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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

New screening software shows most recent large 16S rRNA gene clone libraries1 contain chimeras.2  

E-Print Network [OSTI]

1 New screening software shows most recent large 16S rRNA gene clone libraries1 contain chimeras.2 3 Running title4 Detecting chimeras within 16S rRNA gene libraries.5 6 Authors7 Kevin E. Ashelford for screening entire 16S rRNA gene2 libraries, of up to 1,000 sequences, for chimeras and other artifacts

Jones, Antonia J.

2

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

SciTech Connect (OSTI)

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

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

2006-02-01T23:59:59.000Z

3

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

SciTech Connect (OSTI)

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

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

2006-04-10T23:59:59.000Z

4

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

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

electrophoretic types (ETs... , and Brazil. Most strains of the distinctive Colombian ETs carried the same 16S rRNA allele as did strains... alleles. No fully...

5

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

SciTech Connect (OSTI)

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

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

2001-10-01T23:59:59.000Z

6

Greengenes: 16S rRNA Database and Workbench Compatible with ARB  

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

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

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

7

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

SciTech Connect (OSTI)

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

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

2010-01-01T23:59:59.000Z

8

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

SciTech Connect (OSTI)

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

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

2009-10-09T23:59:59.000Z

9

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

DOE Patents [OSTI]

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

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

2007-12-04T23:59:59.000Z

10

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

DOE Patents [OSTI]

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

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

2007-10-30T23:59:59.000Z

11

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

SciTech Connect (OSTI)

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

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

2012-03-26T23:59:59.000Z

12

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

13

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...

14

Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria  

SciTech Connect (OSTI)

Small-subunit (SSU) ribosomal DNA (rDNA) gene clusters are phylogenetically related sets of SSU rRNA genes, commonly encountered in genes amplified from natural populations. Genetic variability in gene clusters could result form artifacts (polymerase error or PCR chimera formation), microevolution (variation among rrn copies within strains), or macroevolution (genetic divergence correlated with long-term evolutionary divergence). To better understand gene clusters, this study assessed genetic diversity and distribution of a single environmental SSU rDNA gene cluster, the SAR11 cluster. SAR11 cluster genes, from an uncultured group of the {alpha} subclass of the class Proteobacteria, have been recovered from coastal and midoceanic waters of the North Atlantic and Pacific. We cloned and bidirectionally sequenced 23 new SAR11 cluster 16S rRNA genes, from 80 and 250 m im the Sargasso Sea and from surface coastal waters of the Atlantic and Pacific, and analyzed them with previously published sequences. Two SAR11 genes were obviously PCR chimeras, but the biological (nonchimeric) origins of most subgroups within the cluster were confirmed by independent recovery from separate gene libraries. Using group-specific oligonucleotide probes, we analyzed depth profiles of nucleic acids, targeting both amplified rDNAs and bulk RNAs. Two subgroups within the SAR11 cluster showed different highly depth-specific distributions. We conclude that some of the genetic diversity within the SAR11 gene cluster represents macroevolutionary divergence correlated with niche specialization. Furthermore, we demonstrate the utility for marine microbial ecology of oligonucleotide probes based on gene sequences amplified from natural populations and show that a detailed knowledge of sequence variability may be needed to effectively design these probes. 48 refs., 7 figs., 3 tabs.

Field, K.G.; Gordon, D.; Wright, T. [Oregon State Univ., Corvallis, OR (United States)] [and others

1997-01-01T23:59:59.000Z

15

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

E-Print Network [OSTI]

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

Shankar Sagaram, U.

2009-01-01T23:59:59.000Z

16

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

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

sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic... and span a broad ... Source: Colorado at Boulder, University of - Alpine Microbial Observatory;...

17

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

SciTech Connect (OSTI)

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

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

2009-01-01T23:59:59.000Z

18

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

E-Print Network [OSTI]

the reef" and further, that; ". . . outside recruitment of corals to the Hower Garden Reef from other sources is apparently minimal. " ! Other researchers have reached similar conclusions, namely that coral reefs are primarily self-seeded (Done 1982...

Holland, Brenden Stephen

1991-01-01T23:59:59.000Z

19

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

20

Databases for rRNA gene profiling of microbial communities  

DOE Patents [OSTI]

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

Ashby, Matthew

2013-07-02T23:59:59.000Z

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

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

E-Print Network [OSTI]

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

22

LS-16 S. Kim  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: VegetationEquipment Surfaces and Interfaces Sample6, 2011 LOS ALAMOS, NewattractsDamping ofLS-1392447 M.

23

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

24

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

E-Print Network [OSTI]

A chronology of the Little Ice Age in the tropical Andes of Bolivia (16°S) and its implications; Tropical Andes; Bolivia Introduction The concept of Little Ice Age (LIA) was introduced by Matthes (1939 for glaciers of the Charquini, Bolivia (Rabatel et al., 2005) and the reconstruction of their evolution

Rabatel, Antoine

25

Microfluidic cell culture chambers with nanoporous walls for chemical communication  

E-Print Network [OSTI]

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

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

2013-01-01T23:59:59.000Z

26

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Oct. 2008, p. 64446446 Vol. 74, No. 20 0099-2240/08/$08.00 0 doi:10.1128/AEM.00879-08  

E-Print Network [OSTI]

in Guerrero Negro, Baja Cal- ifornia Sur, Mexico, and from Lindsey Lake, located near Carlsbad, NM. Crust Mobio, Inc. (Carlsbad, CA). 16S rRNA genes were amplified using uni- versal and domain-specific primers

27

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

SciTech Connect (OSTI)

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

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

2009-04-01T23:59:59.000Z

28

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

SciTech Connect (OSTI)

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

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

2009-06-15T23:59:59.000Z

29

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

E-Print Network [OSTI]

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

Brown, Rafe M.

2006-01-01T23:59:59.000Z

30

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

SciTech Connect (OSTI)

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

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

2009-03-25T23:59:59.000Z

31

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

32

Coexistence of mitochondrial 12S rRNA C1494T and CO1/tRNA{sup Ser(UCN)} G7444A mutations in two Han Chinese pedigrees with aminoglycoside-induced and non-syndromic hearing loss  

SciTech Connect (OSTI)

Mutations in mitochondrial DNA are one of the important causes of hearing loss. We report here the clinical, genetic, and molecular characterization of two Han Chinese pedigrees with maternally transmitted aminoglycoside-induced and nonsyndromic bilateral hearing loss. Clinical evaluation revealed the wide range of severity, age-at-onset, and audiometric configuration of hearing impairment in matrilineal relatives in these families. The penetrances of hearing loss in these pedigrees were 20% and 18%, when aminoglycoside-induced deafness was included. When the effect of aminoglycosides was excluded, the penetrances of hearing loss in these seven pedigrees were 10% and 15%. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the presence of the deafness-associated 12S rRNA C1494T and CO1/tRNA{sup Ser(UCN)} G7444A mutations. Their distinct sets of mtDNA polymorphism belonged to Eastern Asian haplogroup C4a1, while other previously identified six Chinese mitochondrial genomes harboring the C1494T mutation belong to haplogroups D5a2, D, R, and F1, respectively. This suggested that the C1494T or G7444A mutation occurred sporadically and multiplied through evolution of the mitochondrial DNA (mtDNA). The absence of functionally significant mutations in tRNA and rRNAs or secondary LHON mutations in their mtDNA suggest that these mtDNA haplogroup-specific variants may not play an important role in the phenotypic expression of the 12S rRNA C1494T and CO1/tRNA{sup Ser(UCN)} G7444A mutations in those Chinese families. However, aminoglycosides and other nuclear modifier genes play a modifying role in the phenotypic manifestation of the C1494T mutation in these Chinese families.

Yuan Huijun; Chen Jing; Liu Xin; Cheng Jing [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China); Wang Xinjian; Yang Li [Division of Human Genetics and Center for Hearing and Deafness Research, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039 (United States); Yang Shuzhi; Cao Juyang; Kang Dongyang; Dai Pu; Zha, Suoqiang [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China); Han Dongyi [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China)], E-mail: HDY301@263.com; Young Wieyen [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China)], E-mail: YWY@263.com; Guan Minxin [Division of Human Genetics and Center for Hearing and Deafness Research, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039 (United States); Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH (United States)], E-mail: min-xin.guan@cchmc.org

2007-10-12T23:59:59.000Z

33

Fecal Microbiome in Dogs with Acute Diarrhea  

E-Print Network [OSTI]

-hemorrhagic diarrhea (NHD), and dogs with acute hemorrhagic diarrhea (AHD) using 16S rRNA gene sequencing and qPCR analysis; (2) to measure fecal concentrations of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs); and (3) to describe...

Guard, Blake Crosby

2013-11-07T23:59:59.000Z

34

Characterization of the Fecal Microbiota in Dogs with Chronic Enteropathies and Acute Hemorrhagic Diarrhea  

E-Print Network [OSTI]

Recent 16S rRNA gene sequencing studies of the duodenal and fecal microbiota have revealed alterations in the abundance of specific bacterial groups in dogs with gastrointestinal (GI) disorders. The aim of this study was to establish a panel...

Markel, Melissa

2012-10-19T23:59:59.000Z

35

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

E-Print Network [OSTI]

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

Murphy, Bob

36

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

37

Trichoderma genes  

DOE Patents [OSTI]

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

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

2012-06-19T23:59:59.000Z

38

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

SciTech Connect (OSTI)

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

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

2007-12-01T23:59:59.000Z

39

Ribosomal Database Project II  

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

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

40

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

SciTech Connect (OSTI)

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

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

2012-03-29T23:59:59.000Z

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

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

E-Print Network [OSTI]

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

42

Extremely low penetrance of deafness associated with the mitochondrial 12S rRNA mutation in 16 Chinese families: Implication for early detection and prevention of deafness  

SciTech Connect (OSTI)

Mutations in mitochondrial DNA (mtDNA) have been found to be associated with sensorineural hearing loss. We report here the clinical, genetic, and molecular characterization of 16 Chinese pedigrees (a total of 246 matrilineal relatives) with aminoglycoside-induced impairment. Clinical evaluation revealed the variable phenotype of hearing impairment including audiometric configuration in these subjects, although these subjects share some common features: being bilateral and sensorineural hearing impairment. Strikingly, these Chinese pedigrees exhibited extremely low penetrance of hearing loss, ranging from 4% to 18%, with an average of 8%. In particular, nineteen of 246 matrilineal relatives in these pedigrees had aminoglycoside-induced hearing loss. Mutational analysis of the mtDNA in these pedigrees showed the presence of homoplasmic 12S rRNA A1555G mutation, which has been associated with hearing impairment in many families worldwide. The extremely low penetrance of hearing loss in these Chinese families carrying the A1555G mutation strongly supports the notion that the A1555G mutation itself is not sufficient to produce the clinical phenotype. Children carrying the A1555G mutation are susceptible to the exposure of aminoglycosides, thereby inducing or worsening hearing impairment, as in the case of these Chinese families. Using those genetic and molecular approaches, we are able to diagnose whether children carry the ototoxic mtDNA mutation. Therefore, these data have been providing valuable information and technology to predict which individuals are at risk for ototoxicity, to improve the safety of aminoglycoside therapy, and eventually to decrease the incidence of deafness.

