expression Programs

    E-Print Network [OSTI]

    Ye, Guibo; Tang, Mengfan; Cai, Jian-Feng; Nie, Qing; Xie, Xiaohui; Muldoon, Mark R

    2013-01-01

    8 | Issue 12 | e82146 Low-Rank for Learning Gene ExpressionWe will call (3) the linear low-rank model in the following.so is its square root K 2 . Low-rank regularized nonlinear

  10. Intrinsic limits to gene regulation by global crosstalk

    E-Print Network [OSTI]

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

    2015-01-01

    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...

  11. Gene Function Prediction Based on Sequence or Expression Data

    E-Print Network [OSTI]

    Horan, Kevin

    2011-01-01

    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.

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

    E-Print Network [OSTI]

    Gerber, Georg Kurt, 1970-

    2007-01-01

    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 ...

  13. 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 ...

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

    DOE Patents [OSTI]

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

    2015-05-19

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

  15. In Vivo Gene Expression Dynamics of Tumor-Targeted Bacteria

    E-Print Network [OSTI]

    Danino, Tal

    The engineering of bacteria to controllably deliver therapeutics is an attractive application for synthetic biology. While most synthetic gene networks have been explored within microbes, there is a need for further ...

  16. The Evolution of a High Copy Gene Array in Arabidopsis

    E-Print Network [OSTI]

    Kane, Joshua; Freeling, Michael; Lyons, Eric

    2010-01-01

    48:597–604 Zhang J (2003) Evolution by gene duplication: an10.1007/s00239-010-9350-2 The Evolution of a High Copy Genein understanding the evolution of genomes and their host

  17. A novel method for finding small highly discriminant gene sets 

    E-Print Network [OSTI]

    Gardner, Jason H.

    2004-11-15

    In a normal microarray classification problem there will be many genes, on the order of thousands, and few samples, on the order of tens. This necessitates a massive feature space reduction before classification can take place. While much time...

  18. Speeding disease gene discovery by sequence based candidate prioritization 

    E-Print Network [OSTI]

    Adie, Euan A; Adams, Richard R; Evans, Kathryn L; Porteous, David; Pickard, Ben S

    2005-03-14

    Background: Regions of interest identified through genetic linkage studies regularly exceed 30 centimorgans in size and can contain hundreds of genes. Traditionally this number is reduced by matching functional annotation ...

  19. 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

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

    DOE Patents [OSTI]

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

    2010-05-11

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

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

    E-Print Network [OSTI]

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

    2009-01-01

    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 ...

  2. Sorghum Ma5 and Ma6 maturity genes 

    E-Print Network [OSTI]

    Brady, Jeffrey Alan

    2009-05-15

    The Ma5 and Ma6 maturity loci in sorghum contain genes interacting epistatically to block flowering until an appropriate daylength is met. Because sorghum is a crop of tropical origin, its critical daylength is close to ...

  3. Should Gene Therapy be Used for Newborns with Hemophilia?

    E-Print Network [OSTI]

    Ponder, Katherine P.

    of genetically-modified fibroblasts for he- mophilia A. The Food and Drug Administration has ruled out gene and initial evaluation in humans with other genetic deficiencies demonstrate safety and efficacy. The use

  4. Isolation and characterization of resistance gene analogs (RGAs) in sorghum 

    E-Print Network [OSTI]

    Cho, Jae-Min

    2005-08-29

    to isolate resistance gene analogs (RGAs) by PCR with degenerate primers and homology searches from public databases. Multiple combinations of degenerate primers were designed from three conserved motifs (one motif was used for a subgroup-specific primer...

  5. The design and evaluation of triazine dendrimers for gene delivery 

    E-Print Network [OSTI]

    Mintzer, Meredith Ann

    2011-02-22

    The interest in using gene therapy to target a variety of both inherited and acquired diseases has intensified over the last two decades. Because free DNA is easily degraded by serum nucleases in the bloodstream, the ...

  6. ; 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

  7. Genome Enabled Discovery of Carbon Sequestration Genes in Poplar

    SciTech Connect (OSTI)

    Filichkin, Sergei; Etherington, Elizabeth; Ma, Caiping; Strauss, Steve

    2007-02-22

    The goals of the S.H. Strauss laboratory portion of 'Genome-enabled discovery of carbon sequestration genes in poplar' are (1) to explore the functions of candidate genes using Populus transformation by inserting genes provided by Oakridge National Laboratory (ORNL) and the University of Florida (UF) into poplar; (2) to expand the poplar transformation toolkit by developing transformation methods for important genotypes; and (3) to allow induced expression, and efficient gene suppression, in roots and other tissues. As part of the transformation improvement effort, OSU developed transformation protocols for Populus trichocarpa 'Nisqually-1' clone and an early flowering P. alba clone, 6K10. Complete descriptions of the transformation systems were published (Ma et. al. 2004, Meilan et. al 2004). Twenty-one 'Nisqually-1' and 622 6K10 transgenic plants were generated. To identify root predominant promoters, a set of three promoters were tested for their tissue-specific expression patterns in poplar and in Arabidopsis as a model system. A novel gene, ET304, was identified by analyzing a collection of poplar enhancer trap lines generated at OSU (Filichkin et. al 2006a, 2006b). Other promoters include the pGgMT1 root-predominant promoter from Casuarina glauca and the pAtPIN2 promoter from Arabidopsis root specific PIN2 gene. OSU tested two induction systems, alcohol- and estrogen-inducible, in multiple poplar transgenics. Ethanol proved to be the more efficient when tested in tissue culture and greenhouse conditions. Two estrogen-inducible systems were evaluated in transgenic Populus, neither of which functioned reliably in tissue culture conditions. GATEWAY-compatible plant binary vectors were designed to compare the silencing efficiency of homologous (direct) RNAi vs. heterologous (transitive) RNAi inverted repeats. A set of genes was targeted for post transcriptional silencing in the model Arabidopsis system; these include the floral meristem identity gene (APETALA1 or AP1), auxin response factor gene (ETTIN), the gene encoding transcriptional factor of WD40 family (TRANSPARENTTESTAGLABRA1 or TTG1), and the auxin efflux carrier (PIN-FORMED2 or PIN2) gene. More than 220 transgenic lines of the 1st, 2nd and 3rd generations were analyzed for RNAi suppression phenotypes (Filichkin et. al., manuscript submitted). A total of 108 constructs were supplied by ORNL, UF and OSU and used to generate over 1,881 PCR verified transgenic Populus and over 300 PCR verified transgenic Arabidopsis events. The Populus transgenics alone required Agrobacterium co-cultivations of 124.406 explants.

  8. New mathematical methods in human gene mapping

    SciTech Connect (OSTI)

    Terwilliger, J.D.

    1993-01-01

    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.

  9. Evaluation and comparison of gene clustering methods in

    E-Print Network [OSTI]

    Tseng, George C. "Chien-Cheng"

    disjoint clusters; i.e. C={C1 , ... , Ck} and .j k j CX 1== U Cluster genes (n: # of genes; p: # of samples. k has to be correctly estimated. .clusterofcentroids),( )( )( 1 2)( jxmeanx xxkW i Cx j k j Cx j i to the cluster centers. .clusterofmedoids),( )( )( 1 2)( jxmedianx xxkW i Cx j k j Cx j i ji ji = = -= #12

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

    E-Print Network [OSTI]

    Morham, Scott Garton

    1985-01-01

    /function 2. MATERIALS AND METHODS Abbreviations . Media and buffers Assay conditions Bacterial strains and constructions Construction of screening vector Induction of liquid cultures Purification of JglacE fusion protein Isolation of plasmid DNA... Biological characterization of the pSM120 screening vector and the JHlacZ fusion gene Selection and characterization of E mutants M13 subcloning Dideoxy sequencing Isolation of single base changes which inactivate gene E function Suppressor studies...

  11. Emerging Use of Gene Expression Microarrays in Plant Physiology

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

    Wullschleger, Stan D.; Difazio, Stephen P.

    2003-01-01

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

  12. Organization and control of genes encoding catabolic enzymes in Rhizobiaceae

    SciTech Connect (OSTI)

    Parke, D.; Ornston, L.N.

    1993-03-01

    Rhizobiaceae, a diverse bacterial group comprising rhizobia and agrobacteria, symbiotic partnership with plants form nitrogen-fixing nodules on plant roots or are plant pathogens. Phenolic compounds produced by plants serve as inducers of rhizobial nodulation genes and agrobacterial virulence genes reflect their capacity to utilize numerous aromatics, including phenolics, as a source of carbon and energy. In many microbes the aerobic degradation of numerous aromatic compounds to tricarboxylic acid cycle intermediates is achieved by the [beta]-ketoadipate pathway. Our initial studies focused on the organization and regulation of the ketoadipate pathway in Agrobacterium tumefaciens. We have cloned, identified and characterized a novel regulatory gene that modulates expression of an adjacent pca (protocatechuate) structural gene, pcaD. Regulation of pcaD is mediated by the regulatory gene, termed pcaQ, in concert with the intermediate [beta]-carboxy-cis,cis-muconate. [beta]-carboxy-cis,cismuconate is an unstable chemical, not marketed commercially, and it is unlikely to permeate Escherichia coli cells if supplied in media. Because of these factors, characterization of pcaQ in E. coli required an in vivo delivery system for [beta]-carboxycis,cis-muconate. This was accomplished by designing an E. coli strain that expressed an Acinetobacter calcoaceticus pcaA gene for conversion of protocatechuate to [beta]-carboxy-cis,cis-muconate.

  13. GENOME-ENABLED DISCOVERY OF CARBON SEQUESTRATION GENES IN POPLAR

    SciTech Connect (OSTI)

    DAVIS J M

    2007-10-11

    Plants utilize carbon by partitioning the reduced carbon obtained through photosynthesis into different compartments and into different chemistries within a cell and subsequently allocating such carbon to sink tissues throughout the plant. Since the phytohormones auxin and cytokinin are known to influence sink strength in tissues such as roots (Skoog & Miller 1957, Nordstrom et al. 2004), we hypothesized that altering the expression of genes that regulate auxin-mediated (e.g., AUX/IAA or ARF transcription factors) or cytokinin-mediated (e.g., RR transcription factors) control of root growth and development would impact carbon allocation and partitioning belowground (Fig. 1 - Renewal Proposal). Specifically, the ARF, AUX/IAA and RR transcription factor gene families mediate the effects of the growth regulators auxin and cytokinin on cell expansion, cell division and differentiation into root primordia. Invertases (IVR), whose transcript abundance is enhanced by both auxin and cytokinin, are critical components of carbon movement and therefore of carbon allocation. Thus, we initiated comparative genomic studies to identify the AUX/IAA, ARF, RR and IVR gene families in the Populus genome that could impact carbon allocation and partitioning. Bioinformatics searches using Arabidopsis gene sequences as queries identified regions with high degrees of sequence similarities in the Populus genome. These Populus sequences formed the basis of our transgenic experiments. Transgenic modification of gene expression involving members of these gene families was hypothesized to have profound effects on carbon allocation and partitioning.

