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Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


1

Bacterial Diversity Analysis of Huanglongbing Pathogen-Infected Citrus, Using PhyloChip Arrays and 16S rRNA Gene Clone Library Sequencing  

Science Journals Connector (OSTI)

...Arrays and 16S rRNA Gene Clone Library Sequencing Published ahead...total community 16S rDNA clone libraries. Mol. Ecol. 6: 475-482...RDP-II): introducing myRDP space and quality controlled public...diversity than typical clone library when sampling the environment...

Uma Shankar Sagaram; Kristen M. DeAngelis; Pankaj Trivedi; Gary L. Andersen; Shi-En Lu; Nian Wang

2009-01-16T23:59:59.000Z

2

Bacterial Diversity Analysis of Huanglongbing Pathogen-Infected Citrus, Using PhyloChip Arrays and 16S rRNA Gene Clone Library Sequencing  

Science Journals Connector (OSTI)

...16S rRNA Gene Clone Library Sequencing Published...community 16S rDNA clone libraries. Mol. Ecol. 6...introducing myRDP space and quality controlled public data. Nucleic Acids...than typical clone library when sampling the environment...

Uma Shankar Sagaram; Kristen M. DeAngelis; Pankaj Trivedi; Gary L. Andersen; Shi-En Lu; Nian Wang

2009-01-16T23:59:59.000Z

3

Alignment-Independent Comparisons of Human Gastrointestinal Tract Microbial Communities in a Multidimensional 16S rRNA Gene Evolutionary Space  

Science Journals Connector (OSTI)

...The coordinate space was generated by...analyses for clone library comparisons were...gene evolutionary space. | We present a...16S rRNA gene clone libraries that is independent...The coordinate space was generated by...analyses for clone library comparisons were...

Knut Rudi; Monika Zimonja; Bente Kvenshagen; Jarle Rugtveit; Tore Midtvedt; Merete Eggesbø

2007-03-02T23:59:59.000Z

4

E-Print Network 3.0 - archaeal 16s rrna Sample Search Results  

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

recovered that were... and archaeal taxa. We have demonstrated in silico that this primer set should amplify 16S rRNA genes from... of ... Source: Colorado at Boulder,...

5

Alignment-Independent Comparisons of Human Gastrointestinal Tract Microbial Communities in a Multidimensional 16S rRNA Gene Evolutionary Space  

Science Journals Connector (OSTI)

...Gene Evolutionary Space Published ahead...Norwegian National Public Health Institute...rRNA gene clone libraries that is independent...evolutionary coordinate space. The coordinate...gene sequences in public databases, and...multidimensional coordinate space, using multimer...very large clone libraries. A further benefit...

Knut Rudi; Monika Zimonja; Bente Kvenshagen; Jarle Rugtveit; Tore Midtvedt; Merete Eggesbø

2007-03-02T23:59:59.000Z

6

E-Print Network 3.0 - amplified rrna gene Sample Search Results  

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

Summary: number 54, overexpressing rRNA from an inducible promoter 66, deleting the fis gene 20,67 (see... response specifically associated with changes in rRNA gene dosage...

7

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

E-Print Network [OSTI]

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...

Lostak, Tracy Karon

2009-05-15T23:59:59.000Z

8

Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases  

Science Journals Connector (OSTI)

...et al. estimated the costs to be $144 for a single...finding that the material costs, excluding labor, amounted...and the processing of a control) (109). Cook et al. (22) found even lower costs for identification of...without estimating capital equipment charges, the...

Jill E. Clarridge III

2004-10-01T23:59:59.000Z

9

Selective Phylogenetic Analysis Targeting 16S rRNA Genes of Hyperthermophilic Archaea in the Deep-Subsurface Hot Biosphere  

Science Journals Connector (OSTI)

...surface of the mound and from the top of chimney structures. Prior to sampling, the temperature...fluid (343C) was found at the top of the chimney, the temperature of the shimmering fluid...cycle of a hypersaline stratified lake (Solar Lake, Sinai, Egypt). Appl. Environ...

Hiroyuki Kimura; Jun-Ichiro Ishibashi; Harue Masuda; Kenji Kato; Satoshi Hanada

2007-02-02T23:59:59.000Z

10

Phylogenetic analysis of Euthyneura (Gastropoda) by means of the 16S rRNA gene: use of a ‘fast’gene for ‘higher–level’ phylogenies  

Science Journals Connector (OSTI)

...by Haszprunar (1985), who proposed a revised taxonomy. He rede ned Heterobranchia so that it was more inclu- sive, and introduced...Lindberg (1997) in their analysis of gastropod phylogeny rede ned some taxa based on these ideas (for example, they de ned...

1999-01-01T23:59:59.000Z

11

Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment  

Science Journals Connector (OSTI)

...sulfate reduction for energy generation hamper cultivation-independent...Solar Lake (Sinai, Egypt) was sectioned horizontally...control of hybridization efficiency and for straightforward...Solar Lake (Sinai, Egypt). Appl. Environ...Solar Lake (Sinai, Egypt). Consistent with previous...

Alexander Loy; Angelika Lehner; Natuschka Lee; Justyna Adamczyk; Harald Meier; Jens Ernst; Karl-Heinz Schleifer; Michael Wagner

2002-10-01T23:59:59.000Z

12

Analysis of 16S rRNA and 51-Kilodalton Antigen Gene and Transmission in Mice of Ehrlichia risticii in Virgulate Trematodes from Elimia livescens Snails in Ohio  

Science Journals Connector (OSTI)

...residing in Klamath Falls, Oreg. Isolate...Horse residing in Klamath Falls, Oreg. Isolate...unweighted pair-group method of analysis...Stagnicola sp.) from Klamath Falls, Oregon, which...the E. risticii group, is of greater...

Manuel Kanter; Jason Mott; Norio Ohashi; Bernard Fried; Stephen Reed; Young C. Lin; Yasuko Rikihisa

2000-09-01T23:59:59.000Z

13

Subfossil 16S rRNA Gene Sequences of Green Sulfur Bacteria in the Black Sea and Their Implications for Past Photic Zone Anoxia  

Science Journals Connector (OSTI)

...sampling on the ship. Distribution...and all known marine phylotypes...Therefore, the rare detection and low abundance...Within the radiation of the Chlorobiaceae, the marine species can be...The fourth marine sequence type...dropped below the detection limit at a depth...

Ann K. Manske; Uta Henßge; Jens Glaeser; Jörg Overmann

2007-11-26T23:59:59.000Z

14

Phylogenetic Differences in Attached and Free-Living Bacterial Communities in a Temperate Coastal Lagoon during Summer, Revealed via High-Throughput 16S rRNA Gene Sequencing  

Science Journals Connector (OSTI)

...significant correlation of POM with rain and wind events going back 5 days prior to sampling...2007.12.010 . 38. Byers, SC , EL Mills and PL Stewart. 1978. A comparison of...Supplement: Supplemental file 1 - Strongest wind gust and rain data recorded by Environment...

Vani Mohit; Philippe Archambault; Nicolas Toupoint; Connie Lovejoy

2014-01-24T23:59:59.000Z

15

Characterization of C1-Metabolizing Prokaryotic Communities in Methane Seep Habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by Analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA Genes  

Science Journals Connector (OSTI)

...other bacteria in sediments above gas hydrate (Cascadia Margin, Oregon...associated with Gulf of Mexico gas hydrates. Appl. Environ. Microbiol...reduction in sediment from a marine gas hydrate area. Environ. Microbiol. 4...

Fumio Inagaki; Urumu Tsunogai; Masae Suzuki; Ayako Kosaka; Hideaki Machiyama; Ken Takai; Takuro Nunoura; Kenneth H. Nealson; Koki Horikoshi

2004-12-01T23:59:59.000Z

16

Genetic Diversity among ArthrobacterSpecies Collected across a Heterogeneous Series of Terrestrial Deep-Subsurface Sediments as Determined on the Basis of 16S rRNA and recA Gene Sequences  

Science Journals Connector (OSTI)

...that most of the large taxonomic groups...collected during drilling of the Yakima Barricade borehole (YBB) at the...present in fairly large numbers in this...to advance the borehole without the use of drilling fluids, which...

Lorraine G. van Waasbergen; David L. Balkwill; Fiona H. Crocker; Bruce N. Bjornstad; Robert V. Miller

2000-08-01T23:59:59.000Z

17

Analysis of Dissimilatory Sulfite Reductase and 16S rRNA Gene Fragments from Deep-Sea Hydrothermal Sites of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific  

Science Journals Connector (OSTI)

...Proteobacteria as well as the occurrence...previously from other geothermal environments. Deep-sea...Gulf of California, Mexico (26). Recently...Further studies, as well as microscopy observations...epsilon-Proteobacteria as well as the occurrence...previously from other geothermal environments...

Tatsunori Nakagawa; Jun-Ichiro Ishibashi; Akihiko Maruyama; Toshiro Yamanaka; Yusuke Morimoto; Hiroyuki Kimura; Tetsuro Urabe; Manabu Fukui

2004-01-01T23:59:59.000Z

18

16S rRNA Phylogenetic Investigation of the Candidate Division “Korarchaeota”  

Science Journals Connector (OSTI)

...surface soil of Cambridge, MA), sand (Harvard University campus), river...Except the DNA of sediment, soil, and sand that was extracted by using a Bio...associated with surface-breaching gas hydrate mounds in the Gulf of Mexico. FEMS...

Thomas A. Auchtung; Cristina D. Takacs-Vesbach; Colleen M. Cavanaugh

2006-07-01T23:59:59.000Z

19

16S rRNA Phylogenetic Investigation of the Candidate Division “Korarchaeota”  

Science Journals Connector (OSTI)

...sequence. Superscript letters: a, hot springs and mudpots are terrestrial; b...separated cold ambient seawater and hot hydrothermal fluid; i, previously...collection and analysis of the Chena, Alaska, spring water; and Irene Newton for help...

Thomas A. Auchtung; Cristina D. Takacs-Vesbach; Colleen M. Cavanaugh

2006-07-01T23:59:59.000Z

20

Bacterial 16S Sequence Analysis of Severe Caries in Young Permanent Teeth  

Science Journals Connector (OSTI)

...enzyme in the arginine deiminase system, which converts arginine to...amplification. Finally, the resolving power of even full-length 16S genes...for the arginine deiminase system from Streptococcus gordonii...ed.), The prokaryotes: a handbook on the biology of bacteria...

Erin L. Gross; Eugene J. Leys; Stephen R. Gasparovich; Noah D. Firestone; Judith A. Schwartzbaum; Daniel A. Janies; Kashmira Asnani; Ann L. Griffen

2010-09-08T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Methylation of 16S RNA during ribosome assembly in vitro  

Science Journals Connector (OSTI)

... 16S RNA. Little is known, however, about the role of ribosomal proteins in the processing of precursor 16S RNA7. Recent experiments which demonstrated that 16S RNA from kasugamycin-resistant ... RNA and the assembly map (Fig. 4)14,16 indicates these proteins are strongly interrelated and occupy an early part of the map. In addition to S4, S8, ...

Pallaiah Thammana; William A. Held

1974-10-25T23:59:59.000Z

22

Distinguishing the Roles of Topoisomerases I and II in Relief of Transcription-Induced Torsional Stress in Yeast rRNA Genes  

Science Journals Connector (OSTI)

...melting. The observed DNA bubbles were not R-loops and did...considerably shorter than topo-bubbles and/or less amenable to visualization...which is preferred due to the stability conferred by base-pairing...Our observations of DNA bubbles in active genes after in vivo...

Sarah L. French; Martha L. Sikes; Robert D. Hontz; Yvonne N. Osheim; Tashima E. Lambert; Aziz El Hage; Mitchell M. Smith; David Tollervey; Jeffrey S. Smith; Ann L. Beyer

2010-11-22T23:59:59.000Z

23

Molecular Characterization of the Diversity and Distribution of a Thermal Spring Microbial Community by Using rRNA and Metabolic Genes  

Science Journals Connector (OSTI)

...considered here, the chemical affinities were well within the ranges previously reported...Conserved regions of the gene corresponded well to those found in A. pyrophilus in both...Sulfurihydrogenibium sequences are present in situ as well. We suspect that stochastic overamplification...

Justine R. Hall; Kendra R. Mitchell; Olan Jackson-Weaver; Ara S. Kooser; Brandi R. Cron; Laura J. Crossey; Cristina D. Takacs-Vesbach

2008-06-06T23:59:59.000Z

24

Renibacterium salmoninarum, the causative agent of bacterial kidney disease in salmonid fish, detected by nested reverse transcription-PCR of 16S rRNA sequences.  

Science Journals Connector (OSTI)

...chinook salmon for control of bacterial kidney disease, annual report FY. U.S. Department of Energy Bonneville Power Administration Division of Fish and Wildlife, Oreg. 17. Kawasaki, E. S. 1990. Amplification of RNA, p. 21-27...

H B Magnússon; O H Fridjónsson; O S Andrésson; E Benediktsdóttir; S Gudmundsdóttir; V Andrésdóttir

1994-12-01T23:59:59.000Z

25

Genetic Diversity in Microcystis Populations of a French Storage Reservoir Assessed by Sequencing of the 16S-23S rRNA  

E-Print Network [OSTI]

Genetic Diversity in Microcystis Populations of a French Storage Reservoir Assessed by Sequencing stations with different depths and at two dif- ferent sampling times (winter and summer) in the French allows this microorganism to growth in a broad range of environmental conditions. These papers

Jacquet, Stéphan

26

Clinical and Microbiological Features of a Cystic Fibrosis Patient Chronically Colonized with Pandoraea sputorum Identified by Combining 16S rRNA Sequencing and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry  

Science Journals Connector (OSTI)

...instruments for identification of isolates of the Burkholderia cepacia complex. J. Clin. Microbiol. 40 :1743-1748. 4. Caraher E , et al . 2008. Evaluation of in vitro virulence characteristics of the genus Pandoraea in lung epithelial cells. J. Med...

A. Fernández-Olmos; M. I. Morosini; A. Lamas; M. García-Castillo; L. García-García; R. Cantón; L. Máiz

2011-12-14T23:59:59.000Z

27

Phylogeny of bacterial methylotrophy genes reveals robustness in Methylobacterium mxaF sequences and mxa operon construction  

Science Journals Connector (OSTI)

mxaF, the structural gene for the methanol dehydrogenase (MDH enzyme), encodes for alpha subunit of the MDH enzyme. This member of the mxa family is required for production of a functional MDH enzyme. Methylobacterium species, pink-pigmented facultatively methylotrophic bacteria (PPFMs), are plant colonizing, methylotrophic bacteria that utilize methanol as a carbon and energy source during phyllosphere and rhizosphere growth. In a previous study that examined the phylogeny of soil and blueberry skin biofilm isolates, mxaF sequence was found to be a more useful indicator of species distinction within the Methylobacterium genus than 16S rRNA gene sequence and that it was not influenced by several environmental properties, including pH. Here, the phylogeny of methylotrophy genes including mxaF is examined to assess the potential for use of mxaF sequence as a biomarker for the Methylobacterium genus. A phylogenetic comparison of 311 archived PPFM and non-PPFM GenBank bacterial sequences of mxaF, xoxF, and generically annotated PQQ-dependent dehydrogenase genes in the methanol/ethanol family was conducted, including 270 mxaF, mxaF? and mxaF-like sequences. In addition, construction of operons within the mxa gene family was compared using GenBank completed genome sequences to investigate potential horizontal gene transfer (HGT) events within the mxa methylotrophy system. mxaF sequence and mxa gene family operon construction was found to be highly conserved within the genus Methylobacterium as compared to other bacterial genera. The data reveal evidence of HGT events between Methylobacterium species and other bacterial genera as well as the potential for mxaF sequence to be used as a taxonomic indicator for environmental Methylobacterium strains.

Jennifer Kist; Robert L. Tate III

2013-01-01T23:59:59.000Z

28

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

SciTech Connect (OSTI)

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.

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.

2007-07-30T23:59:59.000Z

29

LS-16 S. Kim  

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

S. Kim March 20, 1985 Parameters and Spectral Brilliance of the Aladdin Undulators This note shows tunable ranges of photon energies and the brilliances for different undulator periods and electron beam parameters. 1. Undulator Parameter Undulator parameters of Table 1 are generated with a minimum gap of 3.5 em and with a peak field B on the axis of the undulator where B 1.30 x 0.95 exp(- ng/A u )' undulator gap, undulator period. (1) Here a filling factor for the assembly of the undulator is assumed to be 95%. 2. Electron Beam Parameter The horizontal and vertical beam emittances are determined by a coupling constant K2 and natural emittance £xo: ~ / (1 + K2), c.. xo Parameters of beam size and beam divergence are related as = (6 £ )1/2 x,y ,

30

Physiological Ageing as it is Related to Gene Function in the Lone Star Tick, Amblyomma americanum  

E-Print Network [OSTI]

............................ 15 Figure 4 Electrophoresis gel results for the expression of the 16S gene in Amblyomma americanum subdivided by the mortality percentile to the right of the result, the sample number over the top of the result, and the group... as assessed by Image J software displaying the expression of Amblyomma americaum gene 16S for the female control (FC), male control (MC), female experimental (FE), and male experimental (ME) groups from Day 0 to Day 77...

Catena, Amanda M.

2010-07-14T23:59:59.000Z

31

Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays  

Science Journals Connector (OSTI)

......the amplified 16S rDNA pool by high-throughput...microbes of soils and ocean waters (Eckburg et al., 2005...organisms and because of the conservation of its nucleotide sequence...the simulated genome pool of 400 different microbial...genomic DNA, applying the pool of amplified and total......

Oleg Paliy; Brent D. Foy

2011-08-01T23:59:59.000Z

32

Microbial Communities in Contaminated Sediments, Associated with Bioremediation of Uranium to Submicromolar Levels  

Science Journals Connector (OSTI)

...construction of the clone libraries. REFERENCES 1 Anderson...records currently held in public repositories is estimated...16S rRNA gene clone libraries contain chimeras...introducing myRDP space and quality controlled public data. Nucleic Acids...

Erick Cardenas; Wei-Min Wu; Mary Beth Leigh; Jack Carley; Sue Carroll; Terry Gentry; Jian Luo; David Watson; Baohua Gu; Matthew Ginder-Vogel; Peter K. Kitanidis; Philip M. Jardine; Jizhong Zhou; Craig S. Criddle; Terence L. Marsh; James M. Tiedje

2008-05-02T23:59:59.000Z

33

Assessment of the Diversity, Abundance, and Ecological Distribution of Members of Candidate Division SR1 Reveals a High Level of Phylogenetic Diversity but Limited Morphotypic Diversity  

Science Journals Connector (OSTI)

...environmental clone libraries (e.g., candidate...that are deposited in public databases but have...16S rRNA gene clone libraries, especially those...introducing myRDP space and quality controlled public data. Nucleic Acids...

James P. Davis; Noha H. Youssef; Mostafa S. Elshahed

2009-04-24T23:59:59.000Z

34

Foodborne Sources of Bacteria Associated With Human Obesity  

E-Print Network [OSTI]

and anaerobic bacterial loads and to isolate bacteria. The total microbial community was extracted from these food samples and the 16S rRNA gene sequences of the microbiome were PCR amplified. The PCR amplicons were sequenced using pyrosequencing...

McElhany, Katherine Grace

2009-09-30T23:59:59.000Z

35

Phylum XIV. Bacteroidetes phyl. nov.  

Science Journals Connector (OSTI)

The phylum Bacteroidetes is a phenotypically diverse group of Gram-stain-negative rods that do not form endospores. They are circumscribed for this volume on the basis of phylogenetic analysis of 16S rRNA gene se...

Noel R. Krieg; Wolfgang Ludwig; Jean Euzéby…

2010-01-01T23:59:59.000Z

36

Effect of Spatial Differences in Microbial Activity, pH, and Substrate Levels on Methanogenesis Initiation in Refuse  

Science Journals Connector (OSTI)

...Canonical correspondence analysis to correlate environmental...Kingdom). Phylogenetic analysis. Phylogenetic and molecular evolutionary analyses of 16S rRNA gene sequences...performed to evaluate tree reliability (500 replications...to GQ453667. RESULTS Reactor sampling. All three...

Bryan F. Staley; Francis L. de los Reyes III; Morton A. Barlaz

2011-02-04T23:59:59.000Z

37

Characterization of Corynebacterium Species in Macaques  

E-Print Network [OSTI]

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 ...

Venezia, Jaime

38

Balancing protection and release of DNA: tools to address a bottleneck of non-viral gene delivery  

Science Journals Connector (OSTI)

...realizing the potential of genetic medicine. As future therapeutics will increasingly...nano-carriers for drug delivery. Nanotechnology 16, S484-S491. ( doi:10...Williams, D. A. , and C. Baum 2003 Medicine. Gene therapy-new challenges...

2010-01-01T23:59:59.000Z

39

A base pair between tRNA and 235 rRNA in the peptidyl transferase centre of the ribosome  

Science Journals Connector (OSTI)

... 235 rRNA in the peptidyl transferase centre of the ribosome Raymond R.SamahaR. R.RachelGreenR.Harry F.NollerH. F. Nature 377, 309-314(1995)

Raymond R. Samaha; Rachel Green; Harry F. Noller

1995-11-23T23:59:59.000Z

40

Serial Analysis of rRNA Genes and the Unexpected Dominance of Rare Members of Microbial Communities  

Science Journals Connector (OSTI)

...supported in part by Department of Energy Small Business Innovations Research (SBIR) grant...1662-1669. 13 Ewing, B., and P. Green. 1998. Base-calling of automated...Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated...

Matthew N. Ashby; Jasper Rine; Emmanuel F. Mongodin; Karen E. Nelson; Dago Dimster-Denk

2007-05-25T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

Effects of FIS Overexpression on Cell Growth, rRNA Synthesis, and Ribosome Content in Escherichia coli  

E-Print Network [OSTI]

Effects of FIS Overexpression on Cell Growth, rRNA Synthesis, and Ribosome Content in Escherichia of California, Riverside, California 92521 The Escherichia coli DNA binding protein FIS is a transcriptional. High-level overproduction of FIS in early, mid, or late log cultures resulted in growth- phase

Chen, Wilfred

42

Huanglongbing, a Systemic Disease, Restructures the Bacterial Community Associated with Citrus Roots  

Science Journals Connector (OSTI)

...the infected clone library using LIBSHUFF statistics...competition for nutrients and space, production of metabolites...analysis of 16S rRNA gene libraries. Bacterial community...introducing myRDP space and quality controlled public data. Nucleic Acids...

Pankaj Trivedi; Yongping Duan; Nian Wang

2010-04-09T23:59:59.000Z

43

Draft Genome Sequences for Two Metal-Reducing Pelosinus fermentans Strains Isolated from a Cr(VI) Contaminated Site and for Type Strain R7  

SciTech Connect (OSTI)

Pelosinus fermentans 16S rRNA gene sequences have been reported from diverse geographical sites since the recent isolation of the type strain. We present the genome sequence of the P. fermentans type strain R7 (DSM 17108) and genome sequences for two new strains with different abilities to reduce iron, chromate, and uranium.

Brown, Steven D [ORNL; Podar, Mircea [ORNL; Klingeman, Dawn Marie [ORNL; Johnson, Courtney M [ORNL; Yang, Zamin Koo [ORNL; Utturkar, Sagar M [ORNL; Land, Miriam L [ORNL; Mosher, Jennifer J [ORNL; Hurt, Jr., Richard Ashley [ORNL; Phelps, Tommy Joe [ORNL; Palumbo, Anthony Vito [ORNL; Arkin, Adam [Lawrence Berkeley National Laboratory (LBNL); Hazen, Terry C [ORNL; Elias, Dwayne A [ORNL

2012-01-01T23:59:59.000Z

44

Download Full-text PDF  

Science Journals Connector (OSTI)

particles, and prevent them from swimming down to the sediment ... extraction efficiency for ostracods has been reported by other studies ..... T-RFLP analysis of the 16S rRNA gene pool in the ..... and energy transfer to higher trophic levels.

2011-12-23T23:59:59.000Z

45

Enumeration and Characterization of Acidophilic Microorganisms Isolated from a Pilot Plant Stirred-Tank Bioleaching Operation  

Science Journals Connector (OSTI)

...supplied to the reactors by means of a sparger...microbiological analysis were taken a few...times for the three reactors are shown in Table...each of the three reactors were analyzed by...to increase the reliability of 16S rRNA gene...enzyme fragment analysis (double digestion...

Naoko Okibe; Mariekie Gericke; Kevin B. Hallberg; D. Barrie Johnson

2003-04-01T23:59:59.000Z

46

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor  

Science Journals Connector (OSTI)

...reactions used for energy generation in the dark ocean are more...16S rRNA gene surveys, is generally...Processes in the Dark Ocean Although...with secondary energy-generating...Furthermore, a survey of viral genetic...ECOLOGY OF THE DARK OCEAN Building...amount of free energy that is available...

Beth N. Orcutt; Jason B. Sylvan; Nina J. Knab; Katrina J. Edwards

2011-06-01T23:59:59.000Z

47

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)

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.

NONE

1991-12-31T23:59:59.000Z

48

Gabon black population data on the ten short tandem repeat loci D3S1358, VWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01 and FGA  

Science Journals Connector (OSTI)

...Allele frequencies for ten short tandem repeat (STR) loci D3S1358, VWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01 and FGA were determined in a Black African sample population from Gabon. All loc...

M. Steinlechner; K. Schmidt; H. G. Kraft…

2002-06-01T23:59:59.000Z

49

Gene Frequency  

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

Gene Frequency Gene Frequency Name: donna Location: N/A Country: N/A Date: N/A Question: If six fingers is a dominant human trait why do we have only five? Replies: This is simple. There are just not many genes in the human population for six fingers. Steve Sample Look in any high school biology book for what is known as Hardy-Weinberg equilibrium. These two scientists (separately) said that gene frequencies do not change much unless something in the environment selects them over other genes. In other words, unless 6 fingers somehow becomes an advantage, and five-fingered people have less of an advantage, the frequency of six fingered people in the population will not necessarily increase. This is the same reason that recessive traits don't disappear from the population. Also, six fingers is not considered attractive and they may not get as many mates. Also, more people are born with six fingers than you might imagine but just have them amputated shortly after birth.

50

Why Sequence a Group 4 Verrucomicrobium?  

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

a Group 4 Verrucomicrobium? a Group 4 Verrucomicrobium? It is a disturbing reality that we have only fragmentary understanding of the enormous microbial diversity that exists on our planet. This applies not merely to microbes living in extreme environments, which would be expected to possess unusual and perhaps not yet fully characterized properties, but also to those microbes in more mundane habitats, like a gram of soil. One bacterial phylum that has few cultivated representatives, but is found routinely in clone libraries of amplified 16S rRNA genes, is Verrucomicrobia. More than 200 unique verrucomicrobial 16S rRNA genes have been identified from terrestrial and aquatic environments and associated with a variety of eukaryotic hosts. The Verrucomicrobia, most of whose sequences are more than 75% identical to one another, form a monophyletic

51

Diversity analyses of microbial communities in petroleum samples from Brazilian oil fields  

Science Journals Connector (OSTI)

Recent studies of oil fields have shown that the microbial diversity is represented by bacteria and archaea of wide distribution, and that many of these organisms have potential to metabolize organic and inorganic compounds. Biodegradation processes in oil industry are of great relevance, since it may be related with the loss of petroleum quality and can bring problems during production. The aim of this study was to compare the microbial communities present in biodegraded (GMR75) and non-biodegraded (PTS1) terrestrial oils from the Potiguar Basin (RN, Brazil) by using cultivation (microbial enrichments and isolation) and molecular approaches (16S rRNA gene libraries). The cultivated microorganisms recovered were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Both bacterial 16S rRNA gene libraries revealed a great diversity, encompassing representatives from 8 different phyla (Actinobacteria, Bacteroidetes, Deferribacteres, Spirochaetes, Firmicutes, Proteobacteria, Thermotogae and Synergistetes) for the GMR75 sample, and from 5 different phyla (Actinobacteria, Chloroflexi, Firmicutes, Proteobacteria and Thermotoga) for the PTS1 sample. The archaeal 16S rRNA gene library was obtained only for GMR75 oil and all phylotypes were affiliated with the family Methanomicrobiaceae. Diversity results suggest that methanogenesis is the dominant terminal process for hydrocarbon degradation in GMR oil field, driven by anaerobic biodegradation.

T.R. Silva; L.C.L. Verde; E.V. Santos Neto; V.M. Oliveira

2013-01-01T23:59:59.000Z

52

Classification of bacterial isolates of the Jordanian oil refinery petroleum sludge  

Science Journals Connector (OSTI)

The aim of this study is to characterise the bacterial isolates of Jordanian oil refinery sludge for the purpose of using microorganisms in treating industrial wastewater effluents that contains hydrocarbons. Morphological, physiological, biochemical, antimicrobial susceptibility tests and 16S-23S rRNA spacer region polymorphism were used to characterise the isolated thermotolerant Bacillus, with specific reference to Bacillus strains. Data were coded and analysed by numerical techniques using the Gower coefficients and by average linkage (UPGMA) analysis. The study resulted in allocation of strains into two areas at 50.0% similarity levels and ten major phenons at 78.0% similarity level. Amplification of 16S-32S rRNA genes divided all strains into two areas at 48.0% similarity level; however, at 78.0% similarity level five taxonomically distinct phenons were evident.

Mohammed N. Battikhi; Bassam Mrayyan; Manar Atoum

2009-01-01T23:59:59.000Z

53

Seasonal Diversity of Planktonic Protists in Southwestern Alberta Rivers over a 1-Year Period as Revealed by Terminal Restriction Fragment Length Polymorphism and 18S rRNA Gene Library Analyses  

Science Journals Connector (OSTI)

...profiles) in three-dimensional space based on similarity or dissimilarity...apart. Emulsion PCR and clone library construction. Sampling periods...Approximately 500 clones from each library were prescreened by HaeIII...from further analyses. Clone library sequencing and analysis. Sequencing...

Matthew C. Thomas; L. Brent Selinger; G. Douglas Inglis

2012-06-08T23:59:59.000Z

54

Seasonal Diversity of Planktonic Protists in Southwestern Alberta Rivers over a 1-Year Period as Revealed by Terminal Restriction Fragment Length Polymorphism and 18S rRNA Gene Library Analyses  

Science Journals Connector (OSTI)

...in freshwater ecosystems to public health, it is of the utmost...diversity. According to the Public Health Agency of Canada's...profiles) in three-dimensional space based on similarity or dissimilarity...apart. Emulsion PCR and clone library construction. Sampling periods...

Matthew C. Thomas; L. Brent Selinger; G. Douglas Inglis

2012-06-08T23:59:59.000Z

55

Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to Dehalococcoides strains  

SciTech Connect (OSTI)

Dehalogenimonas lykanthroporepellens is the type species of the genus Dehalogenimonas, which belongs to a deeply branching lineage within the phylum Chloroflexi. This strictly anaerobic, mesophilic, non spore forming, Gram negative staining bacterium was first isolated from chlorinated solvent contaminated groundwater at a Superfund site located near Baton Rouge, Louisiana, USA. D. lykanthroporepellens was of interest for genome sequencing for two reasons: (a) its unusual ability to couple growth with reductive dechlorination of environmentally important polychlorinated aliphatic alkanes and (b) its phylogenetic position distant from previously sequenced bacteria. The 1,686,510 bp circular chromosome of strain BL-DC-9{sup T} contains 1,720 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small unit rRNA (16S) locus.