Dai Pu; Liu Xin [Department of Otolaryngology, Chinese PLA General Hospital, Beijing (China); Han Dongyi [Department of Otolaryngology, Chinese PLA General Hospital, Beijing (China)]. E-mail: hdy301@263.net; Qian Yaping [Division and Program in Human Genetics and Center for Hearing and Deafness Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH (United States); Huang Deliang; Yuan Huijun; Li Weiming; Yu Fei [Department of Otolaryngology, Chinese PLA General Hospital, Beijing (China); Zhang Ruining [Department of Otolaryngology, Yuncheng Central Hospital, Yuncheng, Shanxi 044000 (China); Lin Hongyan [Department of Otolaryngology, Anyang Stomatology Hospital, Anyang, Henan 455000 (China); He Yong [Department of Otolaryngology, Fuzhou Second Hospital, Fozhou, Fujian 528000 (China); Yu Youjun [Department of Otolaryngology, Foshan First People's Hospital, Foshan, Guangdong 528000 (China); Sun Quanzhu [Department of Otolaryngology, Datong Third People's Hospital, Datong, Shanxi 037008 (China); Qin Huaiyi [Blind, Deaf and Dumb School, Liuzhou, Guangxi 545005 (China); Li Ronghua [Division and Program in Human Genetics and Center for Hearing and Deafness Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH (United States); Zhang Xin; Kang Dongyang; Cao Juyang [Department of Otolaryngology, Chinese PLA General Hospital, Beijing (China); Young Wieyen [Department of Otolaryngology, Chinese PLA General Hospital, Beijing (China)]. E-mail: ywy301@163.net; Guan Minxin [Division and Program in Human Genetics and Center for Hearing and Deafness Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH (United States)]|[Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 (United States)]. E-mail: min-xin.guan@cchmc.org

2006-02-03T23:59:59.000Z

43

Microfluidic gene synthesis  

E-Print Network [OSTI]

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

Kong, David Sun, 1979-

2008-01-01T23:59:59.000Z

44

Microbiological and Geochemical Heterogeneity in an In Situ  

E-Print Network [OSTI]

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

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

2005-01-01T23:59:59.000Z

45

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

46

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

David Kirchman

2011-12-31T23:59:59.000Z

47

Clinical and molecular analysis of a four-generation Chinese family with aminoglycoside-induced and nonsyndromic hearing loss associated with the mitochondrial 12S rRNA C1494T mutation  

SciTech Connect (OSTI)

We report here the clinical, genetic, and molecular characterization of a four-generation Chinese family with aminoglycoside-induced and nonsyndromic hearing loss. Five of nine matrilineal relatives had aminoglycoside-induced hearing loss. These matrilineal relatives exhibited variable severity and audiometric configuration of hearing impairment, despite sharing some common features: being bilateral and having sensorineural hearing impairment. Sequence analysis of mitochondrial DNA (mtDNA) in the pedigree identified 16 variants and the homoplasmic 12S rRNA C1494T mutation, which was associated with hearing loss in the other large Chinese family. In fact, the occurrence of the C1494T mutation in these genetically unrelated pedigrees affected by hearing impairment strongly indicated that this mutation is involved in the pathogenesis of aminoglycoside-induced and nonsyndromic hearing loss. However, incomplete penetrance of hearing loss indicated that the C1494T mutation itself is not sufficient to produce a clinical phenotype but requires the involvement of modifier factors for the phenotypic expression. Those mtDNA variants, showing no evolutional conservation, may not have a potential modifying role in the pathogenesis of the C1494T mutation. However, nuclear background seems to contribute to the phenotypic variability of matrilineal relatives in this family. Furthermore, aminoglycosides modulate the expressivity and penetrance of deafness associated with the C1494T mutation in this family.

Wang Qiuju [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China); Li Qingzhong [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China); Han Dongyi [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China)]. E-mail: hdy301@263.net; Zhao Yali [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China); Zhao Lidong [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China); Qian Yaping [Division and Program in Human Genetics and Center for Hearing and Deafness Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039 (United States); Yuan Hu [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China); Li Ronghua [Division and Program in Human Genetics and Center for Hearing and Deafness Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039 (United States); Zhai Suoqiang [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China); Young Wieyen [Institute of Otolaryngology, Chinese PLA General Hospital, Beijing (China)]. E-mail: ywy301@263.net; Guan Minxin [Division and Program in Human Genetics and Center for Hearing and Deafness Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039 (United States) and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH (United States)]. E-mail: min-xin.guan@chmcc.org

2006-02-10T23:59:59.000Z

48

E-Print Network 3.0 - algumas algas verdes Sample Search Results  

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

Portions of the 12S and 16S rRNA mitochondrial regions of 30... specimens from Kenya, Uganda, Niger, Mali, Burkina-Faso, Ghana, Guinea-Bissau and Cape Verde were used Source:...

49

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

SciTech Connect (OSTI)

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

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

2009-12-01T23:59:59.000Z

50

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

SciTech Connect (OSTI)

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

Lee Kerkhof

2013-01-01T23:59:59.000Z

51

Nonviral Vectors for Gene Delivery  

E-Print Network [OSTI]

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

Baoum, Abdulgader Ahmed

2011-04-26T23:59:59.000Z

52

Genetic Diversity Among Botulinum Neurotoxin Producing Clostridial Strains  

SciTech Connect (OSTI)

Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore forming rod-shaped bacteria which have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and even death in humans and various other animal species. A collection of 174 C. botulinum strains were examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT A-G). Analysis of the16S rRNA sequences confirmed earlier reports of at least four distinct genomic backgrounds (Groups I-IV) each of which has independently acquired one or more BoNT serotypes through horizontal gene transfer. AFLP analysis provided higher resolution, and can be used to further subdivide the four groups into sub-groups. Sequencing of the BoNT genes from serotypes A, B and E in multiple strains confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes, and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven serotypes of BoNT were compared and show varying degrees of interrelatedness and recombination as has been previously noted for the NTNH gene which is linked to BoNT. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for treatment of botulism.

Hill, K K; Smith, T J; Helma, C H; Ticknor, L O; Foley, B T; Svennson, R T; Brown, J L; Johnson, E A; Smith, L A; Okinaka, R T; Jackson, P J; Marks, J D

2006-07-06T23:59:59.000Z

53

Metazoan Gene Families from Metazome  

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

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

54

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

55

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

56

GenePRIMP: Improving Microbial Gene Prediction Quality  

SciTech Connect (OSTI)

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

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

2009-05-29T23:59:59.000Z

57

20 Cd4In16S35 14-Supertetrahedral T4 Clusters as  

E-Print Network [OSTI]

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

Yaghi, Omar M.

58

E-Print Network 3.0 - ammonia oxidizer 16s Sample Search Results  

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

ammonia emissions... gaseous ammonia (NH3) which through chemical reaction in rainwater changes into ammonium ion (NH4 Source: Aneja, Viney P. - Department of Marine,...

59

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

E-Print Network [OSTI]

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

Craig, Elizabeth A

60

ancestral gene relationships: Topics by E-print Network  

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

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

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

ascl1 target genes: Topics by E-print Network  

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

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

62

abolishes gene targeting: Topics by E-print Network  

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

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

63

Enhanced polymeric nanoparticles for gene delivery  

E-Print Network [OSTI]

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

Green, Jordan Jamieson

2007-01-01T23:59:59.000Z

64

Plant nitrogen regulatory P-PII genes  

DOE Patents [OSTI]

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

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

2001-01-01T23:59:59.000Z

65

Regulation of the genes involved in nitrification.  

SciTech Connect (OSTI)

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

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

2003-08-14T23:59:59.000Z

66

Uses of antimicrobial genes from microbial genome  

DOE Patents [OSTI]

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

Sorek, Rotem; Rubin, Edward M.

2013-08-20T23:59:59.000Z

67

Short Specialist Review Gene structure prediction  

E-Print Network [OSTI]

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

Brendel, Volker

68

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.

69

Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions  

E-Print Network [OSTI]

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

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

2014-06-12T23:59:59.000Z

70

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

2011-09-27T23:59:59.000Z

71

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

72

Thermostable cellulase from a thermomonospora gene  

DOE Patents [OSTI]

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

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

1997-10-14T23:59:59.000Z

73

Apolipoprotein gene involved in lipid metabolism  

DOE Patents [OSTI]

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

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

2007-07-03T23:59:59.000Z

74

Bacterial genes for stress | EMSL  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-Series to someone6 M. Babzien, I. Ben-Zvi, P. Study ofJ U LY 2 9Bacterial genes

75

FAMeS: Fidelity of Analysis of Metagenomic Samples  

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

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

76

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

77

Methods for monitoring multiple gene expression  

DOE Patents [OSTI]

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

Berka, Randy; Bachkirova, Elena; Rey, Michael

2013-10-01T23:59:59.000Z

78

Methods for monitoring multiple gene expression  

SciTech Connect (OSTI)

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

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

2012-05-01T23:59:59.000Z

79

Atmospheric cloud water contains a diverse bacterial community  

SciTech Connect (OSTI)

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

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

2011-06-15T23:59:59.000Z

80

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

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

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

82

Nucleotide Frequency Variation Across Human Genes  

E-Print Network [OSTI]

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

Majewski, Jacek

83

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

84

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.

85

Tissue-specific gene silencing monitored in circulating RNA  

E-Print Network [OSTI]

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

Sehgal, Alfica

86

Effects of Pinealectomy on Hypothalamic Metabolic and Clock Gene Rhythms  

E-Print Network [OSTI]

by comparing the affects of pinealectomy on 2DG uptake and canonical "clock" gene expression in the hypothalamus of house sparrows, Passer domesticus. Since other brain structures exhibit metabolic and clock gene rhythms, investigation of clock gene expression...

Clauson, Amanda

2006-07-11T23:59:59.000Z

87

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

88

angiotensin receptor gene: Topics by E-print Network  

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

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

89

arthritis candidate genes: Topics by E-print Network  

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

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

90

albumin gene expression: Topics by E-print Network  

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

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

91

Coregulation of terpenoid pathway genes and prediction of isoprene...  

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

Coregulation of terpenoid pathway genes and prediction of isoprene production in Bacillus subtilis using transcriptomics. Coregulation of terpenoid pathway genes and prediction of...

92

Organization and evolution of the rat tyrosine hydroxylase gene  

SciTech Connect (OSTI)

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

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

1987-08-11T23:59:59.000Z

93

apoptosis related gene: Topics by E-print Network  

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

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

94

apoptosis related genes: Topics by E-print Network  

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

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

95

BESC Submits 32 Gene Disclosures for Patents | ORNL  

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

differences between normal and tension wood and identified 10 genes that appear to affect cellulose deposition. These genes are being overexpressed or underexpressed in poplar...

96

agnostic gene coding: Topics by E-print Network  

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

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

97

Dynamics Modelling of Biolistic Gene Guns  

SciTech Connect (OSTI)

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

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

2009-06-04T23:59:59.000Z

98

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

99

Predicting gene function from images of cells  

E-Print Network [OSTI]

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

Jones, Thouis Raymond, 1971-

2007-01-01T23:59:59.000Z

100

Characterization of a unique embedded gene  

E-Print Network [OSTI]

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

Zhang, Ning

1999-01-01T23:59:59.000Z

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

INVESTIGATION Coding Gene Single Nucleotide Polymorphism  

E-Print Network [OSTI]

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

Bernatchez, Louis

102

Characterization of the Bovine Cathelicidin Gene Family  

E-Print Network [OSTI]

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

Flores, Erin Gillenwaters

2012-10-19T23:59:59.000Z

103

Parallel gene synthesis in a microfluidic device  

E-Print Network [OSTI]

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

Kong, David S.

104

E-Print Network 3.0 - arthritis-associated gene-gene interaction...  

