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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

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

SciTech Connect

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

2

Greengenes: 16S rRNA Database and Workbench Compatible with ARB  

DOE Data Explorer (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.

3

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

Science Conference Proceedings (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.

Tremblay, Julien [DOE JGI

2012-06-01T23:59:59.000Z

4

Development of polymerase chain reaction primer sets for diagnosis of Lyme disease and for species-specific identification of Lyme disease isolates by 16S rRNA signature nucleotide analysis  

E-Print Network (OSTI)

polymerase chain reaction primer sets for diagnosis of Lyme disease and for species-specific identification of Lyme disease isolates by 16S rRNA signature nucleotide analysis.

R T Marconi; C F Garon; Richard T. Marconi; Claude; F. Garon

1992-01-01T23:59:59.000Z

5

16S rRNA gene microarray analysis of microbial communities in ethanol-stimulated subsurface sediment  

E-Print Network (OSTI)

Enrichment of members of the family Geobacteraceae associated with the stimulation of dissimilatory metal reduction in uranium-

Mohanty, S.R.

2012-01-01T23:59:59.000Z

6

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

E-Print Network (OSTI)

and Edwards, 2003), and a dry cell weight (dcw) of 1.33 ¥ 10-13 g cell-1 (Bratbak, 1985) [i.e. X = (Y ¥ DS/dcw of benzene consumed and assuming Y = 9.4 g cells mol benzene-1 (Ulrich and Edwards, 2003), dcw = 1. 33 ¥ 10-13 g cell-1 (Bratbak, 1985), and a soil bulk density (rb) of 1.6 kg l-1 [i.e. X = (Y ¥ DS/rb ¥ dcw

Alvarez, Pedro J.

7

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

E-Print Network (OSTI)

Development of a real-time PCR method for the detection of fossil 16S rDNA fragments- tive real-time PCR methodology for specific detection of 16S rRNA gene sequences of purple and green by polymerase chain reaction (PCR) amplification and sequencing (Coolen & Overmann, 1998). Lake Cadagno

Gilli, Adrian

8

Biolog(TM) ID as compared to 16S ribosomal RNA ID for environmental isolates from the deep subsurface  

SciTech Connect

The U.S. Dept of Energy (DOE) Subsurface Microbial Culture Collection (SMCC) contains nearly 10,000 strains of microorganisms isolated from terrestrial subsurface environments. Many of the aerobic, gram-negative, chemoheterotrophs isolated from the DOE Savannah River Site (SRS) have previously been identified by phylogenetic analysis of 16S ribosomal RNA (rRNA) gene nucleotide sequences. These SMCC isolates are currently being examined using Biolog GN Microplates and the Biolog Microstation System in order to gain knowledge of their metabolic capabilities and to compare Biolog IDs with 16S IDs. To accommodate the particular needs of these subsurface isolates, which are often incapable of growing under high-nutrient conditions, Biolog's recommendations for inoculating isolates into Biolog GN Microplates have been altered. The isolates are grown on low nutrient media, sodium thioglycolate (3mM) is added to the culture media to inhibit capsule formation, and a low density of bacteria is inoculated into the microplate. Using these altered inoculation criteria, 60 percent of these SMCC isolates have a Biolog genus ID that matches the 16S rRNA ID. These results indicate that the Biolog System can be a good means of identifying unusual environmental isolates, even when recommended inoculation procedures are altered to accommodate particular isolate needs.

McKinsey, P.C.

2000-05-05T23:59:59.000Z

9

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes  

Science Conference Proceedings (OSTI)

Technologies for massively parallel sequencing are revolutionizing microbial ecology and are vastly increasing the scale of ribosomal RNA (rRNA) gene studies. Although pyrosequencing has increased the breadth and depth of possible rRNA gene sampling, one drawback is that the number of reads obtained per sample is difficult to control. Pyrosequencing libraries typically vary widely in the number of sequences per sample, even within individual studies, and there is a need to revisit the behaviour of richness estimators and diversity indices with variable gene sequence library sizes. Multiple reports and review papers have demonstrated the bias in non-parametric richness estimators (e.g. Chao1 and ACE) and diversity indices when using clone libraries. However, we found that biased community comparisons are accumulating in the literature. Here we demonstrate the effects of sample size on Chao1, ACE, CatchAll, Shannon, Chao-Shen and Simpson's estimations specifically using pyrosequencing libraries. The need to equalize the number of reads being compared across libraries is reiterated, and investigators are directed towards available tools for making unbiased diversity comparisons.

Gihring, Thomas [ORNL; Green, Stefan [Florida State University; Schadt, Christopher Warren [ORNL

2011-01-01T23:59:59.000Z

10

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

E-Print Network (OSTI)

template mismatch by real-time PCR using the 16S rRNA geneWelch DB (2009). Effect of PCR amplicon size on assessmentsof mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol

Engelbrektson, Anna

2010-01-01T23:59:59.000Z

11

LS-16 S. Kim  

NLE Websites -- All DOE Office Websites (Extended Search)

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

12

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

13

16S ribosomal DNA sequence analysis confirms the close relationship between the genera Xanthobacter, Azorhizobium, and Aquabacter and reveals a lack of phylogenetic coherence among Xanthobacter species  

Science Conference Proceedings (OSTI)

A comparative 16S ribosomal DNA (rDNA) sequence analysis was used to investigate the phylogenetic position of members of the genus Xanthobacter. We determined 16S rDNA sequence data for the type strains of the three Xanthobacter species and five additional Xanthobacter strains. The close relationship between the genera Xanthobacter, Azorhizobium, and Aquabacter previously demonstrated by DNA-rRNA hybridization studies was confirmed. The results of our phylogenetic analysis indicate that members of the genera Xanthobacter, Azorhizobium, and Aquabacter are intermixed and that there is no clear genetic cluster consisting of the Xanthobacter species. A comparison of the Xanthobacter sequences with the 16S rDNA sequences available from environmental clone studies indicated that members of this genus have not been detected by nonculturing approaches.