Siddaramappa, Shivakumara [Los Alamos National Laboratory (LANL); Delano, Susana [Los Alamos National Laboratory (LANL); Green, Lance D. [Los Alamos National Laboratory (LANL); Daligault, Hajnalka E. [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Chang, Yun-Juan [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Hauser, Loren John [ORNL; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Yan, Jun [Louisiana State University; Bowman, Kimberly [Louisiana State University; Da Costa, Milton S, [University of Coimbra, Coimbra Portugal; Rainey, Fred A. [University of Alaska; Moe, William M. [Louisiana State University

2012-01-01T23:59:59.000Z

56

Gene expression and evolution  

E-Print Network [OSTI]

Visualization of individual Scr mRNAs during Drosophilaof the homeotic gene Scr associated with a crustacean leg-as in Kosman et al. , 2004. SCR and ABD-B antibodies were

Lemons, Derek Scott

2010-01-01T23:59:59.000Z

57

Nanomedicine for gene therapy  

Science Journals Connector (OSTI)

Viruses are promising vehicles that result in high gene expression level, but issues of safety and virulent nature prevented its extensive use. Therefore, nonviral approach was investigated with the intervention ...

Susan Muthe Alex; Chandra P. Sharma

2013-10-01T23:59:59.000Z

58

CAP‘n’Collar Genes (CNC)  

Science Journals Connector (OSTI)

CNC genes are basic leucine zipper transcription factor... DNA binding protein domains , homeotic genes

2008-01-01T23:59:59.000Z

59

OVARIAN CANCER GENE THERAPY  

Science Journals Connector (OSTI)

Although systemic gene therapy is certainly the ultimate goal for strategies directed towards patient cancer therapy, present problems with systemic vector delivery suggest that initial gene therapy strategies may involve regional approaches directed towards the few specific tumors that exhibit a predominantly regional pattern of spread: ovarian cancers and brain tumors. The model system of metastatic ovarian cancer growing within peritoneal fluid has several advantages of safety and efficacy for retroviral-mediated gene transfer into solid tumors. First, the pathology of metastasis into mesothelial-lined spaces consists of relatively thin tumor plaques with extravasation of cancer cells into the fluid, potentially allowing a reservoir for delivering retroviral vectors to malignant cells. This spreading pattern is in contrast to primary tumors and more solid metastatic sites, where cancer grows as a large three-dimensional mass that could prevent delivery of retroviral vectors or other agents into the majority of tumor cells. In addition, infusion of retroviral vectors into these fluids should produce a greater effect on the growing cells within the fluid (predominantly cancer cells) than on proliferating host cells in regions of the body that do not directly connect to the mesothelial-lined spaces. Second, ovarian cancer provides a model system in which regional therapy could be curative in a high percentage of cases. This is true because ovarian cancer is confined to the peritoneal cavity at patient presentation in 60% of cases. The uptake and expression of the viral vectors can be readily assessed in these model systems because these fluids are readily accessible for cytologic, biochemical, and molecular analysis. Cancer gene therapy strategies include immunotherapy, introduction of drug sensitivity or resistance genes, oncogene inactivation, introduction of cytolytic genes, and tumor suppressor gene replacement. Examples of gene therapy protocols designed to target ovarian cancer include immunotherapy approaches, introduction of cytolytic genes, and tumor suppressor gene therapy approaches (reviewed in Roth and Cristiano22). The BRCA1 gene is mutated in the majority of cases of hereditary breast and ovarian cancer and exhibits loss of heterozygosity (LOH) and/or decreased expression in many sporadic cases.5,6,7,9,11,16,17,30,31 Multiple studies have demonstrated that overexpression of the BRCA1 gene results in growth inhibition and/or cell death, suggesting that BRCA1 can function directly as a growth inhibitor or tumor suppressor.10,21,28,31,33,34 Alternatively, growth inhibition may not be the major or sole mechanism for tumor suppression,13 because BRCA1 also functions during differentiation8,14,15 and may modulate DNA repair.13,27 The antitumor effect may be due to secretion of the BRCA1 gene product and a resulting paracrine inhibitory effect,12 although the precise biochemical function of BRCA1 is controversial and may involve nuclear functions4,26 such as DNA repair27 or transcriptional activation.3,18 Preclinical studies in nude mice xenografts have shown that intraperitoneal injection of retroviral vectors expressing \\{BRCA1sv\\} (a normal splice variant form of BRCA1) can inhibit the growth of established intraperitoneal tumors.10 Control retroviral vectors do not exhibit a significant antitumor effect, indicating that this is not merely a nonspecific effect of retroviral injection, but an effect of BRCA1 gene transfer.10 These studies showed transduction of tumor cells and expression of BRCA1 mRNA and protein following intraperitoneal injection of established intraperitoneal tumors10 or intratumoral injection of subcutaneous tumors (Obermiller and Holt, unpublished data). This article describes the development and phase I testing of BRCA1 gene therapy for the treatment of ovarian cancer.

David L. Tait; Patrice S. Obermiller; Roy A. Jensen; Jeffrey T. Holt

1998-01-01T23:59:59.000Z

60

Nonviral Vectors for Gene Delivery  

E-Print Network [OSTI]

been conducted (http://www.wiley.com/legacy/wileychi/genmed/clinical/). Gene therapies can be categorized on the basis of therapy as gene inhibitors, gene vaccines and gene substitutes. Gene inhibitors (i.e. siRNA) are potent therapies that silence... in formulation design and can be tailored to fit the size and topology of the gene. 1.4.2.1. Natural polymers Over the years, a significant number of natural polymers, such as chitosan 174 , cationic proteins (e.g., polylysine, protamine and histones...

Baoum, Abdulgader Ahmed

2011-04-26T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

Huntington's disease Between genes and  

E-Print Network [OSTI]

-base stutter in the DNA of the gene concerned. To a large extent, the length of the repeated section determines

Levin, Yan

62

Mitochondrial DNA variants observed in Alzheimer disease and Parkinson disease patients  

SciTech Connect (OSTI)

Mitochondrial DNA (mtDNA) variants associated with Alzheimer disease (AD) and Parkinson disease (PD) were sought by restriction endonuclease analysis in a cohort of 71 late-onset Caucasian patients. A tRNA[sup Gln] gene variant at nucleotide pair (np) 4336 that altered a moderately conserved nucleotide was present in 9/173 (5.2%) of the patients surveyed but in only 0.7% of the general Caucasian controls. One of these patients harbored an additional novel 12S rRNA 5-nucleotide insertion at np 956-965, while a second had a missense variant at np 3397 that converted a highly conserved methionine to a valine. This latter mutation was also found in an independent AD + PD patient, as was a heteroplasmic 16S rRNA variant at np 3196. Additional studies will be required to determine the significance, if any, of these mutations. 122 refs., 4 figs., 2 tabs.

Shoffner, J.M.; Brown, M.D.; Torroni, A.; Lott, M.T.; Cabell, M.F.; Mirra, S.S.; Yang, C.C.; Gearing, M.; Salvo, R. (Emory Univ. School of Medicine, Atlanta, GA (United States)); Beal, M.F. (Harvard Medical School, Boston, MA (United States)) (and others)

1993-07-01T23:59:59.000Z

63

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

SciTech Connect (OSTI)

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? 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?). 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.

David Kirchman

2011-12-31T23:59:59.000Z

64

Traits and Multiple Genes  

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

Traits and Multiple Genes Traits and Multiple Genes Name: Frank Location: N/A Country: N/A Date: N/A Question: Please, could you give me an example of how human traits are controlled by more than one pair of alleles? Replies: Your question is just a bit vague, there are different answers depending on just what your question is. I will answer it in terms of polygenic traits also known as additive alleles. When you think of traits such as skin color, hair color and eye color, or traits where there is a wide range of phenotypes they are usually under the control of more than one pair of alleles. These alleles can even be on different chromosomes! Each pair of additive alleles adds to the phenotype. For instance in the case of skin color, scientists now believe that 3 genes control skin color. You then get 3 sets from your mother and 3 from your father for 6 possibilities. If all 6 of the alleles are for dark skin, you will have the darkest possible skin. If you have 5 dark alleles and one light, you will have very dark skin. If you have all 6 light alleles then you will have the lightest skin possible. Is it possible to have a child that is light skinned when both parents are dark-skinned? Well, not if both have all 6 dark alleles, but if they have some light alleles and the child inherits all of the possible light alleles available, then yes, the child could have lighter skin than either parent. It is now believed that eye color is not simply brown being dominant over blue because how many people do you know that have the same shade of brown or blue eyes? Eye color must also be polygenic.

65

Recessive and Dominant Gene Action  

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

Recessive and Dominant Gene Action Recessive and Dominant Gene Action Name: Katie Location: N/A Country: N/A Date: N/A Question: What Causes some genes to be ressesive and other genes to be dominant? Replies: Think about the fact that genes code for directions for making proteins. There are many different kinds of proteins in our body-enzymes for regulating metabolism, structural proteins for building our bodies, hormones for regulating processes etc. If the gene for the protein is structural, then it is important to have the right kind and the right amount. If the gene is defective (usually recessive genes are defective, but not always) the right protein will not be made and the structure will either be defective and won't work at all or there won't be enough to maintain the structure. Sometimes you need both genes to be working to get enough of the structure. So a homozygous person will have the strongest structure. A heterozygote would have one gene that is working a may produce enough of the protein to maintain the structure, but maybe not. So in some cases, just having one copy of the dominant (working) gene is enough. If it is a trait for something like eye color, this is not going to cause a defect, just a difference. In this case, being heterozygous or homozgyous for the dominant trait produces the same color of eye. In the case of sickle cell anemia, the recessive gene changes the protein structure of the shape of the red blood cell. If you have one good copy and one bad copy of the gene, some of your cells will be normal and some will be sickle cells. One good copy of the gene gives you enough normal red blood cells to stay healthy. But if you don't have a normal copy, all of your cells have the capability to sickle under certain conditions and this can be fatal. So think of dominant and recessive genes in terms of what they produce and what that protein is supposed to do and then think of what would happen if the dominant gene was able to overtake the effect of the recessive gene.

66

The Home Microbiome and Childhood Asthma  

E-Print Network [OSTI]

. 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...

Ciaccio, Christina Elizabeth

2014-05-31T23:59:59.000Z

67

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

E-Print Network [OSTI]

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 ...

Preheim, Sarah Pacocha

68

A turbine oil-degrading bacterial consortium from soils of oil fields and its characteristics  

Science Journals Connector (OSTI)

A microbial consortium capable of degrading turbine oil (TuO), which consisted mainly of recalcitrant cycloalkanes and isoalkanes, was obtained from a soil sample collected from oil fields using repeated enrichment. When this consortium, named Atsuta A, was cultured in minimal salts medium containing 0.5% (w/v) TuO, it degraded 90% of TuO at 30 °C and pH 7 over 5 days. Although nine bacterial strains were isolated from the Atsuta A consortium, TuO degradation by the individual isolates and by a mixture of them was negligible. The community structure of the consortium, which was investigated by PCR–denaturing gradient gel electrophoresis (DGGE) targeting 16S rRNA genes, changed significantly during the degradation of TuO. Four major bands (F, K, N and T) out of at least 23 DGGE bands significantly increased in intensity over time during incubation. The DGGE bands F, K and N corresponded to those of previously isolated species. However, DGGE band T did not correspond to any isolated strain. The 16S rRNA gene sequence collected from band T was 98% homologous to that of an unculturable strain belonging to the ?-Proteobacteria. The degradation of TuO in the consortium may occur by cooperation between the unculturable species corresponding to band T and other strains in the consortium, including species corresponding to bands F, K and N.

Hitoshi Ito; Reia Hosokawa; Masaaki Morikawa; Hidetoshi Okuyama

2008-01-01T23:59:59.000Z

69

The Honorable Gene Dean  

Office of Legacy Management (LM)

Energy' .' Energy' .' Washington, DC 20585 DE! 14 1gg4 The Honorable Gene Dean \ P.O. Box 1659~ L Huntington, West Virginia 25717 _ ',.. : Dear Mayor Dean: Secretary of Energy Hazel O'Leary has'announced,a new approach ,to openness in the'Department of Energy (DOE) and its communications with the public. In support of this in.itiative, we are pleased,to forward the..enclosed information related to the former Reduction Pilot Plant sitein your jurisdiction that performed work for DOE predecessor agencies. This information is provided.for your information, use,.band retention., DDE's Formerly Utilized Sites Remedial.Action Program is responsible for identification of sitesused by DOE's predecessor agencies, determini,ng theirs current radiological condition and, where it has authority, performing

70

GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes  

SciTech Connect (OSTI)

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.

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

2010-04-01T23:59:59.000Z

71

Genome sequencing and annotation of Amycolatopsis azurea DSM 43854T  

Science Journals Connector (OSTI)

Abstract We report the 9.2 Mb genome of the azureomycin A and B antibiotic producing strain Amycolatopsis azurea isolated from a Japanese soil sample. The draft genome of strain DSM 43854T consists of 9,223,451 bp with a G + C content of 69.0% and the genome contains 3 rRNA genes (5S–23S–16S) and 58 aminoacyl-tRNA synthetase genes. The homology searches revealed that the PKS gene clusters are supposed to be responsible for the biosynthesis of naptomycin, macbecin, rifamycin, mitomycin, maduropeptin enediyne, neocarzinostatin enediyne, C-1027 enediyne, calicheamicin enediyne, landomycin, simocyclinone, medermycin, granaticin, polyketomycin, teicoplanin, balhimycin, vancomycin, staurosporine, rubradirin and complestatin.

Indu Khatri; Srikrishna Subramanian; Shanmugam Mayilraj

2014-01-01T23:59:59.000Z

72

Prodigal: Microbial Gene Prediction Software  

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

Screenshot Screenshot Artemis Screenshot of Prodigal Results Compared with Curated Annotations and other Computational Genefinders for Anaeromyxobacter dehalogenans 2CP-C (Click to enlarge) Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include: Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less. Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very

73

Whose genes can stomach cancer?  

Science Journals Connector (OSTI)

... a person develops stomach cancer depends partly on their genes, new research suggests. As John Whitfield reports, this discovery could help prevent the disease. El-Omar,E. M. ...

John Whitfield

2000-03-23T23:59:59.000Z

74

Ethics of Gene Therapy Debated  

Science Journals Connector (OSTI)

Ethics of Gene Therapy Debated ... A press conference at the annual meeting of the American Association for the Advancement of Science in Washington, D.C., last month turned into an impromptu debate on the ethical and policy implications of human gene therapy. ... The protagonists were biomedical ethicist LeRoy Walters of Georgetown University, and attorney Andrew Kimbrell of the Foundation on Economic Trends, an activist group that has filed many lawsuits relating to biotechnology. ...

STU BORMAN

1991-03-04T23:59:59.000Z

75

Fusion genes in breast cancer  

E-Print Network [OSTI]

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...

Batty, Elizabeth

2012-02-07T23:59:59.000Z

76

The need for a human gene index  

Science Journals Connector (OSTI)

......need for a human gene index. | Editorial | Abstracting...NEED FOR A HUMAN GENE INDEX Much noise has been made...the year 2000 about the completion of a "draft" of the...changes in assembly and completion of the draft genome...need for a human gene index Towards a true gene index......

C. Victor Jongeneel

2000-12-01T23:59:59.000Z

77

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)

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.

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

2012-01-01T23:59:59.000Z

78

Mining Virulence Genes Using Metagenomics  

E-Print Network [OSTI]

When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are totally absent in recruitment plots, representing therefore genes unique to individual bacterial isolates. We show that these Metagenomic Islands (MIs) are also visible in bacteria living in human hosts when their genomes are compared to sequences from the human microbiome, despite the compartmentalized structure of human-related environments such as the gut. From an applied point of view, MIs of human pathogens (e.g. those identified in enterohaemorragic Escherichia coli against the gut metagenome or in pathogenic Neisseria meningitidis against the oral metagenome) include virulence genes that appear to be absent in related strains or species present in the microbiome of healthy individuals. We propose that this strategy (i.e. recruitment analysis of pathogenic bacteria against the metagenome of healthy subjects) can be used to detect pathogenicity regions in species where the genes involved in virulence are poorly characterized. Using this approach, we detect well-known pathogenicity islands and identify new potential virulence genes in several human pathogens.

Pedro Belda-ferre; Raúl Cabrera-rubio; Andrés Moya; Alex Mira

2011-01-01T23:59:59.000Z

79

Gene encoding plant asparagine synthetase  

DOE Patents [OSTI]

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.

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

1993-10-26T23:59:59.000Z

80

Using co-expression to redefine functional gene sets for gene set enrichment analysis  

E-Print Network [OSTI]

Manually curated gene sets related to a biological function often contain genes that are not tightly co-regulated transcriptionally. which obscures the evidence of coordinated differential expression of these gene sets in ...

Kodysh, Yuliya

2007-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

Gene 240 (1999) 4555 www.elsevier.com/locate/gene  

E-Print Network [OSTI]

gene of E. coli, which encodes an essentialtide(s); ORF, open reading frame; PAC, P1 artificial; Protein expression from ARD-1 cDNA in E. coli resultsSDS, sodium dodecyl sulfate; snRNP, small nuclear Abstract ARD-1 is an endoribonuclease identified initially as the product of a human cDNA that complements

Trinkle-Mulcahy, Laura

82

Antibody library project could unlock mysteries of human gene...  

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

Mysteries of human gene function Antibody library project could unlock mysteries of human gene function By looking at antibodies, researchers can identify where, in a cell, genes...

83

Regulation of Alpha-Amylase Gene Expression  

Science Journals Connector (OSTI)

The aim of our studies is to elucidate in molecular detail the principles underlying the tissue specific expression of eucaryotic genes. It is hoped that by understanding how a particular gene becomes activated i...

H. C. Hurst; O. Hagenbüchle; U. Schibler…

1986-01-01T23:59:59.000Z

84

Gene synthesis by circular assembly amplification  

E-Print Network [OSTI]

Gene synthesis by circular assembly amplification Duhee Bang & George M Church Here we report the development of a gene-synthesis technology, circular assembly amplification. In this approach, we first error-rich products, thereby substantially improving gene-synthesis quality. We used this method

Church, George M.

85

Genes, Themes and Microarrays Using Information Retrieval for LargeScale Gene Analysis  

E-Print Network [OSTI]

research effort. 4. Due to the interrelated nature of biological processes, genes may have more than

Shatkay, Hagit

86

Magnetotactic Bacteria: A Study of Mam Genes and Metabolism  

E-Print Network [OSTI]

, lacks several hemerythrin genes that might represent a gene island that harbors genes that encode hemerythrin island causes the non-magnetic phenotype or if deletion of magnetosome genes is involved as well

Walker, Lawrence R.

87

Method for determining gene knockouts  

DOE Patents [OSTI]

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.

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

2013-06-04T23:59:59.000Z

88

Gene Therapy for Color Blindness  

Science Journals Connector (OSTI)

...injection of a recombinant, replication-defective adeno-associated virus (AAV) (Figure 1). Before injection, blue-green and red-violet colors were invisible to the monkeys, as determined by a computer-based test of color vision. Five months after injection, the monkeys were found to have trichromatic vision... The subretinal introduction of a gene encoding an opsin into two color-blind monkeys lacking that opsin resulted in the acquisition of trichromatic vision.

Bennett J.

2009-12-17T23:59:59.000Z

89

Sexual and Apomictic Seed Formation in Hieracium Requires the Plant Polycomb-Group Gene FERTILIZATION INDEPENDENT ENDOSPERM  

Science Journals Connector (OSTI)

...essential for multiple developmental processes during plant growth (Figure 2), similar...Hieracium subgenus Pilosella are closely interrelated developmental pathways. Plant Cell 15...Experimental analysis of the fertilization process. Plant Cell 16: S107-S118. Wood...

Julio C.M. Rodrigues; Matthew R. Tucker; Susan D. Johnson; Maria Hrmova; Anna M.G. Koltunow

2008-09-23T23:59:59.000Z

90

Gene Therapy and Biological Pacing  

Science Journals Connector (OSTI)

...stem-cell vehicles to deliver ion-channel genes to the heart, and with the injection of biological pacemakers derived from embryonic stem cells (Figure 1), the report by Hu et al. is only the second in large animals to describe a biological pacemaker that induces heart rates and autonomic function that... TBX18 is a transcription factor critical to the specification of the sinoatrial node during normal development. A recent pig model of heart block suggests that the injection of a vector carrying TBX18 induces physiologically relevant pacemaker activity for 11 days.

Rosen M.R.

2014-09-18T23:59:59.000Z

91

Cross-Ontological Analytics: Combining Associative and Hierarchical Relations in the Gene Ontologies to Assess Gene Product Similarity  

SciTech Connect (OSTI)

Gene and gene product similarity is a fundamental diagnostic measure in analyzing biological data and constructing predictive models for functional genomics. With the rising influence of the gene ontologies, two complementary approaches have emerged where the similarity between two genes/gene products is obtained by comparing gene ontology (GO) annotations associated with the gene/gene products. One approach captures GO-based similarity in terms of hierarchical relations within each gene ontology. The other approach identifies GO-based similarity in terms of associative relations across the three gene ontologies. We propose a novel methodology where the two approaches can be merged with ensuing benefits in coverage and accuracy.

Posse, Christian; Sanfilippo, Antonio P.; Gopalan, Banu; Riensche, Roderick M.; Beagley, Nathaniel; Baddeley, Bob L.

2006-05-28T23:59:59.000Z

92

A fruit quality gene map of Prunus  

E-Print Network [OSTI]

Central Open Access A fruit quality gene map of PrunusAbstract Background: Prunus fruit development, growth,and maintaining stone fruit quality from production and

Ogundiwin, Ebenezer A; Peace, Cameron P; Gradziel, Thomas M; Parfitt, Dan E; Bliss, Fredrick A; Crisosto, Carlos H

2009-01-01T23:59:59.000Z

93

Imaging Gene Expression | The Ames Laboratory  

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

Imaging Gene Expression FWPProject Description: Project Leader(s): Marit Nilsen-Hamilton Principal Investigators: George Kraus We are developing apatmers to use as cellular...

94

LSUHSC NEW ORLEANS GENE THERAPY PUBLICATIONS  

E-Print Network [OSTI]

delivery of galactocerebrosidase tagged with the HIV Tat protein transduction domain. Journal-Negative Rev Gene Into Human CD34(+) Hematopoietic Progenitor Cells Potently Inhibits HIV-1 Replication

95

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network  

E-Print Network [OSTI]

, and more secure planning and design of experiments. The purpose of the GeneFarmprojectis to obtain

Gent, Universiteit

96

Gene-set Cohesion Analysis Tool (GCAT): A literature based web tool for calculating functional cohesiveness of gene groups  

Science Journals Connector (OSTI)

Numerous algorithms exist for producing gene sets from high-throughput genomic and proteomic technologies. However, analysis of the functional significance of these groups of genes or proteins remains a big challenge. We developed a Web based system ... Keywords: interferon, gene set cohesion analysis tool, functional cohesiveness, gene groups, genomics, proteomics, latent semantic indexing, gene ontology, embryonic fibroblasts, literature based Web tool, gene-gene literature similarities, microarray data analysis

Lijing Xu; R. Homayouni; N. A. Furlotte; K. E. Heinrich; E. O. George; M. W. Berry

2009-11-01T23:59:59.000Z

97

O R I G I N A L P A P E R Thermodesulfobacterium  

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

Thermodesulfobacterium Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park Scott D. Hamilton-Brehm * Robert A. Gibson * Stefan J. Green * Ellen C. Hopmans * Stefan Schouten * Marcel T. J. van der Meer * John P. Shields * Jaap S. S. Damste ´ * James G. Elkins Received: 20 July 2012 / Accepted: 4 January 2013 Ó Springer Japan (outside the USA) 2013 Abstract A novel sulfate-reducing bacterium designated OPF15 T was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism dis- played hyperthermophilic temperature requirements for growth with a range of 70-90 °C and an optimum of 83 °C. Optimal pH was around 6.5-7.0 and the organism required the presence of H 2 or formate

98

the Family Prochloraceae Florenzano, Balloni, and Materassi 1986, and the Family Prochlorotrichaceae Burger-Wiersma,  

E-Print Network [OSTI]

Systematic Bacteriology under the rules of the Bacteriological Code, be rejected because of the imperfection of ordinal diagnosis. The oxygenic-phototrophic prokaryotes involved are proposed to be incorporated under their validly published names into the orders Chroococcales and Oscillatoriales of the “Cyanobacteria ” group. Correspondingly, the latter is proposed to be upgraded to equal “Oxygenic photosynthetic bacteria ” (Section 19 in Bergey’s Manual). Oxygenic phototrophy is the generation of proton motive force due to light-driven transport of electrons which are extracted from water; a universal complement of the genomes in oxygenic phototrophs are the psa, psb, and wox gene assemblages (12). Oxygenic phototrophs are assigned to 1 of 11 major bacterial phyla, which has been convincingly demonstrated by the analysis of 16s rRNA sequences (22). The diversity of oxygenic phototrophs comprises, beside the members of Section 19, “Oxygenic photosynthetic bacteria ” (6), bacterium-derived cellular entities: cyanelles and plastids. The

Alexander V. Pinevich; Svetlana G. Averina; Natalia; V. Velichko

99

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

SciTech Connect (OSTI)

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.

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

2007-07-01T23:59:59.000Z

100

Short communication: Characterization of microflora in Mexican Chihuahua cheese  

Science Journals Connector (OSTI)

This work was performed to identify the bacterial species present in 10 Chihuahua cheeses obtained from commercial producers in Mexico using 16S rRNA gene analysis. As expected, some of the agar media initially used for isolation were not very selective, supporting the growth of several unrelated bacterial species. Sequence analysis identified potential pathogens, including Escherichia coli and Staphylococcus aureus, in all raw milk samples and 2 pasteurized milk samples. Streptococcus thermophilus and Lactococcus lactis ssp. lactis were identified in 9 and 6 samples, respectively, and would serve as acidifying agents during cheese production. Lactobacilli were identified in all cheeses, with the most prevalent being Lactobacillus plantarum identified in 7 raw milk and 1 pasteurized milk cheeses. Leuconostoc mesenteroides and Streptococcus macedonicus were identified in 4 raw milk cheeses and both were present in all pasteurized milk samples, suggesting that they may play a role in the development of traditional Chihuahua cheese attributes.

J.A. Renye Jr.; G.A. Somkuti; D.L. Van Hekken; V.M. Guerrero Prieto

2011-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

Gene therapy in alcoholic rats  

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

70 70 Sept. 9, 2001 Gene Therapy Reduces Drinking in "Alcoholic" Rats UPTON, NY - Scientists at the U.S. Department of Energy's Brookhaven National Laboratory have shown that increasing the level of a brain protein important for transmitting pleasure signals can turn rats that prefer alcohol into light drinkers, and those with no preference into near teetotalers. The findings, published in the first September 2001 issue of the Journal of Neurochemistry (Vol. 78, No. 5), may have implications for the prevention and treatment of alcoholism in humans. "This is a preliminary study, but when you see a rat that chooses to drink 80 to 90 percent of its daily fluid as alcohol, and then three days later it's down to 20 percent, that's a dramatic drop in alcohol intake - a very clear change in behavior," said Panayotis Thanos, the lead researcher. "This gives us great hope that we can refine this treatment for future clinical use."

102

Assignment of Orthologous Genes via Genome Rearrangement  

E-Print Network [OSTI]

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

Lonardi, Stefano

103

Gene prediction by multiple spliced alignment  

Science Journals Connector (OSTI)

With recent advances in sequencing technologies, a huge amount of DNA sequences become available year after year. In order to obtain useful information on these sequences, we need to process them in search of biologically meaningful regions. The genes ... Keywords: comparative genomics, gene prediction, multiple spliced alignment

Rodrigo Mitsuo Kishi; Ronaldo Fiorilo dos Santos; Said Sadique Adi

2011-08-01T23:59:59.000Z

104

Targets and indicators for gene level biodiversity  

E-Print Network [OSTI]

Targets and indicators for gene level biodiversity Resilience and future adaptation in forests, inland waters and marine environments depend on genetic variation Welcome to the Side-event on Lunch.weibull@naturvardsverket.se BaltGene­BalticSeaGeneticBiodiversity www.tmbl.gu.se:16080/baltgene GeneticMonitoring http

105

Gene coding for the E1 endoglucanase  

DOE Patents [OSTI]

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.

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

1996-07-16T23:59:59.000Z

106

Dynamic characteristics of bacterial community in a sulphate-reducing bioreactor fed with acetate and intermittent ethanol  

Science Journals Connector (OSTI)

Acetotrophic Sulphate-Reducing Bacteria (ASRB) were enriched in a sulphidogenic Continuous Stirred Tank Reactor (CSTR) fed with acetate/ethanol and diagnosed by Single-Strand Conformation Polymorphism (SSCP) and 16S rRNA gene clone library. The CSTR was run for 65 days with synthetic wastewater containing sulphate and acetate with intermittent ethanol at hydraulic retention time of 10 h. The Sulphate-Removal Rate (SRR) reached to 3.8 g/(Lâ?¢day) after 35 days of start-up. The SSCP profiles of bacterial community changed rapidly at the beginning of start-up before Desulphococcus sp., Desulphomicrobium sp., Aminomonas and Anaerolinea formed a stable community. Bacterial diversity decreased when the ethanol in the influent was replaced by acetate of equal Chemical Oxygen Demand (COD). Desulphomicrobium sp. was enriched and found to have a significant role in acetate utilisation. When ethanol was re-added instead of acetate of equal COD strength, microbial diversity increased and the Desulphomicrobium band of SSCP profiles became weak. At the later start-up stage, the 16S rRNA gene clone library indicated the presence of bacteria belonging to six different known phyla and sequences with similarities to those of sulphate-reducing bacteria accounted for 22%. The SSCP band sequences revealed that the characteristics of bacterial community populations resembled those of clone library sequences. The present study showed the addition of ethanol to influent would enhance bacterial diversity and SRR, ASRB could be enriched and Desulphomicrobium sp. was the primary source of acetate oxidation.

Yangguo Zhao; Nanqi Ren; Aijie Wang; Yiwei Liu

2008-01-01T23:59:59.000Z

107

Association and Interactions between DNA Repair Gene Polymorphisms and Adult Glioma  

Science Journals Connector (OSTI)

...analyzing gene-gene and gene-environment interactions. First, using...professions were also pilots and engineers. Of the 373 cases, 214...Gene-Gene and Gene-Environment Interactions Analysis Cumulative...for gene-gene and gene-environment interactions on glioma risk...

Yanhong Liu; Michael E. Scheurer; Randa El-Zein; Yumei Cao; Kim-Anh Do; Mark Gilbert; Kenneth D. Aldape; Qingyi Wei; Carol Etzel; and Melissa L. Bondy

2009-01-01T23:59:59.000Z

108

Tissue-Specific Gene Delivery via Nanoparticle Coating  

E-Print Network [OSTI]

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 ...