  14. 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

  15. Directed evolution of specific receptorligand pairs for use in the creation of gene switches

    E-Print Network [OSTI]

    Zhao, Huimin

    Directed evolution of specific receptor­ligand pairs for use in the creation of gene switches in the creation of gene switches for the control of heterologous gene expression in applications such as gene switch-like'' attributes: rapid induction kinetics (6­8), dose-dependent ligand response, and readily

  16. Should genes with missing data be excluded from phylogenetic Wei Jiang a,b,c

    E-Print Network [OSTI]

    Wiens, John J.

    their studies to maximize the number of genes included but minimize the overall amount of missing data. However genes). Detailed analyses suggest that adding incom- plete genes is especially helpful for resolving taxa and genes are deliberately excluded in order to avoid them. For example, the issue of missing data

  17. DNA zip codes control an ancient mechanism for gene targeting to the nuclear periphery

    E-Print Network [OSTI]

    Brickner, Jason

    ARTICLES DNA zip codes control an ancient mechanism for gene targeting to the nuclear periphery are recruited to the nuclear periphery after transcriptional activation. We have identified two gene recruitment sequences (GRS I and II) from the promoter of the INO1 gene that target the gene to the nuclear periphery

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

    SciTech Connect (OSTI)

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

    2011-05-15

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

  19. New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes forMethanosarcinaspecies

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

    Guss, Adam M.; Rother, Michael; Zhang, Jun Kai; Kulkkarni, Gargi; Metcalf, William W.

    2008-01-01

    A highly efficient method for chromosomal integration of cloned DNA intoMethanosarcina spp.was developed utilizing the site-specific recombination system from theStreptomycesphage ?C31. Host strains expressing the ?C31 integrase gene and carrying an appropriate recombination site can be transformed with non-replicating plasmids carrying the complementary recombination site at efficiencies similar to those obtained with self-replicating vectors. We have also constructed a series of hybrid promoters that combine the highly expressedM. barkeriPmcrBpromoter with binding sites for the tetracycline-responsive, bacterial TetR protein. These promoters are tightly regulated by the presence or absence of tetracycline in strains that express thetetRgene. The hybrid promoters can bemore »used in genetic experiments to test gene essentiality by placing a gene of interest under their control. Thus, growth of strains withtetR-regulated essential genes becomes tetracycline-dependent. A series of plasmid vectors that utilize the site-specific recombination system for construction of reporter gene fusions and for tetracycline regulated expression of cloned genes are reported. These vectors were used to test the efficiency of translation at a variety of start codons. Fusions using an ATG start site were the most active, whereas those using GTG and TTG were approximately one half or one fourth as active, respectively. The CTG fusion was 95% less active than the ATG fusion.« less

  20. Progesterone and interferon tau regulated genes in the endometrium of the ovine uterus and expression of interferon stimulated genes in the corpus luteum during early pregnancy in sheep 

    E-Print Network [OSTI]

    Ahn, Hyo Won

    2008-10-10

    During early pregnancy in ruminants, progesterone (P4) from the corpus luteum (CL) and interferon tau (IFNT) from the conceptus act on the endometrium to regulate genes including interferon stimulated genes (ISGs) that are hypothesized...

  1. Table 2 (Supplemental): Complete data for all 100 expression programs discovered by GeneProgram from the Novartis Gene Atlas v2

    E-Print Network [OSTI]

    Gerber, Georg K.

    2007-06-25

    Table 2 (Supplemental): Complete data for all 100 recurrent expression programs (EPs) discovered by GeneProgram. Each EP has two identifying rows, a list of meta-genes, and a list of significantly enriched GO categories. ...

  2. 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.

    1989-04-01

    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 ...

  3. 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

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

    E-Print Network [OSTI]

    McElhany, Katherine

    2012-02-14

    Environmental microbiology has traditionally been performed using culture-based methods. However, in the last few decades, the emergence of molecular methods has changed the field considerably. The latest development in ...

  6. A functional gene array for detection of bacterial virulence elements

    SciTech Connect (OSTI)

    Jaing, C

    2007-11-01

    We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistance gene families in a greatly expanded set of organisms.

  7. The naphthalene catabolic (nag) genes of Polaromonas naphthalenivorans CJ2: Evolutionary implications for two gene clusters and novel regulatory control

    SciTech Connect (OSTI)

    Jeon, C.O.; Park, M.; Ro, H.S.; Park, W.; Madsen, E.L.

    2006-02-15

    Polaromonas naphthalenivorans CJ2, found to be responsible for the degradation of naphthalene in situ at a coal tar waste-contaminated site, is able to grow on mineral salts agar media with naphthalene as the sole carbon source. Beginning from a 484-bp nagAc-like region, we used a genome walking strategy to sequence genes encoding the entire naphthalene degradation pathway and additional flanking regions. We found that the naphthalene catabolic genes in P. naphthalenivorans CJ2 were divided into one large and one small gene cluster, separated by an unknown distance. The large gene cluster is bounded by a LysR-type regulator (nagR). The small cluster is bounded by a MarR-type regulator (nagR2). The catabolic genes of P. naphthalenivorans CJ2 were homologous to many of those of Ralstonia U2, which uses the gentisate pathway to convert naphthalene to central metabolites. However, three open reading frames (nagY, nagM, and nagN), present in Ralstonia U2, were absent. Also, P. naphthalenivorans carries two copies of gentisate dioxygenase (nagI) with 77.4% DNA sequence identity to one another and 82% amino acid identity to their homologue in Ralstonia sp. strain U2. Investigation of the operons using reverse transcription PCR showed that each cluster was controlled independently by its respective promoter. Insertional inactivation and lacZ reporter assays showed that nagR2 is a negative regulator and that expression of the small cluster is not induced by naphthalene, salicylate, or gentisate. Association of two putative Azoarcus-related transposases with the large cluster and one Azoarcus-related putative salicylate 5-hydroxylase gene (ORF2) in the small cluster suggests that mobile genetic elements were likely involved in creating the novel arrangement of catabolic and regulatory genes in P. naphthalenivorans.

  8. Molecular characterization of Theileria spp. using ribosomal RNA 

    E-Print Network [OSTI]

    Bendele, Kylie Gayle

    2005-11-01

    The molecular characterization of twenty six Theileria spp. isolates and one C. felis isolate were done on the small subunit ribosomal RNA (SSU rRNA) gene, the 5.8S gene, and the two internal transcribed spacer regions ...

  9. 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

    2013-03-05

    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.

  10. Detection of gene communities in multiplex networks reveals cancer drivers

    E-Print Network [OSTI]

    Cantini, Laura; Fortunato, Santo; Caselle, Michele

    2015-01-01

    We propose a new multiplex-based strategy to integrate different layers of genomic information and use them in a coordinate way to identify driving cancer genes. The multiplex networks that we consider combine transcription factor co-targeting, microRNA co-targeting, protein-protein interaction and gene co-expression networks. The rationale behind this choice is that gene coexpression and protein-protein interactions require a tight coregulation of the partners and that such a fine tuned regulation can be obtained only combining both the transcriptional and post-transcriptional layers of regulation. . To extract the relevant biological information from the multiplex we studied its partition into communities. To this end we applied a consensus clustering algorithm to the single-layer partitions obtained using state of art community detection methods, combined with a filtering preprocessing of the individual networks. Even if our procedure is valid in principle for any pathology in this work we concentrate in p...

  11. Bioluminescent reporters for catabolic gene expression and pollutant bioavailability

    SciTech Connect (OSTI)

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

    1991-01-01

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

  12. Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

    SciTech Connect (OSTI)

    Makarova, Kira S.; Omelchenko, Marina V.; Gaidamakova, Elena K.; Matrosova, Vera Y.; Vasilenko, Alexander; Zhai, Min; Lapidus, Alla; Copeland, Alex; Kim, Edwin; Land, Miriam; Mavrommatis, Konstantinos; Pitluck, Samuel; Richardson, Paul M.; Detter, Chris; Brettin, Thomas; Saunders, Elizabeth; Lai, Barry; Ravel, Bruce; Kemner, Kenneth M.; Wolf, Yuri I.; Sorokin, Alexander; Gerasimova, Anna V.; Gelfand, Mikhail S.; Fredrickson, James K.; Koonin, Eugene V.; Daly, Michael J.

    2007-07-24

    Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at itsoptimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.

  13. Molecular mechanisms of extensive mitochondrial gene rearrangementin plethodontid salamanders

    SciTech Connect (OSTI)

    Mueller, Rachel Lockridge; Boore, Jeffrey L.

    2005-06-01

    Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light strand replication and the nearby tRNA genes or the regions flanking the origin of heavy strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and non-tandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mtDNAs, up to 25 percent of the total length is composed of tandem duplications of non-coding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intra-molecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.

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

    SciTech Connect (OSTI)

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

    2013-10-01

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

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

    E-Print Network [OSTI]

    Filipe Tostevin; Wiet de Ronde; Pieter Rein ten Wolde

    2012-02-07

    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.

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

    DOE Patents [OSTI]

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

    2011-09-13

    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.

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

    DOE Patents [OSTI]

    Woychik, Richard P. (Knoxville, TN)

    1998-01-01

    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.

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

    DOE Patents [OSTI]

    Woychik, Richard P. (Knoxville, TN)

    2000-06-27

    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.

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

    E-Print Network [OSTI]

    Terrill, Cooper

    2012-02-14

    expression for primer CCL-8. ......................... 48 10 Amplification plot of gene expression for primer CCR-9 .......................... 49 11 Amplification plot of gene expression for primer TNFSF13 ...................... 50 12 Amplification plot... of gene expression for primer IFIT-5 ........................... 51 13 Amplification plot of gene expression for primer IL-1RN ......................... 52 14 Amplification plot of gene expression for primer IL-2RA. ........................ 53 xi...

  20. Lifestyle Evolution in Cyanobacterial Symbionts of Sponges

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

    Burgsdorf, Ilia; Slaby, Beate M.; Handley, Kim M.; Haber, Markus; Blom, Jochen; Marshall, Christopher W.; Gilbert, Jack A.; Hentschel, Ute; Steindler, Laura

    2015-06-02

    The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The first draft genome of a “Ca. Synechococcus spongiarum” group member was recently published, providing evidence of genome reduction by loss of genes involved in several nonessential functions. However, “Ca. Synechococcus spongiarum” includes a variety of clades that may differ widely in genomic repertoire and consequently in physiology and symbiotic function. Here, we present three additional draft genomes of “Ca. Synechococcus spongiarum,” each from a different clade. By comparing all fourmore »symbiont genomes to those of free-living cyanobacteria, we revealed general adaptations to life inside sponges and specific adaptations of each phylotype. Symbiont genomes shared about half of their total number of coding genes. Common traits of “Ca. Synechococcus spongiarum” members were a high abundance of DNA modification and recombination genes and a reduction in genes involved in inorganic ion transport and metabolism, cell wall biogenesis, and signal transduction mechanisms. Moreover, these symbionts were characterized by a reduced number of antioxidant enzymes and low-weight peptides of photosystem II compared to their free-living relatives. Variability within the “Ca. Synechococcus spongiarum” group was mostly related to immune system features, potential for siderophore-mediated iron transport, and dependency on methionine from external sources. The common absence of genes involved in synthesis of residues, typical of the O antigen of free-living Synechococcus species, suggests a novel mechanism utilized by these symbionts to avoid sponge predation and phage attack.« less

  1. GenEd Subject Area St. Pete GE

    E-Print Network [OSTI]

    Meyers, Steven D.