Rainey, F.A. [Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig (Germany); Wiegel, J. [Univ. of Georgia, Athens, GA (United States)

1996-04-01T23:59:59.000Z

14

D16S39 Variants  

Science Conference Proceedings (OSTI)

... 3 extractions, 3 PCR in Identifilier and 3 PCR in PP16 and confirmation with the father profile which has the same allele. ...

2013-10-17T23:59:59.000Z

15

Task 1: Hydrate Code release, Maintenance and Support  

NLE Websites -- All DOE Office Websites (Extended Search)

abundance by direct microscopy and abundance of bacteria and archaea by quantitative PCR. Ultimately, the metagenomic and 16S rRNA gene data will be combined with other...

16

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  

Science Conference Proceedings (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

17

Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing  

E-Print Network (OSTI)

The UPF0054 protein family is highly conserved with homologues present in nearly every sequenced bacterium. In some bacteria, the respective gene is essential, while in others its loss results in a highly pleiotropic ...

Davies, Bryan W.

18

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

Science Conference Proceedings (OSTI)

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

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

2012-01-01T23:59:59.000Z

19

The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing  

Science Conference Proceedings (OSTI)

The essential RNA helicase, Mtr4, performs a critical role in RNA processing and degradation as an activator of the nuclear exosome. The molecular basis for this vital function is not understood and detailed analysis is significantly limited by the lack of structural data. In this study, we present the crystal structure of Mtr4. The structure reveals a new arch-like domain that is specific to Mtr4 and Ski2 (the cytosolic homologue of Mtr4). In vivo and in vitro analyses demonstrate that the Mtr4 arch domain is required for proper 5.8S rRNA processing, and suggest that the arch functions independently of canonical helicase activity. In addition, extensive conservation along the face of the putative RNA exit site highlights a potential interface with the exosome. These studies provide a molecular framework for understanding fundamental aspects of helicase function in exosome activation, and more broadly define the molecular architecture of Ski2-like helicases.

Jackson, R.N.; Robinson, H.; Klauer, A. A.; Hintze, B. J.; van Hoof, A.; Johnson, S. J.

2010-07-01T23:59:59.000Z

20

Advances in diapriid (Hymenoptera: diapriidae) systematics, with contributions to cybertaxonomy and the analysis of rRNA sequence data  

E-Print Network (OSTI)

Diapriids (Hymenoptera: Diapriidae) are small parasitic wasps. Though found throughout the world they are relatively unknown. A framework for advancing diapriid systematics is developed by introducing a new web-based application/database capable of storing a broad range of systematic data, and the first molecular phylogeny specifically focused at examining intrafamilial relationships. In addition to these efforts, a description of a new taxon is provided. Several advantages of digital description, including linking descriptions to an ontology of morphological terms, are highlighted. The functionality of the database is further illustrated in the production of a catalog of diapriid host associations. The hosts database currently holds over 450 association records, for over 500 named taxa (parasitoids and hosts), and over 180 references. Diapriids are found to be primarily endoparasitoids of Diptera emerging from the host pupa. Phylogenetic inference for a molecular dataset of 28S and 18S rRNA sequence data, derived from a diverse selection of diapriids, is accomplished with a new suite of tools developed for handling complex rRNA datasets. Several parsimony-based methodologies, including an alignment-free method of analyzing multiple sequences, are reviewed and applied using the new software tools. Diapriid phylogenetic relationships are shown to be broadly congruent with existing morphology-based classifications. Methods for analyzing typically excluded sequence data are shown to recover phylogenetic signal that would otherwise be lost and the alignment-free method performed remarkably well in this regard. Empirically, phylogenetic approaches that incorporate structural data were not notably different than those that did not.

Yoder, Matthew Jon

2007-05-01T23:59:59.000Z

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.


21

Aging gene  

NLE Websites -- All DOE Office Websites (Extended Search)

Aging gene Name: Linda S Martinez Location: NA Country: NA Date: NA Question: Have the aging gene or genes been located on the human chromosomes, and, if yes, will removing that...

22

A possible mechanism for the inhibition of ribosomal RNA gene transcription during mitosis  

E-Print Network (OSTI)

Abstract. When cells enter mitosis, RNA synthesis ceases. Yet the RNA polymerase I (pol I) transcription machinery involved in the production of pre-rRNA remains bound to the nucleolus organizing region (NOR), the chromosome site harboring the tandemly repeated rRNA genes. Here we examine whether rDNA transcription units are transiently blocked or "frozen " during mitosis. By using fluorescent in situ hybridization we were unable to detect nascent prerRNA chains on the NORs of mouse 3T3 and rat kangaroo PtK2 cells. Appropriate controls showed that our approach was sensitive enough to visualize, at the light microscopic level, individual transcriptionally active rRNA genes both in situ after experimental unfolding of nucleoli and in chromatin spreads ("Miller

Dieter Weisenberger; Ulrich Scheer

1995-01-01T23:59:59.000Z

23

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

24

Why Sequence a Group 4 Verrucomicrobium?  

NLE Websites -- All DOE Office Websites (Extended Search)

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

25

Gene Frequency  

NLE Websites -- All DOE Office Websites (Extended Search)

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

26

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

Science Conference Proceedings (OSTI)

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

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

2012-01-01T23:59:59.000Z

27

Proto-genes and de novo gene birth  

E-Print Network (OSTI)

Novel protein-coding genes can arise either through re-organization of pre-existing genes or de novo. Processes involving re-organization of pre-existing genes, notably after gene duplication, have been extensively described. ...