Harris, Todd J.

109

Comparative gene identification in mammalian, fly, and fungal genomes  

E-Print Network [OSTI]

An important step in genome interpretation is the accurate identification of protein-coding genes. One approach to gene identification is comparative analysis of the genomes of several related species, to find genes that ...

Lin, Michael F. (Michael Fong-Jay)

2006-01-01T23:59:59.000Z

110

Computationally Optimised DNA Assembly of synthetic genes  

Science Journals Connector (OSTI)

Gene synthesis is hampered by two obstacles: improper assembly of oligonucleotides; oligonucleotide defects incurred during chemical synthesis. To overcome the first problem, we describe the employment of a Computationally Optimised DNA Assembly (CODA) algorithm that uses the degeneracy of the genetic code to design overlapping oligonucleotides with thermodynamic properties for self-assembly into a single, linear, DNA product. To address the second problem, we describe a hierarchical assembly strategy that reduces the incorporation of defective oligonucleotides into full-length gene constructs. The CODA algorithm and these biological methods enable fast, simple and reliable assemblies of sequence-correct full-length genes.

Liza S.Z. Larsen; Christopher D. Wassman; G. Wesley Hatfield; Richard H. Lathrop

2008-01-01T23:59:59.000Z

111

Heat induces gene amplification in cancer cells  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer This study discovered that heat exposure (hyperthermia) results in gene amplification in cancer cells. Black-Right-Pointing-Pointer Hyperthermia induces DNA double strand breaks. Black-Right-Pointing-Pointer DNA double strand breaks are considered to be required for the initiation of gene amplification. Black-Right-Pointing-Pointer The underlying mechanism of heat-induced gene amplification is generation of DNA double strand breaks. -- Abstract: Background: Hyperthermia plays an important role in cancer therapy. However, as with radiation, it can cause DNA damage and therefore genetic instability. We studied whether hyperthermia can induce gene amplification in cancer cells and explored potential underlying molecular mechanisms. Materials and methods: (1) Hyperthermia: HCT116 colon cancer cells received water-submerged heating treatment at 42 or 44 Degree-Sign C for 30 min; (2) gene amplification assay using N-(phosphoacetyl)-L-aspartate (PALA) selection of cabamyl-P-synthetase, aspartate transcarbarmylase, dihydro-orotase (cad) gene amplified cells; (3) southern blotting for confirmation of increased cad gene copies in PALA-resistant cells; (4) {gamma}H2AX immunostaining to detect {gamma}H2AX foci as an indication for DNA double strand breaks. Results: (1) Heat exposure at 42 or 44 Degree-Sign C for 30 min induces gene amplification. The frequency of cad gene amplification increased by 2.8 and 6.5 folds respectively; (2) heat exposure at both 42 and 44 Degree-Sign C for 30 min induces DNA double strand breaks in HCT116 cells as shown by {gamma}H2AX immunostaining. Conclusion: This study shows that heat exposure can induce gene amplification in cancer cells, likely through the generation of DNA double strand breaks, which are believed to be required for the initiation of gene amplification. This process may be promoted by heat when cellular proteins that are responsible for checkpoints, DNA replication, DNA repair and telomere functions are denatured. To our knowledge, this is the first study to provide direct evidence of hyperthermia induced gene amplification.

Yan, Bin, E-mail: yanbin@mercyhealth.com [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States) [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States); Mercy Cancer Center, Mercy Medical Center-North Iowa, Mason City, IA 50401 (United States); Ouyang, Ruoyun [Department of Respiratory Medicine, The Second Xiangya Hospital, Xinagya School of Medicine, Central South University, Changsha 410011 (China)] [Department of Respiratory Medicine, The Second Xiangya Hospital, Xinagya School of Medicine, Central South University, Changsha 410011 (China); Huang, Chenghui [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States) [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States); Department of Oncology, The Third Xiangya Hospital, Xinagya School of Medicine, Central South University, Changsha 410013 (China); Liu, Franklin [Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710 (United States)] [Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710 (United States); Neill, Daniel [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States)] [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States); Li, Chuanyuan [Dermatology, Duke University Medical Center, Durham, NC 27710 (United States)] [Dermatology, Duke University Medical Center, Durham, NC 27710 (United States); Dewhirst, Mark [Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710 (United States)] [Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710 (United States)

2012-10-26T23:59:59.000Z

112

Finding a gene in a haystack  

Science Journals Connector (OSTI)

... the size of sample, double or triple samples can be processed simultaneously. Packaged under cleanroom conditions, Gene Frame II can be autoclaved and sterilized by ultraviolet irradiation. The adhesives ...

1997-02-27T23:59:59.000Z

113

Horizontal gene transfer in Bacteroides fragilis   

E-Print Network [OSTI]

Horizontal gene transfer (HGT) is one of the man driving forces of evolution in prokaryotes, and can also promote within-strain variation of bacterial species. The genomes of three previously sequenced Bacteroides fragilis ...

Jobling, Kelly Louise

2014-11-27T23:59:59.000Z

114

Validation of Gene Therapy Manufacturing Processes  

Science Journals Connector (OSTI)

Specific issues of concern in the validation of gene therapy viral vector manufacturing processes include quality of raw materials, safety testing of cell and viral banks, production and purification of the ve...

Dominick Vacante; Gail Sofer; Stephen Morris…

2002-01-01T23:59:59.000Z

115

Post transcriptional regulation of chloroplast gene expression by nuclear encoded gene products  

SciTech Connect (OSTI)

Many individual chloroplast genes require the products of a collection of nuclear genes for their successful expression. These nuclear gene products apparently work with great specificity, each committed to the expression of a single chloroplast gene. We have chosen as a model nuclear mutants of Chlamydomonas affected in different stages in the expression of the chloroplast encoded Photosystem II polypeptide, D2. We have made the progress in understanding how nuclear gene products affect the translation of the D2 encoding MRNA. Two nuclear genes are required for this process which have been mapped genetically. In contrast to other examples of nuclear control of translation in the chloroplast, these nuclear gene products appear to be required either for specific stages in translation elongation or for the post-translational stabilization of the nascent D2 protein. Pseudoreversion analysis has led us to a locus which may be directly involved in D2 expression. We have made considerable progress in pursuing the molecular basis of psbd MRNA stabilization. psbD 5' UTR specific transcripts have been synthesized in vitro and used in gel mobility shift assays. UV-crosslinking studies are underway to identify the transacting factors which bind to these sequences. The continued examination of these mutants will help us to understand how nuclear gene products work in this specific case of chloroplast gene expression, and will elucidate how two distinct genomes can interact generally.

Kuchka, M.R.

1992-01-01T23:59:59.000Z

116

GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes  

E-Print Network [OSTI]

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

Pati, Amrita

2012-01-01T23:59:59.000Z

117

Reverse Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles Using High-Performance Computing  

Science Journals Connector (OSTI)

Regulation of gene expression is a carefully regulated phenomenon in the cell. "Reverse-engineering” algorithms try to reconstruct the regulatory interactions among genes from genome-scale measurements of gene expression profiles (microarrays). ... Keywords: Reverse engineering, gene regulatory network, clustering algorithm, parallel computing.

Vincenzo Belcastro; Francesco Gregoretti; Velia Siciliano; Michele Santoro; Giovanni D'Angelo; Gennaro Oliva; Diego di Bernardo

2012-05-01T23:59:59.000Z

118

Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression  

Science Journals Connector (OSTI)

......lists of genes with EASE. Genome Biol. 4 R70 Liu, G., Loraine, A.E., Shigeta, R., Cline, M., Cheng, J., Valmeekam...of genes with EASE. Genome Biol., 4, R70. Liu,G., Loraine,A.E., Shigeta,R., Cline,M., Cheng,J., Valmeekam......

Yoram Ben-Shaul; Hagai Bergman; Hermona Soreq

2005-04-01T23:59:59.000Z

119

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

E-Print Network [OSTI]

for the selected genes of this project. 4 Genetic variation in pines has been studied extensively because of a high level of variation in natural populations (Hamrick and Godt 1996; Ledig 1998). Gene expression analysis is a valuable tool for generating...

Palle, Sreenath Reddy

2011-10-21T23:59:59.000Z

120

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

DOE Patents [OSTI]

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.

Desprez, Pierre-Yves; Campisi, Judith

2014-08-19T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1T)  

SciTech Connect (OSTI)

Polynucleobacter necessarius subsp. asymbioticus Hahn et al. 2009 is one of currently two subspecies of P. necessarius. While P. necessarius subsp. asymbioticus is a free-living bacterium, the closely related second subspecies, P. necessarius subsp. necessarius is an obligate endosymbiont living in the cytoplasm of freshwater ciliates of the genus Euplotes aediculatus. The two P. necessarius subspecies were the closest thus far reported phylogenetic neighbors that differ in their lifestyle as obligately free-living vs. obligate endosymbiontic, and they are the only members of the genus Polynucleobacter with completely sequenced genomes. The genome-sequenced strain represents a group of closely related strains not distinguishable by 16S rRNA, 16S-23S ITS or glnA sequences, which is persistent in the home habitat of the strain and frequently contributes > 10% of total bacterial numbers in water samples of the habitat. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006.

Meincke, Linda [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Berry, Kerrie W. [United States Department of Energy Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Schmutz, Jeremy [Stanford University; Brettin, Thomas S [ORNL; Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Wu, Qinglong L. [Austrian Academy of Sciences, Institute for Limnology, Mondsee, Austria; Pockl, Matthias [Austrian Academy of Sciences, Institute for Limnology, Mondsee, Austria; Hahn, Martin W. [Austrian Academy of Sciences, Institute for Limnology, Mondsee, Austria; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

2012-01-01T23:59:59.000Z

122

(for Gene Recognition Analysis Internet Link),  

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

5 6/1/2011 5 6/1/2011 6.6 Speeding Up the Process of Gene Discovery The human genome contains information that could be used to prevent birth defects and treat or cure devastating diseases, but it is written in a language that scientists are only beginning to understand. To help decipher the code, Ed Uberbacher and colleagues at Oak Ridge National Laboratory combined cutting- edge computer technology with their knowledge of human biology to develop GRAIL (for Gene Recognition Analysis Internet Link), a "thinking" computer program that imitates the human learning process as it searches for genetic meaning. GRAIL and successor software programs can rapidly identify key instructions in genes from within vast stretches of DNA that appear to be meaningless-a critical contribution to the

123

Retroviral vectors for human gene delivery  

Science Journals Connector (OSTI)

The potential for gene therapy to cure a wide range of diseases has lead to high expectations and a great increase in research efforts in this area. At present, viral vectors are the most efficient means of delivering a corrective gene into human cells. While a number of different viral vectors are under development, retroviral vectors are currently the most common type used in clinical trials today. However, the production of retroviral vectors for gene therapy applications faces a number of challenges. Of primary concern is the low titre of vector stocks produced by packaging cells in culture and the inherent instability of retroviral vector activity. The problems facing large-scale retroviral vector production are outlined in this review and the research efforts by a number of groups who have attempted to optimise production methods are presented.

Sally McTaggart; Mohamed Al-Rubeai

2002-01-01T23:59:59.000Z

124

Thauera linaloolentis sp. nov. and Thauera terpenica sp. nov., Isolated on Oxygen-containing Monoterpenes (Linalool, Menthol, and Eucalyptol and Nitrate  

Science Journals Connector (OSTI)

Summary The monoterpenes menthol, linalool, and eucalyptol were recently used as sole electron donor and carbon source for the isolation of three denitrifying bacterial strains 21Mol, 47Lol, and 58Eu. The motile, mesophilic, Gram-negative rods had a strictly respiratory metabolism. Monoterpenes were completely mineralised to carbon dioxide, nitrate was reduced to dinitrogen. Strain 47Lol utilised aliphatic monoterpenes, strain 21Mol oxygenated monocyclic monoterpenes, and strain 58Eu the bicyclic eucalyptol and monocyclic monoterpene alkenes. The fatty acid composition of the strains indicated an allocation to the rRNA group III of pseudomonads. Comparative 16S rRNA gene sequence analyses revealed that the new isolates can be assigned as members of the genus Thauera within the beta subclass of Proteobacteria. DNA-DNA hybridisation studies indicated a relateness of 68.5% between strains 21Mol and 58Eu which shared 36.0% and 40.6% DNA similarity with strain 47Lol. The strains are described as new species belonging to the genus Thauera, strain 47Lol (DSM 12138T) as T. linaloolentis sp. nov. and strains 21Mol and 58Eu as T. terpenica sp. nov. with strain 58Eu (DSM 12139T) as type strain.

S. Foss; J. Harder

1998-01-01T23:59:59.000Z

125

Regulation of methane genes and genome expression  

SciTech Connect (OSTI)

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

John N. Reeve

2009-09-09T23:59:59.000Z

126

Basidiomycete Mating Type Genes and Pheromone Signaling  

Science Journals Connector (OSTI)

...behavior and only a slight reduction of aerial hyphal formation were seen in the homokaryotic...and gpc genes, reduces the growth of aerial hyphae and, when homoallelic in a dikaryon...S. Fox, V. Grinberg, J. Fu, M. Fukushima, B. J. Haas, J. C. Huang, G. Janbon...

Marjatta Raudaskoski; Erika Kothe

2010-02-26T23:59:59.000Z

127

Expression of the MHC Class III Genes  

Science Journals Connector (OSTI)

...biosynthesis of the MHC class III products; for example...C2-producing cells is greater in freshly isolated macrophages...to expression of the class III MHC gene products...biosynthesis of the MHC class III products; for example...C2-producing cells is greater in freshly isolated macrophages...

1984-01-01T23:59:59.000Z

128

Inferring differentiation pathways from gene expression  

Science Journals Connector (OSTI)

......as finding the pdf p t [x] that...multivariate Gaussian pdf is defined (Cover...From genomics to chemical genomics: new...Som toolbox for matlab. In: Technical...Supplementary Data - pdf file Inferring...underlying molecular processes. In previous...physiology Computer Simulation Gene Expression......

Ivan G. Costa; Stefan Roepcke; Christoph Hafemeister; Alexander Schliep

2008-07-01T23:59:59.000Z

129

Should there be property rights in genes?  

Science Journals Connector (OSTI)

...whether large or small, can be `owned' in the same way as cars and houses, and so be subject to being bought and sold? Society...which produce them would be to prevent the transmission of defective genes to subsequent generations. Some would prohibit all such...

1997-01-01T23:59:59.000Z

130

Disentangling Mental Disorders : from Genes to Circuits  

E-Print Network [OSTI]

Summer Program 2014 Disentangling Mental Disorders : from Genes to Circuits RIKEN Brain Science Application : http://www.brain.riken.jp/en/summer/ Inquiries : info.summer@brain.riken.jp RIKEN Brain Science July 15-July 22, 2014 Summer Program 2014 Summer Program 2014 RIKEN Brain Science InstituteRIKEN Brain

Kazama, Hokto

131

E-Print Network 3.0 - acid metabolism-related genes Sample Search...  

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

attempt... Genes in the environment Genes and Ecosystems Dr Eshwar Mahenthiralingam (Esh) Cardiff University... 12;Genes in the environment Ecosystems (food, medicine, soil...

132

E-Print Network 3.0 - atctl2 gene enhances Sample Search Results  

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

Genes in the environment Genes and Ecosystems Dr Eshwar Mahenthiralingam (Esh) Cardiff University... 12;Genes in the environment Ecosystems (food, medicine, soil...

133

E-Print Network 3.0 - antifreeze protein gene Sample Search Results  

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

and nuclear gene sequences Summary: ribosomal protein intron 1), and combined dataset containing the mtDNA and nuclear genes resulted... complete gene sequences from...

134

E-Print Network 3.0 - atherosclerosis gene expression Sample...  

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

Gene Sequences In Drosophila melanogaster... , USA We performed a systematic BLAST analysis of 929 human disease gene entries associated... disease genes (77% of disease...

135

E-Print Network 3.0 - animal gene families Sample Search Results  

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

a curated database of phylogenetic trees of animal gene families... Fam: a curated database of phylogenetic trees of animal gene families 12,400 animal gene ... Source:...

136

E-Print Network 3.0 - akt-mediated gene repression Sample Search...  

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

rapid reactivation of transcription, a phenomenon known... - scription results in gene looping. After repression, genes can remain looped through interac- tions... that gene...

137

Regulation of HIV-1 gene expression  

SciTech Connect (OSTI)

The quantity and quality of HIV-1 gene expression is temporally controlled by a cascade of sequential regulatory interactions. basal HIV-1 transcription is determined by interaction of cellular regulatory proteins with specific DNA target sequences within the HIV-1 long-terminal repeat. The most notable of these protein: DNA interactions involves NF-{aleph}B, a transcription factor that plays a pivotal role in the activation of genes important for cellular responses to infection and inflammation. A second level of control involves the virally encoded Tat trans-activator. Tat, in combination with as yet unidentified cellular proteins, activates HIV-1 gene expression through a specific interaction with the viral TAR RNA stem-loop target sequence. A final level of regulation is mediated by the viral Rev protein. Rev acts posttranscriptionally to induce the expression of HIV-1 structural proteins and thereby commits HIV-1 to the late, cytopathic phase of the viral replication cycle. Rev activity appears to require a critical, threshold level of Rev protein expression, thus preventing entry into this late phase in cells that are unable to support efficient HIV-1 gene expression. In total, this cascade of regulatory levels allow the HIV-1 provirus to respond appropriately to the intracellular milieu present in each infected cell. In activated cells, the combination of Tat and Rev can stimulate a very high level of viral gene expression and replication. In quiescent or resting cells, in contrast, these same regulatory proteins are predicted to maintain the HIV-1 provirus in a latent or nonproductive state.

Cullen, B.R. (Duke Univ., Durham, NC (United States))

1991-07-01T23:59:59.000Z

138

Abnormal Gene Expression of Four Genes in Cells from Family Members of  

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

Abnormal Gene Expression of Four Genes in Cells from Family Members of Abnormal Gene Expression of Four Genes in Cells from Family Members of Hereditary-type Retinoblastoma Patients relative to Normal Individuals Chin-Yu Wang, 1 Yuanlin Peng, 1 Zhonghui Yang, 2 Chuan-Yuan Li, 2 Hatsumi Nagasawa, 1 Markus M. Fitzek, 3 John B. Little, 4 Joel S. Bedford, 1 and Eric Y. Chuang 5 1 Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado; 2 Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina; 3 Department of Radiation Oncology, Tufts-New England Medical Center; 4 Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts; and 5 Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan

139

E-Print Network 3.0 - allelic based gene-gene Sample Search Results  

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

identify many common alleles of major effect... to that in humans7,8 , the resulting SNP density of one SNP per 500 base pairs is considerably higher than... number of genes (Fig....

140

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

SciTech Connect (OSTI)

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

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

2013-01-20T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


141

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

E-Print Network [OSTI]

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 ...

Bolliet, Catherine

2007-01-01T23:59:59.000Z

142

Nonsyntenic Genes Drive Highly Dynamic Complementation of Gene Expression in Maize Hybrids  

Science Journals Connector (OSTI)

...Authors ( www.plantcell.org ) is: Frank Hochholdinger ( hochholdinger@uni-bonn.de ). [W] Online version contains Web-only data. This study analyzes how transcriptome diversity between two maize inbred lines affects gene expression patterns...

Anja Paschold; Nick B. Larson; Caroline Marcon; James C. Schnable; Cheng-Ting Yeh; Christa Lanz; Dan Nettleton; Hans-Peter Piepho; Patrick S. Schnable; Frank Hochholdinger

2014-10-14T23:59:59.000Z

143

Family- and Genus-Level 16S rRNA-Targeted Oligonucleotide Probes for Ecological Studies of Methanotrophic Bacteria  

Science Journals Connector (OSTI)

...methanotroph from Antarctic marine-salinity, meromictic lakes...Ajello A. F. Kaufmann D. J. Wear J. D. Wenger Proposal of Afipia...Anderson A methanotrophic marine molluscan (Bivalvia, Mytilidae...trichloroethylene and dimethyl sulfide by a marine Methylomicrobium strain containing...

Jay Gulledge; Azeem Ahmad; Paul A. Steudler; William J. Pomerantz; Colleen M. Cavanaugh

2001-10-01T23:59:59.000Z

144

Monitoring Precursor 16S rRNAs ofAcinetobacter spp. in Activated Sludge Wastewater Treatment Systems  

Science Journals Connector (OSTI)

...Sanitary District, Northeast Wastewater Treatment Plant (UCSD, NEWWTP), and...gallons/day) of municipal wastewater. The treatment plant reduces the average influent...community structure of wastewater treatment plants: a comparison of old...

Daniel B. Oerther; Jakob Pernthaler; Andreas Schramm; Rudolf Amann; Lutgarde Raskin

2000-05-01T23:59:59.000Z

145

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies  

E-Print Network [OSTI]

The advent of next generation sequencing has coincided with a growth in interest in using these approaches to better understand the role of the structure and function of the microbial communities in human, animal, and ...

Gevers, Dirk

146

Rapid sequence determination of late simian virus 40 16S mRNA leader by using inhibitors of reverse transcriptase  

Science Journals Connector (OSTI)

...The fragments were fractionated by RPC5 (gift from Bruce Roe) column chromatography (19-21). Digestion of the Alu I...Res. 5, 13-21. 22. Deely, R. G., Gordon, J. I., Burns, A. T., Mullinex, K. P., Bina- Stein, M. & Goldberger...

M Bina-Stein; M Thoren; N Salzman; J A Thomspon

1979-01-01T23:59:59.000Z

147

Mutational Analysis of the Wilms' Tumor (WTI) Gene  

Science Journals Connector (OSTI)

Mutations of the Wilms’ tumor (WT1) gene have been shown to underlie a proportion of cases of Wilms’ tumor, an embryonal kidney cancer occurring mainly in childhood. The WTl gene comprtses ten exons spanning a...

Linda King-Underwood; Kathy Pritchard-Jones

1996-01-01T23:59:59.000Z

148

Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes  

E-Print Network [OSTI]

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

Babu, M. Madan

149

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

SciTech Connect (OSTI)

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.

Edlund, A.; Jansson, J.

2008-05-01T23:59:59.000Z

150

Regulation of Gene Expression by Synthetic DNA-Binding Ligands  

E-Print Network [OSTI]

Regulation of Gene Expression by Synthetic DNA-Binding Ligands Peter B. Dervan ( ) · Adam T. Poulin

Dervan, Peter B.

151

Alteration in Copy Numbers of Genes as a Mechanism for Acquired Drug Resistance  

Science Journals Connector (OSTI)

...RP11-334D3 and RP11-95P2 (containing markers D16S525 and SHGC-11838, respectively) distal to ABCC1 (Fig. 1I) . SK3...BCL2L2 lay on the region spanning between markers D14S879 and SHGC-101614 (BACs, RP11-146E13 and RP11-144C18, respectively...

Kohichiroh Yasui; Saori Mihara; Chen Zhao; Hiroyuki Okamoto; Fumiko Saito-Ohara; Akihiro Tomida; Tadao Funato; Akira Yokomizo; Seiji Naito; Issei Imoto; Takashi Tsuruo; Johji Inazawa

2004-02-15T23:59:59.000Z

152

Evidence Combination in Hidden Markov Models for Gene Bronislava Brejova  

E-Print Network [OSTI]

the human and fruit fly genomes. The use of sequence evolutionary conservation as a source of evidence introduces new techniques for finding genes in genomic sequences. Genes are regions of a genome encoding proteins of an organism. Identification of genes in a genome is an important step in the annotation process

Brejova, Brona

153

2005 Nature Publishing Group Photosynthesis genes in marine viruses yield  

E-Print Network [OSTI]

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

Church, George M.

154

An Adaptive GA—PSO Approach with Gene Clustering to Infer S-system Models of Gene Regulatory Networks  

Science Journals Connector (OSTI)

......In addition, we plan to develop advanced...analysis of gene regulatory networks. Nat...simulation of genetic regulatory systems: a literature review. J. Comput. Biol...Inference of Gene Regulatory Networks Using S-system......

Wei-Po Lee; Yu-Ting Hsiao

2011-09-01T23:59:59.000Z

155

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

E-Print Network [OSTI]

of root-knot nematode resistance (RNR) in Auburn 623 - one of the most desirable sources for RNR in Upland cottons, identification of DNA markers for the RNR genes and characterization of disease resistance gene candidates in cotton. Genetic analysis...

He, Limei

2000-01-01T23:59:59.000Z

156

Human interactome resource and gene set linkage analysis for the functional interpretation of biologically meaningful gene sets  

Science Journals Connector (OSTI)

......interactome resource and gene set linkage analysis for the functional interpretation of biologically meaningful gene sets Xi Zhou Pengcheng Chen Qiang Wei Xueling Shen Xin Chen * *To whom correspondence should be addressed. Department of Bioinformatics, College......

Xi Zhou; Pengcheng Chen; Qiang Wei; Xueling Shen; Xin Chen

2013-08-15T23:59:59.000Z

157

E-Print Network 3.0 - arctica gene cloning Sample Search Results  

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

Summary: 19 GENE2147X KIAA0282 KIAA0282 protein GENE2906X Homo sapiens cDNA FLJ13700 fis, clone PLACE2000216... 2DTL protein GENE3683X LAD1 ladinin 1 GENE6843X Homo sapiens...

158

HyDRA: Gene Prioritization via Hybrid Distance-Score Rank Aggregation  

Science Journals Connector (OSTI)

......computational techniques for inferring disease genes through a set of training genes and carefully chosen similarity criteria. Test genes are scored based on their average similarity to the training set, and the rankings of genes under various similarity criteria......

Minji Kim; Farzad Farnoud; Olgica Milenkovic

2014-11-01T23:59:59.000Z

159

E-Print Network 3.0 - anoxia-responsive gene expression Sample...  

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

. . . . . . . . . . . . . . . . . . . . . 266 3. Anoxia-responsive gene expression in turtle organs... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ....

160

The impact of long-distance horizontal gene transfer on prokaryotic genome size  

E-Print Network [OSTI]

Horizontal gene transfer (HGT) is one of the most dominant forces molding prokaryotic gene repertoires. These repertoires can be as small as ?200 genes in intracellular organisms or as large as ?9,000 genes in large, ...

Cordero Sanchez, Otto Xavier

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

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

ScienceCinema (OSTI)

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.

Lukjancenko, Oksana [Technical University of Denmark

2013-01-25T23:59:59.000Z

162

Archaeal Communities in Surface Stream Sediments Contact: Tony Palumbo (palumboav@ornl.gov, 865-574-5845)  

E-Print Network [OSTI]

Archaeal Communities in Surface Stream Sediments Contact: Tony Palumbo (palumboav@ornl.gov, 865 freshwater stream sediments and compared to those present in an uncontaminated stream located in the vicinity region of 16S rRNA amplified from twelve sediment samples. Crenarchaeota composed 76 % of the 1

163

AQUATIC MICROBIAL ECOLOGY Aquat Microb Ecol  

E-Print Network [OSTI]

Net production of dissolved organic carbon (DOC) in the open sea is ultimately derived from of the `malfunctioning microbial loop' during late spring and summer at BATS. Objectives of the study were to determine carbon · Nutrient limitation · 16S rRNA · BATS Resale or republication not permitted without written

Hansell, Dennis

164

Characterization of a unique embedded gene  

E-Print Network [OSTI]

and RzlW38am alleles. . . . . Is the A(SR) deletion also Rz and Rzl defective?. . . . . . . . , . . . . . . . . . . . . . . . . . . . . Epitope-tags on Rz and Rzl genes for localization of Rz1 protein and interaction analysis between Rz and Rzl proteins... in the envelope fractions of infected cells (Kedzierska et al. , 1996). However, this protein species identified in immunoblots as the Rz1 product was not present in the envelope fractions of induced lysogens carrying the I A(SR) prophage, although the deletion...

Zhang, Ning

1999-01-01T23:59:59.000Z

165

Molecular characterization of Theileria spp. using ribosomal RNA  

E-Print Network [OSTI]

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 using gDNA. The SSU rRNA gene...

Bendele, Kylie Gayle

2005-11-01T23:59:59.000Z

166

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

SciTech Connect (OSTI)

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

Chakraborty, Romy; Chakraborty, Romy

2008-08-12T23:59:59.000Z

167

An iterative searching and ranking algorithm for prioritising pharmacogenomics genes  

Science Journals Connector (OSTI)

Pharmacogenomics (PGx) studies are to identify genetic variants that may affect drug efficacy and toxicity. A machine understandable drug-gene relationship knowledge is important for many computational PGx studies and for personalised medicine. A comprehensive and accurate PGx-specific gene lexicon is important for automatic drug-gene relationship extraction from the scientific literature, rich knowledge source for PGx studies. In this study, we present a bootstrapping learning technique to rank 33,310 human genes with respect to their relevance to drug response. The algorithm uses only one seed PGx gene to iteratively extract and rank co-occurred genes using 20 million MEDLINE abstracts. Our ranking method is able to accurately rank PGx-specific genes highly among all human genes. Compared to randomly ranked genes (precision: 0.032, recall: 0.013, F1: 0.018), the algorithm has achieved significantly better performance (precision: 0.861, recall: 0.548, F1: 0.662) in ranking the top 2.5% of genes.

Rong Xu; QuanQiu Wang

2013-01-01T23:59:59.000Z

168

Metagenomic gene annotation by a homology-independent approach  

SciTech Connect (OSTI)

Fully understanding the genetic potential of a microbial community requires functional annotation of all the genes it encodes. The recently developed deep metagenome sequencing approach has enabled rapid identification of millions of genes from a complex microbial community without cultivation. Current homology-based gene annotation fails to detect distantly-related or structural homologs. Furthermore, homology searches with millions of genes are very computational intensive. To overcome these limitations, we developed rhModeller, a homology-independent software pipeline to efficiently annotate genes from metagenomic sequencing projects. Using cellulases and carbonic anhydrases as two independent test cases, we demonstrated that rhModeller is much faster than HMMER but with comparable accuracy, at 94.5percent and 99.9percent accuracy, respectively. More importantly, rhModeller has the ability to detect novel proteins that do not share significant homology to any known protein families. As {approx}50percent of the 2 million genes derived from the cow rumen metagenome failed to be annotated based on sequence homology, we tested whether rhModeller could be used to annotate these genes. Preliminary results suggest that rhModeller is robust in the presence of missense and frameshift mutations, two common errors in metagenomic genes. Applying the pipeline to the cow rumen genes identified 4,990 novel cellulases candidates and 8,196 novel carbonic anhydrase candidates.In summary, we expect rhModeller to dramatically increase the speed and quality of metagnomic gene annotation.