    Fundamentals of Physics PHY 2020 Conceptual Physics CANP SMNS Natural Sciences PHY X048 General Physics with Calculus PHY 2048 General Physics I - Calculus Based CANP Natural Sciences PHY X053 General Physics I PHY 2053 General Physics I CANP SPNS SMNS 3/20/2015 2015-2016 8.005 Regulation GenEd Core USF Institution

  2. 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

  3. 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

  4. HYBRID PETRI NET REPRESENTATION OF GENE REGULATORY NETWORK

    E-Print Network [OSTI]

    Breitling, Rainer

    HYBRID PETRI NET REPRESENTATION OF GENE REGULATORY NETWORK HIROSHI MATSUNO, ATSUSHI DOI Faculty regulatory networks. The HPN is an extension of Petri nets which have been used to represent many kinds networks which realizes the intuitions of biologists while keeping the universality in its com- putational

  5. Energy Costs Constrain the Evolution of Gene Expression

    E-Print Network [OSTI]

    Wagner, Andreas

    Energy Costs Constrain the Evolution of Gene Expression ANDREAS WAGNERĂ Department of Biochemistry.) 308B:322­ 324, 2007. r 2007 Wiley-Liss, Inc. How to cite this article: Wagner A. 2007. Energy costs of nucleotides and amino acids, as well as their polymerization into RNA and proteins cost energy. Changes

  6. TECHNICAL ADVANCES Semi-quantitative differences in gene transcription

    E-Print Network [OSTI]

    Bernatchez, Louis

    of data also demonstrates sexual dimorphism in somatic tissues from nematodes, insects, fish, birds and females from a population showing no apparent sexual dimorphism. The results confirm that the method can sexual dimorphic species. Keywords: cDNA polymorphism, expression differences, gene expression, sex

  7. Measuring Power Consumption on IBM Blue Gene/Q

    E-Print Network [OSTI]

    Lan, Zhiling

    their usefulness and how well they match up against the environmental data. I. INTRODUCTION As the field, soft- ware will also have a big role to play namely in ensuring power is not wasted by dynamically on the Blue Gene/Q (BGQ): one is an environmental database and the other is profiling code built on vendor

  8. Characterization of candidate genes in English cocker spaniel hereditary nephritis 

    E-Print Network [OSTI]

    Camacho, Zenaido

    2005-02-17

    are expressed in the canine GBM. Many inherited diseases of the kidney have been reported and mutations in genes regulating kidney function have been identified. Alport syndrome (AS) is the most common form of human hereditary nephritis (HN). AS is defined...

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

    E-Print Network [OSTI]

    Chauve, Cedric

    Montrâ??eal Comparative Genomics, RECOMB 2005 International Workshop, RCG 2005, volume 3678 of Lecture reconstruction based on gene order for whole genomes. We define three genomic distances between whole genomes reconstruction methods to compute a phy­ logeny for a group of 12 complete genomes of #­Proteobacteria. Keywords

  10. 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

  11. Coral Thermal Tolerance: Tuning Gene Expression to Resist Thermal Stress

    E-Print Network [OSTI]

    Coral Thermal Tolerance: Tuning Gene Expression to Resist Thermal Stress Anthony J. Bellantuono1 thermal tolerance in the scleractinian coral Acropora millepora, corals preconditioned to a sub under which non-preconditioned corals bleached and preconditioned corals (thermal-tolerant) maintained

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

    E-Print Network [OSTI]

    Babu, M. Madan

    . In particular, we reveal that the target genes (TGs) of transcription factors (TFs) for the yeast, Saccharo show that (i) the TGs of a majority of TFs show a strong preference to be encoded on specific chromosomes, (ii) the TGs of a significant number of TFs display a strong preference (or avoidance

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

    E-Print Network [OSTI]

    Hu, Wei-Li

    1999-01-01

    in sequence and requires some of the earlier genes expressed for anterior-posterior and dorsal-ventral axes development. Development in the P- D axis can be divided into two phases: initiation of the axis in imaginal discs in the larva, and growth...

  14. Graduate Studies in the Gene and Linda Voiland

    E-Print Network [OSTI]

    Collins, Gary S.

    Graduate Studies in the Gene and Linda Voiland School of Chemical Engineering and Bioengineering www.wsu.edu School Faculty Nehal Abu-Lail, Associate Professor, 2003 Ph.D. Chemical Engineering of Copenhagen. Haluk Beyenal, Associate Professor, 1997 Ph.D. Chemical Engineering, Hacettepe University.. Wenji

  15. Stochastic Models of Gene Expression Bachelor of Engineering

    E-Print Network [OSTI]

    Dix, Daniel B.

    of the state of a chemical system. The Master equation is built on a Markov model foundation. We deriveStochastic Models of Gene Expression by Lanjia Lin Bachelor of Engineering Wuhan University, 2003 gratitude to my advisor, Dr. Daniel Dix, for his invaluable guidance and constant patience. Second, I wish

  16. Comparisons of Statistical Modeling for Constructing Gene Regulatory

    E-Print Network [OSTI]

    Murphy, Kevin Patrick

    Comparisons of Statistical Modeling for Constructing Gene Regulatory Networks by Xiaohui Chen B. In this thesis, we compare a variety of existing regression models and apply them to construct regulatory network construction algorithm. Finally, we apply our models on a p53-related data set, NCI-60 data

  17. Retinoblastoma-like RRB gene of arabidopsis thaliana

    DOE Patents [OSTI]

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

    2004-02-24

    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.

  18. Increased anxiety in mice lacking vitamin D receptor gene

    E-Print Network [OSTI]

    Kalueff, Allan V.

    ,University of Tampere; 3 Department of Clinical Chemistry,University of Tampere Hospital, FIN-33014 Tampere, Finland CA Subjects were 30 adult male mice (age 24­30 weeks) bred in the University of Tampere (Finland). VDR gene mutant mice were bred in the University of Tampere from the line initially generated in the University

  19. Doug Brutlag 2015 Your Genes and Your Health

    E-Print Network [OSTI]

    Brutlag, Doug

    © Doug Brutlag 2015 Your Genes and Your Health http://bio84.stanford.edu/ The Human Genome Project;© Doug Brutlag 2015 The Human Genome Project: Should we do it? · Service, R. F. (2001). The human genome Human Genome Project Strategy http://www.nhgri.nih.gov/ Courtesy Eric Green #12;© Doug Brutlag 2015

  20. 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

  1. Support Vector Machine Classification of Microarray Gene Expression Data

    E-Print Network [OSTI]

    Noble, William Stafford

    using expression data. In addition, SVM performance is compared to four standard machine learningSupport Vector Machine Classification of Microarray Gene Expression Data UCSC-CRL-99-09 Michael P 95065 mpbrown,bgrundy,dave,haussler @cse.ucsc.edu ß Center for Molecular Biology of RNA Department

  2. Modeling and control of gene regulatory Madalena Chaves

    E-Print Network [OSTI]

    Sontag, Eduardo

    network Model: concentrations of mRNA and proteins, for a group of 5 genes responsible for generating.5 1, if hhc0.5 { CIR EN hh hh hhc CIR CIRc EN ENc Dynamics: synchronous or asynchronous algorithms 2005 #12;18 Boolean models: updates and dynamics t Synchronous T k All variables simultaneously updated

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

    E-Print Network [OSTI]

    Mella Herrera, Rodrigo Andres

    2010-10-12

    , 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...

  4. ORIGINAL ARTICLE Regulation of nif gene expression and the

    E-Print Network [OSTI]

    Nitrogen fixation, a prokaryotic, O2-inhibited process that reduces N2 gas to biomass, is of paramount importance in biogeochemical cycling of nitrogen. We analyzed the levels of nif transcripts of Synechococcus: Synechococcus; microsensor; gene expression; nitrogen fixation; Yellowstone National Park; in situ Introduction

  5. Extracting yeast stress genes by dependencies between stress treatments

    E-Print Network [OSTI]

    Kaski, Samuel

    Extracting yeast stress genes by dependencies between stress treatments Arto Klamia,b , Janne, Finland c Medicel Oy, Helsinki, Finland 17 data sets from different stress treatments, obtained from two different sources (Gasch et al. 2000, Causton et al. 2001) Heat (3), acid, alkali, peroxide, Na

  6. Gene Fusion Technology NEW METHODS FOR ENHANCING FUNCTIONAL PROTEIN

    E-Print Network [OSTI]

    Lebendiker, Mario

    SUMOpro-3® Gene Fusion Technology NEW METHODS FOR ENHANCING FUNCTIONAL PROTEIN EXPRESSION packed globular fold with -sheets wrapped around an -helix. SUMO3 Fusions Human SUMO3 fused (ubiquitin or SUMO) at the N-terminus of a partner protein increases the recombinant fusion protein yield

  7. Gene Fusion Technology NEW METHODS FOR ENHANCING FUNCTIONAL PROTEIN

    E-Print Network [OSTI]

    Lebendiker, Mario

    SUMOpro® Gene Fusion Technology NEW METHODS FOR ENHANCING FUNCTIONAL PROTEIN EXPRESSION packed globular fold with -sheets wrapped around an -helix. Smt3 Fusions Yeast SUMO (Smt3) fused (ubiquitin or SUMO) at the N-terminus of a partner protein increases the recombinant fusion protein yield

  8. 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

    2013-06-17

    — 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.

  9. Sorghum gene expression modulated by water deficit and cold stress 

    E-Print Network [OSTI]

    Lim, Sanghyun

    2007-04-25

    Global gene expression in Sorghum bicolor, an important crop showing drought tolerance in arid and semi-arid cultivated areas, was monitored to exposure of 8-days seedlings to water deficit (20% polyethylene glycol) or cold stress (4 Ă?ÂşC). A...

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

    E-Print Network [OSTI]

    Hemminki, Akseli

    REVIEW Transcriptional Targeting for Ovarian Cancer Gene Therapy E. Casado,*, D. M. Nettelbeck Paz, Madrid, Spain Received November 10, 2000 Ovarian carcinoma is a leading cause of cancer death patients diagnosed with ovarian cancer are still low. Therefore, novel molecular therapeutic strat- egies

  11. Characterization of a Gene Abundantly Expressed in Stallion Testis 

    E-Print Network [OSTI]

    Shields, Jordan Elizabeth

    2012-02-14

    .................................................................................... 12 3.3 Sequencing ........................................................................................... 12 3.4 Primer Design ....................................................................................... 13 3.5 RLM... Page Table 1 Complete list of primers used for sequencing CH241-11J8 ............. 14 1 1. INTRODUCTION The NMES1 gene was first identified in humans and is predicted to encode a relatively small protein (83 amino acids)of unknown function...

  12. 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

  13. 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

  14. Algorithmic Methods for the Analysis of Gene Expression Data

    E-Print Network [OSTI]

    Obradovic, Zoran

    are a very valuable tool for biomedical science. First, a brief overview of the microarray technology is present in DNA, while uracil replaces it in RNA. Genes are fundamental blocks of DNA that encode genetic are then translated into proteins, Handbook of Applied Algorithms: Solving Scientific, Engineering and Practical

  15. 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)

    2009-04-28

    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.