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

Keywords: microarray, gene expression, prostate cancer... , interaction patterns, F-statistic Author for correspondence 1 Bioinformatics Oxford University Press 2004 Source:...

105

Analyzing Gene Relationships for Down Syndrome with Labeled Transition Graphs  

E-Print Network [OSTI]

Analyzing Gene Relationships for Down Syndrome with Labeled Transition Graphs Neha Rungta, Hyrum changes in gene expres- sion and physical characteristics associated with Down syndrome is not well understood. Chromosome 21 genes interact with non- chromosome 21 genes to produce Down syndrome

Brigham Young University

106

Pathogenicity island mobility and gene content.  

SciTech Connect (OSTI)

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

Williams, Kelly Porter

2013-10-01T23:59:59.000Z

107

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

SciTech Connect (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

108

Universal light-switchable gene promoter system  

DOE Patents [OSTI]

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

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

2005-02-22T23:59:59.000Z

109

Quantitative trait loci analysis to identify modifiers genes of the gene opaque2 in maize endosperm  

E-Print Network [OSTI]

fraction represents 9.5% of the 4 kernel, while other plants like soybean or beans contain 38% and 23% of protein, respectively (National Research Council, 1988). The Prolamins of Maize: The Zeins According to the classification system of cereal...Da ?-zein gene is located on chromosome 6S (bin 6.01) (Weerakoon et al., 1993). The gene encoding the 10kDa d-zein is located in chromosome 9L near the centromere (bin 9.03) (Benner et al., 1989), and the 18 kDa ?-zein gene mapped to the chromosome 6L...

Gutierrez Rojas, Libardo Andres

2009-05-15T23:59:59.000Z

110

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

E-Print Network [OSTI]

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

McElhany, Katherine

2012-02-14T23:59:59.000Z

111

SHORT REVIEW Ecological genomics: understanding gene and  

E-Print Network [OSTI]

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

Kaufman, Glennis A.

112

Gene encoding acetyl-coenzyme A carboxylase  

DOE Patents [OSTI]

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

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

1996-09-24T23:59:59.000Z

113

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

114

Gene duplications, robustness and evolutionary innovations  

E-Print Network [OSTI]

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

Wagner, Andreas

115

Gene encoding acetyl-coenzyme A carboxylase  

DOE Patents [OSTI]

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

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

1996-01-01T23:59:59.000Z

116

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

117

adjacent rrna nucleotide: Topics by E-print Network  

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

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

118

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...

119

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:...

120

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...

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

E-Print Network 3.0 - acid degradation genes Sample Search Results  

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

degradation, necessitating a gene inactivation... ). Several genes involved in steroid degradation were cloned by functional complementation of different UV... , a kstD gene...

122

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

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

genes involved in oxidative... Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets KILIAN BARTHOLOME,1... produced by microarray ex- periments, the...

123

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

124

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

125

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....

126

asthma candidate genes: Topics by E-print Network  

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

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

127

autism candidate gene: Topics by E-print Network  

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

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

128

adhd candidate gene: Topics by E-print Network  

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

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

129

axon guidance gene: Topics by E-print Network  

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

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

130

asthma susceptibility gene: Topics by E-print Network  

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

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

131

amoa gene analysis: Topics by E-print Network  

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

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

132

analysis reveals genes: Topics by E-print Network  

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

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

133

analysis identifies genes: Topics by E-print Network  

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

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

134

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

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

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

135

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

136

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

137

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

E-Print Network [OSTI]

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

Vercruysse, Maarten

138

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

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

139

Geomicrobiology Journal, 26:189198, 2009 Copyright Taylor & Francis Group, LLC  

E-Print Network [OSTI]

and Ocean Sciences, Inha University, Incheon 402­751, Republic of Korea 4 Rankin Science South, Appalachian from the dorsal surface of a hydrother- mal vent tubeworm. 16S rRNA analysis reveals Aurantimonas. Other organisms within this clade have been isolated from disparate environments such as surface

Dick, Christopher

140

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

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

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.

142

Message from ISCB Getting Started in Gene Orthology and Functional  

E-Print Network [OSTI]

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

Gerstein, Mark

143

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

144

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

145

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...

146

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

147

The Role of Multiple Transcription Factors In Archaeal Gene Expression  

SciTech Connect (OSTI)

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

Charles J. Daniels

2008-09-23T23:59:59.000Z

148

Gene Calling Standards (GSC8 Meeting)  

ScienceCinema (OSTI)

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

Kyrpides, Nikos [Genome Biology Program, DOE JGI

2011-04-28T23:59:59.000Z

149

Imaging Gene Expression | The Ames Laboratory  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation ProposedUsingFun withconfinementEtching. |Endecaheme c-Type|Iltt:ImagingImprovedImaging Gene

150

BlueGene/Q Optimization Bob Walkup  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-Series to someone6 M.Extracellular Polysaccharides and Blue Gene/Q

151

G. E. (Gene) Ice | ornl.gov  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-SeriesFlickr Flickr Editor's note:ComputingFusion roadmapping about a majorGene

152

Surface enhanced Raman gene probe and methods thereof  

DOE Patents [OSTI]

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

Vo-Dinh, T.

1998-09-29T23:59:59.000Z

153

Surface enhanced Raman gene probe and methods thereof  

DOE Patents [OSTI]

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

Vo-Dinh, T.

1998-07-21T23:59:59.000Z

154

Surface enhanced Raman gene probe and methods thereof  

DOE Patents [OSTI]

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

Vo-Dinh, T.

1998-02-24T23:59:59.000Z

155

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

E-Print Network [OSTI]

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

Xie, Xiaoliang Sunney

156

Petascale Debugging via Allinea DDT for IBM Blue Gene /P  

E-Print Network [OSTI]

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

Kemner, Ken

157

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

158

Engineering disease resistance with pectate lyase-like genes  

DOE Patents [OSTI]

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

Vogel, John; Somerville, Shauna

2005-03-08T23:59:59.000Z

159

autoimmunity susceptibility gene: Topics by E-print Network  

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

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

160

autism susceptibility genes: Topics by E-print Network  

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

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

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

arthritis susceptibility genes: Topics by E-print Network  

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

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

162

apoptosis gene profiling: Topics by E-print Network  

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

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

163

arom gene cluster: Topics by E-print Network  

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

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

164

almt1 gene cluster: Topics by E-print Network  

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

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

165

aspartyl proteinase gene: Topics by E-print Network  

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

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

166

adenovirus early gene: Topics by E-print Network  

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

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

167

acquired resistance genes: Topics by E-print Network  

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

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

168

Genomics, Gene Expression and Other Studies in Soybean Rust  

E-Print Network [OSTI]

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

Posada-Buitrago, Martha Lucia

2005-01-01T23:59:59.000Z

169

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

170

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

SciTech Connect (OSTI)

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

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

1989-04-01T23:59:59.000Z

171

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

172

Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph  

SciTech Connect (OSTI)

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

Daniel J Arp

2005-06-15T23:59:59.000Z

173

Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph  

SciTech Connect (OSTI)

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

Daniel J. Arp

2005-05-25T23:59:59.000Z

174

INTRODUCTION Cascades of gene interactions are critical for the establishment  

E-Print Network [OSTI]

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

Quake, Stephen R.

175

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

176

Lipophilic Peptides for Gene Delivery Carla A. H. Prata,  

E-Print Network [OSTI]

University, Boston, Massachusetts 02215, Department of Biological and Environmental Engineering, Cornell laboratories and in ViVo gene delivery holds the promise for curing many diseases. The synthetic carriers of lipophilic peptides including the synthesis, physio- chemical properties, cytotoxicity, and in Vitro gene

177

GenePRIMP: A software quality control tool  

SciTech Connect (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

2010-05-05T23:59:59.000Z

178

Hotspots of Biased Nucleotide Substitutions in Human Genes  

E-Print Network [OSTI]

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

Sorenson, Michael

179

Photoacoustic microscopy of tyrosinase reporter gene in vivo  

E-Print Network [OSTI]

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

Wang, Lihong

180

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

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

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

182

RESEARCH Open Access Transient receptor potential genes, smoking,  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

183

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

184

Genomic Analyses of Bacterial Porin-Cytochrome Gene Clusters  

SciTech Connect (OSTI)

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

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

2014-11-26T23:59:59.000Z

185

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

186

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

SciTech Connect (OSTI)

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

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

2010-02-28T23:59:59.000Z

187

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:...

188

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

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:...

189

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:...

190

A study of mammalian microRNA-mediated repression of gene expression by ribosome profiling  

E-Print Network [OSTI]

All cells in a multicellular organism carry the same genes, yet these same genes direct the differentiation of many different cell types. This is facilitated by differential gene expression, the control of which can be ...

Guo, Huili

2011-01-01T23:59:59.000Z

191

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

E-Print Network [OSTI]

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

Nedelcu, Aurora M.

192

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

193

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

SciTech Connect (OSTI)

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

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

2011-01-01T23:59:59.000Z

194

E-Print Network 3.0 - alternative oxidase gene Sample Search...  

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

alternative oxidase gene from T. hominis, G. plecoglossi... a high frequency of fast-evolving genes. ... Source: Keeling, Patrick - Department of Botany, University of British...

195

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,...

196

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...

197

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....

198

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

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

Summary: matched bone marrow donor. A clinical trial using stem cell gene therapy for sickle cell patients... team includes experts in stem cell gene therapy, clinical bone c...

199

E-Print Network 3.0 - anemia gene fancc 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....

200

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...

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 - anoxia-responsive gene expression Sample...  

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

Abstract Motivation: A central step in the analysis of gene expression data is the identification of groups... of genes that exhibit similar expression patterns. ... Source:...

202

E-Print Network 3.0 - aopex11-1 gene involved Sample Search Results  

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

genes involved in Embden... networks 4. essential genes 5. host-phage co-evolution robust phenomena new mathematical measures... . Clyde Hutchison, 1999 (Science 286, 2165-2169):...

203

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

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

normalization... : In this paper, we present a gene normalization strategy based on the identification of gene and ... Source: Srinivasan, Padmini - School of Library and...

204

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

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

normalization... : In this paper, we present a gene normalization strategy based on the identification of gene and ... Source: Srinivasan, Padmini - School of Library and...

205

E-Print Network 3.0 - antipsychotic-induced gene regulation Sample...  

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

and Information Sciences 42 Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets Summary: methods which are focused on significance, our approach...

206

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

E-Print Network [OSTI]

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

Tian, Weidong

207

E-Print Network 3.0 - acid metabolic genes Sample Search Results  

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

Sciences and Ecology 3 Genes in the environment Genes and Ecosystems Summary: secretion Sulphur assimilation Amino acid metabolism Hypothetical proteins Sulphur...

208

E-Print Network 3.0 - accelerated gene evolution Sample Search...  

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

Search Powered by Explorit Topic List Advanced Search Sample search results for: accelerated gene evolution Page: << < 1 2 3 4 5 > >> 1 Gene conversion and diversification of...

209

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...

210

E-Print Network 3.0 - alkaloid gene dmaw Sample Search Results  

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

search results for: alkaloid gene dmaw Page: << < 1 2 3 4 5 > >> 1 exploiting biodiversity for the improvement of natural product-based drug discovery Summary: genes thus...

211

E-Print Network 3.0 - alligator cyp3a77 gene Sample Search Results  

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

Genetree: A TOOL FOR EXPLORING GENE FAMILY EVOLUTION Roderic D. M. Page James A. Cotton Molecular... biologists interested in the evolution of gene families and molecular...