Froula, Jeff; Zhang, Tao; Salmeen, Annette; Hess, Matthias; Kerfeld, Cheryl A.; Wang, Zhong; Du, Changbin

2011-06-02T23:59:59.000Z

169

IBM Blue Gene Parallel Supercomputer, Brookhaven National Laboratory, (BNL)  

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

L L Overview Simple Example: Compile, Link, Run Compiler Invocation Compile and Link Tips Batch Job Submission Applications Support Math Libraries MPI Version IBM Fortran Blue Gene & Linux Manuals (IBM Redbooks) Much of the info you need will be in the Linux manual, but there is also some Blue Gene-specific info in the Blue Gene manual. Current Fortran compiler version number can be determined on fen by typing: ls /opt/ibmcmp/xlf/bg, will be highest number listed. IBM C/C++ Blue Gene & Linux Manuals (IBM Redbooks) Much of the info you need will be in the Linux manual, but there is also some Blue Gene-specific info in the Blue Gene manual. Linux Manual: Go to XL C/C++ for Linux, choose the Product Library link, then select current version number in tab at page top. (Current C/C++

170

IBM Blue Gene Parallel Supercomputer, Brookhaven National Laboratory, (BNL)  

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

How to Login How to Login Please note, New York Blue/L has been decommissioned and these web pages have not yet been updated to reflect its removal from service. The New York Blue/P is now one rack and remains in service. The BNL Blue Gene/Q also remains in service. Introduction Accessing the Blue Gene SSH Gateways Accessing the Blue Gene Front-End Nodes Accessing the Visualization Cluster Accessing the CSC GPU Cluster SSH Tunneling Introduction The only way to access Blue Gene computing resources remotely (outside the Blue Gene network enclave) is through the Blue Gene ssh gateways. Even users connecting from inside the BNL campus network need to go through the gateways. Outside the BNL campus the gateways are known as: ssh.bluegene.bnl.gov Inside the BNL campus they are known as: ssh.bluegene.bnl.local

171

Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics  

Science Journals Connector (OSTI)

......E-value cutoff (currently set to 0.1). For each reference...nodes without BLAST hits (N is set to 5). This process is repeated...threshold) and (iii) the alignment covers at least 40% of the length of...The identity threshold is set to 60%, since genes may not......

Yu-Wei Wu; Mina Rho; Thomas G. Doak; Yuzhen Ye

2012-09-15T23:59:59.000Z

172

Characterization of the functional gene and several processed pseudogenes in the human triosephosphate isomerase gene family.  

Science Journals Connector (OSTI)

...hybridized TPI probe and rehybridized with nick- translated pBR322 DNA. TPI gene and...nitrocellulose, and hybridized with a nick-translated cDNA insert from pHTPI-5a...certain sequences with the TPI promoter that merit mention. These sequences include the GTGGCC...

J R Brown; I O Daar; J R Krug; L E Maquat

1985-07-01T23:59:59.000Z

173

STUDY OF GENE SILENCING IN RICE: A ROOT PREFERENTIAL GENE RCG2  

E-Print Network [OSTI]

involved in the gene silencing of the YXB lines. DNA methylation analysis, northern blotting, RT-PCR and small RNA analysis supported the conclusion that PTGS and TGS are present in the silenced plants. Promoter analysis in silico and using promoter...

Shi, Xiangyu

2010-07-14T23:59:59.000Z

174

From Green to Red: Horizontal Gene Transfer of the Phycoerythrin Gene Cluster between Planktothrix Strains  

Science Journals Connector (OSTI)

...Evolutionary and Genomic Microbiology From Green to Red: Horizontal Gene Transfer of the...phycoerythrin, which are responsible for green and red appearance, respectively. Sequence...that is otherwise more closely related to green strains. Our data show that the insertion...

Ave Tooming-Klunderud; Hanne Sogge; Trine Ballestad Rounge; Alexander J. Nederbragt; Karin Lagesen; Gernot Glöckner; Paul K. Hayes; Thomas Rohrlack; Kjetill S. Jakobsen

2013-08-30T23:59:59.000Z

175

Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes  

Science Journals Connector (OSTI)

......sequence. Using a large gene family as a test case, Figmop was found to be more sensitive...but this may not be enough to make and test evolutionary and functional hypotheses...confirmed full-length proteins from the test species. The user runs the MEME software......

David M. Curran; John S. Gilleard; James D. Wasmuth

2014-11-15T23:59:59.000Z

176

Heterocyst Morphogenesis and Gene Expression in Anabaena sp. PCC 7120  

E-Print Network [OSTI]

experiments we found that conR (all0187) gene is necessary for normal septum-formation of vegetative cells, diazotrophic grow, and heterocyst morphogenesis. In our studies we characterized the expression of sigma factors genes in Anabaena PCC 7120 during... are developmentally regulated................... 15 Heterocyst pattern formation requires dynamic signaling............................ 17 II Anabaena SP. STRAIN PCC 7120 GENE conR (ALL0187) CONTAINS A LytR-CpsA-Psr DOMAIN, IS DEVELOPMENTALLY REGULATED...

Mella Herrera, Rodrigo Andres

2010-10-12T23:59:59.000Z

177

Mutator gene and hereditary non-polyposis colorectal cancer  

DOE Patents [OSTI]

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.

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

2008-02-05T23:59:59.000Z

178

Gene Geracao Eolica Do Nordeste | Open Energy Information  

Open Energy Info (EERE)

Place: Brazil Sector: Wind energy Product: Aims to manufacture and commercialize wind turbines generators between 3 and 10kW. Incubated by Padetec. References: Gene - Geracao...

179

Crystallization of Hfq protein: a bacterial gene-expression regulator  

Science Journals Connector (OSTI)

A global regulator of gene expression in bacteria, Hfq protein, has been crystallized and X-ray diffraction data have been collected to 2.1 ? resolution.

Vassilieva, I.M.

2003-05-23T23:59:59.000Z

180

Gene Controls Flowering Time in Corn - Energy Innovation Portal  

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

Gene Controls Flowering Time in Corn Great Lakes Bioenergy Research Center Contact GLBRC About This Technology Technology Marketing Summary Plant development is marked by three...

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

Post transcriptional regulation of chloroplast gene expression by nuclear encoded gene products. Progress report, June 1, 1990--June 30, 1992  

SciTech Connect (OSTI)

Many individual chloroplast genes require the products of a collection of nuclear genes for their successful expression. These nuclear gene products apparently work with great specificity, each committed to the expression of a single chloroplast gene. We have chosen as a model nuclear mutants of Chlamydomonas affected in different stages in the expression of the chloroplast encoded Photosystem II polypeptide, D2. We have made the progress in understanding how nuclear gene products affect the translation of the D2 encoding MRNA. Two nuclear genes are required for this process which have been mapped genetically. In contrast to other examples of nuclear control of translation in the chloroplast, these nuclear gene products appear to be required either for specific stages in translation elongation or for the post-translational stabilization of the nascent D2 protein. Pseudoreversion analysis has led us to a locus which may be directly involved in D2 expression. We have made considerable progress in pursuing the molecular basis of psbd MRNA stabilization. psbD 5` UTR specific transcripts have been synthesized in vitro and used in gel mobility shift assays. UV-crosslinking studies are underway to identify the transacting factors which bind to these sequences. The continued examination of these mutants will help us to understand how nuclear gene products work in this specific case of chloroplast gene expression, and will elucidate how two distinct genomes can interact generally.

Kuchka, M.R.

1992-08-01T23:59:59.000Z

182

The use of microarrays in microbial ecology  

SciTech Connect (OSTI)

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

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

2009-09-15T23:59:59.000Z

183

Evolutionary analyses of nonfamily genes in plants  

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

73 73 © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd Received Date : 11-May-2012 Revised Date : 16-Oct-2012 Accepted Date : 07-Nov-2012 Article type : Original Article Evolutionary analyses of non-family genes in plants Chu-Yu Ye 1,2,3,4 , Ting Li 1,3,4 , Hengfu Yin 1 , David J. Weston 1 , Gerald A. Tuskan 1,2 , Timothy J. Tschaplinski 1,2 , Xiaohan Yang 1,2,* 1 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA 2 BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA 3 Present addresses: Beijing Forestry University, Beijing 100083, China (C.-Y.Y.); Pioneer Hi- Bred International, Johnston, IA 50131, USA (T.L.) 4 These authors contributed equally to this work. * Corresponding author:

184

HumanMouse Gene Identification by Comparative Evidence Integration and  

E-Print Network [OSTI]

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

Pavlovic, Vladimir

185

A novel method for finding small highly discriminant gene sets  

E-Print Network [OSTI]

-modified algorithm uses the best aspects of the filter algorithms and the best aspects of the wrapper algorithms to find very small yet highly discriminant gene sets. We also discuss methods to evaluate alternate, ambiguous gene sets. Applying our new mixed model...

Gardner, Jason H.

2004-11-15T23:59:59.000Z

186

Parallel evolution of chimeric fusion genes Corbin D. Jones*  

E-Print Network [OSTI]

Parallel evolution of chimeric fusion genes Corbin D. Jones* and David J. Begun *Department in Drosophila to guide our analyses. We discovered a fundamental similarity in the temporal, spatial, and types in the evolution of chimeric fusion genes. We suggest that the patterns we observed are both general and predictive

Begun, David

187

Coding Tandem Repeats Generate Diversity in Aspergillus fumigatus Genes  

Science Journals Connector (OSTI)

...Genes containing multiple coding mini- and microsatellite repeats...growth was observed under a grid-mounted Olympus CK inverted...conidia were counted under a grid-mounted Olympus CK inverted...Genes containing multiple coding mini- and microsatellite repeats...

Emma Levdansky; Jacob Romano; Yona Shadkchan; Haim Sharon; Kevin J. Verstrepen; Gerald R. Fink; Nir Osherov

2007-06-08T23:59:59.000Z

188

Analogue Circuit Control through Gene Kester Clegg, Susan Stepney  

E-Print Network [OSTI]

offer an intriguing plat- form for automated design by evolutionary algorithms. Like previous evolvable) or adaptable control (homoeostasis). 1 Background and motivation We present a system for the automated example, ana- logue filters) are modelled as `genes'. Genes are `expressed' in response to circuit output

Stepney, Susan

189

Grouped graphical Granger modeling for gene expression regulatory networks discovery  

Science Journals Connector (OSTI)

......Hinkley (2006) for a review]. More precisely...method to uncover gene regulatory networks for the human...As future work we plan to consider a variant...time-delayed gene regulatory networks based on temporal...et al. Modelling regulatory pathways in E.coli......

Aurélie C. Lozano; Naoki Abe; Yan Liu; Saharon Rosset

2009-06-15T23:59:59.000Z

190

Morphological evolution in land plants: new designs with old genes  

Science Journals Connector (OSTI)

...February 2012 review-article Articles...of their body plans that included...flowers. In this review, we discuss...leaves|flowers|regulatory genes| 1. The...N. 2006 Gene regulatory networks in the...of their body plans that included...flowers. In this review, we discuss...

2012-01-01T23:59:59.000Z

191

DETECTION AND DECOMPOSITION: TREATMENT-INDUCED CYCLIC GENE EXPRESSION  

E-Print Network [OSTI]

*,, , WENSHENG QIN,,|||| and JIN CHEN*,§,§§,|||| *MSU-DOE Plant Research Laboratory Michigan State University-induced disruption of the core set of cyclic genes (which control many downstream pathways) occurs in almost all the disruptions of two core circadian clock genes due to cold treatment in Arabidopsis.9 When a stress treatment

Qin, Wensheng

192

Gene for Improved Nutritional Value in Barley Seed Protein  

Science Journals Connector (OSTI)

...adhere to the starch grains in meal...screening of single seeds without affecting...Acids analysis Cereals Genes, Recessive...Proteins analysis metabolism Seeds analysis Gene...adhere to the starch grains in meal...and selection. Cereals have a low content...

L. Munck; K. E. Karlsson; A. Hagberg; B. O. Eggum

1970-05-22T23:59:59.000Z

193

Prediction of Complete Gene Structures in Human Genomic DNA  

E-Print Network [OSTI]

and RNA splicing. On the other hand, with the recent shift in the emphasis of the Human Genome ProjectPrediction of Complete Gene Structures in Human Genomic DNA Chris Burge* and Samuel Karlin model of the gene structure of human genomic sequences which incorporates descriptions of the basic

Shatkay, Hagit

194

Characterization of candidate genes in English cocker spaniel hereditary nephritis  

E-Print Network [OSTI]

Six different isoforms of Type IV collagen (colIV?1-6) have been identified. The individual isoforms of colIV are termed alpha chains and are translated from six different COLIV genes (COLIVA1-A6). Collagen Type IV gene products compose...

Camacho, Zenaido

2005-02-17T23:59:59.000Z

195

GenePRIMP: A software quality control tool  

ScienceCinema (OSTI)

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.

Amrita Pati

2010-09-01T23:59:59.000Z

196

Issue: April 2013 Algae Go to Extremes with "Borrowed" Genes  

E-Print Network [OSTI]

Issue: April 2013 Algae Go to Extremes with "Borrowed" Genes by Patricia Waldron Brand-New Genes their extreme environment. For example, some bacteria that live at high temperatures have special molecules that are highly acidic, or full of toxic metals. While most microbes that live in extreme environments

Schönknecht, Gerald

197

Comprehensive detection of cancer gene expression profiles and gene networks are impacted by the choice of pre-processing algorithm and gene-selection method  

Science Journals Connector (OSTI)

Pre-processing algorithms (PPA) and gene-selection methods (GSM) are commonly employed to select Differentially Expressed Genes (DEGs) from microarray data. Previous studies established that different combinations of PPAs and GSMs are intrinsically different in their performance to select biologically relevant DEGs. In this study, we evaluated eight combinations of PPAs and GSMs for their ability to select DEGs for prioritising gene-networks. Although the different combinations yielded dissimilar DEG-lists, all DEG-lists selected could segregate tumour from normal. Nevertheless, the DEG-list selected significantly impacted the prioritisation of cancer-associated gene-networks; hence the initial choice of PPA and GSM is crucial for subsequent interactome investigations.

N. Baskaran; Chee Keong Kwoh; Kam M. Hui

2013-01-01T23:59:59.000Z

198

BESC Submits 32 Gene Disclosures for Patents | ORNL  

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

News Careers Work with ORNL About ORNL Visiting ORNL Events and Conferences Highlights Success Stories Contact Us Index Home | ORNL | Highlights SHARE BESC submits 32 gene disclosures for future patents July 01, 2012 Plant geneticist Wellington Muchero examines phenotypic traits of Populus transgenic lines grown in a greenhouse. The Bioenergy Science Center (BESC) at Oak Ridge National Laboratory (ORNL) is preparing invention disclosures for 32 different genes that can help improve the yield of ethanol from cellulosic biomass. These genes or their variants function to overcome recalcitrance-difficulty in breaking down cellulosic biomass to release sugars. Several members of ORNL's Biosciences Division are submitting disclosures: 16 genes by Wellington Muchero, 10 genes by Udaya Kalluri, and

199

Cell number regulator genes in Prunus provide candidate genes for the control of fruit size in sweet and sour cherry  

E-Print Network [OSTI]

Cell number regulator genes in Prunus provide candidate genes for the control of fruit size at Springerlink.com Abstract Striking increases in fruit size distinguish cultivated descendants from small-fruited wild progen- itors for fleshy fruited species such as Solanum lycopersicum (tomato) and Prunus spp

van der Knaap, Esther

200

Ontogenomic study of the relationship between number of gene splice variants and GO categorization  

Science Journals Connector (OSTI)

......Ashburner et al., 2000a; Gene Ontology Consortium, 2006; Little...has been analyzed. The Gene Ontology (GO; Ashburner et al., 2000b; Gene Ontology Consortium, 2006) and tools...form of clustered image map (CIM) highlighted GO categories......

Ari B. Kahn; Barry R. Zeeberg; Michael C. Ryan; D. Curtis Jamison; David M. Rockoff; Yves Pommier; John N. Weinstein

2010-08-15T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

E-Print Network 3.0 - amp-binding protein gene Sample Search...  

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

2 protein... 19 GENE2147X KIAA0282 KIAA0282 protein GENE2906X Homo sapiens cDNA FLJ13700 fis, clone PLACE2000216... GENE3053X HMGIY high-mobility group (nonhistone ... Source:...

202

E-Print Network 3.0 - arenaviruses genes proteins Sample Search...  

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

2 protein... 19 GENE2147X KIAA0282 KIAA0282 protein GENE2906X Homo sapiens cDNA FLJ13700 fis, clone PLACE2000216... GENE3053X HMGIY high-mobility group (nonhistone ... Source:...

203

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

E-Print Network [OSTI]

significantly expressed genes in response to bioethanol conversion inhibitor 5-hydroxymethylfurfural model, esti- mated from time course gene expression measurements during the earlier exposure to 5-hydroxymethylfurfural, reveals known transcriptional reg- ulations as well as potential significant genes involved

Song, Joe

204

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

SciTech Connect (OSTI)

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.

Zylstra, Gerben; van der Meer, Jan Roelof

2013-03-05T23:59:59.000Z

205

E-Print Network 3.0 - adaptive gene expression Sample Search...  

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

in splice site predictors adapted from the Gene... A Critical Review of Gene Prediction Software Mark ... Source: Bejerano, Gill - Departments of Computer Science & Developmental...

206

Gene expression in human fungal pathogen Coccidioides immitis changes as arthroconidia differentiate into spherules and mature  

E-Print Network [OSTI]

transform- ation is the alpha amylase (AMY1) gene. This geneJT, Goldman WE: An alpha-(1,4)-amylase is essential for

Viriyakosol, Suganya; Singhania, Akul; Fierer, Joshua; Goldberg, Jonathan; Kirkland, Theo N; Woelk, Christopher H

2013-01-01T23:59:59.000Z

207

E-Print Network 3.0 - adenoviral gene therapy Sample Search Results  

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

Stanford University Collection: Biology and Medicine 46 THE JOURNAL OF GENE MEDICINE RESEARCH ARTICLE J Gene Med 2003; 5: 300310. Summary: . Alvarez RD, Gomez-Navarro J, Wang...

208

E-Print Network 3.0 - alpha gene family Sample Search Results  

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

birds, such as expansions in the keratin gene family, which are the pro- teinaceous building... in the study of gene family evolution. ... Source: Kellis, Manolis - Computer...

209

E-Print Network 3.0 - active genes based Sample Search Results  

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

Biology and Medicine 69 GeneTracer: Gene Sequence Analysis of Disease Mutations VAST 2010 Mini Challenge 3 Award: Excellent Process Explanation Summary: for a disease outbreak,...

210

E-Print Network 3.0 - acads gene variation Sample Search Results  

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

of vertebrate gene deserts Summary: deserts). However, there is a wide variation in ECR density among different gene deserts, which cannot... Evolution and functional...

211

E-Print Network 3.0 - acetyl-coa carboxylase-alpha gene Sample...  

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

is to deter- mine the biological function of all the gene pro... microbial genomes highlights the need for func- tional characterization of the gene ... Source: Gerstein,...

212

E-Print Network 3.0 - anemia gene facc Sample Search Results  

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

FRAMEWORKS FOR ENGINEERS Summary: disease and nature of the mutation that leads to Sickle Cell Anemia? E. The gene defective in Sickle Cell... Anemia is a recessive gene....

213

E-Print Network 3.0 - abca3 gene leads Sample Search Results  

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

and Medicine 11 RESOVING THE GENE TREE AND SPECIES TREE PROBLEM BY PHYLOGENETIC MINING Summary: RESOVING THE GENE TREE AND SPECIES TREE PROBLEM BY PHYLOGENETIC MINING XIAOXU...

214

E-Print Network 3.0 - arsenite oxidase gene Sample Search Results  

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

gene pgpA in arsenite-resistant Leishmania tarentolae. EMBO J 16: 30573065 Howell N, Gilbert K... (1989) Internal frameshifts within the mitochondrial genes for cytochrome ......

215

E-Print Network 3.0 - acquired cns gene Sample Search Results  

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

Summary: . Then, in the insect lineage, maternal expression of zen was lost and the bcd gene was acquired through... genes in different lineages have one, two or three...

216

E-Print Network 3.0 - adenoviral gene delivery Sample Search...  

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

for both inter and intra species gene therapy delivery in adults. The gene therapy vehicle is tolerated... cell potential Nonviral delivery of selected ... Source:...

217

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

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

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

218

E-Print Network 3.0 - autism candidate gene Sample Search Results  

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

, presumably causing ASD. For extracting ASD candidate genes, we developed an analysis pipeline for rare... Atlas", ASD candidate genes have ... Source: Hochreiter, Sepp -...

219

Apoptotic detection methods — from morphology to gene  

Science Journals Connector (OSTI)

To date, many terms have been given for cell death and forgotten before they became widely accepted. Most researchers studying cell death use some terms for cell death that have survived over centuries and regard apoptosis and programmed cell death (PCD), and necrosis and oncosis as synonymous. The different terminologies used for cell death depending on the preference of researchers sometimes cause confusion in the study of apoptosis. The study of apoptosis was first based on cell morphology using transmission electron microscopy (TEM): chromatin condensation, cellular shrinkage, budding and apoptotic body formation. Recently, marked progress in biochemistry, molecular biology and genetics provided researchers of apoptosis various tools for apoptotsis detection, such as the terminal deoxynucleotidyl transferase (TdT)-mediated dUTP-biotin nick end-labeling (TUNEL) method, agarose gel electrophoresis using extracted DNA, staining methods using fluorescence dyes, and flow cytometry. This review focuses on the following topics: history of the study of cell death and its classification, apoptosis-related proteins and their signal pathways, morphological, biochemical and molecular biological methods of apoptosis detection, and the transcriptional regulation of bcl-2 using the real-time Southwestern method and cancer gene therapy. In addition, the merits and demerits of the above-mentioned apoptosis detection methods are discussed.

Yoshinori Otsuki; Zhonglian Li; Masa-Aki Shibata

2003-01-01T23:59:59.000Z

220

Mutational analysis of the [phi] X174 E Gene  

E-Print Network [OSTI]

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

Morham, Scott Garton

1985-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

Analysis of the [lambda] S? gene function by mutational suppressors  

E-Print Network [OSTI]

the ssb-ral region. The ~sl C mutation which confers resistance to the plasmid borne S gene was mapped to 3 min on the E. coli chromosome and shown to impart a 6-9 minute delay in lysis by wild type The lysis regulator proposed by Campbell and Rolfe... genes transcribed from the strong pR' promoter, beginning about 8-10 minutes after induction of a l lysogen. The product of the R gene is a transglycosylase or endolysin (Campbell and Rolfe, 1975; Bienkowska and Taylor, 1980; Bienkowska et al...

Sohaskey, Charles David

2012-06-07T23:59:59.000Z

222

Single, Key Gene Discovery Could Streamline Production of Biofuels |  

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

Single, Key Gene Discovery Could Streamline Production of Biofuels 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, DC -- A team of researchers at the Department of Energy's BioEnergy Science Center (BESC) have pinpointed the exact, single gene that controls ethanol production capacity in a microorganism. This discovery could be the missing link in developing biomass crops that produce higher concentrations of ethanol at lower costs. "The Department of Energy relies on the scientific discoveries of its labs and research centers to improve the production of clean energy sources," said Energy Secretary Steven Chu. "This discovery is an important step in developing biomass crops that could increase yield of

223

; Evolution of genes and genomes on the Drosophila phylogeny  

E-Print Network [OSTI]

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

Kellis, Manolis

224

Visually Relating Gene Expression and in vivo DNA Binding Data  

SciTech Connect (OSTI)

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

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

2011-09-20T23:59:59.000Z

225

Circadian clock genes and risk of fatal prostate cancer  

Science Journals Connector (OSTI)

Circadian genes may be involved in regulating cancer-related pathways, including cell proliferation, DNA damage response, and apoptosis. We aimed to assess the role of genetic variation in core circadian rhyth...

Sarah C. Markt; Unnur A. Valdimarsdottir; Irene M. Shui…

2014-11-01T23:59:59.000Z

226

Scaling up accurate phylogenetic reconstruction from gene-order data  

Science Journals Connector (OSTI)

......not a problem; for nuclear genomes with a thousand...workable size. Thus datasets of nuclear genomes with large pairwise...computation. As larger datasets of gene-order data...to the much larger nuclear genomes (thousands......

Jijun Tang; Bernard M.E. Moret

2003-07-01T23:59:59.000Z

227

Low-Rank Regularization for Learning Gene Expression Programs  

E-Print Network [OSTI]

8 | Issue 12 | e82146 Low-Rank for Learning Gene Expressiona convex relaxation of the rank of W [22,23]. Since nuclearcall (3) the linear low-rank model in the following. The

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

2013-01-01T23:59:59.000Z

228

Polyelectrolyte-based Nanoparticles for Gene and Protein Delivery  

E-Print Network [OSTI]

were used to systematically inspect gene transfection efficiency and cytotoxicity. Transfection efficiency of non-degradable nanogels increased with increasing amounts of positive charge. Intriguingly, acid-labile nanogels bearing low charge showed...

Khondee, Supang

2011-05-31T23:59:59.000Z

229

A mathematical programming approach for gene selection and tissue classification  

Science Journals Connector (OSTI)

......programming approach for gene selection...Department of Management Science and Statistics...programming approach can rival...Department of Management Science and Statistics...Innovative Approaches to the Science of Management . Quorum Books......

Minghe Sun; Momiao Xiong

2003-07-01T23:59:59.000Z

230

Dynamics of gene expression and signal transduction in single cells  

E-Print Network [OSTI]

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 ...

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

2009-01-01T23:59:59.000Z

231

The zebrafish progranulin gene family and antisense transcripts  

Science Journals Connector (OSTI)

The progranulin gene family in zebrafish has four members encoding growth factors that evolved from a single ancestor, as is seen in mammals. Their diverse structural makeup and distinct expression patterns point to diversified functions in the four fish proteins.

Benoît Cadieux; Babykumari P Chitramuthu; David Baranowski; Hugh PJ Bennett

2005-11-08T23:59:59.000Z

232

4.2 Selection Changes in gene frequency  

E-Print Network [OSTI]

the best-known example of this situation in man concerns the phenomenon of sickle-cell anaemia. The maintenance of high frequencies for both the sickle cell gene and its normal allele in certain East African

Hsu, Sze-Bi

233

Brief Communication 1195 A gene trap approach in Xenopus  

E-Print Network [OSTI]

developed several gene trap vectors, using the green fluorescent protein (GFP) as a marker. Using, including expression in the epiphysis, the olfactory bulb and placodes, the eyes, ear, brain, muscles, tail

Amaya, Enrique

234

Expression of Genes Linked to NOx Detoxification in Aerobic Bacteria  

E-Print Network [OSTI]

operons referred to as the nif cluster. This suite of genesgenes not found in the nif clusters of K. pneumoniae (i.e.is high conservation among nif gene organization based on

Cua, Lynnie

2010-01-01T23:59:59.000Z

235

Highly Effective Gene Transfection In Vivo by Alkylated Polyethylenimine  

E-Print Network [OSTI]

We mechanistically explored the effect of increased hydrophobicity of the polycation on the efficacy and specificity of gene delivery in mice. N-Alkylated linear PEIs with varying alkyl chain lengths and extent of substitution ...

Fortune, Jennifer A.

236

RESEARCH Open Access Gene expression and fractionation resistance  

E-Print Network [OSTI]

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

Sankoff, David

237

A compendium of gene expression in normal human tissues  

E-Print Network [OSTI]

Gene Expression Index, the HuGE In- dex, http://www.hugeindex.org) for future studies of patho completion of the human genome project (8, 37a), greater attention is now focused on defining the biological

Weng, Zhiping

238

PI Control of Gene Expression in Tumorous Cell Lines  

E-Print Network [OSTI]

3 HT29 cell line data for starved and then fed 20% FBS group (Group 1), starved with no FBS group (Group 2), and no starvation group (Group 3) for the genes JUN, MYC, and EGR1......................................................... 15 4... Normalized HEK cell line data for starved and then fed 20% FBS group (Group 1), starved with no FBS group (Group 2), and no starvation group (Group 3) for the genes JUN, MYC, and EGR1........................................ 16 5 Normalized HT29 cell...

Mendonca, Rouella J.

2010-01-16T23:59:59.000Z

239

Adaptations to Endosymbiosis in a Cnidarian- Dinoflagellate Association: Differential Gene Expression and Specific Gene Duplications  

E-Print Network [OSTI]

Trophic endosymbiosis between anthozoans and photosynthetic dinoflagellates forms the key foundation of reef ecosystems. Dysfunction and collapse of symbiosis lead to bleaching (symbiont expulsion), which is responsible for the severe worldwide decline of coral reefs. Molecular signals are central to the stability of this partnership and are therefore closely related to coral health. To decipher inter-partner signaling, we developed genomic resources (cDNA library and microarrays) from the symbiotic sea anemone Anemonia viridis. Here we describe differential expression between symbiotic (also called zooxanthellate anemones) or aposymbiotic (also called bleached) A. viridis specimens, using microarray hybridizations and qPCR experiments. We mapped, for the first time, transcript abundance separately in the epidermal cell layer and the gastrodermal cells that host photosynthetic symbionts. Transcriptomic profiles showed large inter-individual variability, indicating that aposymbiosis could be induced by different pathways. We defined a restricted subset of 39 common genes that are characteristic of the symbiotic or aposymbiotic states. We demonstrated that transcription of many genes belonging to this set is specifically enhanced in the symbiotic cells (gastroderm). A model is proposed where the aposymbiotic and therefore heterotrophic state triggers vesicular trafficking, whereas the symbiotic and therefore autotrophic state favors metabolic exchanges between host and symbiont. Several genetic pathways were investigated in more detail: i) a key vitamin K–dependant process involved in the dinoflagellate-cnidarian recognition; ii) two cnidarian

Aurélie Moya; Virginie Magnone; Denis Allem; Paola Furla; Cécile Sabourault

240

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks  

SciTech Connect (OSTI)

The whole-genome sequence of Deinococcus geothermalis is the second for an extremely ionizing radiation (IR) resistant bacterium. The first was for Deinococcus radiodurans, which for 50 years has been the subject of extensive investigations aimed at solving the mystery of how this microbe can survive immense doses of ?-rays. So far, comparative analyses between the genome of D. radiodurans and genomes of other bacteria have failed to produce a coherent picture of the underlying resistance systems. Most surprisingly, many critical DNA repair genes identified in D. radiodurans are present in sensitive bacteria, whereas the involvement of many uncharacterized genes implicated in resistance by transcriptome analyses has not been borne out by mutant studies. Genomic subtraction of D. geothermalis from D. radiodurans was used to define a minimal gene set for extreme resistance, whereby unique genes were ruled out, and shared genes were pooled as candidates for resistance. We revise down substantially the number of potential genetic determinants of extreme radiation resistance, identify a putative regulator and a palindromic binding site for genes which comprise a distinct Deinococcus radiation response regulon, and consider the impact of those findings on the prevailing models of extreme radiation resistance.

Makarova, Kira S.; Omelchenko, M. V.; Gaidamakova, E.; Matrosova, V.; Vasilenko, A.; Zhai, M.; Lapidus, Alla; Copeland, A.; Kim, E.; Land, M.; Mavromatis, Konstantinos; Pitluck, S.; Richardson, P. M.; Detter, J. C.; Brettin, T.; Saunders, Elizabeth; Lai, Barry; Ravel, B.; Kemmer, K. M.; Wolf, Y. I.; Sorokin, Alexander; Gerasimova, A. V.; Gelfand, Mikhail S.; Fredrickson, Jim K.; Koonin, Eugene V.; Daly, M. J.