Carvunis, Anne-Ruxandra

28

Human and Gorilla Genes  

NLE Websites -- All DOE Office Websites (Extended Search)

Human and Gorilla Genes Name: Eileen B Status: NA Age: NA Location: NA Country: NA Date: NA Question: What are the differences between the genetic mechanisms which affect...

29

Ward-Rainey N. Proposal for a new hierarchic classification system, Actinobacteria classis nov  

E-Print Network (OSTI)

A new hierarchic classification structure for the taxa between the taxonomic levels of genus and class is proposed for the actinomycete line of descent as defined by analysis of small subunit (16s) rRNA and genes coding for this molecule (rDNA). While the traditional circumscription of a genus of the actinomycete subphylum is by and large in accord with the 16s rRNA/rDNA-based phylogenetic clustering of these organisms, most of the higher taxa proposed in the past do not take into account the phylogenetic clustering of genera. The rich chemical, morphological and physiological diversity of phylogenetically closely related genera makes the description of families and higher taxa so broad that they become meaningless for the description of the enclosed taxa. Here we present a classification system in which phylogenetically neighboring taxa at the genus level are clustered into families, suborders, orders, subclasses, and a class irrespective of those phenotypic characteristics on which the delineation of taxa has been based in the past. Rather than being based on a listing of a wide array of chemotaxonomic, morphological, and physiological properties, the delineation is based solely on 16s rDNA/rRNA sequence-based phylogenetic clustering and the presence of taxon-specific 16s rDNA/RNA signature nucleotides. In their publication On the nature of global classification, Wheelis et al. (177) based the definition of higher taxa on the

Erko Stackebrandt; Fred A. Rainey; Naomi; L. Ward-rainey

1997-01-01T23:59:59.000Z

30

Why Sequence Microbial Communities from a Uranium-Contaminated...  

NLE Websites -- All DOE Office Websites (Extended Search)

of contaminatd subsurface sediments. area 300 photo from the air The 300 Area of the Hanford Site near Richland, Washington. For this project, JGI will sequence 16S rRNA from...

31

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

32

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

SciTech Connect

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 (??Methane in the Arctic Shelf? 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 (??metagenomes?). 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

33

Biological Treatment of Ammonia-Rich Wastewaters by Natural Microbial Communities in the ATOXIC/ASSET Purification System  

Science Conference Proceedings (OSTI)

Analyses of bacterial and archaeal 16S rRNA genes along with high throughput 454 pyrosequencing technology were used to identify microbial communities present at a novel passive wastewater treatment system designed to remove ammonium, nitrate, and heavy metals from fossil plant effluents. Seasonal changes in microbial community composition were observed, however significant (p=0.001) changes were detected in bacterial and archaeal communities consistent with ammonium removal throughout the treatment systems. Phylogenetic analysis of 16S rRNA gene sequences revealed presence of potential ammonium-oxidizing bacteria (AOB), Nitrosomonas, Nitrosococcus, Planctomycetes, and OD1. Other bacteria, such as Nitrospira, Nitrococcus, Nitrobacter, Thiobacillus, -Proteobacteria, Firmicutes, Acidobacteria, which play roles in nitrification and denitrification, were also detected. The relative abundance of the potential ammonium-oxidizing archaea (AOA) (Thermoprotei within the phylum Crenarchaeota) increased with ammonium availability at the splitter box and zero-valent iron extraction trenches even though AOB removed half of the ammonium in the trickling filters at the beginning of the treatment system. The microbial community removed the ammonium from the wastewater within both pilot-scale treatment systems, thus the treatment system components provided an effective environment for the treatment of ammonium enriched wastewater from coal burning power plants equipped with selective catalytic reducers for nitrogen oxide removal.

Vishnivetskaya, Tatiana A [ORNL; Fisher, L. Suzanne [Tennessee Valley Authority (TVA); Brodie, Greg A [Tennessee Valley Authority (TVA); Phelps, Tommy Joe [ORNL

2013-01-01T23:59:59.000Z

34

Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean  

SciTech Connect

A novel marine bacterial strain, PV-4T, isolated from a microbial mat located at a hydrothermal vent of Loihi Seamount in the Pacific Ocean, has been characterized. This micro-organism is orange in color, Gram-negative, polarly flagellated, facultatively anaerobic and psychrotolerant (temperature range, 0-42 C). No growth was observed with nitrate, nitrite, DMSO or thiosulfate as the electron acceptor and lactate as the electron donor. The major fatty acid detected in strain PV-4T was iso-C15 : 0. Strain PV-4T had ubiquinones consisting mainly of Q-7 and Q-8, and possessed menaquinone MK-7. The DNA G+C content of the strain was 53.8 mol% and the genome size was about 4.5 Mbp. Phylogenetic analyses based on 16S rRNA gene sequences placed PV-4T within the genus Shewanella. PV-4T exhibited 16S rRNA gene sequence similarity levels of 99.6 and 97.5 %, respectively, with respect to the type strains of Shewanella aquimarina and Shewanella marisflavi. DNA from strain PV-4T showed low mean levels of relatedness to the DNAs of S. aquimarina (50.5%) and S. marisflavi (8.5%). On the basis of phylogenetic and phenotypic characteristics, the bacterium was classified in the genus Shewanella within a distinct novel species, for which the name Shewanella loihica sp. nov. is proposed. The type strain is PV-4T (=ATCC BAA-1088T=DSM 17748T).