  16. 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

  17. Characterizing the function of T-box target genes in mesoderm development

    E-Print Network [OSTI]

    Maxwell, Adrienne Alecia

    2012-01-01

    shifted into the anterior PSM. Based on the above results,by cells in the intermediate PSM in all embryos except spt;genes ntl and wnt8a, for the induction of anterior PSM gene

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

    E-Print Network [OSTI]

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

    2011-01-01

    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 ...

  19. Disruption of DNA methylation induces genome-specific changes in gene expression in Arabidopsis allotetraploids 

    E-Print Network [OSTI]

    Chen, Meng

    2007-04-25

    Allopolyploids are formed by the combination of evolutionarily-diverged genomes, the union of which leads to dynamic changes in gene expression and genome organization. Expression patterns of orthologous genes are rapidly and stochastically...

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

    E-Print Network [OSTI]

    Gray, Catherine Allison

    2005-08-29

    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...

  1. Molecular and cytological analysis of a novel leaf rust resistance gene in wheat 

    E-Print Network [OSTI]

    Franks, Cleve Douglas

    2002-01-01

    A novel wheat leaf rust resistance gene from Aegilops cylindricum accession TTCC295 was investigated, using both cytogenetic and molecular tools. Previous work had introgressed this gene into adapted wheat germplasm, which was crossed to 'Chinese...

  2. Virus vector gene inserts are stabilized in the presence of satellite panicum mosaic virus coat protein 

    E-Print Network [OSTI]

    Everett, Anthany Laurence

    2009-05-15

    The coat protein of satellite panicum mosaic virus (SPMV) was used to stabilize viral vector gene inserts in planta. A Potato virus X (PVX) vector carrying the SPMV capsid protein (CP) gene was successfully stabilized through three serial passages...

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

    E-Print Network [OSTI]

    Curry, Edward William James

    2011-06-27

    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) ...

  4. TOM: a web-based integrated approach for identification of candidate disease genes

    E-Print Network [OSTI]

    Nardini, Christine

    TOM: a web-based integrated approach for identification of candidate disease genes Simona Rossi on this principle, we present here TOM, a web-based resource for the efficient extraction of candidate genes

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

    E-Print Network [OSTI]

    Anthes, Emily Kennedy

    2006-01-01

    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 ...

  6. An algorithm for identifying clusters of functionally related genes in genomes 

    E-Print Network [OSTI]

    Yi, Gang Man

    2009-05-15

    An increasing body of literature shows that genomes of eukaryotes can contain clusters of functionally related genes. Most approaches to identify gene clusters utilize microarray data or metabolic pathway databases to find ...

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

    E-Print Network [OSTI]

    Maizels, Rick; Blaxter, Mark; Scott, Alan

    2001-01-01

    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 ...

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

    E-Print Network [OSTI]

    Kalezi, Artemis

    2007-01-01

    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 ...

  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)

    2011-06-07

    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.

  10. Cycloheximide inhibition of delayed early gene expression in baculovirus-infected cells 

    E-Print Network [OSTI]

    Ross, Larry Dale

    1998-01-01

    The baculovirus protein IE I is required for the transactivation of many early viral genes in transient expression assays. However, cycloheximide inhibition studies have failed to reveal a dependence of early gene transcription on expression of IE I...

  11. Gene knockouts reveal separate functions for two cytoplasmic dyneins in Tetrahymena thermophila

    E-Print Network [OSTI]

    Lee, Seungwon; Wisniewski, J. C.; Dentler, William L., Jr; Asai, D. J.

    1999-03-01

    presents the opportunity to determine the contributions of individual dynein isoforms in a single cell that expresses multiple dynein heavy chain genes. Substantial portions of two Tetrahymena cytoplasmic dynein heavy chain genes were cloned...

  12. Identification of new genes and pathways that act to delay C. elegans aging

    E-Print Network [OSTI]

    Berdichevsky, Alina

    2008-01-01

    Aging of an organism is determined by both stochastic and genetic components. The importance of genes is illustrated by the discovery of single gene mutations that alter lifespans of species ranging from invertebrates C. ...

  13. The investigation of controlled release microchips, nanoparticles, and sirna for gene therapy in tissue engineering applications 

    E-Print Network [OSTI]

    Chern, Christina

    2009-05-15

    The study of drug delivery for the treatment of illnesses and injuries is an important area of pharmaceutical technology. A relatively new area of drug delivery being explored is gene therapy, which utilizes the idea that genes can be used...

  14. Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae)

    E-Print Network [OSTI]

    Kwak, Myounghai; Gepts, Paul

    2009-01-01

    AFLP analysis of gene pools of a wild bean core collection.in the two major gene pools of common bean (Phaseolusand Mesoamerican gene pools. Using a model-based approach,

  15. 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) displays terms indexed under the selected field (C). Highlighting a term (D) automatically enters

  16. Emerging technologies / Technologies naissantes The role of viroids in gene silencing: the model

    E-Print Network [OSTI]

    Perreault, Jean-Pierre

    -mediated transcriptional gene silenc- ing (TGS) and PTGS. RNA-mediated TGS occurs when double-stranded RNA (ds

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

    DOE Patents [OSTI]

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

    2006-07-04

    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.

  18. 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

    2007-12-10

    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.

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

    SciTech Connect (OSTI)

    Huang, Shi; Fulbright, Scott P; Zeng, Xiaowei; Yates, Tracy; Wardle, Greg; Chisholm, Stephen T; Xu, Jian; Lammers, Peter

    2011-03-16

    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.

  20. 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

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

    DOE Patents [OSTI]

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

    1999-07-27

    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.

  2. Axons Mediate the Distribution of Arylsulfatase A within the Mouse Hippocampus upon Gene Delivery

    E-Print Network [OSTI]

    Bongarzone, Ernesto R.

    Naldini,1,2 and Ernesto R. Bongarzone1,y 1 Telethon Institute for Gene Therapy, San Raffaele Scientific-time observation and tracking of axon­dendritic transport of the enzyme after lentiviral gene therapy. Tagged ARSA brain after direct gene therapy, demonstrating the use of neural processes for enzyme transport. Key

  3. 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

  4. Retargeting of pre-set regions on chromosome for high gene expression in mammalian cells

    E-Print Network [OSTI]

    Jiao, Peng

    We have developed a system to hunt and reuse special gene integration sites that allow for high and stable gene expression. A vector, named pRGFP8, was constructed. The plasmid pRGFP8 contains a reporter gene, gfp2 and two ...

  5. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation

    E-Print Network [OSTI]

    Cai, Long

    Gene identification signature (GIS) analysis for transcriptome characterization and genome a DNA tag sequencing and mapping strategy called gene identification signature (GIS) analysis, in which of every gene. GIS analysis is potentially 30-fold more efficient than standard cDNA sequencing approaches

  6. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

    SciTech Connect (OSTI)

    Elias, Dwayne A.; Mukhopadhyay, Aindrila; Joachimiak, Marcin P.; Drury, Elliott C.; Redding, Alyssa M.; Yen, Huei-Che B.; Fields, Matthew W.; Hazen, Terry C.; Arkin, Adam P.; Keasling, Jay D.; Wall, Judy D.

    2008-10-27

    Hypothetical and conserved hypothetical genes account for>30percent of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved hypothetical (9.5percent) along with 887 hypothetical genes (24.4percent). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 hypothetical and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC-MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. 1212 of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes. Except for the latter, monocistronic gene annotation was expanded using the above criteria along with matching Clusters of Orthologous Groups. Polycistronic genes were annotated in the same manner with inferences from their proximity to more confidently annotated genes. Two targeted deletion mutants were used as test cases to determine the relevance of the inferred functional annotations.

  7. GENOME-WIDE COMPUTATIONAL ANALYSIS OF SMALL NUCLEAR RNA GENES OF ORYZA SATIVA (INDICA AND JAPONICA)

    E-Print Network [OSTI]

    Wong, Limsoon

    GENOME-WIDE COMPUTATIONAL ANALYSIS OF SMALL NUCLEAR RNA GENES OF ORYZA SATIVA (INDICA AND JAPONICA analysis for small nuclear RNA (snRNA) genes resulted in identification of 76 and 73 putative snRNA genes from the primary transcripts (pre-mRNA) by the process of splicing.1 Splicing of nuclear pre

  8. Distinguishing protein-coding and noncoding genes in the human genome

    E-Print Network [OSTI]

    Kellis, Manolis

    ) Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding genesDistinguishing protein-coding and noncoding genes in the human genome Michele Clamp* , Ben Fry An accurate catalog of the protein-coding genes encoded in the human genome is fundamental to the study

  9. Supplementary Information: A Simple and Ecient Algorithm for Gene Selection using Sparse Logistic Regression

    E-Print Network [OSTI]

    Keerthi, S. Sathiya

    . The pseudocode for the proposed gene selection algorithm is also given. Di#11;erent variables and equations for the discovery genes overexpressed in ovarian carcinomas. Gene, 238, 375{385. Pseudocode for the Algorithm Notes for the pseudocode given below: 1. The index i runs over the number of examples while the index j runs over

  10. 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

  11. Potential for hydrogen production with inducible chloroplast gene expression in Chlamydomonas

    E-Print Network [OSTI]

    Halazonetis, Thanos

    Potential for hydrogen production with inducible chloroplast gene expression in Chlamydomonas for hydrogen production. Upon addition of copper to cells pregrown in copper-deficient medium, PSII levels- gen production. Moreover, this inducible gene expression system is applicable to any chloroplast gene

  12. COMPARATIVE ANALYSIS OF GENE PREDICTION METHODS AND DEVELOPMENT OF A FUNGAL GENOME DATABASE SYSTEM

    E-Print Network [OSTI]

    Moriyama, Etsuko

    COMPARATIVE ANALYSIS OF GENE PREDICTION METHODS AND DEVELOPMENT OF A FUNGAL GENOME DATABASE SYSTEM;COMPARATIVE ANALYSIS OF GENE PREDICTION METHODS AND DEVELOPMENT OF A FUNGAL GENOME DATABASE SYSTEM Skanth genome projects have been planned and some new draft genomes have been recently completed. Multiple gene

  13. On the Approximability of the Exemplar Adjacency Number Problem for Genomes with Gene Repetitions

    E-Print Network [OSTI]

    Zhu, Binhai

    On the Approximability of the Exemplar Adjacency Number Problem for Genomes with Gene Repetitions the similarity between two genomes (or in general, be- tween any two sequences drawn from the same alphabet). For two genomes G and H drawn from the same set of n gene families and containing gene repeti- tions, we

  14. Evolution of gene expression and expression plasticity in long-term experimental populations of Drosophila

    E-Print Network [OSTI]

    Fry, James D.

    Evolution of gene expression and expression plasticity in long-term experimental populations to a particular type of stress involves changes in the within- generation (`plastic') responses of gene expression to the stress. We used microarrays to quantify gene expression plasticity in response to ethanol in laboratory

  15. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

    SciTech Connect (OSTI)

    Goldfarb, K.C.; Karaoz, U.; Hanson, C.A.; Santee, C.A.; Bradford, M.A.; Treseder, K.K.; Wallenstein, M.D.; Brodie, E.L.

    2011-04-18

    Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.