212

Sorghum Ma5 and Ma6 maturity genes  

E-Print Network [OSTI]

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

Brady, Jeffrey Alan

2009-05-15T23:59:59.000Z

213

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

214

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

215

Logical Gene Ontology Annotations (GOAL): Exploring gene ontology annotations with OWL  

E-Print Network [OSTI]

for each annotation): Class: MGI_2685072 oboInOwl: hasDefinition ”trace amine–associated receptor 4”, rdfs: label ”Taar4” SubClassOf: Annotations: oboInOwl: evidenceCode ”IEA” ro: located_in some GO: GO_0016021, (integral to membrane) Annotations: obo... N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A: Gene Expression Atlas update - a value-added database of microarray and sequencing- based functional genomics experiments. Nucleic Acids Research 2011. 19. Jupp S...

2012-04-24T23:59:59.000Z

216

Blue Gene/Q Versus Blue Gene/P | Argonne Leadership Computing Facility  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-Series to someone6 M.Extracellular Polysaccharides and Blue Gene/Q Versus Blue

217

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

E-Print Network [OSTI]

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

McMillin, David Edwin

1977-01-01T23:59:59.000Z

218

aneurysm susceptibility genes: Topics by E-print Network  

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

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

219

atrophy susceptibility gene: Topics by E-print Network  

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

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

220

adenosine receptor gene: Topics by E-print Network  

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

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

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

adenosine deaminase gene: Topics by E-print Network  

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

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

222

Auxiliary metabolic genes in viruses infecting marine cyanobacteria  

E-Print Network [OSTI]

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

Thompson, Luke Richard

2010-01-01T23:59:59.000Z

223

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

224

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

225

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

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

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

226

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

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

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

227

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

228

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

229

adipose tissue gene: Topics by E-print Network  

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

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

230

The wheat ?-gliadin genes: structure and EST analysis  

E-Print Network [OSTI]

Gu : G. R. Lazo : J. Wu Genomics and Gene Discovery ResearchFunct Integr Genomics (2009) 9:397–410 DOI 10.1007/s10142-physical–chemical Funct Integr Genomics (2009) 9:397–410

Anderson, Olin D.; Gu, Yong Q.; Kong, Xiuying; Lazo, Gerard R.; Wu, Jiajie

2009-01-01T23:59:59.000Z

231

aldosterone synthase gene: Topics by E-print Network  

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

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

232

High-throughput comparison of gene fitness among related bacteria  

E-Print Network [OSTI]

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

2012-01-01T23:59:59.000Z

233

antagonist gene polymorphism: Topics by E-print Network  

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

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

234

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

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

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

235

antagonist gene polymorphisms: Topics by E-print Network  

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

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

236

alpha gene polymorphisms: Topics by E-print Network  

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

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

237

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

238

Genome Enabled Discovery of Carbon Sequestration Genes in Poplar  

SciTech Connect (OSTI)

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

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

2007-02-22T23:59:59.000Z

239

Unique ER Cistromes Control Cell Type-Specific Gene Regulation  

E-Print Network [OSTI]

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

Brown, Myles

240

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

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

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

SciTech Connect (OSTI)

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

Armour, G.A.

1988-01-01T23:59:59.000Z

242

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

243

A Performance Counter Based Workload Characterization on Blue Gene/P  

E-Print Network [OSTI]

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

John, Lizy Kurian

244

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

245

Bitumen fume-induced gene expression profile in rat lung  

SciTech Connect (OSTI)

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

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

2006-08-15T23:59:59.000Z

246

Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters  

SciTech Connect (OSTI)

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

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

2003-12-31T23:59:59.000Z

247

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

248

Reliability of frequency- and amplitude-decoding in gene regulation  

E-Print Network [OSTI]

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

Filipe Tostevin; Wiet de Ronde; Pieter Rein ten Wolde

2012-02-07T23:59:59.000Z

249

Divinyl ether synthase gene and protein, and uses thereof  

DOE Patents [OSTI]

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

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

2011-09-13T23:59:59.000Z

250

Divinyl ether synthase gene, and protein and uses thereof  

DOE Patents [OSTI]

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

Howe, Gregg A.; Itoh, Aya

2006-12-26T23:59:59.000Z

251

LINGUISTIC ANALYSIS OF THE NUCLEOPROTEIN GENE OF INFLUENZA A VIRUS  

SciTech Connect (OSTI)

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

A. SKOURIKHINE; T. BURR

2000-05-01T23:59:59.000Z

252

Mutations of the tyrosinase gene produce autosomal recessive ocular albinism  

SciTech Connect (OSTI)

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

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

1994-09-01T23:59:59.000Z

253

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

254

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

255

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

256

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

257

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

258

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

259

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

SciTech Connect (OSTI)

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

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

2010-01-01T23:59:59.000Z

260

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

SciTech Connect (OSTI)

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

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

2006-01-01T23:59:59.000Z

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
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261

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

SciTech Connect (OSTI)

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

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

2010-01-01T23:59:59.000Z

262

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

SciTech Connect (OSTI)

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

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

2009-11-15T23:59:59.000Z

263

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)  

SciTech Connect (OSTI)

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

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

2011-01-01T23:59:59.000Z

264

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

265

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

266

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

267

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

268

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.

269

Symbolic Discriminant Analysis for Mining Gene Expression Patterns Jason Moore  

E-Print Network [OSTI]

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

Fernandez, Thomas

270

Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes  

E-Print Network [OSTI]

, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Apartado Postal 565-A, Av Universidad, Cuernavaca, Morelos, 62100 Mexico D.F., Mexico Edited by Aaron Klug, Medical Research Council to influence gene expression (6­11). Thus, unlike in prokaryotes, transcription in eukaryotes is an energy

Babu, M. Madan

271

Diet, nutrients, phytochemicals, and cancer metastasis suppressor genes  

E-Print Network [OSTI]

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

Collins, Gary S.

272

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

273

NUCLEOTIDE SUBSTITUTIONS AND THE EVOLUTION OF DUPLICATE GENES  

E-Print Network [OSTI]

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

Oregon, University of

274

ORIGINAL ARTICLE Regulation of nif gene expression and the  

E-Print Network [OSTI]

ORIGINAL ARTICLE Regulation of nif gene expression and the energetics of N2 fixation over the diel importance in biogeochemical cycling of nitrogen. We analyzed the levels of nif transcripts of Synechococcus ecotypes, NifH subunit and nitrogenase activity over the diel cycle in the microbial mat of an alkaline hot

275

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

276

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.

277

Plasticity of opsin gene expression in cichlids from Lake Malawi  

E-Print Network [OSTI]

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

Carleton, Karen L.

278

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

279

Inflammatory Gene Expression in Goats in Response to Transport  

E-Print Network [OSTI]

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

Carter, Mark

2012-10-19T23:59:59.000Z

280

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

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

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.

282

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

283

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

284

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

E-Print Network [OSTI]

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

Elkhoury, Jean

285

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

286

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

E-Print Network [OSTI]

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

2010-01-01T23:59:59.000Z

287

Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification  

E-Print Network [OSTI]

Background: Previous studies on tumor classification based on gene expression profiles suggest that gene selection plays a key role in improving the classification performance. Moreover, finding important tumor-related ...

Wang, Shu-Lin; Li, Xue-Ling; Fang, Jianwen

2012-07-25T23:59:59.000Z

288

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

E-Print Network [OSTI]

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

Kalezi, Artemis

2007-01-01T23:59:59.000Z

289

E-Print Network 3.0 - alpha-amylase inhibitor genes Sample Search...  

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

amylase inhibitor genes Search Powered by Explorit Topic List Advanced Search Sample search results for: alpha-amylase inhibitor genes Page: << < 1 2 3 4 5 > >> 1 1 Stryer,L....

290

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

E-Print Network [OSTI]

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

Takada, Shoji

291

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

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

2009-04-28T23:59:59.000Z

292

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

293

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...

294

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...

295

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...

296

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...

297

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...

298

E-Print Network 3.0 - alter genes involved Sample Search Results  

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

5 MAY 2006 537 Gene prioritization through genomic Summary: Carmeliet2 & Yves Moreau4 The identification of genes involved in health and disease remains a challenge. We... on their...

299

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 fĂĽr molekulare Genetik

300

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

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

E-Print Network 3.0 - arabinoside-metabolizing enzyme genes Sample...  

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

genes The tropical tree whose fruit... of its genome -- about 372 million letters of DNA code -- the papaya has surprisingly few genes -- under... roughly the same size, but have...

302

Cancer gene therapy with oncolytic adenoviruses K. Guse,A. Hemminki  

E-Print Network [OSTI]

Cancer gene therapy with oncolytic adenoviruses K. Guse,A. Hemminki Cancer Gene Therapy Group, Molecular Cancer Biology Program & Transplantation Laboratory & Haartman Institute & Finnish Institute, Helsinki, Finland Summary Metastatic cancer remains difficult to treat effectively and treatments

Hemminki, Akseli

303

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

E-Print Network [OSTI]

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

Paria, Nandina

2012-02-14T23:59:59.000Z

304

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

305

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

E-Print Network [OSTI]

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

Gray, Catherine Allison

2005-08-29T23:59:59.000Z

306

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

307

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

E-Print Network [OSTI]

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

Hong,Seokhee

308

Identification of a novel gene family that includes the interferon-inducible human genes 6–16and ISG12  

E-Print Network [OSTI]

renamed as ISG12(a)) are ISGs that encode small hydro- phobic proteins (Mr 12.9 kDa and 11.5 kDa, respec- tively). The predicted proteins share 36% overall amino- acid identity and 49% identity over an ~80 amino acid length. Both genes are regulated...

Parker, Nadeene; Porter, Andrew C G

2004-01-19T23:59:59.000Z

309

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

310

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

E-Print Network [OSTI]

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

McAvin, James Charles

1986-01-01T23:59:59.000Z

311

The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion  

E-Print Network [OSTI]

MB TIF) Figure S2 The CAX (calcium exchanger) transporterFor example, two CAX (calcium exchange) transporter genes

Coleman, J.J.

2010-01-01T23:59:59.000Z

312

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

E-Print Network [OSTI]

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

Alwood, Amanda Raquel

2011-01-01T23:59:59.000Z

313

A flood-based information flow analysis and network minimization method for gene regulatory networks  

E-Print Network [OSTI]

tend to have high interconnectivity, complex topologies andSince feedback and high interconnectivity is common in gene

Pavlogiannis, Andreas; Mozhayskiy, Vadim; Tagkopoulos, Ilias

2013-01-01T23:59:59.000Z

314

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,...

315

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

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

genes'). Acknowledgment This ... Source: Stotz, Karola - Department of History and Philosophy of Science, Indiana University Collection: Multidisciplinary Databases and...

316

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

SciTech Connect (OSTI)

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

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

2013-05-01T23:59:59.000Z

317

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

E-Print Network [OSTI]

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

2007-08-16T23:59:59.000Z

318

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

E-Print Network [OSTI]

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

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

2011-08-26T23:59:59.000Z

319

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

E-Print Network [OSTI]

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

Peng, Qianqian; Zhao, Jinghua; Xue, Fuzhong

2010-01-26T23:59:59.000Z

320

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

E-Print Network [OSTI]

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

Gruber, Jonathan

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

LETTER doi:10.1038/nature11279 The long-range interaction landscape of gene  

E-Print Network [OSTI]

engage in looping interactions that have been implicated in gene regulation1 . Here we have applied chromosome conforma- tion capture carbon copy (5C2 ) to interrogate comprehensively interactions between gene domains. Furthermore, only 7% of looping interactions are with the nearest gene, indicating

Dean, Matthew D.