Gao, Haichun; Obraztova, Anna; Stewart, Nathan; Popa, Radu; Fredrickson, Jim K.; Tiedje, James M.; Nealson, Kenneth; Zhou, Jizhong

2006-08-28T23:59:59.000Z

35

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

DOE Green Energy (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

36

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

E-Print Network (OSTI)

Environmental microbiology has traditionally been performed using culture-based methods. However, in the last few decades, the emergence of molecular methods has changed the field considerably. The latest development in this area has been the introduction of next-generation sequencing, including pyrosequencing. These technologies allow the massively parallel sequencing of millions of DNA strands and represent a major development in sequencing technologies. The purpose of this study was to use both 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 Texas. Milk samples were analyzed by plating, pyrosequencing, and an assay for the presence of cell-cell signaling molecules. Samples were processed, stored, and then evaluated again for spoilage microflora. The results of this study showed that raw milk had a considerably higher bacterial load, more diversity between samples, and a significantly higher concentration of pathogens than pasteurized milk. Additionally, this study provided evidence for varying spoilage microflora between raw and pasteurized milk, as well as evidence for the production of cell-cell signaling molecules by bacterial organisms involved in milk spoilage. Four samplings of untreated sewage sludge were collected from wastewater treatment plants in seven different municipalities across the United States. Samples were subjected to quantification of selected bacterial organisms by culture and a pyrosequencing analysis was performed on extracted community DNA. The results of this study showed that untreated sewage sludge is inhabited by a huge diversity of microorganisms and that certain municipalities may have distinct bacterial populations that are conserved over time. Additionally, this study provided some evidence for seasonal differences in several of the major bacterial phyla. Lastly, this study emphasized the challenges of comparing results obtained by culture and pyrosequencing. In conclusion, this study showed that both milk and sewage are highly diverse, dynamic environments that can contain organisms of public health concern. The use of both culture-based methods and pyrosequencing in this study proved a complementary approach, providing a more comprehensive picture of both microbial environments.

McElhany, Katherine

2010-12-01T23:59:59.000Z

37

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

E-Print Network (OSTI)

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

Gevers, Dirk

38

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

Science Conference Proceedings (OSTI)

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

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

2011-01-01T23:59:59.000Z

39

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

SciTech Connect

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

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

2010-05-17T23:59:59.000Z

40

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

DOE Green Energy (OSTI)

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

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

2012-01-01T23:59:59.000Z

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

Changes in Bacterial And Archaeal Community Structure And Functional Diversity Along a Geochemically Variable Soil Profile  

SciTech Connect

Spatial heterogeneity in physical, chemical, and biological properties of soils allows for the proliferation of diverse microbial communities. Factors influencing the structuring of microbial communities, including availability of nutrients and water, pH, and soil texture, can vary considerably with soil depth and within soil aggregates. Here we investigated changes in the microbial and functional communities within soil aggregates obtained along a soil profile spanning the surface, vadose zone, and saturated soil environments. The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes (amoA and dsrAB) as well as cultivation-based analysis of Fe(III)-reducing organisms. Here we found that the microbial communities and putative ammonia-oxidizing and Fe(III)-reducing communities varied greatly along the soil profile, likely reflecting differences in carbon availability, water content, and pH. In particular, the Crenarchaeota 16S rRNA sequences are largely unique to each horizon, sharing a distribution and diversity similar to those of the putative (amoA-based) ammonia-oxidizing archaeal community. Anaerobic microenvironments within soil aggregates also appear to allow for both anaerobic- and aerobic-based metabolisms, further highlighting the complexity and spatial heterogeneity impacting microbial community structure and metabolic potential within soils.

Hansel, C.M.; Fendorf, S.; Jardine, P.M.; Francis, C.A.

2009-05-18T23:59:59.000Z

42

Evolution of Genes and Gene Networks in Filamentous Fungi  

E-Print Network (OSTI)

The Pezizomycotina, commonly known as the filamentous fungi, are a diverse group of organisms that have a major impact on human life. The filamentous fungi diverged from a common ancestor approximately 200 700 million years ago. Because of the diversity and the wealth of biological and genomic tools for the filamentous fungi it is possible to track the evolutionary history of genes and gene networks in these organisms. In this dissertation I focus on the evolution of two genes (lolC and lolD) in the LOL secondary metabolite gene cluster in Epichlo and Neotyphodium genera, the evolution of the MAP kinase-signaling cascade in the filamentous fungi, the regulation of the gene networks involved in asexual development in Neurospora crassa, and the identification of two genes in the N. crassa asexual development gene network, acon-2 and acon-3. I find that lolC and lolD originated as an ancient duplication in the ancestor of the filamentous fungi, which were later recruited in the LOL gene cluster in the fungal endophyte lineage. In the MAP kinase-signaling cascade, I find that the MAPK component is the most central gene in the gene network. I also find that the MAPK signaling cascade originated as three copies in the ancestor to eukaryotes, an arrangement that is maintained in filamentous fungi. My observations of gene expression profiling during N. crassa asexual development show tissue specific expression of genes. Both the vegetative mycelium and the aerial hyphae contribute to the formation of macroconidiophores. Also, with the help of genomic tools recently developed by researchers in the filamentous fungal community, I identified NCU00478 and NCU07617 as the genes with mutations responsible for two aconidial strains of N. crassa, acon-2 and acon-3 respectively.