  16. Microtargeted gene silencing and ectopic expression in live embryos using biolistic delivery with a pneumatic capillary gun

    E-Print Network [OSTI]

    Shefi, Orit; Simonnet, Claire; Baker, Michael W; Glass, James R; Macagno, Eduardo R; Groisman, Alex

    2006-01-01

    a Pneumatic Capillary Gun Orit Shefi, 1 Claire Simonnet, 2medicinalis; netrin; gene gun Introduction Modulating geneby the current design of “gene guns” used for particle

  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)

    2009-02-17

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

  18. Stochastic models and numerical algorithms for a class of regulatory gene networks

    E-Print Network [OSTI]

    Thomas Fournier; Jean-Pierre Gabriel; Christian Mazza; Jerome Pasquier; Jose Galbete; Nicolas Mermod

    2008-10-01

    Regulatory gene networks contain generic modules like those involving feedback loops, which are essential for the regulation of many biological functions. We consider a class of self-regulated genes which are the building blocks of many regulatory gene networks, and study the steady state distributions of the associated Gillespie algorithm by providing efficient numerical algorithms. We also study a regulatory gene network of interest in synthetic biology and in gene therapy, using mean-field models with time delays. Convergence of the related time-nonhomogeneous Markov chain is established for a class of linear catalytic networks with feedback loops

  19. Plant isoflavone and isoflavanone O-methyltransferase genes

    SciTech Connect (OSTI)

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

    2014-08-19

    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.

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

    DOE Patents [OSTI]

    Shizuya, Hiroaki

    2006-01-31

    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

    2014-12-16

    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. Multiclass cancer diagnosis using tumor gene expression signatures

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

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

    2001-12-11

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

  3. Compositions and methods for detecting gene rearrangements and translocations

    DOE Patents [OSTI]

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

    2000-01-01

    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.

  4. 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.

    2010-08-14

    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.

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

    DOE Patents [OSTI]

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

    2014-09-16

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

  6. Asymptotic and numerical methods for metastable events in stochastic gene networks

    E-Print Network [OSTI]

    Jay Newby

    2014-12-29

    A general class of stochastic gene expression models with self regulation is considered. One or more genes randomly switch between regulatory states, each having a different mRNA transcription rate. The gene or genes are self regulating when the proteins they produce affect the rate of switching between regulatory states. Under weak noise conditions, the deterministic forces are much stronger than fluctuations from gene switching and protein synthesis. Metastable transitions, such as bistable switching, can occur under weak noise conditions, causing dramatic shifts in the expression of a gene. A general tool used to describe metastability is the quasi stationary analysis (QSA). A large deviation principle is derived so that the QSA can explicitly account for random gene switching without using an adiabatic limit or diffusion approximation, which are unreliable and inaccurate for metastable events.This allows the existing asymptotic and numerical methods that have been developed for continuous Markov processes to be used to analyze the full model.

  7. Chromosome mapping of five human cardiac and skeletal muscle sarcoplasmic reticulum protein genes

    SciTech Connect (OSTI)

    Otsu, K.; Fujii, J.; MacLennan, D.H. (Charles H. Best Institute, Univ. of Toronto, Ontario (Canada)); Periasamy, M. (Univ. of Cincinnati College of Medicine, OH (United States)); Difilippantonio, M.; Uppender, M.; Ward, D.C. (Yale Univ. School of Medicine, New Haven, CT (United States))

    1993-08-01

    Fluorescence in situ hybridization (FISH) experiments were performed using genomic and complementary DNA probes in order to determine the location on human chromosomes for five genes expressed in cardiac and skeletal muscle sarcoplasmic reticulum. The chromosome location of each gene was determined in terms of both cytogenetic bands and fractional chromosome length. The ATP2A2 gene, expressing the SERCA2 isoform of the Ca[sup 2+] pump, maps to bands 12q23-q24.1, the phospholamban gene (PLN) to 6q22.1, the human skeletal muscle calsequestrin gene (CASQ1) to band 1q21, the cardiac calsequestrin gene (CASQ2) to bands 1p11-p13.3, and the cardiac calcium release channel gene (RYR2) to the interval between band 1q42.1 (distal) and band 1q43 (proximal). 13 refs., 1 fig.

  8. 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)

    1995-04-01

    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.

  9. Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site

    SciTech Connect (OSTI)

    Lin, Xueju; Kennedy, David W.; Fredrickson, Jim K.; Bjornstad, Bruce N.; Konopka, Allan

    2011-11-29

    Microbial diversity in subsurface sediments at the Hanford Site 300 Area near Richland, Washington State (USA) was investigated by analyzing samples recovered from depths of 9 to 52 m. Approximately 8000 near full-length 16S rRNA gene sequences were analyzed across geological strata that include a natural redox transition zone. These strata included the oxic coarse-grained Hanford formation, fine-grained oxic and anoxic Ringold Formation sediments, and the weathered basalt group. We detected 1233 and 120 unique bacterial and archaeal OTUs (Operational Taxonomic Units at the 97% identity level), respectively. Microbial community structure and richness varied substantially across the different geological strata. Bacterial OTU richness (Chao1 estimator) was highest (>700) in the upper Hanford formation, and declined to about 120 at the bottom of the Hanford formation. Just above the Ringold oxic-anoxic interface, richness was about 325 and declined to less than 50 in the deeper reduced zones. The deeper Ringold strata were characterized by a preponderance (ca. 90%) of Proteobacteria. The Bacterial community in the oxic sediments contained not only members of 9 well-recognized phyla but also an unusually high proportion of 3 candidate divisions (GAL15, NC10, and SPAM). Additionally, novel phylogenetic orders were identified within the Delta-proteobacteria, a clade rich in microbes that carry out redox transformations of metals that are important contaminants on the Hanford Site.

  10. Changes in the composition of the human fecal microbiome following bacteriotherapy for recurrent Clostridium difficile-associated diarrhea

    SciTech Connect (OSTI)

    Khoruts, A.; Dicksved, J.; Jansson, J.K.; Sadowsky, M.J.

    2009-08-15

    CDAD is the major known cause of antibiotic-induced diarrhea and colitis, and the disease is thought to result from persistent disruption of commensal gut microbiota. Bacteriotherapy by way of fecal transplantation can be used to treat recurrent CDAD and is thought to re-establish the normal colonic microflora. However, limitations of conventional microbiologic techniques have until recently precluded testing of this idea. In this study we used T-RFLP and 16S rRNA gene sequencing approaches to characterize the bacterial composition of the colonic microflora in a patient suffering from recurrent CDAD, before and after treatment by fecal transplantation from a healthy donor. While the patient's residual colonic microbiota, prior to therapy, was deficient in members of the bacterial divisions-Firmicutes and Bacteriodetes, transplantation had a dramatic impact on the composition of the patient's gut microbiota. By 14 days post transplantation, the fecal bacterial composition of the recipient was highly similar to the donor and was dominated by Bacteroides spp. strains and an uncharacterized butyrate producing bacterium. The change in bacterial composition was accompanied by resolution of the patient's symptoms. The striking similarity of the recipient's and donor's intestinal microbiota following bacteriotherapy suggests that the donor's bacteria quickly occupied their requisite niches, resulting in restoration of both the structure and function of the microbial communities present.

  11. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

    SciTech Connect (OSTI)

    Hodkinson, Brendan P; Gottel, Neil R; Schadt, Christopher Warren; Lutzoni, Francois

    2011-01-01

    Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e. green algal vs. cyanobacterial), mycobiont-types and large-scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant and taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large-scale geography, photobiont-type and mycobiont-type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.

  12. 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.

    2013-11-19

    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.

  13. Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093T)

    SciTech Connect (OSTI)

    Kappler, Ulrike; Davenport, Karen W.; Beatson, Scott; Lucas, Susan; Lapidus, Alla L.; Copeland, A; Berry, Kerrie W.; Glavina Del Rio, Tijana; Hammon, Nancy; Dalin, Eileen; Tice, Hope; Pitluck, Sam; Richardson, P M; Bruce, David; Goodwin, Lynne A.; Han, Cliff; Tapia, Roxanne; Detter, J. Chris; Chang, Yun-Juan; Jeffries, Cynthia; Land, Miriam L; Hauser, Loren John; Kyrpides, Nikos C; Goker, Markus; Ivanova, N; Klenk, Hans-Peter; Woyke, Tanja

    2012-01-01

    Starkeya novella (Starkey 1934) Kelly et al. 2000 is a member of the family Xanthobacteraceae in the order Rhizobiales , which is thus far poorly characterized at the genome level. Cultures from this spe- cies are most interesting due to their facultatively chemolithoautotrophic lifestyle, which allows them to both consume carbon dioxide and to produce it. This feature makes S. novella an interesting model or- ganism for studying the genomic basis of regulatory networks required for the switch between con- sumption and production of carbon dioxide, a key component of the global carbon cycle. In addition, S. novella is of interest for its ability to grow on various inorganic sulfur compounds and several C1- compounds such as methanol. Besides Azorhizobium caulinodans, S. novella is only the second spe- cies in the family Xanthobacteraceae with a completely sequenced genome of a type strain. The cur- rent taxonomic classification of this group is in significant conflict with the 16S rRNA data. The ge- nomic data indicate that the physiological capabilities of the organism might have been underestimat- ed. The 4,765,023 bp long chromosome with its 4,511 protein-coding and 52 RNA genes was se- quenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.

  14. 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.

    2010-05-17

    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.

  15. 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.

    2013-12-01

    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.

  16. 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

    2010-01-01

    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).

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

    SciTech Connect (OSTI)

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

    2013-07-31

    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.

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

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

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

    2013-07-31

    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

  19. Associations between bacterial communities of house dust and infant gut

    SciTech Connect (OSTI)

    Konya, T.; Koster, B.; Maughan, H.; Escobar, M.; Azad, M.B.; Guttman, D.S.; Sears, M.R.; Becker, A.B.; Brook, J.R.; Takaro, T.K.; Kozyrskyj, A.L.; Scott, J.A.

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  20. Intrinsically Multivariate Predictive Genes David C. Martins-Jr, Ulisses Braga-Neto, Ronaldo F. Hashimoto, Michael L. Bittner and

    E-Print Network [OSTI]

    Braga-Neto, Ulisses

    Intrinsically Multivariate Predictive Genes David C. Martins-Jr, Ulisses Braga-Neto, Ronaldo F multivariate predictive (IMP) genes for binary gene expression, and present a mathematical study of IMP;INTRINSICALLY MULTIVARIATE PREDICTIVE GENES 1 Index Terms Intrinsically Multivariate Prediction, Biological

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

    E-Print Network [OSTI]

    Gent, Universiteit

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

  2. Selection on the Structural Stability of a Ribosomal RNA Expansion Segment in Daphnia obtusa

    E-Print Network [OSTI]

    Obbard, Darren

    , Canada The high rate of sequence divergence in nuclear ribosomal RNA (rRNA) expansion segments offersSelection on the Structural Stability of a Ribosomal RNA Expansion Segment in Daphnia obtusa Seanna polymerase chain reaction amplified and cloned a 589-nt fragment of the 18S rRNA gene containing expansion

  3. Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes

    SciTech Connect (OSTI)

    Wang, Xuting; Tomso, Daniel J.; Liu Xuemei; Bell, Douglas A. . E-mail: BELL1@niehs.nih.gov

    2005-09-01

    Single nucleotide polymorphisms (SNPs) in the human genome are DNA sequence variations that can alter an individual's response to environmental exposure. SNPs in gene coding regions can lead to changes in the biological properties of the encoded protein. In contrast, SNPs in non-coding gene regulatory regions may affect gene expression levels in an allele-specific manner, and these functional polymorphisms represent an important but relatively unexplored class of genetic variation. The main challenge in analyzing these SNPs is a lack of robust computational and experimental methods. Here, we first outline mechanisms by which genetic variation can impact gene regulation, and review recent findings in this area; then, we describe a methodology for bioinformatic discovery and functional analysis of regulatory SNPs in cis-regulatory regions using the assembled human genome sequence and databases on sequence polymorphism and gene expression. Our method integrates SNP and gene databases and uses a set of computer programs that allow us to: (1) select SNPs, from among the >9 million human SNPs in the NCBI dbSNP database, that are similar to cis-regulatory element (RE) consensus sequences; (2) map the selected dbSNP entries to the human genome assembly in order to identify polymorphic REs near gene start sites; (3) prioritize the candidate polymorphic RE containing genes by searching the existing genotype and gene expression data sets. The applicability of this system has been demonstrated through studies on p53 responsive elements and is being extended to additional pathways and environmentally responsive genes.