2007-09-26T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

Glucose Regulates the Expression of the Apolipoprotein A5 Gene  

SciTech Connect (OSTI)

The apolipoprotein A5 gene (APOA5) is a key player in determining triglyceride concentrations in humans and mice. Since diabetes is often associated with hypertriglyceridemia, this study explores whether APOA5 gene expression is regulated by alteration in glucose homeostasis and the related pathways. D-glucose activates APOA5 gene expression in a time- and dose-dependent manner in hepatocytes, and the glycolytic pathway involved was determined using D-glucose analogs and metabolites. Together, transient transfections, electrophoretic mobility shift assays and chromatin immunoprecipitation assays show that this regulation occurs at the transcriptional level through an increase of USF1/2 binding to an E-box in the APOA5 promoter. We show that this phenomenon is not due to an increase of mRNA or protein expression levels of USF. Using protein phosphatases 1 and 2A inhibitor, we demonstrate that D-glucose regulates APOA5 gene via a dephosphorylation mechanism, thereby resulting in an enhanced USF1/2-promoter binding. Last, subsequent suppressions of USF1/2 and phosphatases mRNA through siRNA gene silencing abolished the regulation. We demonstrate that APOA5 gene is up regulated by D-glucose and USF through phosphatase activation. These findings may provide a new cross talk between glucose and lipid metabolism.

Fruchart, Jamila; Nowak, Maxime; Helleboid-Chapman, Audrey; Jakel, Heidelinde; Moitrot, Emmanuelle; Rommens, Corinne; Pennacchio, Len A.; Fruchart-Najib, Jamila; Fruchart, Jean-Charles

2008-04-07T23:59:59.000Z

242

Confirmation of the chromosomal localization of human lamp genes and their exclusion as candidate genes for Salla disease  

Science Journals Connector (OSTI)

Salla disease is an inherited lysosomal storage disorder caused by accumulation of free sialic acid in the lysosomes. Lamp genes, lamp A and lamp B (lysosome associated membrane proteins), are the first known ...

Johanna Schleutker; Leena Haataja; Martin Renlund; Lea Puhakka…

1991-11-01T23:59:59.000Z

243

Efficient mutagenesis of the rhodopsin gene in rod photoreceptor neurons in mice  

E-Print Network [OSTI]

, 2011; Accepted March 17, 2011 ABSTRACT Dominant mutations in the rhodopsin gene, which is expressed

Wensel, Theodore G.

244

Analysis of mixed C-means clustering approach for brain tumour gene expression data  

Science Journals Connector (OSTI)

Data mining has become an important topic in effective analysis of gene expression data due to its wide application in the biomedical industry. A gene cluster is a set of two or more genes that serve to encode for the same or similar products. Gene clustering ...

S. Selva Kumar; H. Hannah Inbarani

2013-05-01T23:59:59.000Z

245

Gene expression profiling of candidate genes in peripheral blood mononuclear cells for predicting toxicity of diesel exhaust particles  

Science Journals Connector (OSTI)

Abstract To validate gene expression profiling of peripheral blood mononuclear cells (PBMCs) as a surrogate for monitoring tissue expression, this study using RT-PCR-based TaqMan low-density array (TLDA) was initiated to investigate similarities in the mRNA expression of target genes altered by exposure to diesel exhaust particles (DEPs) in freshly prepared \\{PBMCs\\} and in lungs. Adult Wistar rats were treated transtracheally with a single dose of 7.5 or 15 or 30 mg/kg \\{DEPs\\} and sacrificed 24 h later. Blood and lungs were immediately taken out and processed for RT-PCR. DEP treatment induced similar patterns of increase in the expression of polycyclic aromatic hydrocarbon-responsive cytochrome P450s, the phase II enzymes, and their associated transcription factors in both lungs and PBMCs, at all doses. Similar to that seen in lungs, a dose-dependent increase was observed in the expression of genes involved in inflammation, such as cytokines, chemokines, and adhesion molecules, in PBMCs. The expression of various genes involved in DNA repair and apoptosis was also increased in a dose-dependent manner in \\{PBMCs\\} and lungs. The present TLDA data indicating similarities in the responsiveness of candidate genes involved in the toxicity of \\{DEPs\\} between \\{PBMCs\\} and lungs after exposure to \\{DEPs\\} demonstrate that expression profiles of genes in \\{PBMCs\\} could be used as a surrogate for monitoring the acute toxicity of fine and ultrafine particulate matter present in vehicular emissions.

Ankita Srivastava; Amit Sharma; Sanjay Yadav; Swaran J.S. Flora; Uppendra N. Dwivedi; Devendra Parmar

2014-01-01T23:59:59.000Z

246

Biochemical and genetic analysis of hydrogen metabolism in Escherichia coli: The hydB gene. [Hydrogenase  

SciTech Connect (OSTI)

Production of active hyrodgenase by Escherichia coli requires several gene products. One of the essential genes, hydB, is encoded by a DNA fragment of approximately 1.0 kilobase. The hydB gene produced a protein with an apparent molecular weight of 32,000. The hydB gene was transcribed only under anaerobic conditions. Oxygen and nitrate repressed transcription of this gene. hydB gene transcription also required {sigma}{sup 60}, the product of the rpoN gene.

Sankar, P.; Shanmugam, K.T. (Univ. of Florida, Gainesville (USA))

1988-12-01T23:59:59.000Z

247

Supplementary Figure 1: Bayesian 50% majority-rule consensus trees for the combined dataset of mitochondrial genes (left) and nuclear genes (right). Color coding distinguishes  

E-Print Network [OSTI]

1 Supplementary Figure 1: Bayesian 50% majority-rule consensus trees for the combined dataset of mitochondrial genes (left) and nuclear genes (right). Color coding distinguishes groups supported by PP 99 for individual nuclear genes: Rag-1, Rag-2 and C-mos. Color coding distinguishes groups supported by PP 99

248

Running Title: LXR Regulated Genes in As4.1 cells Identification of a Novel Set of Genes Regulated by a Unique LXR-Mediated  

E-Print Network [OSTI]

Running Title: LXR Regulated Genes in As4.1 cells 1 Identification of a Novel Set of Genes Regulated by a Unique LXR-Mediated Transcription Mechanism Leonard M. Anderson1 , Sung E. Choe2 , Rustam Y, Genomic #12;Running Title: LXR Regulated Genes in As4.1 cells 2 SUMMARY We have reported previously

Church, George M.

249

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

E-Print Network [OSTI]

Chitosan-based therapeutic nanoparticles for combination gene therapy and gene silencing 2011 Keywords: Type 2 diabetes Glucagon like peptide 1 Dipeptydil-peptidase IV siRNA Chitosan Gene-IV) endoprotease. In this study, the glucosamine-based polymer chitosan was used as a cationic polymer

Buschmann, Michael

250

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

DOE Patents [OSTI]

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

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

2003-03-04T23:59:59.000Z

251

A functional gene array for detection of bacterial virulence elements  

SciTech Connect (OSTI)

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.

Jaing, C

2007-11-01T23:59:59.000Z

252

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks  

SciTech Connect (OSTI)

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.

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.

2007-07-24T23:59:59.000Z

253

Modelling gene functional linkages using yeast microarray data  

Science Journals Connector (OSTI)

Understanding how genes are functionally related requires efficient algorithms to model networks from expression data. We report a heuristic search algorithm called Two-Level Simulated Annealing (TLSA) that is more likely to find the global optimal network structure compared to conventional simulated annealing and other searching schemes. We have applied this method to search for a global optimised network structure from a synthetic data set and an expression data set of S. cerevisiae mutants. We have achieved better precision and recall compared to other searching algorithms and are able to map relationships more accurately among functionally-linked genes.

Tie Wang; Guoliang Xue; Jeffrey W. Touchman

2007-01-01T23:59:59.000Z

254

The lysis genes of bacteriophage 21: structure and function  

E-Print Network [OSTI]

(Campbell and Rolfe, 1975, Garret et al. , 1981). The most distal gene in the lysis "overlappon", le, is of unknown function and is required for lysis only under conditions of high osmolarity such as 10mH HgC12 (Young et al. , 1979). The fl gene encodes.... As mentioned above, respiratory poisons such as cyanide or dinitrophenol have been shown to trigger pg pr'ematurely in the lytic cycle, presumably by subverting the delayed action timing of pS (Campbell and Rolfe, 1975, Garret et al. , 1981). This model...

Bonovich, Maria Teresa

2012-06-07T23:59:59.000Z

255

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

SciTech Connect (OSTI)

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.

Suflita, Joseph M.; Duncan, Kathleen E.

2010-08-14T23:59:59.000Z

256

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

DOE Patents [OSTI]

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.

Woychik, Richard P. (Knoxville, TN)

2000-06-27T23:59:59.000Z

257

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

DOE Patents [OSTI]

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.

Woychik, Richard P. (Knoxville, TN)

1998-01-01T23:59:59.000Z

258

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

SciTech Connect (OSTI)

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.

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

2013-12-01T23:59:59.000Z

259

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

SciTech Connect (OSTI)

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.

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

2013-11-19T23:59:59.000Z

260

The potential of glycerol in freezing preservation of turbine oil-degrading bacterial consortium and the ability of the revised consortium to degrade petroleum wastes  

Science Journals Connector (OSTI)

Abstract The turbine oil (TuO)-degrading bacterial consortium Tank-2 (original Tank-2) was preserved as a glycerol stock at ?80 °C from 2009 to 2012. Storage methods have been unavailable so far for any TuO-degrading bacterial consortia or isolates. To evaluate the usefulness of glycerol stock, the original Tank-2 consortium frozen in glycerol at ?80 °C was thawed and then revived by repeated culture in mineral salts medium (MSM) containing 0.5% (w/w) TuO (revived Tank-2). The revived Tank-2 consortium exhibited a high activity to degrade TuO, which was equivalent to that of original Tank-2. It also degraded car engine oil, used car engine oil, Arabian light and Vityaz crude oils and TuO in wastewater. These results indicated that a glycerol stock at ?80 °C was useful for storing Tank-2. PCR-denaturing gradient gel electrophoresis (DGGE) that targeted the V3 regions of 16S rRNA gene sequences showed that the DGGE band profiles of principal bacteria were significantly different between the original and revived Tank-2 consortia and between the revived Tank-2 culture grown in MSM containing TuO and that grown in MSM containing other types of petroleum products. This suggested that bacterial strains inherently residing in Tank-2 could adjust their compositions based on the storage and culture conditions.

Kumiko Kurachi; Reia Hosokawa; Marina Takahashi; Hidetoshi Okuyama

2014-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Tr  

SciTech Connect (OSTI)

Spirochaeta caldaria Pohlschroeder et al. 1995 is an obligately anaerobic, spiral-shaped bac- terium that is motile via periplasmic flagella. The type strain, H1T, was isolated in 1990 from cyanobacterial mat samples collected at a freshwater hot spring in Oregon, USA, and is of in- terest because it enhances the degradation of cellulose when grown in co-culture with Clos- tridium thermocellum. Here we provide a taxonomic re-evaluation for S. caldaria based on phylogenetic analyses of 16S rRNA sequences and whole genomes, and propose the reclassi- fication of S. caldaria and two other Spirochaeta species as members of the emended genus Treponema. Whereas genera such as Borrelia and Sphaerochaeta possess well-distinguished genomic features related to their divergent lifestyles, the physiological and functional ge- nomic characteristics of Spirochaeta and Treponema appear to be intermixed and are of little taxonomic value. The 3,239,340 bp long genome of strain H1T with its 2,869 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Scheuner, Carmen [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Han, Cliff [Los Alamos National Laboratory (LANL); Lu, Megan [Los Alamos National Laboratory (LANL); Misra, Monica [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

2013-01-01T23:59:59.000Z

262

Thermophilic anaerobic digestion of thermal pretreated sludge: Role of microbial community structure and correlation with process performances  

Science Journals Connector (OSTI)

Abstract Thermal hydrolysis pretreatment coupled with Thermophilic Anaerobic Digestion (TAD) for Waste Activated Sludge (WAS) treatment is a promising combination to improve biodegradation kinetics during stabilization. However, to date there is a limited knowledge of the anaerobic biomass composition and its impact on TAD process performances. In this study, the structure and dynamics of the microbial communities selected in two semi-continuous anaerobic digesters, fed with untreated and thermal pretreated sludge, were investigated. The systems were operated for 250 days at different organic loading rate. 16S rRNA gene clonal analysis and Fluorescence In Situ Hybridization (FISH) analyses allowed us to identify the majority of bacterial and archaeal populations. Proteolytic Coprothermobacter spp. and hydrogenotrophic Methanothermobacter spp. living in strict syntrophic association were found to dominate in TAD process. The establishment of a syntrophic proteolytic pathway was favoured by the high temperature of the process and enhanced by the thermal pretreatment of the feeding sludge. Proteolytic activity, alone or with thermal pretreatment, occurred during TAD as proven by increasing concentration of soluble ammonia and soluble COD (sCOD) during the process. However, the availability of a readily biodegradable substrate due to pretreatment allowed to significant sCOD removals (more than 55%) corresponding to higher biogas production in the reactor fed with thermal pretreated sludge. Microbial population dynamics analysed by FISH showed that Coprothermobacter and Methanothermobacter immediately established a stable syntrophic association in the reactor fed with pretreated sludge in line with the overall improved TAD performances observed under these conditions.

M.C. Gagliano; C.M. Braguglia; A. Gianico; G. Mininni; K. Nakamura; S. Rossetti

2015-01-01T23:59:59.000Z

263

Characterization of the Deltaproteobacteria in contaminated and uncontaminated stream sediments and identification of potential mercury methylators  

SciTech Connect (OSTI)

Microbial communities were examined in surface stream sediments at 5 contaminated sites and 1 control site near Oak Ridge, TN, USA, to identify bacteria that could be contributing to mercury (Hg) methylation. The phylogenetic composition of the sediment bacterial community was examined over 3 quarterly sampling periods (36 samples) using 16S rRNA gene pyrosequencing. Only 3064 sequences (0.85% of the total community) were identified as Deltaproteobacteria, the only group known to methylate Hg, using the Ribosomal Database Project classifier at the 99% confidence threshold. Constrained ordination techniques indicated statistically significant positive linear correlations between Desulfobulbus spp., Desulfonema spp. and Desulfobacca spp. and methyl-Hg concentrations at the Hg-contaminated sites. In contrast, the distribution of organisms related to Byssovorax spp. was significantly correlated to inorganic carbon, nitrate and uranium concentrations but not to Hg or methyl-Hg. Overall, the abundance and richness of Deltaproteobacteria sequences were higher in uncontaminated sediments, while the majority of the members present at the contaminated sites were either known potential metal-reducers/methylators or metal tolerant species. Given the abundance relative to other known Hg methylators and the association with methyl-Hg, Desulfobulbus spp. is considered a prime candidate for involvement in Hg methylation in these streams.

Mosher, Jennifer [ORNL; Vishnivetskaya, Tatiana A [ORNL; Elias, Dwayne A [ORNL; Podar, Mircea [ORNL; Brooks, Scott C [ORNL; Brown, Steven D [ORNL; Brandt, Craig C [ORNL; Palumbo, Anthony Vito [ORNL

2012-01-01T23:59:59.000Z

264

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

SciTech Connect (OSTI)

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.

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

2011-11-29T23:59:59.000Z

265

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

SciTech Connect (OSTI)

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.

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

2010-05-17T23:59:59.000Z

266

A comprehensive insight into bacterial virulence in drinking water using 454 pyrosequencing and Illumina high-throughput sequencing  

Science Journals Connector (OSTI)

Abstract In order to comprehensively investigate bacterial virulence in drinking water, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential pathogenic bacteria and virulence factors (VFs) in a full-scale drinking water treatment and distribution system. 16S rRNA gene pyrosequencing revealed high bacterial diversity in the drinking water (441–586 operational taxonomic units). Bacterial diversity decreased after chlorine disinfection, but increased after pipeline distribution. ?-Proteobacteria was the most dominant taxonomic class. Alignment against the established pathogen database showed that several types of putative pathogens were present in the drinking water and Pseudomonas aeruginosa had the highest abundance (over 11‰ of total sequencing reads). Many pathogens disappeared after chlorine disinfection, but P. aeruginosa and Leptospira interrogans were still detected in the tap water. High-throughput sequencing revealed prevalence of various pathogenicity islands and virulence proteins in the drinking water, and translocases, transposons, Clp proteases and flagellar motor switch proteins were the predominant VFs. Both diversity and abundance of the detectable \\{VFs\\} increased after the chlorination, and decreased after the pipeline distribution. This study indicates that joint use of 454 pyrosequencing and Illumina sequencing can comprehensively characterize environmental pathogenesis, and several types of putative pathogens and various \\{VFs\\} are prevalent in drinking water.

Kailong Huang; Xu-Xiang Zhang; Peng Shi; Bing Wu; Hongqiang Ren

2014-01-01T23:59:59.000Z

267

Continuous syngas fermentation for the production of ethanol, n-propanol and n-butanol  

Science Journals Connector (OSTI)

Abstract Syngas fermentation to fuels is a technology on the verge of commercialization. Low cost of fermentation medium is important for process feasibility. The use of corn steep liquor (CSL) instead of yeast extract (YE) in Alkalibaculum bacchi strain CP15 bottle fermentations reduced the medium cost by 27% and produced 78% more ethanol. When continuous fermentation was performed in a 7-L fermentor, 6 g/L ethanol was obtained in the YE and YE-free media. When CSL medium was used in continuous fermentation, the maximum produced concentrations of ethanol, n-propanol and n-butanol were 8 g/L, 6 g/L and 1 g/L, respectively. n-Propanol and n-butanol were not typical products of strain CP15. A 16S rRNA gene-based survey revealed a mixed culture in the fermentor dominated by A. bacchi strain CP15 (56%) and Clostridium propionicum (34%). The mixed culture presents an opportunity for higher alcohols production from syngas.

Kan Liu; Hasan K. Atiyeh; Bradley S. Stevenson; Ralph S. Tanner; Mark R. Wilkins; Raymond L. Huhnke

2014-01-01T23:59:59.000Z

268

Molecular analysis of intestinal bacterial communities in Cipangopaludina chinensis used in aquatic ecological restorations  

Science Journals Connector (OSTI)

High pollutant concentrations have led to the breakout of planktonic bloom and the breakdown of the ecosystem in several bodies of water in China. Some restoration projects using constructed wetlands have been enacted to increase the water clarity and rebuild the aquatic ecosystem in these bodies of water. Cipangopaludina chinensis were usually placed to manage the particles and microbes adhering to the surface of the aquatic plants in the wetlands. In the current study, the intestinal bacteria in C. chinensis collected from three restoration projects in Shanghai, China were investigated using denaturing gradient gel electrophoresis and 16S rRNA gene clone library analyses. The species affiliated to Firmicutes were proven the dominant species in the intestinal bacterial population in C. chinensis. The most dominant phylotypes are closely related to Pseudobutyrivibrio ruminis and Faecalibacterium prausnitzii. Furthermore, significant differences between the intestinal bacterial community constructs and different structures were found in C. chinensis collected from different restoration projects. This information on the intestinal bacteria of C. chinensis is helpful in further understanding the function of these mollusks and in screening for useful bacterial strains.

Kejun Li

2012-01-01T23:59:59.000Z

269

Genome Organization and Gene Expression Shape the Transposable Element Distribution  

E-Print Network [OSTI]

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

Alvarez, Nadir

270

Genes order and phylogenetic reconstruction: application to #Proteobacteria  

E-Print Network [OSTI]

@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

Fertin, Guillaume

271

Genes order and phylogenetic reconstruction: application to -Proteobacteria  

E-Print Network [OSTI]

@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

Fertin, Guillaume

272

Gene Delivery DOI: 10.1002/anie.201302820  

E-Print Network [OSTI]

(10­25 peptide residues) and lack adequate cationic charge to efficiently condense and deliver genes vehicles to improve delivery efficiencies.[11] We recently developed high-molecular-weight (MW), cationic efficiency and chemotoxicity of these polymeric vectors are often closely related to the density

Cheng, Jianjun

273

The genes that turned wildcats into kitty cats  

Science Journals Connector (OSTI)

...humans as well. “We're hitting on genes that allow our brains to develop and make us interact socially.” The team also...explaining why domestic animals share common traits, such as smaller brains and certain pigmentation patterns—a mystery first noted...

David Grimm

2014-11-14T23:59:59.000Z

274

Identification of Genes Expressed in Malignant Cells That Promote Invasion  

Science Journals Connector (OSTI)

...vacuum. The resulting space was filled with tumor...and Analysis of SAGE Libraries. SAGE libraries for...described (24) . The SAGE libraries corresponding to each...proprietary database or the public Gene Expression Omnibus...information for the libraries. Tag counts were normalized...

Jennifer Walter-Yohrling; Xiaohong Cao; Michele Callahan; William Weber; Sharon Morgenbesser; Stephen L. Madden; Clarence Wang; and Beverly A. Teicher

2003-12-15T23:59:59.000Z

275

A genome-wide association study of global gene expression  

E-Print Network [OSTI]

map of the effects of polymorphism on gene expression in 400 children from families recruited through descriptors for response to unfolded protein (chaperonins and heat shock proteins), regulation of progression may be mapped with considerable power1,2. As a consequence, our objective was to build a database

Liang, Liming

276

Multi-objective gene-pool optimal mixing evolutionary algorithms  

Science Journals Connector (OSTI)

The recently introduced Gene-pool Optimal Mixing Evolutionary Algorithm (GOMEA), with a lean, but sufficient, linkage model and an efficient variation operator, has been shown to be a robust and efficient methodology for solving single objective (SO) ... Keywords: clustering, linkage tree genetic algorithm, multi-objective optimization, optimal mixing

Ngoc Hoang Luong; Han La Poutré; Peter A.N. Bosman

2014-07-01T23:59:59.000Z

277

RESEARCH ARTICLE Open Access Identification of lignin genes and regulatory  

E-Print Network [OSTI]

RESEARCH ARTICLE Open Access Identification of lignin genes and regulatory sequences involved analysis revealed 18 lignin isoforms for each species. We also identified five contigs homologous to R2R3 wall formation and lignin deposition. We searched the contigs against public microRNA database

278

Duplicated genes evolve independently after polyploid formation in cotton  

E-Print Network [OSTI]

Duplicated genes evolve independently after polyploid formation in cotton Richard C. Cronn to characterize the evolution of homoeologous loci in allopolyploid cotton (Gossypium hirsutum) and in species from organismal history was recovered. In contrast to observations involving repetitive DNAs in cotton

Wendel, Jonathan F.

279

Nonlinear estimation in a class of gene transcription process  

Science Journals Connector (OSTI)

In this work the Goodwin model applied to gene transcription is employed as a benchmark system for estimation purposes, considering two dynamic behaviors, monotone decreasing and sustained oscillations, each one under a specific parameter's set. The ... Keywords: Asymptotic convergence, Goodwin model, Model uncertainties, Nonlinear observer, Observability analysis

Ricardo Aguilar-López, M. Isabel Neria-González, Rafael Martínez-Guerra, Juan L. Mata-Machuca

2014-01-01T23:59:59.000Z

280

Expression of Early Growth Response Genes in Human Prostate Cancer  

Science Journals Connector (OSTI)

...recent observation of a heterozygous somatic WTI mutation in one PLNR of a patient with Wilms...tumors arise from events at or near the WTI locus with birth weights lower than the...alterations in the tumor suppressor gene WTI. J. Pediatr., 123: 673-678, 1993...

Manal A. Eid; M. Vijay Kumar; Kenneth A. Iczkowski; David G. Bostwick; Donald J. Tindall

1998-06-01T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

Morphological evolution in land plants: new designs with old genes  

Science Journals Connector (OSTI)

...and of different chlorophyte algae have greatly increased the evolutionary...these are present in chlorophyte algae [77,78]. This indicates...87]. Gene duplication can fuel evolution because a duplicate...are not present in chlorophyte algae [96,97], suggesting that...

2012-01-01T23:59:59.000Z

282

Genome Function and Nuclear Architecture: From Gene Expression to Nanoscience  

E-Print Network [OSTI]

Genome Function and Nuclear Architecture: From Gene Expression to Nanoscience Timothy P. O'Brien,1, and nanoscience approaches to the study of nuclear structure and activity have been developing recently and hold, and nanoscience to relate genome organization and nuclear archi- tecture with development and disease. Integrating

Langowski, Jörg

283

Evolutionary simulations to detect functional lineage-specific genes  

Science Journals Connector (OSTI)

......Goodman, M. 1999The genomic record of Humankind's evolutionary roots. Am. J. Hum...1996; Yang, 1997, Methods). To this end, we use the sequences of the gene copy...after the humanchimpanzee split). To this end, we performed testdis on the human lineage......

Isabelle Dupanloup; Henrik Kaessmann

2006-08-01T23:59:59.000Z

284

Coordinately Up-Regulated Genes in Ovarian Cancer  

Science Journals Connector (OSTI)

...Furusato M., LiVolsi V. A., Menzin A. W., Liu P. C., Benjamin I., Morgan M. A., King S. A., Rebane B. A., Cardonick...carcinomas. Gene, 238: 375-385, 1999. 21 Wang K., Gan L., Jeffery E., Gayle M., Gown A. M., Skelly M., Nelson P. S...

Colleen D. Hough; Kathleen R. Cho; Alan B. Zonderman; Donald R. Schwartz; and Patrice J. Morin

2001-05-15T23:59:59.000Z

285

Classification and evolution of alpha-amylase genes in plants.  

Science Journals Connector (OSTI)

...which most of the a-amylase genes of rice belong...the grass family. a-Amylase (EC 3.2.1.1...endoglycolytic cleavage of amylose and amylopectin, the principal components...biochemistry of plant a-amylases have been reviewed by...

N Huang; G L Stebbins; R L Rodriguez

1992-01-01T23:59:59.000Z

286

Systematic identification of human mitochondrial disease genes through integrative genomics  

E-Print Network [OSTI]

encoding proteins targeted to this organelle. Elucidation of the molecular basis for these disorders of all 33,860 Ensembl human proteins. The genome-wide false discovery rate was estimated from large gold disorders are due to mutations not in the mitochondrial genome (mtDNA) but rather in the nuclear genes

287

GeneVis: visualization tools for genetic regulatory network dynamics  

Science Journals Connector (OSTI)

GeneVis provides a visual environment for exploring the dynamics of genetic regulatory networks. At present time, genetic regulation is the focus of intensive research worldwide, and computational aids are being called for to help in the research of ... Keywords: biological visualization, focus and context, genetic networks, lenses, multirepresentation, visualization

C. A. H Baker; M. S. T Carpendale; P. Prusinkiewicz; M. G. Surette

2002-10-01T23:59:59.000Z

288

Trends in Antibiotic Resistance Genes Occurrence in the Haihe  

E-Print Network [OSTI]

D P E D R O J . J . A L V A R E Z * , | Tianjin Key Laboratory of Environmental Remediation and antibiotic resistance genes (ARGs) was quantified in water and sediment samples collected from a 72 km leads the world in antibiotic use, about 210 000 tons of antibiotics are produced every year, with 180

Alvarez, Pedro J.

289

A Bayesian Framework for Combining Gene Predictions Vladimir Pavlovic  

E-Print Network [OSTI]

deployed in several highly visible genome analysis projects. Popular gene finding systems include Glimmer systems have been made available to the public. Such projects include the genomes of over thirty microbial of the Drosophila genome and Genscan ([2]) was used for analysis of human chromo- some 22. In addition

290

Human Diversity: Our Genes Tell Where we Live  

E-Print Network [OSTI]

of Human Polymorphism (CEPH) in the framework of the Human Genome Diversity Project initiated by LucaHuman Diversity: Our Genes Tell Where we Live Dispatch Laurent Excoffier A detailed genetic analysis of more than a thousand human subjects clusters them into five groups corresponding to major

Rosenberg, Noah

291

Identification and analysis of bacterial virulence genes in vivo  

Science Journals Connector (OSTI)

...mixed population of mutants. Searches have been carried out by screening...provide the basis for long-term studies into their functions...in the classical sense of the term, many of the S. aureus genes...phate and occurs as cells enter the stationary phase of growth...

2000-01-01T23:59:59.000Z

292

ANALYSIS OF GENE EXPRESSION PROFILES AND DRUG ACTIVITY PATTERNS BY  

E-Print Network [OSTI]

are more related to the kind of cancer than to drug activity patterns. Dependency analysis using Bayesian1 11 ANALYSIS OF GENE EXPRESSION PROFILES AND DRUG ACTIVITY PATTERNS BY CLUSTERING AND BAYESIAN of data produced from up- to-date biological experimental processes needs appropriate data mining

293

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;Uncorrected Proof Copy 86 Davuluri and Zhang Job: Plant Functional Genomics--Grotewold Compositor: Nettype Job: Plant Functional Genomics--Grotewold Compositor: Nettype Chapter: Chapter 6 Date: 3/15/2003 Pub

294

MICROFLUIDIC DEVICES FOR GENENTIC ANAYLSIS AND GENE EXPRESSION STUDIES  

E-Print Network [OSTI]

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

Quake, Stephen R.

295

POSTER PRESENTATION Open Access Combinatorial RNA interference as a gene  

E-Print Network [OSTI]

and HIV-1 tat/rev and vif sequences were inserted into a lentiviral vector under the control of eitherPOSTER PRESENTATION Open Access Combinatorial RNA interference as a gene therapy strategy for HIV-1 in treating HIV-1 infection, as single short hairpin RNAs (shRNAs) are rapidly rendered ineffective

Paris-Sud XI, Université de

296

Prospective on the potential of imaging gene expression  

SciTech Connect (OSTI)

The feasibility of the non-invasive imaging of gene expression is explored. Calculations of the possibility of the direct imaging of specific messenger RNA with radiolabeled antisense are discussed. In addition, possible mechanism for the amplification of the biological signal to enhance image detection are discussed.

Taylor, Scott E; Budinger, Thomas F.

2000-06-01T23:59:59.000Z

297

From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation  

E-Print Network [OSTI]

be explained in terms of their gene numbers. If, however, a biological function requires the concerted action histones, chromatin, micro-RNAs etc. become relevant, which are just entering the stage of model building in bioinformatics, with the aim of identifying statistical characteristics of functional loci and of building search

Lässig, Michael

298

Energy Costs Constrain the Evolution of Gene Expression  

E-Print Network [OSTI]

Energy Costs Constrain the Evolution of Gene Expression ANDREAS WAGNER� 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

Wagner, Andreas

299

Lower Oil Prices: A Reason to Give Thanks GENE EPSTEIN  

E-Print Network [OSTI]

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

California at Davis, University of

300

Increased expression of the insulin-like growth factor I receptor gene, IGF1R, in Wilms tumor is correlated with modulation of IGF1R promoter activity by the WT1 Wilms tumor gene product  

Science Journals Connector (OSTI)

...expression of the Wilms tumor suppressor gene WTI, whose inactivation appears to be a key step...constructs driving luciferase reporter genes and with WTI expression vectors showed that the active WTI gene product represses IGF-IR promoter activity...