322

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

DOE Patents [OSTI]

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

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

1999-07-27T23:59:59.000Z

323

Red Algae Lose Key Mitochondrial Genes in Response to Becoming Parasitic  

E-Print Network [OSTI]

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

Lane, Chris

324

Carotenoid Gene Nucleotide Diversity Reflects Carrot History and J. Clotault1  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

325

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

E-Print Network [OSTI]

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

Fernandez, Thomas

326

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

327

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

SciTech Connect (OSTI)

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

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

2013-01-01T23:59:59.000Z

328

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

SciTech Connect (OSTI)

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

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

2013-01-01T23:59:59.000Z

329

Analysis of genes regulated by the peroxide response regulator PerR in Borrelia burgdorferi using real-time RT-PCR  

E-Print Network [OSTI]

encodes a peroxide response regulator (PerR) which regulates gene expression in response to oxidative stress in other organisms. Several borrelial genes with homology to known oxidative stress genes, and the pathogenesis-associated gene dbpA, contain...

Swingle, Kristen Lynn

2002-01-01T23:59:59.000Z

330

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

331

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

332

GENE E. LIKENS FOUNDING DIRECTOR AND PRESIDENT EMERITUS  

E-Print Network [OSTI]

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

Canham, Charles D.

333

Transcriptional regulation of the Arabidopsis thaliana chalcone synthase gene  

SciTech Connect (OSTI)

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

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

1988-05-01T23:59:59.000Z

334

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

335

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

336

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

337

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

SciTech Connect (OSTI)

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

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

1989-06-01T23:59:59.000Z

338

Could the gene coding for human uteroglobin (clara cell 10 kDa protein) be a candidate gene for atopy?  

SciTech Connect (OSTI)

It has been proposed that human immune response to allergens is genetically determined. Most of these allergic responses are directed to environmental proteins and are mediated by immunoglobulin E (IgE). These allergic disorders (eg. allergic asthma) are commonly known as atopy. IgE activates phospholipase A{sub 2} (PLA{sub 2}) which hydrolyzes cell membrane phospholipids generating free fatty acids, such as arachidonic acid (AA). AA is utilized as the substrate for the generation of pro-inflammatory eicosanoids and platelet activating factor (PAF). These agents can cause inflammation as well as bronchoconstriction, hallmarks of asthma. IgE-induced mast cell degranulation and accumulation of basophils and eosinophils in the lung are also characteristic immunological processes commonly found in atopic asthma. Recent investigations suggest that a group I PLA{sub 2} may be associated with the secretory granules of these cells. An inverse relationship between the levels of eicosanoids and hUG has been found in the nasopharyngeal lavage fluid of children with viral infections of the upper respiratory tract, often a precipitating factor in asthma. Results of genetic linkage studies mapped a putative atopy gene in human chromosome 11q{sup 13}, the same region in which we localized the hUG gene. Moreover, a genetic linkage between atopic IgE responses and chromosome 11q{sup 13} has been reported. In addition, hUG is: (i) a potent inhibitor of PLA{sub 2} activity, (ii) a potent antiinflammatory/immunomodulatory and antichemotactic protein and has a hitherto undetermined receptor-mediated activity. Taken together, these findings suggest that a mutation either in the hUG or its receptor genes may manifest symptoms characteristic of atopy. Hence, we raise the question whether hUG is a candidate gene for this disease.

Mukherjee, A.B.; Peri, A.; Miele, L. [SDG, Bethesda, MD (United States)] [and others

1994-09-01T23:59:59.000Z

339

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

340

[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

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

The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion  

SciTech Connect (OSTI)

The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of .50 species known as the"Fusarium solani species complex". Members of this complex have diverse biological properties including the ability to cause disease on .100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches.

Coleman, J.J.; Rounsley, S.D.; Rodriguez-Carres, M.; Kuo, A.; Wasmann, C.c.; Grimwood, J.; Schmutz, J.; Taga, M.; White, G.J.; Zhuo, S.; Schwartz, D.C.; Freitag, M.; Ma, L.-J.; Danchin, E.G.J.; Henrissat, B.; Cutinho, P.M.; Nelson, D.R.; Straney, D.; Napoli, C.A.; Baker, B.M.; Gribskov, M.; Rep, M.; Kroken, S.; Molnar, I.; Rensing, C.; Kennell, J.C.; Zamora, J.; Farman, M.L.; Selker, E.U.; Salamov, A.; Shapiro, H.; Pangilinan, J.; Lindquist, E.; Lamers, C.; Grigoriev, I.V.; Geiser, D.M.; Covert, S.F.; Temporini, S.; VanEtten, H.D.

2009-04-20T23:59:59.000Z

342

Prolactin receptor and signal transduction to milk protein genes  

SciTech Connect (OSTI)

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

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

1994-06-01T23:59:59.000Z

343

Imaging gene expression in real-time using aptamers  

SciTech Connect (OSTI)

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

Shin, Il Chung

2011-12-13T23:59:59.000Z

344

Deciphering c-MYC-regulated genes in two distinct tissues  

E-Print Network [OSTI]

of Warwick, CV4 7AL, UK Full list of author information is available at the end of the article Robson et al. BMC Genomics 2011, 12:476 http://www.biomedcentral.com/1471-2164/12/476 © 2011 Robson et al; licensee BioMed Central Ltd. This is an Open Access... ] and subtractive hybridization [25]. It has been hypothesized that MYC may have the potential to regu- late up to 15% of the entire genome [26], leading to it being described as a ‘master regulator’ of gene expression. Regulatable transgenic mouse models have...

Robson, Samuel C; Ward, Lesley; Brown, Helen; Turner, Heather; Hunter, Ewan; Pelengaris, Stella; Khan, Michael

2011-09-30T23:59:59.000Z

345

Ayuda:Imágenes | Open Energy Information  

Open Energy Info (EERE)

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home5b9fcbce19 NoPublic Utilities Address: 160 EastMaine: EnergyAustin Energy Place: TexasAvoyelles Parish,Ayuda:EcuacionesImágenes

346

Gene Geracao Eolica Do Nordeste | Open Energy Information  

Open Energy Info (EERE)

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Office of Inspector GeneralDepartmentAUDIT REPORTOpen EnergyBoard" form. To createResearch Groups JumpGenDriveGene

347

Sandia National Laboratories: GeneSiC Semiconductor  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 -theErik Spoerke SSLS Exhibit at Explora MuseumFloatingFrontGTO Sandia WinsGeneSiC

348

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

E-Print Network [OSTI]

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

349

arbuscular mycorrhizal hyphae: Topics by E-print Network  

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

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

350

arbuscular mycorrhizal status: Topics by E-print Network  

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

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

351

arbuscular mycorrhiza enhanced: Topics by E-print Network  

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

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

352

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

SciTech Connect (OSTI)

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

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

2011-10-15T23:59:59.000Z

353

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

354

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

355

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

SciTech Connect (OSTI)

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

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

1990-04-01T23:59:59.000Z

356

E-Print Network 3.0 - archaeal amoa genes Sample Search Results  

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

genes involved in its transformations Source: Center for Coastal Margin Observation and Prediction (CMOP) Collection: Environmental Sciences and Ecology ; Geosciences 18...

357

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...

358

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,...

359

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

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

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

360

E-Print Network 3.0 - alter legume gene Sample Search Results  

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

Collection: Biology and Medicine 2 Meeting Report Legumes as a Model Plant Family. Genomics for Food and Summary: biochemical genes will be mapped across major crop legumes in...

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

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...

362

E-Print Network 3.0 - alstrom syndrome gene Sample Search Results  

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

Powered by Explorit Topic List Advanced Search Sample search results for: alstrom syndrome gene Page: << < 1 2 3 4 5 > >> 1 LIFE SCIENCE NEWSPublished by the Institute of...

363

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

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

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

364

E-Print Network 3.0 - alkane hydroxylase gene Sample Search Results  

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

gene. Sequence and expression... . In Vivo ... Source: Arnold, Frances H. - Division of Chemistry and Chemical Engineering, California Institute of Technology Collection:...

365

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

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

to normal cells Summary: amplify the genes for photosynthesis in the presence of dye-labeled nucleotides and incubate the products... . I cannot make a reasonable guess....

366

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting  

E-Print Network [OSTI]

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

Pignatta, Daniela

367

E-Print Network 3.0 - aluminum tolerance genes Sample Search...  

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

expression and soil aluminum tolerance Summary: to exhibit enhanced tolerance to Al, alfalfa was engineered by introducing the CS gene controlled... that were more...

368

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...

369

E-Print Network 3.0 - analyse gene patterns Sample Search Results  

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

Nebraska-Lincoln Collection: Environmental Sciences and Ecology ; Biology and Medicine 31 Identification of a nematode chemosensory gene family Summary: - ical clustering patterns....

370

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...

371

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...

372

E-Print Network 3.0 - auto-regulation increase gene Sample Search...  

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

and feed-forward motifs. Figure 2 illustrates the automatic... 100 to N 104 genes. Code is available online and from the authors. 1 Introduction ... Source: Oxford,...

373

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

374

E-Print Network 3.0 - acvr1 gene mutation Sample Search Results  

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

Emerging from an increasing number of mouse gene knockout, dominant... of cytoplasmic Stat-5 and translocation of Stat-5-phosphate to the nucleus for promo- tion of milk...

375

E-Print Network 3.0 - acid gene cluster Sample Search Results  

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

The most common method for analyzing gene expression data is ... Source: Friedman, Nir - School of Computer Science and Engineering, Hebrew University of Jerusalem Collection:...

376

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

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

1724, Detroit, June 2005. c 2005 Association for Computational Linguistics Summary: .2 Generating orthographic variants Our previous work on gene and protein name synonyms...

377

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

378

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

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

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...

379

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

380

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

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

Summary: Biologists Mutation of a Chitinase-Like Gene Causes Ectopic Deposition of Lignin, Aberrant Cell Shapes... growth and development, but no muta- tions in chitinase-like...

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

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...

382

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

383

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

384

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

E-Print Network [OSTI]

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

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

2002-01-01T23:59:59.000Z

385

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...

386

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. -...

387

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

388

The Exiguobacterium genus: biodiversity and biogeography  

SciTech Connect (OSTI)

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

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

2009-01-01T23:59:59.000Z

389

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

SciTech Connect (OSTI)

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

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

2007-03-01T23:59:59.000Z

390

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

SciTech Connect (OSTI)

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

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

2010-01-15T23:59:59.000Z

391

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

E-Print Network [OSTI]

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

Gao, Wenxiang

2005-02-17T23:59:59.000Z

392

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.

393

a1555g 12s rrna: Topics by E-print Network  

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

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

394

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

395

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

396

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; Lasure, Linda L; Magnuson, Jon K

2014-05-27T23:59:59.000Z

397

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

398

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

399

Recombinant cells that highly express chromosomally-integrated heterologous genes  

DOE Patents [OSTI]

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

Ingram, Lonnie O. (Gainesville, FL); Ohta, Kazuyoshi (Gainesville, FL); Wood, Brent E. (Gainesville, FL)

2000-08-22T23:59:59.000Z

400

Recombinant cells that highly express chromosomally-integrated heterologous genes  

DOE Patents [OSTI]

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

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

1998-10-13T23:59:59.000Z

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.