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

    SciTech Connect (OSTI)

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

    2004-02-25

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

  5. Imaging gene expression in real-time using aptamers

    SciTech Connect (OSTI)

    Shin, Il Chung

    2011-12-13

    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.

  6. Blue Gene/Q | Argonne Leadership Computing Facility

    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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 OutreachProductswsicloudwsiclouddenDVA N C E D B L O OLaura|BilayerBiomimetic DyeBlue Gene/Q Download original

  7. Ayuda:Imágenes | 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 on Google Bookmark EERE: Alternative Fuels Data Center Home Page on QA:QA J-E-1 SECTION JEnvironmental Jump to:EAandAmminex AAustria Geothermal RegionAvra Valley,Ayuda:EcuacionesImágenes

  8. 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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverse (Journal Article)ForthcomingGENERALProblems ISecurityGene Controls Flowering

  9. Systems Biology of Microbiota Metabolites and Adipocyte Transcription Factor Network 

    E-Print Network [OSTI]

    Choi, Kyungoh

    2013-07-17

    (16, 17). Therefore, it is important to understand the dynamics and interaction between different members of the regulatory network for modulating complex phenotypes such as lipid balance in adipocytes. Phylogenetic (16S rRNA) sequencing... such as Crohn?s disease and dysbiosis of the intestinal microbiota (22). For example, a clinical metabolomics study suggested that poor utilization of tryptophan and an imbalance of tryptophan-derived microbiota metabolites correlated strongly with ileal...

  10. Viunalikeviruses are environmentally common agents of horizontal gene transfer in pathogens and biocontrol bacteria

    E-Print Network [OSTI]

    Matilla, M. A.; Fang, X.; Salmond, George P. C.

    2014-01-01

    plaque-forming unit. We also demonstrate the interstrain transduction of plasmids and chromosomal markers, including genes involved in anabolism, genes for virulence and genes encoding secondary metabolites involved in biocontrol. We propose that all... additional ViI-like phages and three new environmentally isolated viunalike- viruses, all infecting plant and human pathogens, are very efficient generalised transducers capable of transducing chromosomal markers at frequencies of up to 10?4 transductants per...

  11. 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.

    2011-10-15

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

  12. Recognizing genes and other components of genomic structure

    SciTech Connect (OSTI)

    Burks, C. ); Myers, E. . Dept. of Computer Science); Stormo, G.D. . Dept. of Molecular, Cellular and Developmental Biology)

    1991-01-01

    The Aspen Center for Physics (ACP) sponsored a three-week workshop, with 26 scientists participating, from 28 May to 15 June, 1990. The workshop, entitled Recognizing Genes and Other Components of Genomic Structure, focussed on discussion of current needs and future strategies for developing the ability to identify and predict the presence of complex functional units on sequenced, but otherwise uncharacterized, genomic DNA. We addressed the need for computationally-based, automatic tools for synthesizing available data about individual consensus sequences and local compositional patterns into the composite objects (e.g., genes) that are -- as composite entities -- the true object of interest when scanning DNA sequences. The workshop was structured to promote sustained informal contact and exchange of expertise between molecular biologists, computer scientists, and mathematicians. No participant stayed for less than one week, and most attended for two or three weeks. Computers, software, and databases were available for use as electronic blackboards'' and as the basis for collaborative exploration of ideas being discussed and developed at the workshop. 23 refs., 2 tabs.

  13. Single gene insertion drives bioalcohol production by a thermophilic archaeon

    SciTech Connect (OSTI)

    Basen, M; Schut, GJ; Nguyen, DM; Lipscomb, GL; Benn, RA; Prybol, CJ; Vaccaro, BJ; Poole, FL; Kelly, RM; Adams, MWW

    2014-12-09

    Bioethanol production is achieved by only two metabolic pathways and only at moderate temperatures. Herein a fundamentally different synthetic pathway for bioalcohol production at 70 degrees C was constructed by insertion of the gene for bacterial alcohol dehydrogenase (AdhA) into the archaeon Pyrococcus furiosus. The engineered strain converted glucose to ethanol via acetate and acetaldehyde, catalyzed by the host-encoded aldehyde ferredoxin oxidoreductase (AOR) and heterologously expressed AdhA, in an energy-conserving, redox-balanced pathway. Furthermore, the AOR/AdhA pathway also converted exogenously added aliphatic and aromatic carboxylic acids to the corresponding alcohol using glucose, pyruvate, and/or hydrogen as the source of reductant. By heterologous coexpression of a membrane-bound carbon monoxide dehydrogenase, CO was used as a reductant for converting carboxylic acids to alcohols. Redirecting the fermentative metabolism of P. furiosus through strategic insertion of foreign genes creates unprecedented opportunities for thermophilic bioalcohol production. Moreover, the AOR/AdhA pathway is a potentially game-changing strategy for syngas fermentation, especially in combination with carbon chain elongation pathways.

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

    E-Print Network [OSTI]

    Hegarty, Jeffrey Miles

    2011-01-01

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

  15. 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)

    2003-01-01

    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.

  16. Complex gene expression in the dragline silk producing glands of the Western black widow (Latrodectus hesperus)

    E-Print Network [OSTI]

    Lane, Amanda; Hayashi, Cheryl Y; Whitworth, Gregg B; Ayoub, Nadia A

    2013-01-01

    gene expression in the dragline silk producing glands of thematerial properties of spider dragline silk across species.protein superfiber: spider dragline silk. Proc Natl Acad Sci

  17. Sporulation Genes Associated with Sporulation Efficiency in Natural Isolates of Yeast

    E-Print Network [OSTI]

    Sinha, Himanshu

    Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India, 2 Department and sporulation-associated genes. Using two independent methods for association mapping and correcting

  18. 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

    2002-01-01

    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 ...

  19. Functional Metagenomics Reveals Previously Unrecognized Diversity of Antibiotic Resistance Genes in Gulls

    E-Print Network [OSTI]

    Martiny, Adam C; Martiny, Jennifer B. H; Weihe, Claudia; Field, Andrew; Ellis, Julie C

    2011-01-01

    multidrug resistant bacteria and resistance genes have beenbacteria in birds www.frontiersin.org Antibiotic resistanceAntibiotic-resistance pro?le in environmental bacteria

  20. Effects of melatonin and age on gene expression in mouse CNS using microarray analysis

    E-Print Network [OSTI]

    Bondy, SC; Sharman, EH; Sharman, KZ; Lahiri, D; Cotman, CW; Perreau, VM

    2007-01-01

    gene expression in the hypothalamus and cortex of mice. Procovine pre-mammillary hypothalamus: day-night variation innucleus of the hypothalamus (von Gall et al. , 2002), the

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

    E-Print Network [OSTI]

    2014-01-01

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

  2. 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

  3. Molecular decay of enamel matrix protein genes in turtles and other edentulous amniotes

    E-Print Network [OSTI]

    Meredith, Robert W; Gatesy, John; Springer, Mark S

    2013-01-01

    GK, Feng JQ, Yamakoshi F, Simmer JP: Enamel defects andNMRP, Milkovich RN, Kim J-W, Simmer JP, Hu JC-C: Target gene

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

    SciTech Connect (OSTI)

    Desprez, Pierre-Yves; Campisi, Judith

    2011-10-04

    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.

  5. 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)

    2008-09-30

    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.

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

    E-Print Network [OSTI]

    Yamamoto, Miki L.

    2009-01-01

    Alternative Pre-mRNA Splicing Switches Modulate GeneErythroid Stage-Specific Alternative Splicing Number ofin promoter use and alternative splicing that have important

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

    E-Print Network [OSTI]

    2008-01-01

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

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

    SciTech Connect (OSTI)

    Somenahally, Anil C; Mosher, Jennifer J; Yuan, Tong; Podar, Mircea; Phelps, Tommy Joe; Brown, Steven D; Yang, Zamin Koo; Hazen, Terry C; Arkin, Adam; Palumbo, Anthony Vito; Zhou, Jizhong; Elias, Dwayne A

    2013-01-01

    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.

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

    SciTech Connect (OSTI)

    Somenahally, Anil C; Mosher, Jennifer J; Yuan, Tong; Phelps, Tommy Joe; Brown, Steven D; Yang, Zamin Koo; Hazen, Terry C; Arkin, Adam; Palumbo, Anthony Vito; Van Nostrand, Dr. Joy D.; Zhou, Jizhong; Elias, Dwayne A

    2013-01-01

    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. 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.

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

    DOE Patents [OSTI]

    Dai, Ziyu (Richland, WA); Lasure, Linda L. (Fall City, WA); Magnuson, Jon K. (Pasco, WA)

    2008-11-11

    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.

  12. Isolated Fungal Promoters and Gene Transcription Terminators and Methods of Protein and Chemical Production in a Fungus

    DOE Patents [OSTI]

    Dai, Ziyu (Richland, WA); Lasure, Linda L. (Fall City, WA); Magnuson, Jon K. (Pasco, WA)

    2008-11-11

    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.

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

    SciTech Connect (OSTI)

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

    2014-05-27

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

  14. Use of NAP gene to manipulate leaf senescence in plants

    DOE Patents [OSTI]

    Gan, Susheng; Guo, Yongfeng

    2013-04-16

    The present invention discloses transgenic plants having an altered level of NAP protein compared to that of a non-transgenic plant, where the transgenic plants display an altered leaf senescence phenotype relative to a non-transgenic plant, as well as mutant plants comprising an inactivated NAP gene, where mutant plants display a delayed leaf senescence phenotype compared to that of a non-mutant plant. The present invention also discloses methods for delaying leaf senescence in a plant, as well as methods of making a mutant plant having a decreased level of NAP protein compared to that of a non-mutant plant, where the mutant plant displays a delayed leaf senescence phenotype relative to a non-mutant plant. Methods for causing precocious leaf senescence or promoting leaf senescence in a plant are also disclosed. Also disclosed are methods of identifying a candidate plant suitable for breeding that displays a delayed leaf senescence and/or enhanced yield phenotype.

  15. LAMMPS strong scaling performance optimization on Blue Gene/Q

    SciTech Connect (OSTI)

    Coffman, Paul; Jiang, Wei; Romero, Nichols A.