H Werner; G G Re; I A Drummond; V P Sukhatme; F J Rauscher; 3rd; D A Sens; A J Garvin; D LeRoith; C T Roberts; Jr

1993-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


301

ESPM131 Microarrays, Environmental Genomics, Quantification S06 Microarrays (Wilson et al 2002)  

E-Print Network [OSTI]

) 60,000 probes/chip now 500,000/chip - hybridize fluorescently labeled PCR pool, or cDNA pool May miss to Leptospirillium group III Sargasso Sea (Venter et al 2004.) Some numbers: 200 L of filtered surface water (0.1 - 3,901 novel, conserved open reading frames. 60,000 16S rRNA sequences, 148 of which are at least 3% different

California at Berkeley, University of

302

Comparative analysis of synthetic DNA promoters for high-level gene expression in plants  

Science Journals Connector (OSTI)

Plants survive assimilating multiple environmental stress factors (biotic/abiotic) by adjusting inducible and spatio-temporal expression patterns of responsive genes. In plants, the pattern of gene expression is ...

Dipak Kumar Sahoo; Shayan Sarkar; Sumita Raha; Indu B. Maiti; Nrisingha Dey

2014-10-01T23:59:59.000Z

303

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

DOE Patents [OSTI]

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

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

1992-01-01T23:59:59.000Z

304

Evolution of Hox gene expression and function and the effect on limb specification in arthropods  

E-Print Network [OSTI]

of the homeotic genes Scr, Antp, Ubx, and abd-A duringof the homeotic gene Scr associated with a crustacean leg-crustacean, Porcelio scaber, SCR protein is detected in the

Hsia, Cheryl Chih-Jui

2007-01-01T23:59:59.000Z

305

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

E-Print Network [OSTI]

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

MacPherson, David (David P.)

2005-01-01T23:59:59.000Z

306

E-Print Network 3.0 - adenoviral-mediated gene transfer Sample...  

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

Biology and Medicine ; Environmental Sciences and Ecology 11 THE JOURNAL OF GENE MEDICINE RESEARCH ARTICLE J Gene Med 2003; 5: 300310. Summary: . Alvarez RD, Gomez-Navarro J, Wang...

307

E-Print Network 3.0 - adenoviral-mediated mikappabalpha gene...  

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

Health Science Center Collection: Biology and Medicine 9 THE JOURNAL OF GENE MEDICINE RESEARCH ARTICLE J Gene Med 2003; 5: 300310. Summary: . Alvarez RD, Gomez-Navarro J, Wang...

308

E-Print Network 3.0 - acbp gene expression Sample Search Results  

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

acbp gene expression Search Powered by Explorit Topic List Advanced Search Sample search results for: acbp gene expression Page: << < 1 2 3 4 5 > >> 1 Membrane Charge and Curvature...

309

UFO: an Arabidopsis gene involved in both floral meristem and floral organ development.  

Science Journals Connector (OSTI)

RESEARCH ARTICLES UFO: An Arabidopsis Gene Involved in Both Floral...the role of the UNUSUAL FLORAL ORGANS (UFO) gene in Arabidopsis floral development...characterization of the phenotypes of nine ufo alleles. UFO is required for the proper...

310

Gene identification and analysis: an application of neural network-based information fusion  

SciTech Connect (OSTI)

Identifying genes within large regions of uncharacterized DNA is a difficult undertaking and is currently the focus of many research efforts. We describe a gene localization and modeling system called GRAIL. GRAIL is a multiple sensor-neural network based system. It localizes genes in anonymous DNA sequence by recognizing gene features related to protein-coding slice sites, and then combines the recognized features using a neural network system. Localized coding regions are then optimally parsed into a gene mode. RNA polymerase II promoters can also be predicted. Through years of extensive testing, GRAIL consistently localizes about 90 percent of coding portions of test genes with a false positive rate of about 10 percent. A number of genes for major genetic diseases have been located through the use of GRAIL, and over 1000 research laboratories worldwide use GRAIL on regular bases for localization of genes on their newly sequenced DNA.

Matis, S.; Xu, Y.; Shah, M.B.; Mural, R.J.; Einstein, J.R.; Uberbacher, E.C.

1996-10-01T23:59:59.000Z

311

Expression of the Wilms' tumor suppressor gene WT1 during mouse embryogenesis  

Science Journals Connector (OSTI)

...ifferential Regulation of the Wilms' Tumor Gene, WTI, during Differentiation of Embryonal Carcinoma...pattern of the Wilms' tumor suppressor gene, WTI, during embryonal development suggests a role for the WTI proteins in the differentiation of specific...

RR Rackley; AM Flenniken; NP Kuriyan; PM Kessler; MH Stoler; BR Williams

1993-12-01T23:59:59.000Z

312

'Model your genes the mathematical way'—a mathematical biology workshop for secondary school teachers  

Science Journals Connector (OSTI)

......mathematical model for a regulatory network of genes...Brief historical review of biochemistry...Suggested lesson plans M2 Graph theory...to model gene regulatory networks Polynomial...simulation of genetic regulatory systems: a literature review. Journal of......

Ana Margarida Martins; Paola Vera-Licona; Reinhard Laubenbacher

2008-06-01T23:59:59.000Z

313

E-Print Network 3.0 - atrophy gene sma Sample Search Results  

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

of worms mutant for the genes listed (far left) andor carrying... of expression of the cnc-2 reporter gene was unchanged in sma-2- mutant worms treated with sma-4-specific...

314

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

DOE Patents [OSTI]

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.

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

2011-06-07T23:59:59.000Z

315

E-Print Network 3.0 - a5 gene expression Sample Search Results  

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

Genes September 26, 2008 Summary: the filtering function to the expression matrix. > f1 <- kOverA(5, 200) > ffun <- filterfun(f1) > which... genes that are expressed in more...

316

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

E-Print Network [OSTI]

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...

Everett, Anthany Laurence

2009-05-15T23:59:59.000Z

317

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

E-Print Network [OSTI]

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 ...

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

2011-01-01T23:59:59.000Z

318

E-Print Network 3.0 - aurata hemoglobin genes Sample Search Results  

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

University of Rochester Collection: Biology and Medicine 2 25% chance of a child with sickle cell trait Summary: hemoglobin gene D hemoglobin D gene S A A D A A S AA D DA S...

319

E-Print Network 3.0 - auxin-regulated gene expression Sample...  

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

regulated gene expression Search Powered by Explorit Topic List Advanced Search Sample search results for: auxin-regulated gene expression Page: << < 1 2 3 4 5 > >> 1 Funct Integr...

320

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system  

E-Print Network [OSTI]

The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease ...

Zhang, Feng

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

Evolution of a Core Gene Network for Skeletogenesis in Jochen Hecht1,2  

E-Print Network [OSTI]

Evolution of a Core Gene Network for Skeletogenesis in Chordates Jochen Hecht1,2 , Sigmar Stricker2: Hecht J, Stricker S, Wiecha U, Stiege A, Panopoulou G, et al (2008) Evolution of a Core Gene Network

Max-Planck-Institut für molekulare Genetik

322

E-Print Network 3.0 - angiogenic factor genes Sample Search Results  

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

GENE3227X HSA272195 centaurin-alpha 2 protein... GENE6192X SPINT2 serine protease inhibitor, Kunitz type, 2 ... Source: Leng, Chenlei - Department of Statistics and Applied...

323

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

E-Print Network [OSTI]

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 ...

Maizels, Rick; Blaxter, Mark; Scott, Alan

2001-01-01T23:59:59.000Z

324

Regulation of HIV-1 Gene Expression by the Transactivator Protein Tat  

Science Journals Connector (OSTI)

The regulation of HIV-1 gene expression is an area of intense investigation. Like all retroviruses, HIV-1 integrates into cellular DNA, and its gene expression is dependent on host cell transcription factors a...

R. B. Gaynor

1995-01-01T23:59:59.000Z

325

Global depression in gene expression as a response to rapid thermal changes in vent mussels  

Science Journals Connector (OSTI)

...potential relationship between natural genetic variation, stress...attributable to specific gene cascades that can be up- or downregulated...Massive emissions of toxic gas in the Atlantic. Nature 415...explore a relationship between natural genetic variation, gene expression...

2009-01-01T23:59:59.000Z

326

Cell Culture Processes for the Production of Viral Vectors for Gene Therapy Purposes  

Science Journals Connector (OSTI)

Gene therapy is a promising technology for the treatment of several acquired and inherited diseases. However, for gene therapy to be a commercial and clinical success, scalable cell culture processes must be i...

James N. Warnock; Otto-Wilhelm Merten; Mohamed Al-Rubeai

2006-03-01T23:59:59.000Z

327

TABASCO: A single molecule, base-pair resolved gene expression simulator  

E-Print Network [OSTI]

Background Experimental studies of gene expression have identified some of the individual molecular components and elementary reactions that comprise and control cellular behavior. Given our current understanding of gene ...

Kosuri, Sriram

328

Effects of Dietary Energy Restriction on Gene Regulation in Mammary Epithelial Cells  

Science Journals Connector (OSTI)

...Article Prevention Effects of Dietary Energy Restriction on Gene Regulation in Mammary...study was to determine whether dietary energy restriction (DER) affects the pattern of gene expression in three interrelated energy metabolism pathways: glycolysis, gluconeogenesis...

Zongjian Zhu; Weiqin Jiang; John N. McGinley; Jennifer M. Price; Bifeng Gao; Henry J. Thompson

2007-12-15T23:59:59.000Z

329

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information  

Science Journals Connector (OSTI)

......clique graph of all genes). Set L=1. Step-1: L=L+1...If I max (i, j|K)theta, set G(i, j)=0. Return to Step-1...network in Yeast genomes. We set the threshold value 0.1 of...and PCA-PCC, our method can cover non-linear relations between......

Xiujun Zhang; Xing-Ming Zhao; Kun He; Le Lu; Yongwei Cao; Jingdong Liu; Jin-Kao Hao; Zhi-Ping Liu; Luonan Chen

2012-01-01T23:59:59.000Z

330

Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and  

E-Print Network [OSTI]

, with software that retrieves, consolidates, searches, and displays human genome information, has enjoyed. These include the Unified Database (UDB) (http://bioinfo.weizmann.ac.il/udb) for human genome mapping, the human://bioinfo.weizmann.ac.il/ cards/, an automated, integrated database of human genes, genomic maps, proteins, and diseases

Groner, Yoram

331

Completion of the gene coding assignments of SA11 rotavirus: gene products of segments 7, 8, and 9.  

Science Journals Connector (OSTI)

...individual translation in vitro. Segment 7 codes for p31 (NS2), segment 8 codes for p33 (NS1), and the segment 9 gene product...individual translation in vitro. Segment 7 codes for p31 (NS2), segment 8 codes for p33 (NS1), and the...

P Kantharidis; M L Dyall-Smith; I H Holmes

1983-10-01T23:59:59.000Z

332

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

E-Print Network [OSTI]

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

Levin, Judith G.

333

Tissue-Specific Gene Silencing Mediated by a Naturally Occurring Chalcone Synthase Gene Cluster in Glycine max  

Science Journals Connector (OSTI)

...3.5 mM MgCl2, and 0.025 units/muL of AmpliTaq Gold DNA polymerase...deoxynucleotide triphosphate, 2.5 units of Taq polymerase (Invitrogen...to another gene for a house-keeping isoform. Plant J. 13, 267-273...transmitted by grafting from silenced stocks to non-silenced scions. EMBO...

Jigyasa H. Tuteja; Steven J. Clough; Wan-Ching Chan; Lila O. Vodkin

334

Sequencing of rhesus macaque Y chromosome clarifies origins and evolution of the DAZ (Deleted in AZoospermia) genes  

E-Print Network [OSTI]

Studies of Y chromosome evolution often emphasize gene loss, but this loss has been counterbalanced by addition of new genes. The DAZ genes, which are critical to human spermatogenesis, were acquired by the Y chromosome ...

Hughes, Jennifer F.

335

Volume 16S5,number 2 FEBS tO96 January 1984 A nuclear Overhauser enhancement study on the imino proton  

E-Print Network [OSTI]

14 November 1983 A 500 MHz `H-NMR study on a synthetic DNA pentadecamer comprising the specific A DNA (RMS difference of 1.1 A) Synthetic oligonucleotide Imino proton NOE Interproton distance CRP studies to the synthetic DNA pentadecamer 5' AAAGTGTGACGCCGT 3' (-+-) 3' TTTCACACTGCGGCA 5' (-) Pub

Clore, G. Marius

336

Molecular Typing of Papillomatous Digital Dermatitis-Associated Treponema Isolates Based on Analysis of 16S-23S Ribosomal DNA Intergenic Spacer Regions  

Science Journals Connector (OSTI)

...by painful, ulcerative foot lesions. The detection...greater discriminatory power for differentiation of...usually occur on the hind feet and are prone to bleeding...by painful, ulcerative foot lesions. The detection...greater discriminatory power for differentiation of...

L. V. Stamm; H. L. Bergen; R. L. Walker

2002-09-01T23:59:59.000Z

337

Estimation of Bacterial Cell Numbers in Humic Acid-Rich Salt Marsh Sediments with Probes Directed to 16S Ribosomal DNA  

Science Journals Connector (OSTI)

...involved in collection of marsh samples-Dan Wood, Alison...Khalequzzaman, who performed all marsh coring. REFERENCES Amann R. I. Ludwig W. Schleifer...bacteria in a Delaware salt marsh. . Farrelly V. Rainey...species. . Hahn D. Amann R. I. Ludwig W. Akkermans...

Virginia P. Edgcomb; John H. McDonald; Richard Devereux; David W. Smith

1999-04-01T23:59:59.000Z

338

Methanotroph Diversity in Landfill Soil: Isolation of Novel Type I and Type II Methanotrophs Whose Presence Was Suggested by Culture-Independent 16S Ribosomal DNA Analysis  

Science Journals Connector (OSTI)

...Phylogenetic analysis of a natural marine bacterioplankton population...Robertson Viability and isolation of marine bacteria by dilution culture...Dougherty C. B. Fliermans J. Wear C. A. Eddy-Dilek Summary...Murrell Detection of novel marine methanotrophs using phylogenetic...

Mark G. Wise; J Vaun McArthur; Lawrence J. Shimkets

1999-11-01T23:59:59.000Z

339

Identification of Polyphosphate-Accumulating Organisms and Design of 16S rRNA-Directed Probes for Their Detection and Quantitation  

Science Journals Connector (OSTI)

...The performance of reactor GRC fluctuated over...Microbiological analyses. (i) Microscopy of...Enrichment, phylogenetic analysis and detection of a bacterium...Kerdachi K. J. Healey The reliability of cold perchloric acid...Salkinoja-Salonen Comparative analysis of biological phosphate...

Gregory R. Crocetti; Philip Hugenholtz; Philip L. Bond; Andrew Schuler; Jürg Keller; David Jenkins; Linda L. Blackall

2000-03-01T23:59:59.000Z

340

Evaluation of Partial 16S Ribosomal DNA Sequencing for Identification of Nocardia Species by Using the MicroSeq 500 System with an Expanded Database  

Science Journals Connector (OSTI)

...MicroSeq 500 system (Applied BioSystems, Foster City, Calif...species (4). A study was done to...sequencing system with our expanded...MicroSeq 500 system. c See the...description. This study was in compliance...and D. L. Wheeler. 2003. GenBank...

Joann L. Cloud; Patricia S. Conville; Ann Croft; Dag Harmsen; Frank G. Witebsky; Karen C. Carroll

2004-02-01T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

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

E-Print Network [OSTI]

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

342

INSTITUTE OF PHYSICS PUBLISHING JOURNAL OF PHYSICS D: APPLIED PHYSICS J. Phys. D: Appl. Phys. 39 (2006) 34793486 doi:10.1088/0022-3727/39/16/S05  

E-Print Network [OSTI]

that kills bacteria. A culture of Streptococcus mutans (S. mutans) was plated onto the surface of agar. A radio-frequency high voltage is applied to a needle-shaped electrode located inside a concentric gas

Goree, John

343

Single-Molecule Long-Read 16S Sequencing To Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia  

Science Journals Connector (OSTI)

...Bowman (Pacific Biosystems) for bioinformatics support in the installation and use of aligners on Colonial One High Performance Computing cluster is greatly appreciated. Keith Crandall and Eduardo Castro-Nallar have ownership in a commercial startup...

Ian Toma; Marc O. Siegel; John Keiser; Anna Yakovleva; Alvin Kim; Lionel Davenport; Joseph Devaney; Eric P. Hoffman; Rami Alsubail; Keith A. Crandall; Eduardo Castro-Nallar; Marcos Pérez-Losada; Sarah K. Hilton; Lakhmir S. Chawla; Timothy A. McCaffrey; Gary L. Simon

2014-08-20T23:59:59.000Z

344

E-Print Network 3.0 - anti-aging gene klotho Sample Search Results  

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

chemical entities... Gene regulatory networks Inferred from: - protein interaction networks - micro-array data - other... 's Signaling pathwas: rarer reactants,...

345

Systematic analysis of gene expression in human brains before and after death  

E-Print Network [OSTI]

substantially Table 2 Functional analysis of gene expression differences between autopsy and resection samples GO ID Term Expressed genes Significant differences* Change p value Conservation p value GO:0006412 Protein biosynthesis 462 101 (37/64) 0.001 0.999 GO... functional processes. Genes involved in rather basic functions, such as RNA processing, protein bio- synthesis and transport, organelle organization and biogen- esis, the ubiquitin cycle, and DNA repair (Table 1) are over- represented among genes differently...

Franz, Henriette; Ullmann, Claudia; Becker, Albert; Ryan, Margaret; Bahn, Sabine; Arendt, Thomas; Simon, Matthias; Paabo, Svante; Khaitovich, Philipp

2005-12-30T23:59:59.000Z

346

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

SciTech Connect (OSTI)

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.

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

2007-12-10T23:59:59.000Z

347

Orthogonal Control of Endogenous Gene Expression in Mammalian Cells Using Synthetic Ligands  

E-Print Network [OSTI]

ARTICLE Orthogonal Control of Endogenous Gene Expression in Mammalian Cells Using Synthetic Ligands South Mathews Avenue, Urbana, Illinois 61801 ABSTRACT: Gene switches have wide utility in synthetic-finger DNA binding domain (DBD). Our gene switch is specifically and reversibly con- trolled by 4

Zhao, Huimin

348

Zinc finger point mutations within the WT1 gene in Wilms tumor patients  

Science Journals Connector (OSTI)

...Genetics Zinc finger point mutations within the WTI gene in Wilms tumor patients (zinc finger...1992 ABSTRACT A proposed Wilms tumor gene, WTI, which encodes a zinc ringer protein...amino acid change. To our knowl- edge, a WTI gene missense mutation has not been detected...

M H Little; J Prosser; A Condie; P J Smith; V Van Heyningen; N D Hastie

1992-01-01T23:59:59.000Z

349

Patterns of Gene-Specific and Total Transcriptional Activity during the Plasmodium falciparum Intraerythrocytic Developmental Cycle  

Science Journals Connector (OSTI)

...during the IDC, we performed nuclear run-on on whole-transcriptome...genes from gene-specific nuclear run-on hybridization data...activity and RNA stability datasets were available, we found that...points, to gene-specific nuclear run-on data from those time...

Jennifer S. Sims; Kevin T. Militello; Peter A. Sims; Vishal P. Patel; Jacob M. Kasper; Dyann F. Wirth

2009-01-16T23:59:59.000Z

350

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

SciTech Connect (OSTI)

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.

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.

2008-10-27T23:59:59.000Z

351

No Gene-Specific Optimization of Mutation Rate in Escherichia coli  

E-Print Network [OSTI]

selection, E. coli. Because mutation is the ultimate source of genetic variation and evolution, accurately to approximately 0.3 among E. coli genes (Martincorena and Luscombe 2013). Assuming that Áf between genes of multiple genes with similar fractions of deleterious mutations. Analyzing published genome sequences of E

Zhang, Jianzhi

352

Distinguishing protein-coding and noncoding genes in the human genome  

E-Print Network [OSTI]

) 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

Kellis, Manolis

353

Epstein-Barr virus latent gene expression in uncultured peripheral blood lymphocytes.  

Science Journals Connector (OSTI)

...promoter-initiated RNAs. Spliced RNA from the TP gene was detected in all four subjects. Expression of the TP gene was restricted to TP1 promoter-initiated...situ and suggesting a central role for the TP gene in the latency of EBV. Epstein-Barr...

L Qu; D T Rowe

1992-06-01T23:59:59.000Z

354

Synonymous and Nonsynonymous Rate Variation in Nuclear Genes Ziheng Yang,1,2,  

E-Print Network [OSTI]

substitutions in nuclear genes of mammals to test the neutral theory. The index of dispersion is the varianceSynonymous and Nonsynonymous Rate Variation in Nuclear Genes of Mammals Ziheng Yang,1,2, * Rasmus to estimate the synonymous and nonsynonymous substi- tution rates in 48 nuclear genes from primates, artiodac

Nielsen, Rasmus

355

Shotgun DNA microarrays and stage-specic gene expression in Plasmodium falciparum malaria  

E-Print Network [OSTI]

, labour intensive, and expensive to propagate. Second, the experimental power of transfection technology stages can be transfected, gene disruptions are only possible for non-essential genes, as this part there is no negative selection system. Transfection ef®- ciencies in P. falciparum are so poor that no gene function

356

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

E-Print Network [OSTI]

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

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

2006-01-01T23:59:59.000Z

357

E-Print Network 3.0 - ahr-regulated genes cyp1a1 Sample Search...  

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

as the "Ah gene battery"187,188 . The AHR regulates gene... androstane receptor CNC: cap'n'collar ... Source: Hahn, Mark E. - Biology Department, Woods Hole Oceanographic...

358

Manipulating Genes with Hidden TALENs | Advanced Photon Source  

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

A New Discovery Answers an Old Question A New Discovery Answers an Old Question Peering into the Interfaces of Nanoscale Polymeric Materials Ironing Out the Details of the Earth's Core Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed Manipulating Genes with Hidden TALENs FEBRUARY 10, 2012 Bookmark and Share X-ray studies carried out at APS and computer modeling of the data reveal how TALEN intimately winds itself into the major groove of target DNA to form a protein-DNA complex just 60 Å x 60 Å x 90 Å. From Amanda Nga-Sze Mak et al., Science 335(6069), 716 (10 February, 2012). A better understanding of gene function in model plant and animal systems could be used to develop useful traits in livestock and crop plants, and

359

Plant isoflavone and isoflavanone O-methyltransferase genes  

DOE Patents [OSTI]

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.

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

2014-08-19T23:59:59.000Z

360

Pnp gene modification for improved xylose utilization in Zymomonas  

DOE Patents [OSTI]

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.

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

2014-12-16T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


361

Compositions and methods for detecting gene rearrangements and translocations  

DOE Patents [OSTI]

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.

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

2000-01-01T23:59:59.000Z

362

Probing cell-free gene expression noise in femtoliter volumes  

SciTech Connect (OSTI)

Cell-free systems offer a simplified and flexible context that enables important biological reactions while removing complicating factors such as fitness, division, and mutation that are associated with living cells. However, cell-free expression in unconfined spaces is missing important elements of expression in living cells. In particular, the small volume of living cells can give rise to significant stochastic effects, which are negligible in bulk cell-free reactions. Here, we confine cell-free gene expression reactions to cell relevant 20 fL volumes (between the volumes of E. coli and S. cerevisiae), in polydimethylsiloxane (PDMS) containers. We demonstrate that expression efficiency varies widely at this volume, and we analyze gene expression noise. Noise analysis reveals signatures of translational bursting while noise dynamics suggest that overall cell-free expression is limited by a diminishing translation rate. In addition to offering a unique approach to understanding noise in gene circuits, our work contributes to a deeper understanding of the biophysical properties of cell-free expression systems, thus aiding efforts to harness cell-free systems for synthetic biology applications.

Karig, David K [ORNL; Jung, Seung-Yong [ORNL; Srijanto, Bernadeta R [ORNL; Collier, Pat [ORNL; Simpson, Michael L [ORNL

2013-01-01T23:59:59.000Z

363

Ayuda:Imágenes | Open Energy Information  

Open Energy Info (EERE)

Imágenes Imágenes Jump to: navigation, search Esta página trata en detalle la sintaxis de la imagen al momento de editar una página wiki. Usted o algún otro usuario deberá comúnmente cargar una imagen antes de que esta sea visible en la página. Contents 1 Sintaxis 2 Formato 3 Alineación 3.1 Alineación vertical 4 Tamaño y cuadro 5 Detener del movimiento de texto 6 Galería de Imágenes 6.1 Parámetros 7 Enlaces 7.1 Enlace a la página de descripción 7.2 Enlazar directamente al archivo 8 Requisitos 9 Archivos en otras páginas web Sintaxis La sintaxis necesaria para mostrar una imagen: [[Image:{nombre_archivo}|{opciones}]] Donde las opciones que se señalan a continuación, separadas por barras verticales, pueden oscilar entre cero o más: border, frame, thumb, o frameless: Determina el proceso de formato

364

MicroSyn: A user friendly tool for detection of microsynteny in a gene family  

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

O O F T W A R E Open Access MicroSyn: A user friendly tool for detection of microsynteny in a gene family Bin Cai 1,2 , Xiaohan Yang 3,4 , Gerald A Tuskan 3,4 and Zong-Ming Cheng 1,2,4* Abstract Background: The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes. Results: We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene

365

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

DOE Patents [OSTI]

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.

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

2014-09-16T23:59:59.000Z

366

Identification of target genes of synovial sarcoma-associated fusion oncoprotein using human pluripotent stem cells  

SciTech Connect (OSTI)

Highlights: ? We tried to identify targets of synovial sarcoma (SS)-associated SYT–SSX fusion gene. ? We established pluripotent stem cell (PSC) lines with inducible SYT–SSX gene. ? SYT–SSX responsive genes were identified by the induction of SYT–SSX in PSC. ? SS-related genes were selected from database by in silico analyses. ? 51 genes were finally identified among SS-related genes as targets of SYT–SSX in PSC. -- Abstract: Synovial sarcoma (SS) is a malignant soft tissue tumor harboring chromosomal translocation t(X; 18)(p11.2; q11.2), which produces SS-specific fusion gene, SYT–SSX. Although precise function of SYT–SSX remains to be investigated, accumulating evidences suggest its role in gene regulation via epigenetic mechanisms, and the product of SYT–SSX target genes may serve as biomarkers of SS. Lack of knowledge about the cell-of-origin of SS, however, has placed obstacle in the way of target identification. Here we report a novel approach to identify SYT–SSX2 target genes using human pluripotent stem cells (hPSCs) containing a doxycycline-inducible SYT–SSX2 gene. SYT–SSX2 was efficiently induced both at mRNA and protein levels within three hours after doxycycline administration, while no morphological change of hPSCs was observed until 24 h. Serial microarray analyses identified genes of which the expression level changed more than twofold within 24 h. Surprisingly, the majority (297/312, 95.2%) were up-regulated genes and a result inconsistent with the current concept of SYT–SSX as a transcriptional repressor. Comparing these genes with SS-related genes which were selected by a series of in silico analyses, 49 and 2 genes were finally identified as candidates of up- and down-regulated target of SYT–SSX, respectively. Association of these genes with SYT–SSX in SS cells was confirmed by knockdown experiments. Expression profiles of SS-related genes in hPSCs and human mesenchymal stem cells (hMSCs) were strikingly different in response to the induction of SYT–SSX, and more than half of SYT–SSX target genes in hPSCs were not induced in hMSCs. These results suggest the importance of cellular context for correct understanding of SYT–SSX function, and demonstrated how our new system will help to overcome this issue.

Hayakawa, Kazuo [Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto (Japan) [Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto (Japan); Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto (Japan); Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya (Japan); Ikeya, Makoto [Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto (Japan)] [Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto (Japan); Fukuta, Makoto [Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto (Japan) [Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto (Japan); Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto (Japan); Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya (Japan); Woltjen, Knut [Department of Reprogramming Sciences, Center for iPS Cell Research and Application, Kyoto University, Kyoto (Japan)] [Department of Reprogramming Sciences, Center for iPS Cell Research and Application, Kyoto University, Kyoto (Japan); Tamaki, Sakura; Takahara, Naoko; Kato, Tomohisa; Sato, Shingo [Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto (Japan)] [Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto (Japan); Otsuka, Takanobu [Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya (Japan)] [Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya (Japan); Toguchida, Junya, E-mail: togjun@frontier.kyoto-u.ac.jp [Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto (Japan) [Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto (Japan); Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto (Japan); Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto (Japan)

2013-03-22T23:59:59.000Z

367

Evaluation of Gene Breed Type and Expression of Feed Efficiency Candidate Genes, and Their Associations with Carcass Traits in F2 Nellore-Angus Steers  

E-Print Network [OSTI]

determined for 4 candidate genes of feed efficiency: insulin like growth factor-1 (IGF1), leptin (LEP), neuropeptide-Y (NPY) and ghrelin (GHRL). Gene breed types were represented as AA, AN, NA, and NN where A and N denote Angus and Nellore, respectively...

Cardin, Jessica Marie

2011-10-21T23:59:59.000Z

368

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)

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.

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

1995-04-01T23:59:59.000Z

369

Sequence of the 1918 pandemic influenza virus nonstructural gene (NS) segment and characterization of recombinant viruses bearing the 1918 NS genes  

Science Journals Connector (OSTI)

...sequence and a phylogenetic analysis of the smallest influenza gene segment, which codes for the NS1 protein and the nuclear export protein (NEP, previously NS2). To begin to understand the role NS gene products, NS1 and NEP, may have played...

Christopher F. Basler; Ann H. Reid; Jody K. Dybing; Thomas A. Janczewski; Thomas G. Fanning; Hongyong Zheng; Mirella Salvatore; Michael L. Perdue; David E. Swayne; Adolfo García-Sastre; Peter Palese; Jeffery K. Taubenberger

2001-01-01T23:59:59.000Z

370

[CANCER RESEARCH 64, 53905397, August 1, 2004] Effective Gene-Viral Therapy for Telomerase-Positive Cancers by Selective  

E-Print Network [OSTI]

-Positive Cancers by Selective Replicative-Competent Adenovirus Combining with Endostatin Gene Qi Zhang,1 Mingming

Tian, Weidong

371

How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets  

E-Print Network [OSTI]

3 June 2003 Abstract We analyzed 12 combined mitochondrial and nuclear gene datasets in seven orders systematists should increasingly focus on nuclear rather than mitochondrial gene datasets because nuclear genesHow do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian

Danforth, Bryan Nicholas

372

Epstein-Barr virus immediate-early gene product trans-activates gene expression from the human immunodeficiency virus long terminal repeat  

SciTech Connect (OSTI)

Acquired immunodeficiency syndrome patients are frequently coinfected with Epstein-Barr virus (EBV). In this report, the authors demonstrate that an EBV immediate-early gene product, BamHI MLF1, stimulates expression of the bacterial chloramphenicol acetyltransferase (CAT) gene linked to the human immunodeficiency virus (HIV) promoter. The HIV promoter sequences necessary for trans-activation by EBV do not include the tat-responsive sequences. In addition, in contrast to the other herpesvirus trans-activators previously studied, the EBV BamHI MLF1 gene product appears to function in part by a posttranscriptional mechanism, since it increases pHIV-CAT protein activity more than it increases HIV-CAT mRNA. This ability of an EBV gene product to activate HIV gene expression may have biologic consequences in persons coinfected with both viruses.

Kenney, S.; Kamine, J.; Markovitz, D.; Fenrick, R.; Pagano, J.