401

Recombinant cells that highly express chromosomally-integrated heterologous genes  

DOE Patents [OSTI]

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

Ingram, Lonnie O. (Gainesville, FL); Ohta, Kazuyoshi (Gainesville, FL); Wood, Brent E. (Gainesville, FL)

1998-01-01T23:59:59.000Z

402

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

403

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

404

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

405

The Use of EST Expression Matrixes for the Quality Control of Gene Expression Data  

E-Print Network [OSTI]

for tissue typing and quality control of libraries as small as just a few hundred total ESTs. Furthermore, weThe Use of EST Expression Matrixes for the Quality Control of Gene Expression Data Andrew T Expression Matrixes for the Quality Control of Gene Expression Data. PLoS ONE 7(3): e32966. doi:10

Sheldon, Nathan D.

406

Diagnostic test for prenatal identification of Down's syndrome and mental retardation and gene therapy therefor  

DOE Patents [OSTI]

A a diagnostic test useful for prenatal identification of Down syndrome and mental retardation. A method for gene therapy for correction and treatment of Down syndrome. DYRK gene involved in the ability to learn. A method for diagnosing Down's syndrome and mental retardation and an assay therefor. A pharmaceutical composition for treatment of Down's syndrome mental retardation.

Smith, Desmond J. (Oakland, CA); Rubin, Edward M. (Berkeley, CA)

2000-01-01T23:59:59.000Z

407

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

408

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.

409

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

410

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.

411

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

E-Print Network [OSTI]

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

McCorvey, Farah

2007-09-17T23:59:59.000Z

412

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

413

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

414

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

E-Print Network [OSTI]

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

415

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

SciTech Connect (OSTI)

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

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

1994-02-01T23:59:59.000Z

416

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.

417

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

E-Print Network [OSTI]

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

Nyholt, Dale R.

418

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.

419

Evolutionary Conservation of Expression Profiles Between Human and Mouse Orthologous Genes  

E-Print Network [OSTI]

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

Zhang, Jianzhi

420

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

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

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

422

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

423

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

SciTech Connect (OSTI)

Algorithmic methods for gene prediction have been developed and successfully applied to many different prokaryotic genome sequences. As the set of genes in a particular genome is not homogeneous with respect to DNA sequence composition features, the GeneMark.hmm program utilizes two Markov models representing distinct classes of protein coding genes denoted "typical" and "atypical". Atypical genes are those whose DNA features deviate significantly from those classified as typical and they represent approximately 10% of any given genome. In addition to the inherent interest of more accurately predicting genes, the atypical status of these genes may also reflect their separate evolutionary ancestry from other genes in that genome. We hypothesize that atypical genes are largely comprised of those genes that have been relatively recently acquired through lateral gene transfer (LGT). If so, what fraction of atypical genes are such bona fide LGTs? We have made atypical gene predictions for all fully completed prokaryotic genomes; we have been able to compare these results to other "surrogate" methods of LGT prediction.

Borodovsky, M.

2013-04-11T23:59:59.000Z

424

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

E-Print Network [OSTI]

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

Penn, Kevin Matthew

2012-01-01T23:59:59.000Z

425

Using the Cre-loxP system to randomize target gene expression states and generate diverse phenotypes  

E-Print Network [OSTI]

Modifying the expression of multiple genes enables both deeper understanding of their function and the engineering of complex multigenic cellular phenotypes. However, deletion or overexpression of multiple genes is typically ...

Niesner, Bradley (Bradley Joseph)

2013-01-01T23:59:59.000Z

426

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

427

Study Finds that Children with Autism and Gastrointestinal Symptoms Have Altered Expression of Genes Involved in Digestion  

E-Print Network [OSTI]

of Genes Involved in Digestion These changes may also affect the mix of bacteria present in the digestive disturbances have altered expression of genes involved in digestion. These variations may contribute to changes

Salzman, Daniel

428

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

E-Print Network [OSTI]

Gene therapy has been heralded as a possible approach to a variety of diseases and conditions, ranging from cancer and heart disease to blindness and neurodegenerative diseases. However, progress in gene therapy requires ...

Silcox, Christina Elise

2014-01-01T23:59:59.000Z

429

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

E-Print Network [OSTI]

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

Gordan, Raluca

430

6 Gerlai, R. (2001) Gene targeting: technical confounds and potential solutions in behavioral brain research. Behav. Brain Res. 125,  

E-Print Network [OSTI]

at different alternative splice donor sites of the tyrosinase gene in murine albinism. Genomics 37, 245­248 17

Zhang, ZhaoLei

431

redD as a Reporter for Transcriptional Activity 551 Application of redD, the Transcriptional Activator Gene  

E-Print Network [OSTI]

glaucescens, which encodes tyrosinase (Paget et al., 1994), and the EGFP gene for green-fluorescent protein

Bibb, Mervyn

432

Nucleotide sequence of the 2 matrix protein genes (M1 and M2) of hirame rhabdovirus (HRV),  

E-Print Network [OSTI]

Nucleotide sequence of the 2 matrix protein genes (M1 and M2) of hirame rhabdovirus (HRV), a fish of hirame rhabdovirus (HRV). The M1 protein gene was 684 nucleotides long, encoding 227 amino acids.8% at the nucleotide level and 81.1 and 44.8% at the amino acid level. The M2 protein gene was 582 nucleotides long

Boyer, Edmond

433

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.

434

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

E-Print Network [OSTI]

were found in relative quantification for 30 genes in Trial 1 and 36 genes in Trial 2, in which CS calves had greater expression than AS calves (P < 0.047). Fifteen of those genes were common between the two trials with mean treatment differences of RQ...

Terrill, Cooper

2012-02-14T23:59:59.000Z

435

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

436

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

437

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

438

Mapping our genes: The genome projects: How big, how fast  

SciTech Connect (OSTI)

For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for /open quotes/writing the rules/close quotes/ of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. OTA prepared this report with the assistance of several hundred experts throughout the world. 342 refs., 26 figs., 11 tabs.

none,

1988-04-01T23:59:59.000Z

439

Studies on the chalcone synthase gene of two higher plants: petroselinum hortense and matthiola incana  

SciTech Connect (OSTI)

Two higher plant systems are presented which allow to study coordinated gene expression of the light-induced metabolic pathway of flavonoid biosynthesis: tissue culture cells of Petroselinum hortense (Apiaceae) and different developmental stages of various genotypes of Matthiola incana (Brassicaceae). The gene structure of the chalcone synthase is mainly studied. A cDNA clone (pLF56) of parsley has been constructed and characterized conferring the chalcone synthase gene sequence. Strong cross hybridization between the parsley cDNA and Matthiola DNA allowed to identify a HindIII fragment (6000 bp) identical in size for parsley and different Matthiola wild type lines and a mutant line.

Hemleben, V.; Frey, M.; Rall, S.; Koch, M.; Kittel, M.; Kreuzaler, F.; Ragg, H.; Fautz, E.; Hahlbrock, K.

1982-01-01T23:59:59.000Z

440

Expression and rearrangement of the ROS1 gene in human glioblastoma cells  

SciTech Connect (OSTI)

The human ROS1 gene, which possibly encodes a growth factor receptor, was found to be expressed in human tumor cell lines. In a survey of 45 different human cell lines, the authors found ROS1 to be expressed in glioblastoma-derived cell lines at high levels and not to be expressed at all, or expressed at very low levels, in the remaining cell lines. The ROS1 gene was present in normal copy numbers in all cell lines that expressed the gene. However, in one particular glioblastoma line, they detected a potentially activating mutation at the ROS1 locus.

Birchmeier, C.; Sharma, S.; Wigler, M.

1987-12-01T23:59:59.000Z

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.


441

Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate  

SciTech Connect (OSTI)

A thermophilic bacterium that can use O{sub 2}, NO{sub 3}{sup {minus}}, Fe(III), and S{sup 0} as terminal electron acceptors for growth was isolated from groundwater sampled at a 3.2-km depth in a South African gold mine. This organism, designated SA-01, clustered most closely with members of the genus Thermus, as determined by 16S rRNA gene (rDNA) sequence analysis. The 16S rDNA sequence of SA-01 was >98% similar to that of Thermus strain NMX2 A.1, which was previously isolated by other investigators from a thermal spring in New Mexico. Strain NMX2 A.1 was also able to reduce Fe(III) and other electron acceptors. Neither SA-01 nor NMX2 A.1 grew fermentatively, i.e., addition of an external electron acceptor was required for anaerobic growth. Thermus strain SA-01 reduced soluble Fe(III) complexed with citrate or nitrilotriacetic acid (NTA); however, it could reduce only relatively small quantities of hydrous ferric oxide except when the humic acid analog 2,6-anthraquinone disulfonate was added as an electron shuttle, in which case 10 mM Fe(III) was reduced. Fe(III)-NTA was reduced quantitatively to Fe(II); reduction of Fe(III)-NTA was coupled to the oxidation of lactate and supported growth through three consecutive transfers. Suspensions of Thermus strain SA-01 cells also reduced Mn(IV), Co(III)-EDTA, Cr(VI), and U(VI). Mn(IV)-oxide was reduce in the presence of either lactate or H{sub 2}. Both strains were also able to mineralize NTA to CO{sub 2} and to couple its oxidation to Fe(III) reduction and growth. The optimum temperature for growth and Fe(III) reduction by Thermus strains SA-01 and NMX2 A.1 is approximately 65 C; their optimum pH is 6.5 to 7.0. This is the first report of a Thermus sp. being able to couple the oxidation of organic compounds to the reduction of Fe, Mn, or S.

Kieft, T.L. [New Mexico Inst. of Mining and Technology, Socorro, NM (United States). Dept. of Biology; Fredrickson, J.K. [Pacific Northwest National Lab., Richland, WA (United States); Onstott, T.C. [Princeton Univ., NJ (United States). Dept. of Geosciences] [and others

1999-03-01T23:59:59.000Z

442

Mutations of the tyrosinase gene in Indo-Pakistani patients with type I (tyrosinase-deficient) oculocutaneous albinsm (OCA)  

SciTech Connect (OSTI)

Oculocutaneous albinism (OCA) is a group of autosomal recessive disorders characterized by deficient synthesis of melanin pigment. Type I (tyrosinase-deficient) OCA results from mutations of the tyrosinase gene (TYR gene) encoding tyrosinase, the enzyme that catalyzes the first two steps of melanin biosynthesis. Mutations of the TYR gene have been identified in a large number of patients, most of Caucasian ethnic origin, with various forms of type I OCA. The authors present an analysis of the TYR gene in eight Indo-Pakistani patients with type I OCA. The authors describe four novel TYR gene mutations and a fifth mutation previously observed in a Caucasian patient. 16 refs., 6 figs.

Tripathi, R.K.; Droetto, S.; Strunk, K.M.; Holmes, S.A.; Spritz, R.A. (Univ. of Wisconsin, Madison, WI (United States)); Bundey, S.; Musarella, M.A.