Greenwald, Charles Joaquin

2010-08-01T23:59:59.000Z

43

Traits and Multiple Genes  

NLE Websites -- All DOE Office Websites (Extended Search)

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

44

GeneDistillerDistilling Candidate Genes from Linkage Intervals  

E-Print Network (OSTI)

Background: Linkage studies often yield intervals containing several hundred positional candidate genes. Different manual or automatic approaches exist for the determination of the gene most likely to cause the disease. While the manual search is very flexible and takes advantage of the researchers background knowledge and intuition, it may be very cumbersome to collect and study the relevant data. Automatic solutions on the other hand usually focus on certain models, remain black boxes and do not offer the same degree of flexibility. Methodology: We have developed a web-based application that combines the advantages of both approaches. Information from various data sources such as gene-phenotype associations, gene expression patterns and protein-protein interactions was integrated into a central database. Researchers can select which information for the genes within a candidate interval or for single genes shall be displayed. Genes can also interactively be filtered, sorted and prioritised according to criteria derived from the background knowledge and preconception of the disease under scrutiny. Conclusions: GeneDistiller provides knowledge-driven, fully interactive and intuitive access to multiple data sources. It displays maximum relevant information, while saving the user from drowning in the flood of data. A typical query takes less than two seconds, thus allowing an interactive and explorative approach to the hunt for the candidate gene.

Dominik Seelow; Jana Marie Schwarz; Markus Schuelke

2008-01-01T23:59:59.000Z

45

Recessive and Dominant Gene Action  

NLE Websites -- All DOE Office Websites (Extended Search)

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

46

The Honorable Gene Dean  

Office of Legacy Management (LM)

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

47

GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes  

Science Conference Proceedings (OSTI)

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

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

2010-04-01T23:59:59.000Z

48

What is the morphology of a gene?  

NLE Websites -- All DOE Office Websites (Extended Search)

of as structural, operator, and regulatory genes." - Dorland's Illustrated Medical Dictionary, 27th ed. So, in terms of morphology, a gene is a specific sequence of nucleotide in...

49

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

SciTech Connect

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

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

2008-09-30T23:59:59.000Z

50

Prodigal: Microbial Gene Prediction Software  

NLE Websites -- All DOE Office Websites (Extended Search)

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

51

Gene order computation using Alzheimer's DNA microarray gene expression data and the ant colony optimisation algorithm  

Science Conference Proceedings (OSTI)

As Alzheimer's Disease (AD) is the most common form of dementia, the study of AD-related genes via biocomputation is an important research topic. One method of studying AD-related gene is to cluster similar genes together into a gene order. Gene ...

Chaoyang Pang; Gang Jiang; Shipeng Wang; Benqiong Hu; Qingzhong Liu; Youping Deng; Xudong Huang

2012-11-01T23:59:59.000Z

52

Metazoan Gene Families from Metazome  

DOE Data Explorer (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

53

FAMeS: Fidelity of Analysis of Metagenomic Samples  

DOE Data Explorer (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.

54

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

55

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

Science Conference Proceedings (OSTI)

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

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

2006-07-21T23:59:59.000Z

56

THE JOURNAL OF GENE MEDICINE RESEARCH ARTICLE J Gene Med 2008; 10: 583592.  

E-Print Network (OSTI)

-transduction with the two types of viral vectors provided doxycycline- regulated transgene expression in a neuron gene transfer; tetracycline-regulated gene expression; CNS; lentiviral vectors; doxycycline; cell

Bristol, University of

57

Gene expression by software mechanisms  

Science Conference Proceedings (OSTI)

This paper describes the molecular interactions and coordination of cell processes using computer operating system concepts related to synchronization and communication. We argue that in molecular biology, the genes and their chromatin context provide ... Keywords: cell biology, modules, operating systems, pipe, process communication, signals

Gabriel Ciobanu; Bogdan Tanasa

2002-01-01T23:59:59.000Z

58

Culture-independent analysis of bacterial fuel contamination provides insight into the level of concordance with the standard industry practice of aerobis cultivation.  

SciTech Connect

Bacterial diversity in contaminated fuels has not been systematically investigated using cultivation-independent methods. The fuel industry relies on phenotypic cultivation-based contaminant identification, which may lack accuracy and neglect difficult-to-culture taxa. By the use of industry practice aerobic cultivation, 16S rRNA gene sequencing, and strain genotyping, a collection of 152 unique contaminant isolates from 54 fuel samples was assembled, and a dominance of Pseudomonas (21%), Burkholderia (7%), and Bacillus (7%) was demonstrated. Denaturing gradient gel electrophoresis (DGGE) of 15 samples revealed Proteobacteria and Firmicutes to be the most abundant phyla. When 16S rRNA V6 gene pyrosequencing of four selected fuel samples (indicated by 'JW') was performed, Betaproteobacteria (42.8%) and Gammaproteobacteria (30.6%) formed the largest proportion of reads; the most abundant genera were Marinobacter (15.4%; JW57), Achromobacter (41.6%; JW63), Burkholderia (80.7%; JW76), and Halomonas (66.2%; JW78), all of which were also observed by DGGE. However, the Clostridia (38.5%) and Deltaproteobacteria (11.1%) identified by pyrosequencing in sample JW57 were not observed by DGGE or aerobic culture. Genotyping revealed three instances where identical strains were found: (i) a Pseudomonas sp. strain recovered from 2 different diesel fuel tanks at a single industrial site; (ii) a Mangroveibacter sp. strain isolated from 3 biodiesel tanks at a single refinery site; and (iii) a Burkholderia vietnamiensis strain present in two unrelated automotive diesel samples. Overall, aerobic cultivation of fuel contaminants recovered isolates broadly representative of the phyla and classes present but lacked accuracy by overrepresenting members of certain groups such as Pseudomonas.