1988-03-01T23:59:59.000Z

373

Gene selection using rough set based on neighborhood for the analysis of plant stress response  

Science Journals Connector (OSTI)

Abstract Gene selection and sample classification based on gene expression data are important research trends in bioinformatics. It is very difficult to select significant genes closely related to classification because of the high dimension and small sample size of gene expression data. Rough set based on neighborhood has been successfully applied to gene selection, as it selects attributes without redundancy and deals with numerical attributes directly. Construction of neighborhoods, approximation operators and attribute reduction algorithm are three key components in this gene selection approach. In this study, a novel neighborhood named intersection neighborhood for numerical data was defined. The performances of two kinds of approximation operators were compared on gene expression data. A significant gene selection algorithm, which was applied to the analysis of plant stress response, was proposed by using positive region and gene ranking, and then this algorithm with thresholds optimization for intersection neighborhood was extended. The performance of the proposed algorithm, along with a comparison with other related methods, classical algorithms and rough set methods, was analyzed. The results of experiments on four data sets showed that intersection neighborhood was more flexible to adapt to the data with various structure, and approximation operator based on elementary set was more suitable for this application than that based on element. That was to say that the proposed algorithms were effective, as they could select significant gene subsets without redundancy and achieve high classification accuracy.

Jun Meng; Jing Zhang; Rui Li; Yushi Luan

2014-01-01T23:59:59.000Z

374

Green genes: bioinformatics and systems biology innovations drive algal biotechnology  

E-Print Network [OSTI]

for microalgae 4 The nuclear genome of the model green alga Chlamydomonas reinhardtii, sequenced in 2007 5 [1], is approximately 120 Mb and encodes ~15,000 genes. Although C. reinhardtii is commonly 6 used as a reference for the annotation of other microalgae... facilitation of 5 transgene expression comes from the use of 2A peptides [78], which cause self-cleavage to 6 release individual domains from a fusion protein. They thus provide the capacity for operon-7 like transgene expression within the nucleus. Marker...

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

2014-10-21T23:59:59.000Z

375

Anticancer Activity of CX-3543: A Direct Inhibitor of rRNA Biogenesis  

Science Journals Connector (OSTI)

...G-quadruplex interactive agent to enter human clinical trials...G-rich rDNA, we designed a search algorithm (quad_find...telomeric dysfunction. Short-term (48 hours) treatment of...G-quadruplex interactive agent to enter human clinical trials...

Denis Drygin; Adam Siddiqui-Jain; Sean O'Brien; Michael Schwaebe; Amy Lin; Josh Bliesath; Caroline B. Ho; Chris Proffitt; Katy Trent; Jeffrey P. Whitten; John K. C. Lim; Daniel Von Hoff; Kenna Anderes; and William G. Rice

2009-10-01T23:59:59.000Z

376

rRNA and Poly-?-Hydroxybutyrate Dynamics in Bioreactors Subjected to Feast and Famine Cycles  

Science Journals Connector (OSTI)

...wastewater treatment system...activated sludge wastewater treatment plants is subjected...expressed as the mass proportion...degree-of-reduction balances (i.e...activated sludge wastewater treatment. Ph.D...treatment plant before...

Dominic Frigon; Gerard Muyzer; Mark van Loosdrecht; Lutgarde Raskin

2006-04-01T23:59:59.000Z

377

Genome-wide discovery of missing genes in biological pathways of prokaryotes  

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

Genome-wide Genome-wide discovery of missing genes in biological pathways of prokaryotes Yong Chen 1,3,4,5 , Fenglou Mao 1,2 , Guojun Li 1,3 , Ying Xu 1,2,6* From The Ninth Asia Pacific Bioinformatics Conference (APBC 2011) Incheon, Korea. 11-14 January 2011 Abstract Background: Reconstruction of biological pathways is typically done through mapping well-characterized pathways of model organisms to a target genome, through orthologous gene mapping. A limitation of such pathway-mapping approaches is that the mapped pathway models are constrained by the composition of the template pathways, e.g., some genes in a target pathway may not have corresponding genes in the template pathways, the so-called "missing gene" problem. Methods: We present a novel pathway-expansion method for identifying additional genes that are possibly involved in a target pathway after pathway mapping,

378

Nucleotide sequence of the Dpn II DNA methylase gene of Streptococcus pneumoniae and its relationship to the dam gene of Escherichia coli  

SciTech Connect (OSTI)

The structural gene (dpnM) for the Dpn II DNA methylase of Streptococcus pneumoniae, which is part of the Dpn II restriction system and methylates adenine in the sequence 5'-G-A-T-C-3', was identified by subcloning fragments of a chromosomal segment from a Dpn II-producing strain in an S. pneumoniae host/vector cloning system and demonstrating function of the gene also in Bacillus subtilis. Determination of the nucleotide sequence of the gene and adjacent DNA indicates that it encodes a polypeptide of 32,903 daltons. A putative promoter for transcription of the gene lies within a hundred nucleotides of the polypeptide start codon. Comparison of the coding sequence to that of the dam gene of Escherichia coli, which encodes a similar methylase, revealed 30% of the amino acid residues in the two enzymes to be identical. This homology presumably reflects a common origin of the two genes prior to the divergence of Gram-positive and Gram-negative bacteria. It is suggested that the restriction function of the gene is primitive, and that the homologous restriction system in E. coli has evolved to play an accessory role in heteroduplex DNA base mismatch repair.

Mannarelli, B.M.; Balganesh, T.S.; Greenberg, B.; Springhorn, S.S.; Lacks, S.A.

1985-07-01T23:59:59.000Z

379

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

SciTech Connect (OSTI)

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

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

2013-05-03T23:59:59.000Z

380

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

E-Print Network [OSTI]

357307 contribute to band 4 Calculation of gene-centromere genet 'c distance for 7BI. using region I (RI) recombinant progeny Genetic distance bet~~een EP-Bly and Ep-Blz and the frequency of region II (RII) cro. over progeny LIST OF FIGURES... ram Phenot e Total ChrolQo some Co~st. it ut ion 42 43 41 41+telo 42+telo 40+telo and/or not ~f ~1* 8 IU VI IX Chromosome ?BL 42. 17 Centromere ~Ey-El Kp-Blz Chromosome 7AL K -Alz 6. 67 3 90 RII ~E-Alx l0. 67 Figure 8. Linkage...

McMillin, David Edwin

2012-06-07T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


381

Recognizing genes and other components of genomic structure  

SciTech Connect (OSTI)

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.

Burks, C. (Los Alamos National Lab., NM (USA)); Myers, E. (Arizona Univ., Tucson, AZ (USA). Dept. of Computer Science); Stormo, G.D. (Colorado Univ., Boulder, CO (USA). Dept. of Molecular, Cellular and Developmental Biology)

1991-01-01T23:59:59.000Z

382

How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets  

Science Journals Connector (OSTI)

We analyzed 12 combined mitochondrial and nuclear gene datasets in seven orders of insects using both equal weights parsimony (to evaluate phylogenetic utility) and Bayesian methods (to investigate substitution patterns). For the Bayesian analyses we used relatively complex models (e.g., general time reversible models with rate variation) that allowed us to quantitatively compare relative rates among genes and codon positions, patterns of rate variation among genes, and substitution patterns within genes. Our analyses indicate that nuclear and mitochondrial genes differ in a number of important ways, some of which are correlated with phylogenetic utility. First and most obviously, nuclear genes generally evolve more slowly than mitochondrial genes (except in one case), making them better markers for deep divergences. Second, nuclear genes showed universally high values of CI and (generally) contribute more to overall tree resolution than mitochondrial genes (as measured by partitioned Bremer support). Third, nuclear genes show more homogeneous patterns of among-site rate variation (higher values of ? than mitochondrial genes). Finally, nuclear genes show more symmetrical transformation rate matrices than mitochondrial genes. The combination of low values of ? and highly asymmetrical transformation rate matrices may explain the overall poor performance of mitochondrial genes when compared to nuclear genes in the same analysis. Our analyses indicate that some parameters are highly correlated. For example, A/T bias was positively and significantly associated with relative rate and CI was positively and significantly associated with ? (the shape of the gamma distribution). These results provide important insights into the substitution patterns that might characterized high quality genes for phylogenetic analysis: high values of ?, unbiased base composition, and symmetrical transformation rate matrices. We argue that insect molecular systematists should increasingly focus on nuclear rather than mitochondrial gene datasets because nuclear genes do not suffer from the same substitutional biases that characterize mitochondrial genes.

Chung-Ping Lin; Bryan N Danforth

2004-01-01T23:59:59.000Z

383

Combining gene expression and interaction network data to improve kidney lesion score prediction  

Science Journals Connector (OSTI)

Current method of diagnosing kidney rejection based on histopathology of renal biopsies in form of lesion scores is error-prone. Researchers use gene expression microarrays in combination of machine learning to build better kidney rejection predictors. However the high dimensionality of data makes this task challenging and compels application of feature selection methods. We present a method for predicting lesions using combination of statistical and biological feature selection methods along with an ensemble learning technique. Results show that combining highly interacting genes (Hub Genes) from protein-protein interaction network with genes selected by squared t-test method brings the most accurate kidney lesion score predictor.

Davoud Moulavi; Mohsen Hajiloo; Jorg Sander; Philip F. Halloran; Russell Greiner

2012-01-01T23:59:59.000Z

384

E-Print Network 3.0 - artificial gene fusion Sample Search Results  

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

Summary: for their usefulness in gene therapy. We investigated thymidine kinase (TK) fusion proteins including the HIV TAT... 1 General Introduction 12;Chapter 1 10 Cancer...

385

E-Print Network 3.0 - autoimmunity susceptibility gene Sample...  

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

class II haplotypes with 129 unaffected Doberman Pinschers. Three dog-leucocyte antigen (DLA) genes, DLA... hypothyroid disease, other autoimmune dis- eases, cancer and allergic...

386

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

DOE Patents [OSTI]

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.

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

2011-10-04T23:59:59.000Z

387

E-Print Network 3.0 - altered ovarian gene Sample Search Results  

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Sample search results for: altered ovarian gene Page: << < 1 2 3 4 5 > >> 1 Ovarian cancer is the most lethal cause of death among the gynecological cancers. Conventional...

388

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

DOE Patents [OSTI]

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.

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

2008-09-30T23:59:59.000Z

389

E-Print Network 3.0 - ancient immunity gene Sample Search Results  

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

Davis Collection: Environmental Sciences and Ecology 70 Introduction: Molecular Bio-Hacking Department of Bioengineering Summary: of the vertebrate immune system (the RAG gene)...

390

E-Print Network 3.0 - activated human genes Sample Search Results  

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

Indeed, until now, geneticists knew of only 40 such genes... the human genome. The software predicted the existence of 156 ... Source: Hartemink, Alexander - Center for...

391

E-Print Network 3.0 - array-based gene discovery Sample Search...  

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

2001 Summary: 1Mark-A. Krogel, Magdeburg University, Knowledge Discovery and Machine Learning Group KDD Cup 2001... : GeneProtein Function Prediction Using the Multirelational...

392

E-Print Network 3.0 - aldh gene variants Sample Search Results  

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

Collection: Physics 48 ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples Summary: variants recover roughly one...

393

E-Print Network 3.0 - approach matching gene Sample Search Results  

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

COMMON EVIDENCE NETWORK: AN INTEGRATED APPROACH TO INVESTIGATING GENE RELATIONSHIPS by Alison... of Project: Common Evidence Network: An Integrated Approach to Investigating...

394

E-Print Network 3.0 - analysis reveals genes Sample Search Results  

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

is minor at best. Finally, we tested... to be sufficient to generate the substantial functional redundancy seen among the duplicate genes. This analysis... of a large scale...

395

E-Print Network 3.0 - automated eukaryotic gene Sample Search...  

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

origins. The results... relationships for eukaryotic genes ... Source: Cotton, James - School of Biological and Chemical Sciences, Queen Mary, University of London...

396

E-Print Network 3.0 - acute phase gene Sample Search Results  

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

function and metabolism. Recent studies demonstrate that acute... proton nuclear magnetic resonance in mice subjected to acute CR. Liver and muscle showed increased gene... tissues...

397

Identification of cis-regulatory elements in mouse Mab21l2 gene by comparative genomics.  

E-Print Network [OSTI]

??The mab-21 gene was first identified in Caenorhabditis elegans as a critical component required for sensory organ identity determination. Mab21 homologs are highly conserved from… (more)

Shek, Kim Fung

2010-01-01T23:59:59.000Z

398

E-Print Network 3.0 - acyl-coa dehydrogenase gene Sample Search...  

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

Is under the Dual Control... the original work is properly cited. PPAR and HNF4 are nuclear receptors that control gene ... Source: Ecole Polytechnique, Centre de...

399

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades  

Science Journals Connector (OSTI)

We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight...

Shani Blanga-Kanfi; Hector Miranda; Osnat Penn; Tal Pupko…

2009-04-01T23:59:59.000Z

400

E-Print Network 3.0 - alpha rara gene Sample Search Results  

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

found, some of the genes present... the classification, we excluded from Vijver's dataset all samples that presented mutations in the ... Source: Moscato, Pablo - Newcastle...

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

E-Print Network 3.0 - acid sphingomyelinase gene Sample Search...  

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

Microbial Pathogenesis () Summary: CAMP factor in GBS pathogenesis, the cfb gene encoding the pore-forming cytotoxin was deleted... by the combined action of...

402

E-Print Network 3.0 - abscisic-acid-inducible wrky gene Sample...  

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

in the transcriptional activation of the gene. In the meantime, ... Source: Alfan, James R. - Department of Plant Pathology, University of Nebraska-Lincoln Collection: Biology and...

403

E-Print Network 3.0 - acat1 gene expression Sample Search Results  

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

and Medicine 7 Copyright 2002 by the Genetics Society of America Mutations in the midway Gene Disrupt a Drosophila Acyl Coenzyme A Summary: with recombinant baculovirus...

404

Causal Gene Network Inference from Genetical Genomics Experiments via Structural Equation Modeling.  

E-Print Network [OSTI]

??The goal of this research is to construct causal gene networks for genetical genomics experiments using expression Quantitative Trait Loci (eQTL) mapping and Structural Equation… (more)

Liu, Bing

2006-01-01T23:59:59.000Z

405

E-Print Network 3.0 - arthritis candidate genes Sample Search...  

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

spondylitis; RA rheumatoid arthritis. Table 3. Allele... , Birlik, Onen, Bradman, Plaster. REFERENCES 1. French FMF Consortium. A candidate gene for familial... arthritis...

406

E-Print Network 3.0 - akirin gene family Sample Search Results  

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

two species, apparently due to frequent gene duplication... found to be a family of V1rs (Rodriguez et al., 2002). ... Source: Zhang, Jianzhi - Department of Ecology and...

407

E-Print Network 3.0 - adult gene therapy Sample Search Results  

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

potentiates a pound... -lasting tolerance to hFVIII and allows gene ... Source: Ponder, Katherine P. - Departments of Medicine & Biochemistry and Molecular Biophysics, Washington...

408

E-Print Network 3.0 - assessing her2 gene Sample Search Results  

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

; Computer Technologies and Information Sciences 29 The life and death of gene families Jeffery P. Demuth,1 Summary: or for an increased arsenal of molecular weaponry. To assess...

409

E-Print Network 3.0 - avpr2 gene mutations Sample Search Results  

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

; Biology and Medicine 3 Current Pharmacogenomics, 2005, 3, 000-000 1 1570-160305 50.00+.00 2005 Bentham Science Publishers Ltd. Summary: vasopressin receptor gene...

410

E-Print Network 3.0 - analyzing time-series gene Sample Search...  

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

series in terms of number... gene networks from time series include boolean network models, 5 Correlation Metric Construction, 6... - constructed time ... Source: D'haeseleer,...

411

E-Print Network 3.0 - alpha gene variants Sample Search Results  

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

KRT19 keratin... DKFZp564A072) GENE1188X AMACR ... Source: Leng, Chenlei - Department of Statistics and Applied Probability, National University of Singapore Collection:...

412

E-Print Network 3.0 - alpha subunit gene Sample Search Results  

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

KRT19 keratin... DKFZp564A072) GENE1188X AMACR ... Source: Leng, Chenlei - Department of Statistics and Applied Probability, National University of Singapore Collection:...

413

E-Print Network 3.0 - alpha gene expression Sample Search Results  

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

KRT19 keratin... DKFZp564A072) GENE1188X AMACR ... Source: Leng, Chenlei - Department of Statistics and Applied Probability, National University of Singapore Collection:...

414

E-Print Network 3.0 - acid-binding protein-7 gene Sample Search...  

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

top 30 genes for the Brown Data set UID Name ... Source: Leng, Chenlei - Department of Statistics and Applied Probability, National University of Singapore Collection:...

415

A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes  

Science Journals Connector (OSTI)

A mouse embryonic stem cell bank of inducible human chromosome 21 gene expression is shown to be an important resource for investigating trisomy.

Rossella De Cegli; Antonio Romito; Simona Iacobacci; Lei Mao; Mario Lauria; Anthony O Fedele; Joachim Klose; Christelle Borel; Patrick Descombes; Stylianos E Antonarakis; Diego di Bernardo; Sandro Banfi; Andrea Ballabio; Gilda Cobellis

2010-06-22T23:59:59.000Z

416

Haploid genomes illustrate epigenetic constraints and gene dosage effects in mammals  

Science Journals Connector (OSTI)

As part of the Epigenetics Chromatin conference thematic series, Anton Wutz and Martin Leeb discuss how haploid genomes illustrate epigenetic constraints and gene dosage effects in mammals.

Martin Leeb; Anton Wutz

2013-12-05T23:59:59.000Z

417

E-Print Network 3.0 - algorithms gene expression Sample Search...  

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

expression profiles has been developed, where various machine... , which adopts Kruskal-Wallis rank sum test to rank all genes and then apply an algorithm based......

418

E-Print Network 3.0 - alphaviruses gene expression Sample Search...  

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

1994. The alphaviruses: gene... of Marine Mammals: a New Alphavirus Isolated from the Elephant Seal Louse, Lepidophthirus macrorhini MAY LA... Accepted 29 January 2001 A novel...

419

E-Print Network 3.0 - assisted gene insertion Sample Search Results  

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

and noncoding genes in the human genome Michele Clamp* , Ben Fry... ) Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding...

420

E-Print Network 3.0 - approaches gene expression Sample Search...  

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

D: Knowledge Questions 1. You are investigating the changes in gene expression in cancer cells compared to normal cells Summary: Appendix D: Knowledge Questions 1. You are...

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


421

E-Print Network 3.0 - a-amylase inhibitor gene Sample Search...  

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

interaction of monoterpenes Summary: Molecular phylogenetic analysis of the potato a-amylase gene family reveals clustering into two distinct... - mediated tuber bud...

422

E-Print Network 3.0 - aphid resistance gene Sample Search Results  

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

gene confers resistance in tomato to certain clones of Macrosiphum euphorbiae (potato aphid), two... aphids progress through different feeding stages. Interestingly, the...

423

Accelerated Gene Evolution and Subfunctionalization in the Pseudotetraploid Frog Xenopus Laevis  

E-Print Network [OSTI]

Accelerated gene evolution and subfunctionalization in thethese triplets reveals accelerated evolution or relaxationbeen proposed to exhibit accelerated [31] or slowed [32

Hellsten, Uffe; Khokha, Mustafa K.; Grammar, Timothy C.; Harland, Richard M.; Richardson, Paul; Rokhsar, Daniel S.

2007-01-01T23:59:59.000Z

424

E-Print Network 3.0 - autophagy genes protect Sample Search Results  

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

that starvation induced the tran- scription of several autophagy genes... ). To test whether TFEB regulated the expres- sion of autophagy ... Source: Gleeson, Joseph G. -...

425

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

DOE Patents [OSTI]

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.

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

2003-01-01T23:59:59.000Z

426

Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.  

SciTech Connect (OSTI)

A thermophilic, filamentous, heterotrophic bacterium designated strain JAD2T was isolated from sediment of Great Boiling Spring in Nevada, USA. Cells had an average diameter of 0.3 µm and length of 4.0 µm, and formed filaments typically ranging in length from 20 µm to 200 µm. Filaments were negative for the Gram stain reaction, spores were not formed, and motility was not observed. The optimum temperature for growth was 75 °C with a range from 67.5-75 °C, and the optimum pH for growth was 6.75 with a range from 6.5-7.75. Peptone, tryptone or yeast extract were able to support growth when supplemented with a vitamin solution, but no growth was observed using a variety of defined organic substrates. Strain JAD2T was a facultative microaerophile, with optimal growth at 1% v/v O2 and an upper limit of 8% O2, and anaerobic growth was stimulated by fumarate but inhibited by sulfite and elemental sulfur. The major cellular fatty acids (>5%) were C16:0, C19:0, C18:0, C20:0, and C19:1. The genomic DNA G+C content was 69.3%. Phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and other conserved genes placed JAD2T and other members of the yet-uncultivated GAL35 group within the phylum Chloroflexi, but not within any existing class in this phylum. These results indicate that strain JAD2T is the first cultivated representative of a new lineage within the phylum Chloroflexi, for which we propose the name Thermoflexus hugenholtzii gen. nov., sp. nov., type strain JAD2T, within Thermoflexia classis nov., Thermoflexales ord. nov., and Thermoflexaceae fam. nov.

Dodsworth, Jeremy A.; Gevorkian, Jonathan; Despujos, Fairuz; Cole, Jesse; Murugapiran, Senthil K.; Ming, Hong; Li, Wen J.; Zhang, Gengxin; Dohnalkova, Alice; Hedlund, Brian P.

2014-06-06T23:59:59.000Z

427

The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates  

Science Journals Connector (OSTI)

We identified and annotated in the MitoComp2 dataset the orthologs of 68 nuclear genes controlling oxidative phosphorylation in 11 Drosophilidae...Fugu rubripes, Danio rerio and Homo sapiens) and in the cnidarian...

Damiano Porcelli; Paolo Barsanti; Graziano Pesole…

2007-11-01T23:59:59.000Z

428

(E)-β-Ocimene and Myrcene Synthase Genes of Floral Scent Biosynthesis in Snapdragon: Function and Expression of Three Terpene Synthase Genes of a New Terpene Synthase Subfamily  

Science Journals Connector (OSTI)

...Methyl jasmonate-induced terpene synthase gene expression, and cDNA cloning and functional characterization of (+)-3-carene synthase. Plant Mol. Biol. 51, 119-133. Gang, D.R., Lavid, N., Zubieta, C., Chen, F., Beuerle, T., Lewinsohn...

Natalia Dudareva; Diane Martin; Christine M. Kish; Natalia Kolosova; Nina Gorenstein; Jenny Fäldt; Barbara Miller; Jörg Bohlmann

2003-04-11T23:59:59.000Z

429

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)]

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.

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

430

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

DOE Patents [OSTI]

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.

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

2008-11-11T23:59:59.000Z

431

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

DOE Patents [OSTI]

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.

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

2008-11-11T23:59:59.000Z

432

A2 Processor User's Manual for Blue Gene/Q  

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

A2 Processor A2 Processor User's Manual for Blue Gene/Q Note: This document and the information it contains are provided on an as-is basis. There is no plan for providing for future updates and corrections to this document. October 23, 2012 Version 1.3 Title Page ® Copyright and Disclaimer © Copyright International Business Machines Corporation 2010, 2012 Printed in the United States of America October 2012 IBM, the IBM logo, and ibm.com are trademarks or registered trademarks of International Business Machines Corp., registered in many jurisdictions worldwide. Other product and service names might be trademarks of IBM or other compa- nies. A current list of IBM trademarks is available on the Web at "Copyright and trademark information" at www.ibm.com/legal/copytrade.shtml.

433

Cold, Salty and Promiscuous-Gene-shuffling Microbes Dominate  

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

September 30, 2013 September 30, 2013 Cold, Salty and Promiscuous—Gene-shuffling Microbes Dominate Antarctica’s Deep Lake Sequestered in Antarctica's Vestfold Hills, Deep Lake became isolated from the ocean 3,500 years ago by the Antarctic continent rising, resulting in a saltwater ecosystem that remains liquid in extreme cold, and providing researchers a unique niche for studying the evolution of the microbes that now thrive under such conditions. Deep Lake's microscopic inhabitants are dominated by haloarchaea, microbes that require high salt concentrations to grow and are naturally adapted to conditions - at minus 20°C - that would prove lethally cold to other organisms. In a detailed analysis published online the week of September 30, 2013 in the journal Proceedings

434

Microsoft PowerPoint - gene_kight_panelist_presentation  

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

Fossil Energy R&D Fossil Energy R&D American Recovery & Reinvestment Act Projects 10 th Annual U.S. Department of Energy Small Business Conference Small Businesses Leading the Way to Recovery and Reinvestment Gene Kight Director, Finance and Procurement Office of Fossil Energy August 12, 2009 2 Small Businesses Leading the Way to Recovery and Reinvestment Expand and Extend Clean Coal Power Initiative (CCPI) Round 3 (Additional available CCPI funds total >$600 million) Industrial Carbon Capture and Storage Geologic Sequestration Site Characterization Geologic Sequestration Training & Research Carbon Capture and Storage (FutureGen Re-start) FE Program Direction $800 million $1.52 billion $50.0 million $20.0 million $1.0 billion

435

Microarray analysis of IFN-? response genes in astrocytes  

Science Journals Connector (OSTI)

IFN-gamma (IFN-?) has been shown to activate astrocytes to acquire immune functions. In this study the effect of IFN-? on murine astrocytes was investigated via microarray analysis. The activating effect of IFN-? on the astrocyte transcriptome showed predominance toward pathways involved in adaptive immunity, initiation of the immune response and innate immunity. Previously unknown astrocytic genes expressed included members of the p47 \\{GTPases\\} and guanine nucleotide binding protein (GBP) families. Down-regulatory effects of IFN-? stimulation were confined to pathways involved in growth regulation, cell differentiation and cell adhesion. This data supports the notion that astrocytes are an important immunocompetant cell in the brain and indicate that astrocytes may have a significant role in various infectious diseases such as Toxoplasmic Encephalitis and neurological diseases with an immunological component such as Alzheimer's and autoimmune disorders.

Sandra K. Halonen; Tyson Woods; Kate McInnerney; Louis M. Weiss

2006-01-01T23:59:59.000Z

436

Use of NAP gene to manipulate leaf senescence in plants  

DOE Patents [OSTI]

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.

Gan, Susheng; Guo, Yongfeng

2013-04-16T23:59:59.000Z

437

LAMMPS strong scaling performance optimization on Blue Gene/Q  

SciTech Connect (OSTI)

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.

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

2014-11-12T23:59:59.000Z

438

Validation of a novel expressed sequence tag (EST) clustering method and development of a phylogenetic annotation pipeline for livestock gene families  

E-Print Network [OSTI]

Sequence EGAD Expressed Gene Anatomy Database BTGI Bos taurus Gene Indices GO Gene Ontology MAFFT Multiple Alignment Using Fast Fourier Transform viii TABLE OF CONTENTS Page ABSTRACT... Ontology Accession GO:0030295 from the Livestock EST Gene Family Database ........................................ 120 3.8 Search results for Bovine Oligo Microarray Consortium Locus 11695 from the Cattle EST Gene Family Database...

Venkatraman, Anand

2009-05-15T23:59:59.000Z

439

Technology development for gene discovery and full-length sequencing  

SciTech Connect (OSTI)

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.

Marcelo Bento Soares

2004-07-19T23:59:59.000Z

440

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

E-Print Network [OSTI]

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

Petrov, Dmitri

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
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to obtain the most current and comprehensive results.


441

TECHNICAL ADVANCE The ethanol switch: a tool for tissue-specic gene induction  

E-Print Network [OSTI]

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

Murray, J.A.H.

442

Techniques for the removal of marker genes from transgenic plants Charles P. Scutt a,  

E-Print Network [OSTI]

reason to warrant their removal. In addition to environmental and health concerns, there are alsoReview Techniques for the removal of marker genes from transgenic plants Charles P. Scutt a of problems. Various techniques are under development for the removal of unwanted marker genes, while leaving

Meyer, Peter

443

Expression of an Arabidopsis vacuolar -pyrophosphatase gene (AVP1) in cotton improves  

E-Print Network [OSTI]

Expression of an Arabidopsis vacuolar H+ -pyrophosphatase gene (AVP1) in cotton improves drought, pro- ton pump, root development, salt stress, transgenic cotton. Summary The Arabidopsis gene AVP1 conditions. Using the same approach, AVP1-expressing cotton plants were created and tested

Blumwald, Eduardo

444

Expression of an Arabidopsis vacuolar -pyrophosphatase gene (AVP1) in cotton improves  

E-Print Network [OSTI]

Expression of an Arabidopsis vacuolar H+ -pyrophosphatase gene (AVP1) in cotton improves drought- ton pump, root development, salt stress, transgenic cotton. Summary The Arabidopsis gene AVP1 encodes-expressing cotton plants were created and tested for their performance under high-salt and reduced irrigation

Blumwald, Eduardo

445

Alternative splicing and genomic structure of the Wilms tumor gene WT1.  

Science Journals Connector (OSTI)

...chromosome 11p13 WiU tumor suscepti- bility gene WTI appears to play a cucial role in regulating...dfrnai of nephrobasts and god tis- sue. The WTI gene consistsof 1lexons, ig a pattern of...kidney and in various mouse tissues expeing WTI. The conservation in stuctre and relative...

D A Haber; R L Sohn; A J Buckler; J Pelletier; K M Call; D E Housman

1991-01-01T23:59:59.000Z

446

Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the  

E-Print Network [OSTI]

a dataset comprised of one mitochondrial and five nuclear loci, we elucidate the major biogeographicNuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of California. In addition, discordant mitochondrial/ nuclear genetic patterns suggest subsequent gene flow from

Grether, Gregory

447

Single-Copy Nuclear Genes Place Haustorial Hydnoraceae within Piperales and Reveal a Cretaceous  

E-Print Network [OSTI]

Single-Copy Nuclear Genes Place Haustorial Hydnoraceae within Piperales and Reveal a Cretaceous, we extracted 14 nuclear single copy genes (nSCG) from Illumina transcriptome data from one of the ``strangest plants in the world'', Hydnora visseri (Hydnoraceae). A ,15,000 character molecular dataset, based

dePamphilis, Claude

448

Origins of anteroposterior patterning and Hox gene regulation during chordate evolution  

Science Journals Connector (OSTI)

...have a similar basic plan, with an anterior end...many early developmental regulatory genes in protochordates...of the vertebrate body plan it is important to determine...reveal how developmental regulatory genes control AP patterning in vertebrates (for reviews, see Cappechi 1997...

2001-01-01T23:59:59.000Z

449

Evolution of Red Algal Plastid Genomes: Ancient Architectures, Introns, Horizontal Gene Transfer, and  

E-Print Network [OSTI]

Evolution of Red Algal Plastid Genomes: Ancient Architectures, Introns, Horizontal Gene Transfer, Station Biologique, Roscoff, France Abstract Red algae have the most gene-rich plastid genomes known across all available red algal plastid genomes we show they all share a highly compact and slowly

Martone, Patrick T.