    2014-11-12

    LAMMPS "Large-scale Atomic/Molecular Massively Parallel Simulator" is an open-source molecular dynamics package from Sandia National Laboratories. Significant performance improvements in strong-scaling and time-to-solution for this application on IBM's Blue Gene/Q have been achieved through computational optimizations of the OpenMP versions of the short-range Lennard-Jones term of the CHARMM force field and the long-range Coulombic interaction implemented with the PPPM (particle-particle-particle mesh) algorithm, enhanced by runtime parameter settings controlling thread utilization. Additionally, MPI communication performance improvements were made to the PPPM calculation by re-engineering the parallel 3D FFT to use MPICH collectives instead of point-to-point. Performance testing was done using an 8.4-million atom simulation scaling up to 16 racks on the Mira system at Argonne Leadership Computing Facility (ALCF). Speedups resulting from this effort were in some cases over 2x.

  16. 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)

    1998-01-01

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

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

    DOE Patents [OSTI]

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

    1998-10-13

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

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

    DOE Patents [OSTI]

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

    2007-03-20

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

  19. 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)

    2000-08-22

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

  20. Technology development for gene discovery and full-length sequencing

    SciTech Connect (OSTI)

    Marcelo Bento Soares

    2004-07-19

    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.

  1. Evaluation and Comparison of Clustering Algorithms in Analyzing ES Cell Gene Expression Data

    E-Print Network [OSTI]

    1 Evaluation and Comparison of Clustering Algorithms in Analyzing ES Cell Gene Expression Data #12;2 Abstract Many clustering algorithms have been used to analyze microarray gene expression data of clustering algorithms, including hierarchical clustering, k-means, PAM and SOM. The indices were homogeneity

  2. 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

  3. A Lentiviral RNAi Library for Human and Mouse Genes Applied to an

    E-Print Network [OSTI]

    - able libraries of synthetic siRNAs targeting defined gene families have identified mResource A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High short hairpin RNA (shRNA) libraries targeting the human and murine ge- nomes. The libraries currently

  4. 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

  5. Enhanced the expression of an apple gene that switches on a tree's natural defenses

    E-Print Network [OSTI]

    · Enhanced the expression of an apple gene that switches on a tree's natural defenses when fire the roots and killing the tree. Fire blight can kill an apple tree in as little as 30 days. It's called fire Sundin/MSU George Sundin/MSU #12;Enhanced the expression of an apple gene that switches on a tree

  6. 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

  7. LARGE-SCALE BIOLOGY ARTICLE The MORPH Algorithm: Ranking Candidate Genes for

    E-Print Network [OSTI]

    Shamir, Ron

    leading to secondary metabolites in plants. These path- ways have been studied extensively (Saito et al of the nature of interactions between metabolites and gene expression, and we have only a partial grasp, many plant genes remain to be annotated and have no known function (Gerdes et al., 2011

  8. Plasimids containing the gene for DNA polymerase I from Streptococcus pneumoniae

    DOE Patents [OSTI]

    Lacks, Sanford A. (Brookhaven, NY); Martinez, Susana (Sound Beach, NY); Lopez, Paloma (Madrid, ES); Espinosa, Manuel (Madrid, ES)

    1991-01-01

    A method is disclosed for cloning the gene which encodes a DNA polymerase-exonuclease of Streptococcus pneumoniae. Plasmid pSM22, the vector containing the pneumocccal polA gene, facilitates the expression of 50-fold greater amounts of the PolI enzyme.

  9. A. Grothey Solving Large Financial Planning Problems on Blue Gene School of Mathematics

    E-Print Network [OSTI]

    Grothey, Andreas

    . Grothey Solving Large Financial Planning Problems on Blue Gene Overview · Asset and Liability Management Portfolio Optimization: Asset and Liability Management · A set of assets J = {1, ..., J} is given (e Gene Asset and Liability Management as Stochastic Program With every node i = (t, n) we associate

  10. [21] FusionBased Strategies to Identify Genes Involved in Degradation of a Specific Substrate

    E-Print Network [OSTI]

    Hampton, Randy

    [21] FusionBased Strategies to Identify Genes Involved in Degradation of a Specific Substrate By RANDOLPH Y. HAMPTON Abstract Fusion proteins have been used in many instances to allow genetic screening Principles of Using Fusion Reporters to Discover Degradation Genes Because protein degradation is highly

  11. Antibiotic resistance genes in human pathogens such as methicillin-resistant Staphylococcus aureus1

    E-Print Network [OSTI]

    Handelsman, Jo

    , the process by which bacteria acquire genes from the environment5 . Many of the known antibiotic resist- ance bacteria of the same or different species. There is evidence of the transfer of resistance elements bacteria15 . Strikingly, these resistant bacteria can transfer the resistance genes to human pathogens16

  12. Persistence of Extracellular DNA in River Sediment Facilitates Antibiotic Resistance Gene Propagation

    E-Print Network [OSTI]

    Alvarez, Pedro J.

    of multidrug resistant bacteria. It is commonly believed that hospitals are major focal points for resistancePersistence of Extracellular DNA in River Sediment Facilitates Antibiotic Resistance Gene, United States *S Supporting Information ABSTRACT: The propagation of antibiotic resistance genes (ARGs

  13. Tomato tos1 mutation identifies a gene essential for osmotic tolerance and abscisic acid sensitivity

    E-Print Network [OSTI]

    Málaga, Universidad de

    Tomato tos1 mutation identifies a gene essential for osmotic tolerance and abscisic acid; accepted 9 September 2002. Ă For correspondence (fax ţ34 952 132; e-mail mabotella@uma.es). Summary Osmotic plant genes that are required for osmotic stress tolerance in tomato. As a result, we have isolated

  14. A microfluidic processor for gene expression profiling of single human embryonic stem cells

    E-Print Network [OSTI]

    Quake, Stephen R.

    A microfluidic processor for gene expression profiling of single human embryonic stem cells Jiang F and differentiation of individual cells. Here, we report a microfluidic approach that can extract total mRNA from. This feature makes large-scale single-cell gene expression profiling possible. Using this microfluidic device

  15. RESEARCH Open Access Evidence for GC-biased gene conversion as a

    E-Print Network [OSTI]

    Jarvis, Erich D.

    RESEARCH Open Access Evidence for GC-biased gene conversion as a driver of between, consistent with recombination-associated GC biased gene conversion (gBGC) more strongly impacting populations and a greater number of meioses per unit time; that is, a shorter generation time. Thus, in accord

  16. Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1

    E-Print Network [OSTI]

    Halazonetis, Thanos

    University, Nagoya, Japan Introduction Transcriptional gene silencing (TGS) refers to the stable repression suppress the expression of certain protein-coding genes. In multicellular eukaryotes, TGS can persist for plants. Such TGS stability is achieved by the concerted action of multiple epigenetic mechanisms

  17. Progesterone Regulation of Endometrial Gene Expression in the Early Pregnant Ovine Uterus 

    E-Print Network [OSTI]

    Minten, Megan A.

    2012-10-19

    by microarray analysis. The genes included: ANGPTL3, CHGA, CLEC4E, CXCL14, EFNA1, EFNB1, FABP3, IFNG, IL6, LGALS3, PTH, RBP4, SLIT2, SLIT3, and VWF. Early P4 treatment up-regulated CXCL14 gene expression in Day 9 ovine endometrium compared to control...

  18. Establishing novel relationships between genetic variants and gene expression in humans 

    E-Print Network [OSTI]

    Mandhan, Ishita

    2013-02-27

    in humans via three different studies. First, I focus on the impact of the loss-of-function (LoF) mutations on the gene expression. To study the impact of LoF mutations on gene expression, messenger RNA (mRNA) sequences were aligned generating a map...

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

    E-Print Network [OSTI]

    Sinskey, Anthony J.

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

  20. Global variability in gene expression and alternative splicing is modulated by mitochondrial content

    E-Print Network [OSTI]

    Guantes, Raúl

    Global variability in gene expression and alternative splicing is modulated by mitochondrial eukaryotic gene expression is an energy demanding process, differences in the energy budget of each cell and activities. Moreover, we find that mitochondrial levels have a large impact on alternative splicing, thus

  1. RESEARCH PAPER The strawberry gene FaGAST affects plant growth through

    E-Print Network [OSTI]

    Málaga, Universidad de

    RESEARCH PAPER The strawberry gene FaGAST affects plant growth through inhibition of cell The strawberry (Fragaria3ananassa) FaGAST gene encodes a small protein with 12 cysteine residues conserved in strawberry fruits. Ectopic expression of FaGAST in transgenic Fragaria vesca under the control of the CaMV-35

  2. American Journal of Botany 92(6): 10451058. 2005. THE -AMYLASE GENES OF GRASSES AND A

    E-Print Network [OSTI]

    Mason-Gamer, Roberta J.

    1045 American Journal of Botany 92(6): 1045­1058. 2005. THE -AMYLASE GENES OF GRASSES forms of -amylase in the Triticeae crop plants wheat, barley, and rye: an endosperm-specific form phylogenetic analyses of -amylase gene sequences. First, a phylogenetic analysis of coding sequences from wheat

  3. Plasmids containing the gene for DNA polymerase I from Streptococcus pneumoniae

    DOE Patents [OSTI]

    Lacks, S.A.; Martinez, S.; Lopez, P.; Espinosa, M.

    1991-03-26

    A method is disclosed for cloning the gene which encodes a DNA polymerase-exonuclease of Streptococcus pneumoniae. Plasmid pSM22, the vector containing the pneumocccal polA gene, facilitates the expression of 50-fold greater amounts of the PolI enzyme. 1 figure.

  4. 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

  5. Gene-expression programming to predict scour at a bridge abutment

    E-Print Network [OSTI]

    Fernandez, Thomas

    Gene-expression programming to predict scour at a bridge abutment H. Md. Azamathulla ABSTRACT networks, bridge abutments, gene-expression programming, local scour, radial basis function NOTATION L is a major cause of the failure of bridge abutments. Failure of bridges due to scour at their foundations

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

    E-Print Network [OSTI]

    Johnson, Kevin P.

    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

  7. 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

  8. ON PROBE-LEVEL INTERFERENCE AND NOISE MODELING IN GENE EXPRESSION MICROARRAY EXPERIMENTS

    E-Print Network [OSTI]

    ON PROBE-LEVEL INTERFERENCE AND NOISE MODELING IN GENE EXPRESSION MICROARRAY EXPERIMENTS Paul G is received via a cascade of two noisy chan- nels that model noise (uncertainty) before, during, and af- ter processing model of gene expression microarray experiments using oligonucleotide technologies. The objective

  9. Collagen-related gene and protein expression changes in the lung in response to chronic hypoxia

    E-Print Network [OSTI]

    Chesler, Naomi C.

    Collagen-related gene and protein expression changes in the lung in response to chronic hypoxia changes in gene and protein expression in the lungs of mice exposed to hypoxia for 0, 3, 6, 10 and 15 days was increased in whole lungs as early as 6 days of hypoxia and increased monotonically with longer exposures

  10. UNIT 26.2Combinatorial Recombination of Gene Fragments to Construct a Library of

    E-Print Network [OSTI]

    Arnold, Frances H.

    details necessary for creating a combi- natorial gene library. The Basic Protocol limits the size base pairs of identity at the desired recombination site. The Basic Protocol focuses on the mechanistic. Protein Engineering 26.2.1 Supplement 61 #12;Combinatorial Recombination of Gene Fragments 26

  11. Colon Cancer Is colon cancer a func.on of race or gene.cs?

    E-Print Network [OSTI]

    Brutlag, Doug

    Colon Cancer Is colon cancer a func.on of race or gene.cs? #12;Colon Cancer · What is colon cancer? · What genes are associated with colon cancer? · What external factors contribute to colon cancer? · What is done to diagnose

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

    E-Print Network [OSTI]

    Abdel Rahim, Ma'en Ahmad

    2004-09-30

    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 MCF-7 or ZR-75 cells...