White, J.; Gilbert, J. A.; Hill, G.; Hill, E.; Huse, S. M.; Weightman, A. J.; Mahenthiralingam, E. (CLS-CI); (Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University); (ECHA Microbiology Ltd.); (Josephine Bay Paul Centre for Comparative Molecular Biology and Evolution)

2011-07-01T23:59:59.000Z

59

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

60

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

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

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

62

Diversity of bat-associated Leptospira in the Peruvian Amazon inferred by Bayesian phylogenetic analysis of 16S ribosomal DNA sequences  

E-Print Network (OSTI)

Rylands AB, Mittermeier RA, Pilgrim J, Gascon C, Fonseca G,CG, Robles Gil P, Pilgrim J, da Foseca GAB, Brooks T,

2005-01-01T23:59:59.000Z

63

Posters / Parkinsonism and Related Disorders 16S1 (2010) S11S86 S29 study. Apathy was measured using the clinically validated MAI and  

E-Print Network (OSTI)

networked sensing, signal processing and state detection algorithms with its supporting infrastructure to be utilized by researchers, physicians, clinicians and therapists to assess various aspects of human gait participants (age >70) in a community based aging study. Eight variables; velocity, cadence, stride length

He, Lei

64

QB1 - Stochastic Gene Regulation  

Science Conference Proceedings (OSTI)

Summaries of this presentation are: (1) Stochastic fluctuations or 'noise' is present in the cell - Random motion and competition between reactants, Low copy, quantization of reactants, Upstream processes; (2) Fluctuations may be very important - Cell-to-cell variability, Cell fate decisions (switches), Signal amplification or damping, stochastic resonances; and (3) Some tools are available to mode these - Kinetic Monte Carlo simulations (SSA and variants), Moment approximation methods, Finite State Projection. We will see how modeling these reactions can tell us more about the underlying processes of gene regulation.

Munsky, Brian [Los Alamos National Laboratory

2012-07-23T23:59:59.000Z

65

Human gene sequencing makes advances  

SciTech Connect

The Human Genome Project is a federal project that is on the scale of the Manhattan Project of the 1940s. The focus of this project is to map and sequence the 100,000 plus genes and 3 billion base pairs that comprise the human genome. This effort has made two recent advances. First, two of the major companies involved in this project formed a strategic alliance that will pump up to 125 million dollars into this project. Second, researchers at Argonne National Lab. have tested a new sequencing technique that could identify 100 million base pairs a day when fully implemented.

Alper, J.

1993-09-01T23:59:59.000Z

66

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

Science Conference Proceedings (OSTI)

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

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

2012-01-01T23:59:59.000Z

67

Ecological Interactions Between Metals and Microbes That Impact Bioremediation  

DOE Green Energy (OSTI)

Bacterial Community Diversity at a Mixed Waste Contaminated Site The correlation between bacterial population structure and lead, chromium and organic compounds present along a 21.6 m transect was examined. There was a gradient of heavy metal (Cr and Pb) and petroleum hydrocarbon contamination in these soils. A 16S rDNA analysis method and fatty acid methyl esters derived from phospholipids (PLFA) analysis were used to compare microbial communities. Soil microbial DNA was extracted and community fingerprint patterns for each sample location were produced by DGGE separation of the V3 region of the 16S rRNA genes amplified by PCR. Visual analysis of DGGE patterns indicated that sample locations with high concentrations of total toluene (12,000 mg kg-1), xylenes (8,000 mg kg-1), methylene chloride (10,000 mg kg-1), lead (17,000 mg kg-1) and chromium (3,200 mg kg-1) have a different community composition from the community with lower metals (200 mg kg-1) and organics (1200 mg kg-1) content. Microbial biomass, indicated by total phospholipid-P, was greatest in soils with highest organic contamination.

Konopka, Allan E.

2001-06-01T23:59:59.000Z

68

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

69

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

2008-06-01T23:59:59.000Z

70

Nano-vesicles for gene delivery.  

E-Print Network (OSTI)

??Gene therapy was considered an important modality for the potential treatment of cancer. It aimed to correct diseases through the delivery of genetic material encoding (more)

Tan, Karen Li Ping.

2008-01-01T23:59:59.000Z

71

Bayesian survival analysis using gene expression.  

E-Print Network (OSTI)

??This thesis developed and applied Bayesian models for the analysis of survival data. The gene expression was considered as explanatory variables within the Bayesian survival (more)

Thamrin, Sri Astuti

2013-01-01T23:59:59.000Z

72

Gene therapy in alcoholic rats  

NLE Websites -- All DOE Office Websites (Extended Search)

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

73

Microarray gene expression classification with few genes: Criteria to combine attribute selection and classification methods  

Science Conference Proceedings (OSTI)

Microarray data classification is a task involving high dimensionality and small samples sizes. A common criterion to decide on the number of selected genes is maximizing the accuracy, which risks overfitting and usually selects more genes than actually ... Keywords: Efficient classification with few genes, Feature selection, Machine learning, Microarray data classification

Carlos J. Alonso-Gonzlez; Q. Isaac Moro-Sancho; Arancha Simon-Hurtado; Ricardo Varela-Arrabal

2012-06-01T23:59:59.000Z

74

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

Science Conference Proceedings (OSTI)

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

Oosterkamp, Margreet J. [Wageningen University and Research Centre, The Netherlands; Veuskens, Teun [Wageningen University and Research Centre, The Netherlands; Saia, Flavia Talarico [Wageningen University and Research Centre, The Netherlands; Weelink, Sander A.B. [Wageningen University and Research Centre, The Netherlands; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Daligault, Hajnalka E. [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Langenhoff, A. M. [Deltares, The Netherlands; Gerritse, Jan [Deltares, The Netherlands; Van Berkel, Willem J. H. [Wageningen University and Research Centre, The Netherlands; Pieper, Dietmar [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Junca, Howard [CorpoGen, Bogota Colombia; Smidt, Hauke [Wageningen University and Research Centre, The Netherlands; Schraa, Gosse [Wageningen University and Research Centre, The Netherlands; Davids, Mark [Wageningen University and Research Centre, The Netherlands; Schaap, Peter J [Wageningen University and Research Centre, The Netherlands; Plugge, Caroline M. [Wageningen University and Research Centre, The Netherlands; Stams, Alfons J. M. [Wageningen University and Research Centre, The Netherlands