450

Association of isozyme marker-genes on chromosome 6 with resistance to MDMV in maize  

E-Print Network [OSTI]

in the estimated number of resistance genes, even for the same genotype. MATERIALS AND METHODS The choiceAssociation of isozyme marker-genes on chromosome 6 with resistance to MDMV in maize D Ignjatovi homozygous lines were chosen by both divergence in MDMV resistance and presence of segregating isozyme

Boyer, Edmond

451

BioThesaurus: a web-based thesaurus of protein and gene names  

Science Journals Connector (OSTI)

......text mining BioThesaurus: a web-based thesaurus of protein and gene names Hongfang Liu...web-based system BioThesaurus that maps a thesaurus of protein and gene names extracted from...construction is shown in Figure 1. The thesaurus was designed to provide comprehensive......

Hongfang Liu; Zhang-Zhi Hu; Jian Zhang; Cathy Wu

2006-01-01T23:59:59.000Z

452

Genetic analyses of bovine CARD15, a putative disease resistance gene  

E-Print Network [OSTI]

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

Taylor, Kristen Hawkins

2004-09-30T23:59:59.000Z

453

Genetic analysis of a locus on the Bacteroides ovatus chromosome which contains xylan utilization genes.  

Science Journals Connector (OSTI)

...ovatus chromosome which contains xylan utilization genes. J Weaver...O'Brien. 1981. Utilization of xylan by two species of human colonic...in binding of starch to the surface of Bacteroides thetaiotaomicron...1990. The genes for three xylan-degrading activities from...

J Weaver; T R Whitehead; M A Cotta; P C Valentine; A A Salyers

1992-09-01T23:59:59.000Z

454

Gene expression of beta-defensins in chicken white blood cells  

E-Print Network [OSTI]

beta-defensins have been identified; however, the regulation of these genes has not been well-investigated in the chicken. The objective of this research was to understand constitutive and inducible gene expression of beta-defensins in chicken white...

Supak, Tiffany Marie

2009-06-02T23:59:59.000Z

455

Beyond Synexpression Relationships: Local Clustering of Time-shifted and Inverted Gene  

E-Print Network [OSTI]

Beyond Synexpression Relationships: Local Clustering of Time-shifted and Inverted Gene Expression an inverted relationship. Here, we propose a new method, which we call local clus- tering, for identifying these time-delayed and inverted relationships. It is related to conventional gene-expression clustering

Yu, Haiyuan

456

PDGF-Receptor ?-Targeted Adenovirus Redirects Gene Transfer from Hepatocytes to Activated Stellate Cells  

Science Journals Connector (OSTI)

Department of Gastroenterology and Hepatology, Department of Therapeutic Gene Modulation, and Department of Pharmacokinetics and Drug Delivery, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands ... Mailing address: Department of Therapeutic Gene Modulation, University of Groningen, Ant. ... Deusinglaan 1, 9713 AV Groningen, The Netherlands. ...

Marieke H. Schoemaker; Marianne G. Rots; Leonie Beljaars; Arjen Y. Ypma; Peter L. M. Jansen; Klaas Poelstra; Han Moshage; Hidde J. Haisma

2008-01-25T23:59:59.000Z

457

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

E-Print Network [OSTI]

to a decrease in viability of the cells. It was also noted that the method of cell death is likely to be apoptosis. To confirm the efficacy of gene therapy through transfection, the transfection of the serum response factor (SRF) gene plasmid DNA...

Chern, Christina

2009-05-15T23:59:59.000Z

458

The probability distribution of ranked gene trees on a species tree James H. Degnan a,  

E-Print Network [OSTI]

The probability distribution of ranked gene trees on a species tree James H. Degnan a, , Noah A. Rosenberg b , Tanja Stadler c a Department of Mathematics and Statistics, Private Bag 4800, University and the sequence of coalescences for a random gene tree are considered. We derive the probability distribution

Rosenberg, Noah

459

An algorithm for identifying clusters of functionally related genes in genomes  

E-Print Network [OSTI]

rise to them. I present a basis of algorithm to identify gene clusters in eukaryotic genomes that utilizes functional categories defined in graph-based vocabularies such as the Gene Ontology (GO). Clusters identified in this manner need only have a...

Yi, Gang Man

2009-05-15T23:59:59.000Z

460

Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene Trees  

E-Print Network [OSTI]

for human health and environmental remediation. Although it is well understood that the accessory genes is expected to produce conflicting gene tree topologies. The main goal of this study was therefore to infer; Sen et al. 2011), streams (Smalla et al. 2006; Akiyama et al. 2010), and waste- water treatment plants

Sullivan, Jack

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


461

Plasmids containing the gene for DNA polymerase I from Streptococcus pneumoniae  

DOE Patents [OSTI]

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.

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

1987-08-28T23:59:59.000Z

462

Structure and transforming function of transduced mutant alleles of the chicken c-myc gene.  

Science Journals Connector (OSTI)

...chicken c-myc gene. T Patschinsky H W Jansen H Blocker R Frank K Bister A small retroviral...c-myc Gene TILO PATSCHINSKY,' HANS W. JANSEN,1t HELMUT BLOCKER,2 RONALD FRANK...5, 7, 59; K. Bister and H. W. Jansen, Adv. Cancer Res., in press). The...

T Patschinsky; H W Jansen; H Blöcker; R Frank; K Bister

1986-08-01T23:59:59.000Z

463

VALIDATION OF IMPRINTED GENES ON HUMAN CHROMOSOME 6 EXPRESSED IN THE PLACENTA  

E-Print Network [OSTI]

VALIDATION OF IMPRINTED GENES ON HUMAN CHROMOSOME 6 EXPRESSED IN THE PLACENTA Anna Brenneman (Jill, which results in inadequate blood flow and nutrient transfer to the developing fetus. Genomic imprinting in a developmental stage-specific manner in human placenta. Our goal is to better define the set of imprinted genes

Zhou, Yaoqi

464

What is genetic research? Genes are part of every cell in every  

E-Print Network [OSTI]

Genetic Research What is genetic research? Genes are part of every cell in every person. Genes come volunteers More questions? Call: Questions to ask 1. What is the purpose of the study? 2. How will you collect my genetic sample? 3. Will I, or anyone else, receive results from this study? 4. What happens

Church, George M.

465

Gene Expression Profiles during the Initial Phase of Salt Stress in Rice  

Science Journals Connector (OSTI)

...and photoperiodic flowering by the Arabidopsis GIGANTEA gene Price A.H. Young E.M. Tomos A.D. Quantitative trait loci...three rice sucrose synthase genes Yang S.F. Hoffman N.E. Ethylene biosynthesis and its regulation in higher plants Yeo A.R...

Shinji Kawasaki; Chris Borchert; Michael Deyholos; Hong Wang; Susan Brazille; Kiyoshi Kawai; David Galbraith; Hans J. Bohnert

466

Seamless Correction of the Sickle Cell Disease Mutation of the HBB Gene in Human Induced  

E-Print Network [OSTI]

Seamless Correction of the Sickle Cell Disease Mutation of the HBB Gene in Human Induced ABSTRACT: Sickle cell disease (SCD) is the most common human genetic disease which is caused by a single effector nucleases; induced pluripotent stem cells; piggyBac transposon; sickle cell disease; gene therapy

Zhao, Huimin

467

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

SciTech Connect (OSTI)

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

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

2011-10-07T23:59:59.000Z

468

Cell Cycle-regulated Gene Expression in Arabidopsis* Received for publication, July 26, 2002  

E-Print Network [OSTI]

Cell Cycle-regulated Gene Expression in Arabidopsis* Received for publication, July 26, 2002¨rich, Switzerland Regulated gene expression is an important mecha- nism for controlling cell cycle progression regulation de- pendent on cell cycle position. Analysis of cell cycle processes in plants has been hampered

Murray, J.A.H.

469

ATLAS on the BlueGene/L Preliminary Results Keith Seymour Haihang You Jack Dongarra  

E-Print Network [OSTI]

ATLAS on the BlueGene/L ­ Preliminary Results Keith Seymour Haihang You Jack Dongarra Department The goal of this work is to use ATLAS to produce a tuned linear algebra library for the BlueGene/L, while of the machine present a few difficulties for a straightforward port of ATLAS. The compute nodes themselves

Dongarra, Jack

470

Gene–Environment Interaction Involving Recently Identified Colorectal Cancer Susceptibility Loci  

Science Journals Connector (OSTI)

...NY, NC, ND, OH, OK, OR, PA, RI, SC, TN, TX, VA, WA, and WY. PLCO: The...lung datasets were accessed from the dbGaP website ( http://www.ncbi.nlm.nih.gov...Brenner H, Buchanan D, et alGenome-wide search for gene-gene interactions in colorectal...

Elizabeth D. Kantor; Carolyn M. Hutter; Jessica Minnier; Sonja I. Berndt; Hermann Brenner; Bette J. Caan; Peter T. Campbell; Christopher S. Carlson; Graham Casey; Andrew T. Chan; Jenny Chang-Claude; Stephen J. Chanock; Michelle Cotterchio; Mengmeng Du; David Duggan; Charles S. Fuchs; Edward L. Giovannucci; Jian Gong; Tabitha A. Harrison; Richard B. Hayes; Brian E. Henderson; Michael Hoffmeister; John L. Hopper; Mark A. Jenkins; Shuo Jiao; Laurence N. Kolonel; Loic Le Marchand; Mathieu Lemire; Jing Ma; Polly A. Newcomb; Heather M. Ochs-Balcom; Bethann M. Pflugeisen; John D. Potter; Anja Rudolph; Robert E. Schoen; Daniela Seminara; Martha L. Slattery; Deanna L. Stelling; Fridtjof Thomas; Mark Thornquist; Cornelia M. Ulrich; Greg S. Warnick; Brent W. Zanke; Ulrike Peters; Li Hsu; and Emily White

2014-09-01T23:59:59.000Z

471

Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species  

Science Journals Connector (OSTI)

An RFX-binding site is shown to be conserved in the promoters of a subset of ciliary genes and a subsequent screen for this site in two Drosophila species identified novel RFX target genes that are involved in sensory ciliogenesis.

Anne Laurençon; Raphaëlle Dubruille; Evgeni Efimenko; Guillaume Grenier; Ryan Bissett; Elisabeth Cortier; Vivien Rolland; Peter Swoboda; Bénédicte Durand

2007-09-17T23:59:59.000Z

472

Positive selection at the ASPM gene coincides with brain size enlargements in cetaceans  

Science Journals Connector (OSTI)

...selection at the ASPM gene coincides with brain size enlargements in cetaceans Shixia Xu...Republic of China The enlargement of cetacean brain size represents an enigmatic event in mammalian...explored. One candidate gene associated with brain size evolution is the abnormal spindle-like...

2012-01-01T23:59:59.000Z

473

The NGATHA Distal Organ Development Genes Are Essential for Style Specification in Arabidopsis  

Science Journals Connector (OSTI)

...development. Another general process having a patterning role in...additonal understanding as to the processes regulated by NGA gene activity...limits our understanding of the processes of morphogenesis in plants...transport, and these could be interrelated. The NGA Genes Are Essential...

John Paul Alvarez; Alexander Goldshmidt; Idan Efroni; John L. Bowman; Yuval Eshed

2009-05-12T23:59:59.000Z

474

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

E-Print Network [OSTI]

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

Clayton, Dale H.

475

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

E-Print Network [OSTI]

Hierarchical Analysis of Population Genetic Variation in Mitochondrial and Nuclear Genes of Daphnia in part to the limited dispersal ability of Daphnia. However, previous work has shown that fluctuating as rapidly with distance as does that for nuclear genes, which is slower than the neutral expectation

Lynch, Michael

476

Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space  

E-Print Network [OSTI]

1 Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear;2 Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of their dispersal over several chromosomes. Moreover, using Hi-C contact map of the tendency of chromosomal segments

Shamir, Ron

477

Compensatory cis-trans Evolution and the Dysregulation of Gene Expression in Interspecific Hybrids of Drosophila  

E-Print Network [OSTI]

Hybrids of Drosophila Christian R. Landry* , Patricia J. Wittkopp , Clifford H. Taubes , Jose M. Ranz.047449 #12;2 Running head: Gene and expression in interspecific hybrids Key words: Gene regulation, Drosophila, hybrid, dysregulation, allele-specific expression Corresponding author: Daniel L. Hartl

Gruber, Jonathan

478

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

E-Print Network [OSTI]

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

Sinskey, Anthony J.

479

Use of the Transposon Ac as a Gene-Searching Engine in the Maize Genome  

Science Journals Connector (OSTI)

...an excellent gene-searching engine in the highly repetitive maize...The Mutants of Maize. (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press). Parinov...transposon Ac as a gene-searching engine in the maize genome. | We show...

Matthew Cowperthwaite; Wonkeun Park; Zhennan Xu; Xianghe Yan; Steven C. Maurais; Hugo K. Dooner

2002-03-08T23:59:59.000Z

480

Horizontal gene transfer and the evolution of transcriptionalregulation in Escherichia coli  

SciTech Connect (OSTI)

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.

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

2007-12-20T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


481

A comparison of synthetic oligodeoxynucleotides, DNA fragments and AAV-1 for targeted episomal and chromosomal gene repair  

Science Journals Connector (OSTI)

Current strategies for gene therapy of inherited diseases consist in adding functional copies of the gene that is defective. An attractive alternative to these approaches would be to correct the endogenous mutate...

Xavier Leclerc; Olivier Danos; Daniel Scherman; Antoine Kichler

2009-04-01T23:59:59.000Z

482

Mechanisms of hormonal regulation of CAD gene expression and inhibition by Aryl hydrocarbon receptor agonist in human breast cancer cells  

E-Print Network [OSTI]

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 cancer cells, and treatment...

Khan, Shaheen Munawar Ali

2007-04-25T23:59:59.000Z

483

Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network  

Science Journals Connector (OSTI)

......their underlying gene regulatory network (GRN) (Bar-Joseph...Systems Biology, plan cancer 2009-2013...Hecker M , et al. Gene regulatory network inference...in dynamic models-a review. Biosystems (2009...Genomic analysis of regulatory network dynamics reveals......

Nicolas Jung; Frédéric Bertrand; Seiamak Bahram; Laurent Vallat; Myriam Maumy-Bertrand

2014-02-15T23:59:59.000Z

484

Down-Regulation of Homeobox Gene GBX2 Expression Inhibits Human Prostate Cancer Clonogenic Ability and Tumorigenicity  

Science Journals Connector (OSTI)

...283-302. 1992. 3. Shashikant, C. S.. and Violette. S. M. Homeobox genes in mouse development...945-952, 1995. 10. Friedmann, Y.. Daniel. C. A.. Strickland, P., and Daniel, C. W. Hox genes in normal and neoplastic...

Allen C. Gao; Wei Lou; and John T. Isaacs

1998-04-01T23:59:59.000Z

485

Isolation and molecular genetic characterization of the Bacillus subtilis gene (infB) encoding protein synthesis initiation factor 2.  

Science Journals Connector (OSTI)

...genetic characterization of the Bacillus subtilis gene (infB) encoding protein...blot (immunoblot) analysis of Bacillus subtilis cell extracts detected two proteins...genetic characterization of the Bacillus subtilis gene (infB) encoding protein...

K Shazand; J Tucker; R Chiang; K Stansmore; H U Sperling-Petersen; M Grunberg-Manago; J C Rabinowitz; T Leighton

1990-05-01T23:59:59.000Z

486

Inhibition of Repair of Radiation-Induced DNA Damage Enhances Gene Expression from Replication-Defective Adenoviral Vectors  

Science Journals Connector (OSTI)

...those related to increased expression of CAR and integrin are responsible for the enhanced...of gene expression from replication-defective adenoviral vectors: implications for...enhances gene expression from replication-defective adenoviral vectors. | Radiation has been...

Mohan Hingorani; Christine L. White; Andrew Merron; Inge Peerlinck; Martin E. Gore; Andrew Slade; Simon D. Scott; Christopher M. Nutting; Hardev S. Pandha; Alan A. Melcher; Richard G. Vile; Georges Vassaux; and Kevin J. Harrington

2008-12-01T23:59:59.000Z

487

A MACHINE LEARNING APPROACH TO QUERY TIME-SERIES MICROARRAY DATA SETS FOR FUNCTIONALLY RELATED GENES USING HIDDEN MARKOV MODELS  

E-Print Network [OSTI]

Microarray technology captures the rate of expression of genes under varying experimental conditions. Genes encode the information necessary to build proteins; proteins used by cellular functions exhibit higher rates of ...

Senf, Alexander J.

2011-02-04T23:59:59.000Z

488

Automation of Drosophila gene expression pattern image annotation : development of web-based image annotation tool and application of machine learning methods  

E-Print Network [OSTI]

Large-scale in situ hybridization screens are providing an abundance of spatio-temporal patterns of gene expression data that is valuable for understanding the mechanisms of gene regulation. Drosophila gene expression ...

Ayuso, Anna Maria E

2011-01-01T23:59:59.000Z

489

Polymorphic genes of detoxification and mitochondrial enzymes and risk for progressive supranuclear palsy: A case control study  

E-Print Network [OSTI]

and mitochondrial enzymes and risk for progressiveand mitochondrial enzymes and risk for progressivein genes encoding enzymes of xenobiotic detoxification,

2012-01-01T23:59:59.000Z

490

Uncovering the Molecular Secrets of Inflammatory Breast Cancer Biology: An Integrated Analysis of Three Distinct Affymetrix Gene Expression Datasets  

Science Journals Connector (OSTI)

...differentially expressed genes in the datasets generated from the different...multiple gene expression profiling datasets, the common gene signatures...10606 PCNA Proliferating cell nuclear antigen 20pter-p12 5111 PMAIP1...value of proliferating cell nuclear antigen (PCNA) and p53 protein...

Steven J. Van Laere; Naoto T. Ueno; Pascal Finetti; Peter Vermeulen; Anthony Lucci; Fredika M. Robertson; Melike Marsan; Takayuki Iwamoto; Savitri Krishnamurthy; Hiroko Masuda; Peter van Dam; Wendy A. Woodward; Patrice Viens; Massimo Cristofanilli; Daniel Birnbaum; Luc Dirix; James M. Reuben; and François Bertucci

2013-09-01T23:59:59.000Z

491

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima  

E-Print Network [OSTI]

 insect  chemosensory  genes,  included  in  six  gene  families;  three  ligand  binding  protein  families:  Odorant  Binding  Proteins  (OBP;  [56,57]),  Chemosensory  Proteins  (CSP;  [58,59])  and  Che...  proteins,  we  found  only  two  genes  belonging  to  the  CSP  family,  but  no  representatives  of  the  OBP  or  CheA/B  families.  Among  the  membrane  receptor  families,  we  identified  a...

Chipman, Ariel D.; Ferrier, David E. K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S. T.; Schröder, Reinhard; Torres-­Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C.; Alonso, Claudio R.; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C. J.; Blankenburg, Kerstin P.; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K.; Du Pasquier, Louis; Duncan, Elizabeth J.; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D.; Extavour, Cassandra G.; Francisco, Liezl; Gabaldón, Toni; Gillis, William J.; Goodwin-­Horn, Elizabeth A.; Green, Jack E.; Griffiths-­Jones, Sam; Grimmelikhuijzen, Cornelis J. P.; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H. L.; Hunn, Julia P.; Hunnekuhl, Vera S.; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N.; Jiggins, Francis M.; Jones, Tamsin E.; Kaiser, Tobias S.; Kalra, Divya; Kenny, Nathan J.; Korchina, Viktoriya; Kovar, Christie L.; Kraus, F. Bernhard; Lapraz, François; Lee, Sandra L.; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Sandra; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N.; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J.; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling?Ling; Putman, Nicholas H.; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C.; Robertson, Helen E.; Robertson, Hugh M.; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-­Gracia, Alejandro; Scherer, Steven E.; Schurko, Andrew M.; Siggens, Kenneth W.; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J.; Tessmar-­ Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M.; Willis, Judith H.; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M.; Worley, Kim C.; Gibbs, Richard A.; Akam, Michael; Richards, Stephen

2014-01-01T23:59:59.000Z

492

Diversification of the monoterpene synthase gene family (TPSb) in Protium, a highly diverse genus of tropical trees  

E-Print Network [OSTI]

such as the exposure to high temperatures or the oxidative damage due to the accumulation of reactive oxygen (Vickers. These genes are part of the highly diverse TPS gene family (Bohlmann et al., 1998; Chen et al., 2011) and playDiversification of the monoterpene synthase gene family (TPSb) in Protium, a highly diverse genus

Fine, Paul V.A.

493

Systemic Expression of HIV-1 tat Gene in Transgenic Mice Induces Endothelial Proliferation and Tumors of Different Histotypes  

Science Journals Connector (OSTI)

...Articles Virology Systemic Expression of HIV-1 tat Gene in Transgenic Mice Induces Endothelial...progression to a malignant phenotype. The HIV tat gene, introduced into the germ line...containing BKV early region and the HIV tat gene, directed by its own promoter...

Alfredo Corallini; Giuseppe Altavilla; Laura Pozzi; Francesca Bignozzi; Massimo Negrini; Paola Rimessi; Francesca Gualandi; and Giuseppe Barbanti-Brodano

1993-11-15T23:59:59.000Z

494

Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds  

Science Journals Connector (OSTI)

...research-article Research articles 1001 70 Multiple nuclear genes and retroposons support vicariance...the major palaeognath lineages using 27 nuclear genes and 27 archaic retroposon insertions...5]. Recent analyses using multiple nuclear gene sequences of major clades of birds...

2012-01-01T23:59:59.000Z

495

THE ROLE OF SYNTHETIC DNA IN THE PREPARATION OF STRUCTURAL GENES CODING FOR PROTEINS  

Science Journals Connector (OSTI)

Publisher Summary This chapter discusses the role of synthetic DNA in the preparation of structural genes coding for proteins. One of the key steps in the production of proteins by recombinant DNA technology is the preparation of structural genes coding for the desired proteins. There may be two approaches to this goal: (1) artificial gene synthesis and (2) a combination of cloned cDNA sequences and synthetic DNAs. The method of artificial gene synthesis for the preparation of artificial genes was developed for the synthesis of genes for tRNAs in the late 1960s. The approach of combination of cloned cDNA sequences and synthetic DNA has been developed for the preparation of a gene coding for the human growth hormone. The chapter describes an alternative approach for the synthesis of polydeoxyribonucleotides with defined sequences longer than those accessible by conventional chemical methods. Recent advances in the chemical synthesis of oligonucleotides help to synthesize single-stranded oligonucleotides of up to 40 bases in length, rapidly. It is now possible to synthesize double-stranded DNA fragments using DNA polymerase I in the presence of four deoxynucleoside triphosphosphates.

John J. Rossi; Ryszard Kierzek; Ting Huang; Peter Walker; Keiichi Itakura

1982-01-01T23:59:59.000Z

496

Self-assembled pentablock copolymers for selective and sustained gene delivery  

SciTech Connect (OSTI)

The poly(diethylaminoethyl methacrylate) (PDEAEM) - Pluronic F127 - PDEAEM pentablock copolymer (PB) gene delivery vector system has been found to possess an inherent selectivity in transfecting cancer cells over non-cancer cells in vitro, without attaching any targeting ligands. In order to understand the mechanism of this selective transfection, three possible intracellular barriers to transfection were investigated in both cancer and non-cancer cells. We concluded that escape from the endocytic pathway served as the primary intracellular barrier for PB-mediated transfection. Most likely, PB vectors were entrapped and rendered non-functional in acidic lysosomes of non-cancer cells, but survived in less acidic lysosomes of cancer cells. The work highlights the importance of identifying intracellular barriers for different gene delivery systems and provides a new paradigm for designing targeting vectors based on intracellular differences between cell types, rather than through the use of targeting ligands. The PB vector was further developed to simultaneously deliver anticancer drugs and genes, which showed a synergistic effect demonstrated by significantly enhanced gene expression in vitro. Due to the thermosensitive gelation behavior, the PB vector packaging both drug and gene was also investigated for its in vitro sustained release properties by using polyethylene glycol diacrylate as a barrier gel to mimic the tumor matrix in vivo. Overall, this work resulted in the development of a gene delivery vector for sustained and selective gene delivery to tumor cells for cancer therapy.

Zhang, Bingqi

2011-05-15T23:59:59.000Z

497

Differential gene expression in mouse liver associated with the hepatoprotective effect of clofibrate  

SciTech Connect (OSTI)

Pretreatment of mice with the peroxisome proliferator clofibrate (CFB) protects against acetaminophen (APAP)-induced hepatotoxicity. Previous studies have shown that activation of the nuclear peroxisome proliferator activated receptor-alpha (PPAR{alpha}) is required for this effect. The present study utilizes gene expression profile analysis to identify potential pathways contributing to PPAR{alpha}-mediated hepatoprotection. Gene expression profiles were compared between wild type and PPAR{alpha}-null mice pretreated with vehicle or CFB (500 mg/kg, i.p., daily for 10 days) and then challenged with APAP (400 mg/kg, p.o.). Total hepatic RNA was isolated 4 h after APAP treatment and hybridized to Affymetrix Mouse Genome MGU74 v2.0 GeneChips. Gene expression analysis was performed utilizing GeneSpring (registered) software. Our analysis identified 53 genes of interest including vanin-1, cell cycle regulators, lipid-metabolizing enzymes, and aldehyde dehydrogenase 2, an acetaminophen binding protein. Vanin-1 could be important for CFB-mediated hepatoprotection because this protein is involved in the synthesis of cysteamine and cystamine. These are potent antioxidants capable of ameliorating APAP toxicity in rodents and humans. HPLC-ESI/MS/MS analysis of liver extracts indicates that enhanced vanin-1 gene expression results in elevated cystamine levels, which could be mechanistically associated with CFB-mediated hepatoprotection.

Moffit, Jeffrey S. [University of Connecticut, Department of Pharmaceutical Sciences, Storrs, CT (United States); Koza-Taylor, Petra H. [Pfizer, Inc., Groton Laboratories, Molecular and Investigative Toxicology, Groton, CT (United States); Holland, Ricky D. [National Center for Toxicological Research, Division of Systems Toxicology, Jefferson, AR (United States); Thibodeau, Michael S. [University of Connecticut, Department of Pharmaceutical Sciences, Storrs, CT (United States); Beger, Richard D. [National Center for Toxicological Research, Division of Systems Toxicology, Jefferson, AR (United States); Lawton, Michael P. [Pfizer, Inc., Groton Laboratories, Molecular and Investigative Toxicology, Groton, CT (United States); Manautou, Jose E. [University of Connecticut, Department of Pharmaceutical Sciences, Storrs, CT (United States)]. E-mail: jose.manautou@uconn.edu

2007-07-15T23:59:59.000Z

498

Molecular dissection of the roles of the SOD genes in mammalian response to low dose irradiation  

SciTech Connect (OSTI)

It has been long recognized that a significant fraction of the radiation-induced genetic damage to cells are caused by secondary oxidative species. Internal cellular defense systems against oxidative stress play significant roles in countering genetic damage induced by ionizing radiation. The role of the detoxifying enzymes may be even more prominent in the case of low-dose, low-LET irradiation, as the majority of genetic damage may be caused by secondary oxidative species. In this study we have attempted to decipher the roles of the superoxide dismutase (SOD) genes, which are responsible for detoxifying the superoxide anions. We used adenovirus vectors to deliver RNA interference (RNAi or siRNA) technology to down-regulate the expression levels of the SOD genes. We have also over-expressed the SOD genes by use of recombinant adenovirus vectors. Cells infected with the vectors were then subjected to low dose ?-irradiation. Total RNA were extracted from the exposed cells and the expression of 9000 genes were profiled by use of cDNA microarrays. The result showed that low dose radiation had clear effects on gene expression in HCT116 cells. Both over-expression and down-regulation of the SOD1 gene can change the expression profiles of sub-groups of genes. Close to 200 of the 9000 genes examined showed over two-fold difference in expression under various conditions. Genes with changed expression pattern belong to many categories that include: early growth response, DNA-repair, ion transport, apoptosis, and cytokine response.

Eric Y. Chuang

2006-08-31T23:59:59.000Z

499

Identification of human metapneumovirus-induced gene networks in airway epithelial cells by microarray analysis  

SciTech Connect (OSTI)

Human metapneumovirus (hMPV) is a major cause of lower respiratory tract infections in infants, elderly and immunocompromised patients. Little is known about the response to hMPV infection of airway epithelial cells, which play a pivotal role in initiating and shaping innate and adaptive immune responses. In this study, we analyzed the transcriptional profiles of airway epithelial cells infected with hMPV using high-density oligonucleotide microarrays. Of the 47,400 transcripts and variants represented on the Affimetrix GeneChip Human Genome HG-U133 plus 2 array, 1601 genes were significantly altered following hMPV infection. Altered genes were then assigned to functional categories and mapped to signaling pathways. Many up-regulated genes are involved in the initiation of pro-inflammatory and antiviral immune responses, including chemokines, cytokines, type I interferon and interferon-inducible proteins. Other important functional classes up-regulated by hMPV infection include cellular signaling, gene transcription and apoptosis. Notably, genes associated with antioxidant and membrane transport activity, several metabolic pathways and cell proliferation were down-regulated in response to hMPV infection. Real-time PCR and Western blot assays were used to confirm the expression of genes related to several of these functional groups. The overall result of this study provides novel information on host gene expression upon infection with hMPV and also serves as a foundation for future investigations of genes and pathways involved in the pathogenesis of this important viral infection. Furthermore, it can facilitate a comparative analysis of other paramyxoviral infections to determine the transcriptional changes that are conserved versus the one that are specific to individual pathogens.

Bao, X. [Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas (United States); Sinha, M. [Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas (United States)]|[UTMB Bioinformatics Program, University of Texas Medical Branch, Galveston, Texas (United States); Liu, T.; Hong, C. [Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas (United States); Luxon, B.A. [Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas (United States)]|[UTMB Bioinformatics Program, University of Texas Medical Branch, Galveston, Texas (United States); Garofalo, R.P. [Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas (United States)]|[Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas (United States)]|[Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas (United States); Casola, A. [Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas (United States)]|[Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas (United States)]|[Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas (United States)], E-mail: ancasola@utmb.edu

2008-04-25T23:59:59.000Z

500

Barbara McClintock, Jumping Genes, and Transposition  

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

Barbara McClintock and Transposable Genetic Elements McClintock Honored · Woman of Science · Educational Material · Resources with Additional Information Barbara McClintock's remarkable life spanned the history of genetics in the twentieth century. ... [T]he science of genetics, to which McClintock made seminal contributions both experimental and conceptual, has come to dominate all of the biological sciences, from molecular biology, through cell and developmental biology, to medicine and agriculture. ... Barbara McClintock Courtesy of the Cold Spring Harbor Laboratory Archives McClintock made her first significant contribution as a graduate student, developing cytological techniques that allowed her to identify each of the ten maize chromosomes. These early experiments laid the groundwork for a remarkable series of cytogenetic discoveries ... [for which] McClintock was the intellectual driving force ... . These include identification of maize linkage groups with individual chromosomes, the well-known cytological proof of genetic crossing-over, evidence of chromatid crossing-over, cytological determination of the physical location of genes within chromosomes, identification of the genetic consequences of nonhomologous pairing, establishment of the causal relationship between the instability of ring-shaped chromosomes and phenotypic variegation, discovery that the centromere is divisible, and identification of a chromosomal site essential for the formation of the nucleolus. ...