  13. Cancer classification by gradient LDA technique using microarray gene expression data

    E-Print Network [OSTI]

    Cancer classification by gradient LDA technique using microarray gene expression data Alok Sharma a) Dimensionality reduction Cancer classification Feature selection Feature extraction a b s t r a c t Cancer techniques are applied for cancer classification, they face the small sample size (SSS) problem of gene

  14. Plasmids containing the gene for DNA polymerase I from Streptococcus pneumoniae

    DOE Patents [OSTI]

    Lacks, S.A.; Martinez, S.; Lopez, P.; Espinosa, M.

    1987-08-28

    A method is disclosed for cloning the gene which encodes a DNA polymerase-exonuclease of /und Streptococcus/ /und pneumoniae/. Plasmid pSM22, the vector containing the pneumococcal polA gene, facilitates the expression of 50-fold greater amounts of the PolI enzyme. 1 fig., 1 tab.

  15. 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

  16. This ICBG program links the discovery of drugs and genes for agriculture with biodiversity conservation.

    E-Print Network [OSTI]

    Coley, Phyllis

    ABSTRACT This ICBG program links the discovery of drugs and genes for agriculture with biodiversity of Panama's scientific infrastructure for drug and gene discovery, the training of Panamanian scientists in the short- and long-term. INTRODUCTION Over 50% of the most common prescription drugs orig- inate from

  17. Gene Recruitment of the Activated INO1 Locus to the Nuclear Membrane

    E-Print Network [OSTI]

    Walter, Peter

    Gene Recruitment of the Activated INO1 Locus to the Nuclear Membrane Jason H. Brickner* , Peter that activation of INO1 occurs at the nuclear membrane and requires the integral membrane protein Scs2. Scs2, the gene is recruited to the nuclear periphery upon transcriptional activation. Recruitment requires

  18. Hierarchical Analysis of Population Genetic Variation in Mitochondrial and Nuclear Genes of Daphnia pulex'

    E-Print Network [OSTI]

    Lynch, Michael

    Hierarchical Analysis of Population Genetic Variation in Mitochondrial and Nuclear Genes of Daphnia as rapidly with distance as does that for nuclear genes, which is slower than the neutral expectation on the geographic distribution of variability in nuclear and mitochondrial genomes (Birky et al. 1983, 1989

  19. The role of RpoT;3 in chloroplast development and gene expression 

    E-Print Network [OSTI]

    Chandler, Aglaia

    2009-06-02

    ............................. 77 9 Inter-assay variation (n = 2) of ABI Prism 7900 HT real-time PCR 81 10 Primer sequences......................................................................... 94 11 List of plastid genes analyzed in this study... xii LIST OF TABLES (CONTINUED) TABLE Page 15 Sequences of PCR forward (for) and reverse (rev) primers for plastid genes............................................................................ 147 16 PCR forward (for) and reverse...

  20. In vivo gene regulation in Salmonella spp. by a salicylate-dependent control circuit

    E-Print Network [OSTI]

    Cai, Long

    In vivo gene regulation in Salmonella spp. by a salicylate-dependent control circuit Jose´ Luis acid (ASA) in attenuated Salmonella enterica that carries an expression module with a gene of interest in vitro and in vivo. To validate the circuit, we administered Salmonella spp., carrying an expression

  1. The colanic acid gene cluster of Salmonella enterica has a complex history

    E-Print Network [OSTI]

    Lan, Ruiting

    The colanic acid gene cluster of Salmonella enterica has a complex history Gordon Stevenson The colanic acid gene cluster of Salmonella enterica LT2 was sequenced and compared with that of Escherichia rights reserved. Keywords: Colanic acid; Lateral transfer; Amelioration; Salmonella enterica 1

  2. The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during

    E-Print Network [OSTI]

    Domany, Eytan

    The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways.9.05 Deciphering regulatory events that drive malignant transformation represents a major challenge for systemsINK4A tumor suppressors inactivation. This cluster predominantly consists of cell cycle genes

  3. Duplication of the Hoxd11 Gene Causes Alterations in the Axial and Appendicular Skeleton

    E-Print Network [OSTI]

    Capecchi, Mario R.

    , vertebral column, urogenital system, and caudal digestive tract (Dolle´ et al., 1993; Small and Potter, 1993 of the Hoxd11 gene causes reduced male fertility, vertebral transformation, carpal bone fusions complex vertebrate morpholo- gies. Mice with mutations in these genes manifest defects in the limbs

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

    SciTech Connect (OSTI)

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

    2007-12-20

    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.

  5. 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

  6. Analyses of humanchimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging

    E-Print Network [OSTI]

    Church, George M.

    Analyses of human­chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging Joa Abstract Compared to chimpanzees (Pan troglodytes), the onset of aging appears to be delayed in the human acting on genes associated with aging in different model systems, which allowed us to explore

  7. New Markov Model Approaches to Deciphering Microbial Genome Function and Evolution: Comparative Genomics of Laterally Transferred Genes

    SciTech Connect (OSTI)

    Borodovsky, M.

    2013-04-11

    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.

  8. Pluripotency, differentiation, and reprogramming: A gene expression dynamics model with epigenetic feedback regulation

    E-Print Network [OSTI]

    Miyamoto, Tadashi; Kaneko, Kunihiko

    2015-01-01

    Characterization of pluripotent states, in which cells can both self-renew and differentiate, and the irreversible loss of pluripotency are important research areas in developmental biology. In particular, an understanding of these processes is essential to the reprogramming of cells for biomedical applications, i.e., the experimental recovery of pluripotency in differentiated cells. Based on recent advances in dynamical-systems theory for gene expression, we propose a gene-regulatory-network model consisting of several pluripotent and differentiation genes. Our results show that cellular-state transition to differentiated cell types occurs as the number of cells increases, beginning with the pluripotent state and oscillatory expression of pluripotent genes. Cell-cell signaling mediates the differentiation process with robustness to noise, while epigenetic modifications affecting gene expression dynamics fix the cellular state. These modifications ensure the cellular state to be protected against external per...

  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

    2005-11-01

    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. Spatial regulation of a common precursor from two distinct genes generates metabolite diversity

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

    Guo, Chun -Jun; Sun, Wei -Wen; Bruno, Kenneth S.; Oakley, Berl R.; Keller, Nancy P.; Wang, Clay C. C.

    2015-07-13

    In secondary metabolite biosynthesis, core synthetic genes such as polyketide synthase genes usually encode proteins that generate various backbone precursors. These precursors are modified by other tailoring enzymes to yield a large variety of different secondary metabolites. The number of core synthesis genes in a given species correlates, therefore, with the number of types of secondary metabolites the organism can produce. In our study, heterologous expression of all the A. terreus NRPSlike genes showed that two NRPS-like proteins, encoded by atmelA and apvA, release the same natural product, aspulvinone E. In hyphae this compound is converted to aspulvinones whereas inmore »conidia it is converted to melanin. The genes are expressed in different tissues and this spatial control is probably regulated by their own specific promoters. Comparative genomics indicates that atmelA and apvA might share a same ancestral gene and the gene apvA is located in a highly conserved region in Aspergillus species that contains genes coding for life-essential proteins. Our data reveal the first case in secondary metabolite biosynthesis in which the tissue specific production of a single compound directs it into two separate pathways, producing distinct compounds with different functions. Our data also reveal that a single trans-prenyltransferase, AbpB, prenylates two substrates, aspulvinones and butyrolactones, revealing that genes outside of contiguous secondary metabolism gene clusters can modify more than one compound thereby expanding metabolite diversity. Our study raises the possibility of incorporation of spatial, cell-type specificity in expression of secondary metabolites of biological interest and provides new insight into designing and reconstituting their biosynthetic pathways.« less

  11. Copyright 2001 by the Genetics Society of America Genes Involved in Sister Chromatid Separation and Segregation in

    E-Print Network [OSTI]

    Murray, Andrew W.

    , are required for sister chromatid separation and three other LOC genes, CSE4, IPL1, and SMT3, are required replication. We also report an initial characterization of phenotypes associated with the SMT3/SUMO gene

  12. Feasibility of a predictive model of Hsp70b-activated gene therapy protein expression during ultrasound hyperthermia

    E-Print Network [OSTI]

    Silcox, Christina Elise

    2014-01-01

    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 ...

  13. Table 1 (Supplemental): Summary of expression programs discovered by GeneProgram from Novartis Tissue Atlas v2 data

    E-Print Network [OSTI]

    Gerber, Georg K.

    2007-06-25

    Table 1 (Supplemental): Summary of recurrent expression programs (EPs) discovered by GeneProgram. The columns are: (1) the EP identifier (an arbitrarily assigned number), (2) the number of genes in the EP, (3) the number ...

  14. The comparative genomics of salinispora and the distribution and abundance of secondary metabolite genes in marine plankton

    E-Print Network [OSTI]

    Penn, Kevin Matthew

    2012-01-01

    rplB smpB Comparative genomics Gene gain Gene loss Totalbiology and comparative genomics. BMC Bioinformatics 10(1):Intersection of Evolution and Genomics. Science 300(5626):

  15. 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

    2007-04-25

    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 ...

  16. 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 ...

  17. Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes.

    E-Print Network [OSTI]

    2010-01-01

    chloroplast genome lacks petN, a gene found in all knownlist reveals the absence of petN, a gene that is found inchloroplast genome lacks the petN gene because the protein

  18. Melatonin causes gene expression in aged anuimals to respond to inflammatory stimuli in a manner differing from that of younger animals

    E-Print Network [OSTI]

    Bondy, Stephen Bondy C

    2008-01-01

    1, 152' E 53 Melatonin Causes Gene Expression in Aged39;i(6Cl . »1/lelrmuzin Causes Gene Expressiozr in A get! Amice d for 3 ex- Me:5’a:orzi:: Causes Gene Expression 2'

  19. The CER3 wax biosynthetic gene from Arabidopsis thaliana is allelic to WAX2/YRE/FLP1

    E-Print Network [OSTI]

    Kunst, Ljerka

    The CER3 wax biosynthetic gene from Arabidopsis thaliana is allelic to WAX2/YRE/FLP1 Owen Rowlanda with waxes. The Arabidopsis CER3 gene is important for cuticular wax biosynthesis and was reported and instead corresponds to WAX2/ YRE/FLP1 (At5g57800), a gene of unknown function required for wax

  20. Comparative Methods for the Analysis of Gene-Expression Evolution: An Example Using Yeast Functional Genomic Data

    E-Print Network [OSTI]

    Dhindsa, Rajinder

    this increasing database, gene-expression evolution is rarely modeled explicitly. One approach to studying geneComparative Methods for the Analysis of Gene-Expression Evolution: An Example Using Yeast-Hsiung Li* *Ecology and Evolution, and Howard Hughes Medical Institute, University of Chicago Understanding