2013-01-01T23:59:59.000Z

75

Graph theoretic approach to parallel gene assembly  

Science Conference Proceedings (OSTI)

We study parallel complexity of signed graphs motivated by the highly complex genetic recombination processes in ciliates. The molecular gene assembly operations have been modeled by operations of signed graphs, i.e., graphs where the vertices have a ... Keywords: Double-split graphs, Gene assembly, Local complement, Parallel assembly, Perfect matching, Signed graphs, Split graphs

Tero Harju; Chang Li; Ion Petre

2008-11-01T23:59:59.000Z

76

Scalable Time Warp on Blue Gene Supercomputers  

Science Conference Proceedings (OSTI)

n this paper we illustrate scalable parallel performance for the TimeWarp synchronization protocol on the L and P variants of the IBM BlueGene supercomputer. Scalable Time Warp performance for models that communicate a large percentage of the event population ... Keywords: Time Warp, Blue Gene Supercomputer

David W. Bauer Jr.; Christopher D. Carothers; Akintayo Holder

2009-06-01T23:59:59.000Z

77

Noise minimization in eukaryotic gene expression  

Science Conference Proceedings (OSTI)

All organisms have elaborate mechanisms to control rates of protein production. However, protein production is also subject to stochastic fluctuations, or noise. Several recent studies in Saccharomyces cerevisiae and Escherichia coli have investigated the relationship between transcription and translation rates and stochastic fluctuations in protein levels, or more generally, how such randomness is a function of intrinsic and extrinsic factors. However, the fundamental question of whether stochasticity in protein expression is generally biologically relevant has not been addressed, and it remains unknown whether random noise in the protein production rate of most genes significantly affects the fitness of any organism. We propose that organisms should be particularly sensitive to variation in the protein levels of two classes of genes: genes whose deletion is lethal to the organism and genes that encode subunits of multiprotein complexes. Using an experimentally verified model of stochastic gene expression in S. cerevisiae, we estimate the noise in protein production for nearly every yeast gene, and confirm our prediction that the production of essential and complex-forming proteins involves lower levels of noise than does the production of most other genes. Our results support the hypothesis that noise in gene expression is a biologically important variable, is generally detrimental to organismal fitness, and is subject to natural selection.

Fraser, Hunter B.; Hirsh, Aaron E.; Giaever, Guri; Kumm, Jochen; Eisen, Michael B.

2004-01-15T23:59:59.000Z

78

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

79

Induction and selection of the most interesting Gene Ontology based multiattribute rules for descriptions of gene groups  

Science Conference Proceedings (OSTI)

A rules induction algorithm dedicated to describe groups of genes with similar expression profiles by means of Gene Ontology terms is discussed in the paper. The presented algorithm takes into consideration information contained in the Gene Ontology ... Keywords: Decision rules, Gene Ontology, Gene groups descriptions, Rough sets, Rule interestingness measures

Marek Sikora; Aleksandra Gruca

2011-01-01T23:59:59.000Z

80

Article original Inventaire molculaire d'un cosystme  

E-Print Network (OSTI)

, France Abstract - Molecular inventory of an anaerobic digestion microbial ecosystem. The bacterial/Elsevier, Paris anaerobic digestion / biodiversity / microbial ecology / phylogeny / 16S rRNA Résumé - LArticle original Inventaire moléculaire d'un écosystème microbien de digestion anaérobie Jean

Recanati, Catherine

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

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

Science Conference Proceedings (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

2012-06-01T23:59:59.000Z

82

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.

83

Science at LLNL with IBM Blue Gene/Q  

Science Conference Proceedings (OSTI)

Lawrence Livermore National Laboratory (LLNL) has a long history of working with IBM on Blue Gene supercomputers. Beginning in November 2001 with the joint announcement of a partnership to expand the Blue Gene research project (including Blue Gene/L ...

B. Carnes, B. Chan, E. W. Draeger, J.-L. Fattebert, L. Fried, J. Glosli, W. D. Krauss, S. H. Langer, R. McCallen, A. A. Mirin, F. Najjar, A. L. Nichols, T. Oppelstrup, J. A. Rathkopf, D. Richards, F. Streitz, P. M. Vranas, J. J. Rice, J. A. Gunnels, V. Gurev, C. Kim, J. Magerlein, M. Reumann, H.-F. Wen

2013-01-01T23:59:59.000Z

84

Identification of candidate genes in Arabidopsis and Populus...  

NLE Websites -- All DOE Office Websites (Extended Search)

in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database, and additional genes were identified as...

85

Radiation-induced gene responses  

SciTech Connect

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

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

1996-12-31T23:59:59.000Z

86

Visualizing Gene Expression In Situ  

Science Conference Proceedings (OSTI)

Visualizing bacterial cells and describing their responses to the environment are difficult tasks. Their small size is the chief reason for the difficulty, which means that we must often use many millions of cells in a sample in order to determine what the average response of the bacteria is. However, an average response can sometimes mask important events in bacterial physiology, which means that our understanding of these organisms will suffer. We have used a variety of instruments to visualize bacterial cells, all of which tell us something different about the sample. We use a fluorescence activated cell sorter to sort cells based on the fluorescence provided by bioreporter genes, and these can be used to select for particular genetic mutations. Cells can be visualized by epifluorescent microscopy, and sensitive photodetectors can be added that allow us to find a single bacterial cell that is fluorescent or bioluminescent. We have also used standard photomultipliers to examine cell aggregates as field bioreporter microorganisms. Examples of each of these instruments show how our understanding of bacterial physiology has changed with the technology.