1993-12-01T23:59:59.000Z

443

Tyrosinase-positive oculocutaneous albinism in Southern African blacks: P gene-associated haplotypes suggest a major mutation in the 5{prime} region of the gene  

SciTech Connect (OSTI)

Tyrosinase-positive oculocutaneous albinism (ty-pos OCA) occurs with a prevalence of 1 in 3900 among Southern African (SA) blacks. The major contributors to morbidity and mortality are skin cancer and decreased visual acuity. Two distinct phenotypes occur, namely individuals with ephelides (darkly pigmented patches) and those without. There is complete concordance with regard to ephelus status among siblings. The disorder is linked to markers on chromosome 15q11.2-q12, and no obligatory cross-overs were observed with polymophic markers at the human homolog, P, of the mouse pink eyed dilute gene, p. Contrary to what has been shown for Caucasoid ty-pos OCA, this condition shows locus homogeneity among SA blacks. The P gene is an excellent candidate for ty-pos OCA and mutations in this gene will confirm its role in causing the common form of albinism in SA. Numerous P gene mutations have been described in other populations. In an attempt to detect mutations, the P gene cDNA was used to search for structural rearrangements or polymorphisms. Six polymorphisms (plR10/Scal, 912/Xbal, 912/HincII, 912/TaqI, 1412/TaqI [two systems] and 1412/HindIII) were detected with subclones of the P cDNA and haplotypes were determined in each family. None were clearly associated with an albinism-related rearrangement. However, strong linkage disequilibrium was observed with alleles at loci toward the 5{prime} region of the gene ({triangle}=0.65, 0.57 and 0.80 for the three polymorphisms detected with the 912 subclone), suggesting a major ty-pos OCA mutation in this region. Haplotype analysis provides evidence for a major mutation associated with the same haplotype in individuals with ephelides (8/12 OCA chromosomes) and those without ephelides (24:30). The presence of other ty-pos OCA associated haplotypes indicates several other less common mutations.

Ramsay, M.; Stevens, G.; Beukering, J. van [Univ. of the Witwatersrand, Johannesburg (South Africa)] [and others

1994-09-01T23:59:59.000Z

444

E-Print Network 3.0 - a-complementing xpac gene Sample Search...  

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

Johns Hopkins... ,000 genes. See also R.M. Henig's book The Monk in the Garden: The Lost and Found Genius of Gregor Mendel Source: Le Roy, Robert J. - Department of...

445

Sam Wang, Princeton Genes, Brain Circuits, and the Mind: From Optical Imaging to Genomics  

E-Print Network [OSTI]

Sam Wang, Princeton WANG 12-4 Genes, Brain Circuits, and the Mind: From Optical Imaging to Genomics information, my laboratory uses multiphoton optical methods to image activity in the cerebellum, a structure

Glashausser, Charles

446

Phylogenetic diversity of gram-positive bacteria and their secondary metabolite genes  

E-Print Network [OSTI]

in Oceanography by Erin Ann Gontang Committee in charge:The Dissertation of Erin Ann Gontang is approved, and it isMetabolite Genes by Erin Ann Gontang Doctor of Philosophy in

Gontang, Erin Ann

2008-01-01T23:59:59.000Z

447

E-Print Network 3.0 - adenylate cyclase gene Sample Search Results  

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

for: adenylate cyclase gene Page: << < 1 2 3 4 5 > >> 1 Comparative and Functional Genomics Comp Funct Genom 2004; 5: 1738. Summary: Cue et al., 2000) and recently at least two...

448

Correlations Between Gene Expression and Mercury Levels in Blood of Boys With and Without Autism  

E-Print Network [OSTI]

Ingenuity Pathways Analysis (IPA) (Ingenuity Systems Ň ,ed the pathways from the IPA library of canonical pathwaysis not possible. In this case, IPA was used to map the genes

2011-01-01T23:59:59.000Z

449

Molecular cloning and characterization of important stress and redox regulatory genes from Hydra vulgaris  

E-Print Network [OSTI]

In this research, important stress and redox regulatory genes present in Hydra vulgaris were isolated and characterized to facilitate our understanding of the evolution and mechanisms of stress response. H. vulgaris heat shock protein 70 (HvHSP70...

Dash, Bhagirathi

2007-04-25T23:59:59.000Z

450

Molecular studies of longevity-associated genes in yeast and mammalian cells  

E-Print Network [OSTI]

Aging is a complex process affecting diverse organisms from bacteria to humans. Despite strong evolutionary arguments against the conservation of a single mechanism of aging, a variety of conserved single gene mutations ...

Liszt, Gregory (Gregory Birjandi)

2006-01-01T23:59:59.000Z

451

Quantitative analysis of non-viral gene therapy in primary liver culture systems  

E-Print Network [OSTI]

Gene therapy has the potential to cure thousands of diseases caused by genetic abnormalities, provide novel combination therapies for cancers and viral infections, and offer a new and effective platform for next generation ...

Tedford, Nathan C

2007-01-01T23:59:59.000Z

452

A Transient Transgenic RNAi Strategy for Rapid Characterization of Gene Function during Embryonic Development  

E-Print Network [OSTI]

RNA interference (RNAi) is a powerful strategy for studying the phenotypic consequences of reduced gene expression levels in model systems. To develop a method for the rapid characterization of the developmental consequences ...

Bjork, Bryan C.

453

Optimizing a protein-RNA aptamer gene regulatory system using an engineered peptide library  

E-Print Network [OSTI]

For this project, N-terminal and C-terminal peptide library fusions were designed,bconstructed, and screened in order to improve the repression achievable with a novel gene regulatory system. This system, based on the ...

Wong, Jessica Karen

2011-01-01T23:59:59.000Z

454

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

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

Sexually differentiated, androgen-regulated, larynx-specific Summary: the entire xlMyHC-LM gene. The androgen-regulated xtMyHC that predominates in the male larynx of X... -twitch...

455

Identification of sensitivity genes involved in teratogen-induced neural tube defects  

E-Print Network [OSTI]

that NTDs have a strong genetic component to their development. My project is designed to examine differential expression patterns of genes within the neural tube cells of inbred LM/Bc mouse fetuses following exposure to the known teratogenic agent...

Hayes, Blaine G

2013-02-22T23:59:59.000Z

456

Genes related to xylose fermentation and methods of using same for enhanced biofuel production  

DOE Patents [OSTI]

The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

Wohlbach, Dana J.; Gasch, Audrey P.

2014-08-05T23:59:59.000Z

457

Genes: Philosophical Analyses Put to the Test Karola Stotz1 and Paul Griffiths2  

E-Print Network [OSTI]

of the concept of the gene were operationalized and tested against questionnaire data obtained from working of science ­ a case study of conceptual change and its role in science. Empirical science is a powerhouse

Stotz, Karola

458

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

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

CNS 115 Refreshments served 3:40 p.m. CNS 1st floor lobby. ALL... aphid 4:30 Eric Van Fleet (Marina Caillaud) Differential gene expression patterns in host Source: Ithaca...

459

E-Print Network 3.0 - abscisic acid gene Sample Search Results  

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

for: abscisic acid gene Page: << < 1 2 3 4 5 > >> 1 Future Perspectives in Plant Biology Abscisic Acid Receptors Summary: ) Reduced expression of the v-SNAREs AtVAMP71...

460

E-Print Network 3.0 - age-dependent gene expression Sample Search...  

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

search results for: age-dependent gene expression Page: << < 1 2 3 4 5 > >> 1 Current Biology, Vol. 12, 712723, April 30, 2002, 2002 Elsevier Science Ltd. All rights reserved. PII...

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

Hairpin RNAs and Retrotransposon LTRs Effect RNAi and Chromatin-Based Gene Silencing   

E-Print Network [OSTI]

The expression of short hairpin RNAs in several organisms silences gene expression by targeted mRNA degradation. This RNA interference (RNAi) pathway can also affect the genome, as DNA methylation arises at loci homologous ...

Schramke, Vera; Allshire, Robin C

2003-01-01T23:59:59.000Z

462

Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen (2010 JGI User Meeting)  

ScienceCinema (OSTI)

Director Eddy Rubin on "Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

Rubin, Eddy

2011-04-25T23:59:59.000Z

463

Modeling the Fitness Consequences of a Cyanophage-Encoded Photosynthesis Gene  

E-Print Network [OSTI]

Background: Phages infecting marine picocyanobacteria often carry a psbA gene, which encodes a homolog to the photosynthetic reaction center protein, D1. Host encoded D1 decays during phage infection in the light. Phage ...

Chisholm, Sallie (Penny)

464

Genomic Insights into Sexual Selection and the Evolution of Reproductive Genes in Teleost Fishes  

E-Print Network [OSTI]

that genes associated with reproductive biology evolve especially rapidly planted this notion, but many details about the genomics of sex remain elusive. Numerous studies have characterized rapid sequence and expression divergence of sex-related molecules...

Small, Clayton

2012-10-19T23:59:59.000Z

465

Variability in the Stability and Productivity of Transfected Genes in Chinese Hamster Ovary (CHO) cells  

E-Print Network [OSTI]

In the field of biologics production, productivity and stability of the transfected gene of interest are two very important attributes that dictate if a production process is viable. To further understand and improve these ...

Ng, Say Kong

466

E-Print Network 3.0 - activity mia-like gene Sample Search Results  

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

: Castillo-Davis, C. I. and D. L. Hartl. 2003. GeneMerge-- post-genomic analysis, data-mining and hypothesis... testing. Bioinformatics 19(7):891-892 http:www.oeb.harvard.edu...

467

E-Print Network 3.0 - antagonist gene il-1rn Sample Search Results  

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

Information 1 Non-centrality Parameters Summary: Position Gene Control Fam Statistic df P-value IL1RN dad&mom 121 THP 5.17 1 0.023 439154 115064289 IL1... 115068445...

468

Nucleotide diversity and neutrality testing in genes involved in adaptation in Douglas-fir  

E-Print Network [OSTI]

Nucleotide diversity and neutrality testing in genes involved in adaptation in Douglas-fir B. Pande-Oregon region, and 684 SNPs were identified in total. We report the estimation of nucleotide diversity and tests

469

HUMAN GENE THERAPY 18:871880 (October 2007) Mary Ann Liebert, Inc.  

E-Print Network [OSTI]

HUMAN GENE THERAPY 18:871­880 (October 2007) © Mary Ann Liebert, Inc. DOI: 10.1089/hum.2007 of funda- mental questions in retinal biology. 871 INTRODUCTION RNA INTERFERENCE (RNAi) is an approach

Kay, Mark A.

470

HUMAN GENE THERAPY 14:871881 (June 10, 2003) Mary Ann Liebert, Inc.  

E-Print Network [OSTI]

HUMAN GENE THERAPY 14:871­881 (June 10, 2003) © Mary Ann Liebert, Inc. Pathways of Removal of Free ends. These studies shed new light on the molecular mechanisms of rAAV vector transduction in vivo. 871

Kay, Mark A.

471

Identifying genes that are required for the maintenance of pancreatic ductal adenocarcinoma  

E-Print Network [OSTI]

We searched for genes that are potentially important for the maintenance of Pancreatic Ductal Adenocarcinoma (PDAC). PDAC is the 4th leading cause for cancer-related deaths and exhibits a 5-year survival rate of less than ...

Jenq, Harry

2012-01-01T23:59:59.000Z

472

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

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

67 Cancer gene therapy with oncolytic adenoviruses K. Guse,A. Hemminki Summary: , Stricker H, Pegg J et al. Phase I study of replica- tion-competent adenovirus-mediated...

473

E-Print Network 3.0 - affects odontoblast gene Sample Search...  

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

Summary: mice expression of the other non-targeted Runx genes is not affected (Stricker et al., 2002; Yamashiro... in these epithelia is regulated by TGF-b is an interesting...

474

E-Print Network 3.0 - adenovirus-mediated gene therapy Sample...  

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

47 Cancer gene therapy with oncolytic adenoviruses K. Guse,A. Hemminki Summary: , Stricker H, Pegg J et al. Phase I study of replica- tion-competent adenovirus-mediated...

475

E-Print Network 3.0 - adenovirus-mediated gene delivery Sample...  

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

58 Cancer gene therapy with oncolytic adenoviruses K. Guse,A. Hemminki Summary: , Stricker H, Pegg J et al. Phase I study of replica- tion-competent adenovirus-mediated...

476

Exploring the specificity and mechanisms of siRNA-mediated gene silencing in mammalian cells  

E-Print Network [OSTI]

Complementary short interfering RNAs (siRNAs) are routinely used to knockdown gene expression. siRNAs bind to their target sequence and guide transcript cleavage and subsequent degradation. This type of silencing is ...

Alemán, Lourdes Maria

2008-01-01T23:59:59.000Z

477

A fast, robust and tunable synthetic gene oscillator Jesse Stricker1  

E-Print Network [OSTI]

LETTERS A fast, robust and tunable synthetic gene oscillator Jesse Stricker1 *, Scott Cookson1 *, Matthew R. Bennett1,2 *, William H. Mather1 , Lev S. Tsimring2 & Jeff Hasty1,2 One defining goal

Hasty, Jeff

478

Effects of Alcohol on the Regulation of Imprinted Genes in Mouse Stem Cells  

E-Print Network [OSTI]

ABSTRACT Effects of Alcohol on the Regulation of Imprinted Genes in Mouse Stem Cells. (December 2013) Alyssa Crocker Department of Animal Science Texas A&M University Research Advisor: Dr. Michael Golding Department of Veterinary Physiology...

Crocker, Alyssa

2013-02-04T23:59:59.000Z

479

E-Print Network 3.0 - aromatase gene defines Sample Search Results  

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

gene defines Page: << < 1 2 3 4 5 > >> 1 ORIGINAL ARTICLE Aromatase mRNA in the Brain of Adult Green Anole Lizards: Effects of Summary: to previous work using Nissl-stained...

480

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

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

gene expression Page: << < 1 2 3 4 5 > >> 1 ORIGINAL ARTICLE Aromatase mRNA in the Brain of Adult Green Anole Lizards: Effects of Summary: of testosterone to oestradiol (E2)...

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

Examination of dioxin and its alteration of gene expression via DNA Microarray Analysis  

E-Print Network [OSTI]

), and ADD/ADHD. Little evidence has been available to demonstrate how dioxin specifically alters gene expression, both in developing embryos and adults. Recently, Texas A&M University has acquired several DNA Microarray Systems, which are revolutionizing...

Wright, Justin Charles

2013-02-22T23:59:59.000Z

482

Mechanisms of transcriptional activation of estrogen responsive genes in breast cancer cells  

E-Print Network [OSTI]

Estrogen receptor (ER) acts as a ligand-activated transcription factor that regulates the expression of genes. The genomic mechanisms of ER action include ligand-induced dimerization of ER which binds estrogen responsive elements (EREs...

Chen, Chien-Cheng

2009-06-02T23:59:59.000Z

483

Scientific Methods Workshop: Ecological and Agronomic Consequences of Gene Flow from  

E-Print Network [OSTI]

Scientific Methods Workshop: Ecological and Agronomic Consequences of Gene Flow from Transgenic Prevention Division, U.S. EPA" Robert Zemetra, University of Idaho 178 "The evolution of a biological risk

Snow, Allison A.

484

Gene Expression and Association Analyses of Stress Responses in Loblolly Pine (Pinus taeda L.)  

E-Print Network [OSTI]

The molecular mechanisms underlying disease-resistance and drought-resistance in forest trees are not well understood. Linking variation in gene expression with genetic polymorphisms and with variations in disease- and drought-resistance phenotypes...

Seeve, Candace Marie

2012-02-14T23:59:59.000Z

485

Moral obligation and the human germ-line gene therapy debate  

E-Print Network [OSTI]

genetic engineering, there are few arguments made for a positive moral obligation to genetic intervention. This is especially so with respect to human germ-line gene therapy. Burke. K. Zimmerman makes one of the few arguments that society...

Clark, Alan B

1998-01-01T23:59:59.000Z

486

The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants  

SciTech Connect (OSTI)

We report the genome sequence of the nonseed vascular plant, Selaginella moellendorffii, and by comparative genomics identify genes that likely played important roles in the early evolution of vascular plants and their subsequent evolution

Grigoriev, Igor V.; Banks, Jo Ann; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Bowman, John L.; Gribskov, Michael; dePamphilis, Claude; Albert, Victor A.; Aono, Naoki; Aoyama, Tsuyoshi; Ambrose, Barbara A.; Ashton, Neil W.; Axtell, Michael J.; Barker, Elizabeth; Barker, Michael S.; Bennetzen, Jeffrey L.; Bonawitz, Nicholas D.; Chapple, Clint; Cheng, Chaoyang; Correa, Luiz Gustavo Guedes; Dacre, Michael; DeBarry, Jeremy; Dreyer, Ingo; Elias, Marek; Engstrom, Eric M.; Estelle, Mark; Feng, Liang; Finet, Cedric; Floyd, Sandra K.; Frommer, Wolf B.; Fujita, Tomomichi; Gramzow, Lydia; Gutensohn, Michael; Harholt, Jesper; Hattori, Mitsuru; Heyl, Alexander; Hirai, Tadayoshi; Hiwatashi, Yuji; Ishikawa, Masaki; Iwata, Mineko; Karol, Kenneth G.; Koehler, Barbara; Kolukisaoglu, Uener; Kubo, Minoru; Kurata, Tetsuya; Lalonde, Sylvie; Li, Kejie; Li, Ying; Litt, Amy; Lyons, Eric; Manning, Gerard; Maruyama, Takeshi; Michael, Todd P.; Mikami, Koji; Miyazaki, Saori; Morinaga, Shin-ichi; Murata, Takashi; Mueller-Roeber, Bernd; Nelson, David R.; Obara, Mari; Oguri, Yasuko; Olmstead, Richard G.; Onodera, Naoko; Petersen, Bent Larsen; Pils, Birgit; Prigge, Michael; Rensing, Stefan A.; Riano-Pachon, Diego Mauricio; Roberts, Alison W.; Sato, Yoshikatsu; Scheller, Henrik Vibe; Schulz, Burkhard; Schulz, Christian; Shakirov, Eugene V.; Shibagaki, Nakako; Shinohara, Naoki; Shippen, Dorothy E.; Sorensen, Iben; Sotooka, Ryo; Sugimoto, Nagisa; Sugita, Mamoru; Sumikawa, Naomi; Tanurdzic, Milos; Theilsen, Gunter; Ulvskov, Peter; Wakazuki, Sachiko; Weng, Jing-Ke; Willats, William W.G.T.; Wipf, Daniel; Wolf, Paul G.; Yang, Lixing; Zimmer, Andreas D.; Zhu, Qihui; Mitros, Therese; Hellsten, Uffe; Loque, Dominique; Otillar, Robert; Salamov, Asaf; Schmutz, Jeremy; Shapiro, Harris; Lindquist, Erika; Lucas, Susan; Rokhsar, Daniel

2011-04-28T23:59:59.000Z

487

Palindromes on the human X chromosome : testis-biased transcription, gene conversion and evolution  

E-Print Network [OSTI]

Recent genomic studies of the Y chromosome revealed massive, testis-specific palindromes that span 30% of the chromosome and are subject to gene conversion. We conducted studies to determine whether similar palindromes ...

Saionz, Jennifer R., 1976-

2005-01-01T23:59:59.000Z

488

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

E-Print Network [OSTI]

Radiation-induced DNA damage is a precursor to mutagenesis and cytotoxicity. During radiotherapy, exposure of healthy tissues can lead to severe side effects. We explored the potential of mitochondrial SOD (MnSOD) gene ...

Niu, Yunyun

489

Synthesis and chemical modification of degradable polymers to enhance gene delivery  

E-Print Network [OSTI]

Poly([beta]-amino ester)s are a class of cationic, degradable polymers that have shown significant promise as gene delivery agents, more effective than the state-of-the-art, commercially available non-viral systems. The ...

Zugates, Gregory Thomas

2007-01-01T23:59:59.000Z

490

Mysteries of the Deep: What happens inside of MPI on Blue Gene...  

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

Mysteries of the Deep: What happens inside of MPI on Blue GeneQ and why it matters Jeff Hammond Leadership Computing Facility Argonne National Laboratory March 5, 2013 Jeff...

491

E-Print Network 3.0 - anti-cancer target gene Sample Search Results  

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

Search Powered by Explorit Topic List Advanced Search Sample search results for: anti-cancer target gene Page: << < 1 2 3 4 5 > >> 1 THE BETTER WORLD REPORT PART TWO Biotechnology...

492

Heterogeneity of tumor-induced gene expression changes in the human metabolic network  

E-Print Network [OSTI]

Reprogramming of cellular metabolism is an emerging hallmark of neoplastic transformation. However, it is not known how the expression of metabolic genes in tumors differs from that in normal tissues, or whether different ...

Hu, Jie

493

Kiss1 Gene Expression and the Effects of Kisspeptin During Pubertal Development in the Ewe Lamb  

E-Print Network [OSTI]

puberty. In Experiment 1, ovariectomized ewe lambs bearing subcutaneous estradiol implants were used to investigate Kiss1 gene expression in the preoptic area (POA) and hypothalamus during pubertal maturation of the reproductive neuroendocrine system...

Redmond, Jeremy Scott

2012-02-14T23:59:59.000Z

494

Fitting It All Together: How Courtship- and Mating-Responsive Genes Affect Drosophila melanogaster Male Behavior  

E-Print Network [OSTI]

by utilizing microarray technology to assess courtship- or mating-induced gene expression changes in Drosophila male whole bodies or heads. Mutations in candidate loci were tested for effects on reproductive behaviors and present the first data showing...

Ellis, Lisa Lynn

2011-10-21T23:59:59.000Z

495

Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and nonparallel physiological  

E-Print Network [OSTI]

of parallel and nonparallel physiological divergence M. L. EVANS* & L. BERNATCHEZ Institut de Biologie Inte: Coregonus; gene transcription; metabolism; oxidative phosphorylation; phenotypic divergence; physiology mitochondrial and nuclear genome-encoded oxidative phosphorylation (OXPHOS) complexes, the primary physiological

Bernatchez, Louis

496

Whole-Exome Sequencing and Homozygosity Analysis Implicate Depolarization-Regulated Neuronal Genes in Autism  

E-Print Network [OSTI]

Although autism has a clear genetic component, the high genetic heterogeneity of the disorder has been a challenge for the identification of causative genes. We used homozygosity analysis to identify probands from ...

Schubert, Christian R.

497

Novel enabling technologies of gene isolation and plant transformation for improved crop protection  

SciTech Connect (OSTI)

Meeting the needs of agricultural producers requires the continued development of improved transgenic crop protection products. The completed project focused on developing novel enabling technologies of gene discovery and plant transformation to facilitate the generation of such products.

Torok, Tamas

2013-02-04T23:59:59.000Z

498

p63 and p73 Transcriptionally Regulate Genes Involved in DNA Repair  

E-Print Network [OSTI]

The p53 family activates many of the same genes in response to DNA damage. Because p63 and p73 have structural differences from p53 and play distinct biological functions in development and metastasis, it is likely that ...

Lin, Yu-Li

499

Characterization in cochlea of KCTD12/PFET1, an intronless gene with predominant fetal expression  

E-Print Network [OSTI]

The prevalence of severe to profound bilateral congenital hearing loss is estimated at 1 in 1000 births, at least half of which can be attributed to a genetic cause. To date, mutations in at least 67 genes have been ...

Kuo, Sharon Fan

2006-01-01T23:59:59.000Z

500

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

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

Medicine 15 Proc. Natl. Acad. Sci. USA Vol. 93, pp. 3575-3580, April 1996 Summary: and environmental regulation of nitro- genase gene expression and enzyme activity would expand...