Burlage, R.S.

1998-11-02T23:59:59.000Z

87

Algorithms for Gene Clustering Analysis on Genomes  

E-Print Network (OSTI)

The increased availability of data in biological databases provides many opportunities for understanding biological processes through these data. As recent attention has shifted from sequence analysis to higher-level analysis of genes across multiple genomes, there is a need to develop efficient algorithms for these large-scale applications that can help us understand the functions of genes. The overall objective of my research was to develop improved methods which can automatically assign groups of functionally related genes in large-scale data sets by applying new gene clustering algorithms. Proposed gene clustering algorithms that can help us understand gene function and genome evolution include new algorithms for protein family classification, a window-based strategy for gene clustering on chromosomes, and an exhaustive strategy that allows all clusters of small size to be enumerated. I investigate the problems of gene clustering in multiple genomes, and define gene clustering problems using mathematical methodology and solve the problems by developing efficient and effective algorithms. For protein family classification, I developed two supervised classification algorithms that can assign proteins to existing protein families in public databases and, by taking into account similarities between the unclassified proteins, allows for progressive construction of new families from proteins that cannot be assigned. This approach is useful for rapid assignment of protein sequences from genome sequencing projects to protein families. A comparative analysis of the method to other previously developed methods shows that the algorithm has a higher accuracy rate and lower mis-classification rate when compared to algorithms that are based on the use of multiple sequence alignments and hidden Markov models. The proposed algorithm performs well even on families with very few proteins and on families with low sequence similarity. Apart from the analysis of individual sequences, identifying genomic regions that descended from a common ancestor helps us study gene function and genome evolution. In distantly related genomes, clusters of homologous gene pairs serve as evidence used in function prediction, operon detection, etc. Thus, reliable identification of gene clusters is critical to functional annotation and analysis of genes. I developed an efficient gene clustering algorithm that can be applied on hundreds of genomes at the same time. This approach allows for large-scale study of evolutionary relationships of gene clusters and study of operon formation and destruction. By placing a stricter limit on the maximum cluster size, I developed another algorithm that uses a different formulation based on constraining the overall size of a cluster and statistical estimates that allow direct comparisons of clusters of different size. A comparative analysis of proposed algorithms shows that more biological insight can be obtained by analyzing gene clusters across hundreds of genomes, which can help us understand operon occurrences, gene orientations and gene rearrangements.

Yi, Gang Man

2011-05-01T23:59:59.000Z

88

Characterization of the mouse thrombospondin 2 gene  

Science Conference Proceedings (OSTI)

The authors have characterized the exon/intron organization, complete 3[prime] untranslated region (3[prime]-UTR), and approximately 2.5 kb of the promoter/5[prime] flanking region of the mouse thrombospondin 2 (TSP2) gene. The sizes of exons and the pattern of interruption of the reading frame by introns are highly conserved in mouse TSP2 in comparison with mouse or human TSP1, a finding that suggests a close evolutionary relationship between the two genes. The TSP2 and TSP1 genes are also similar in that the 3[prime]-UTRs of both genes contain multiple TATT and ATTT(A) motifs that might function as mediators of mRNA stability. However, the sequences of the promoter regions in TSP1 and TSP2 are very different; in particular, the TSP2 gene lacks the serum response element and the NF-Y binding site that have been implicated in the serum response of the human TSP1 gene. The structure of the TSP2 gene is consistent with emerging evidence supporting the view that TSP1 and TSP2 perform overlapping but distinct functions. 41 refs., 4 figs., 1 tab.

Tetsuji Shingu; Bornstein, P. (Univ. of Washington, Seattle (United States))

1993-04-01T23:59:59.000Z

89

The specificity and evolution of gene regulatory elements  

E-Print Network (OSTI)

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

Friedman, Robin Carl

2010-01-01T23:59:59.000Z

90

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

91

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

SciTech Connect

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

92

Distribution of microbial biomass and the potential for anaerobic respiration in Hanford Site 300 Area subsurface sediment  

Science Conference Proceedings (OSTI)

Subsurface sediments were recovered from a 52 m deep borehole cored in the 300 Area of the Hanford Site in southeastern Washington State to assess the potential for biogeochemical transformation of radionuclide contaminants. Microbial analyses were made on 17 sediment samples traversing multiple geological units: the oxic coarse-grained Hanford formation (9-17.4 m), the oxic fine-grained upper Ringold Formation (17.7-18.1 m), and the reduced Ringold Formation (18.3-52m). Microbial biomass (measured as phospholipid) ranged from 7-974 pmols per g in discrete samples, with the highest numbers found in the Hanford formation. On average, strata below 17.4 m had 13-fold less biomass than those from shallower strata. The nosZ gene encoding nitrous oxide reductase had an abundance of 5-17% relative to total 16S rRNA genes below 18.3 m and Hanford-Ringold formation contact and the Ringold oxic-anoxic interface. Within this zone, copies of the dsrA gene and Geobacteraceae had the highest relative abundance. The majority of dsrA genes detected near the interface were related to Desulfotomaculum sp.. These analyses indicate that the region just below the contact between the Hanford and Ringold formations is a zone of active biogeochemical redox cycling.

Lin, Xueju; Kennedy, David W.; Peacock, Aaron D.; McKinley, James P.; Resch, Charles T.; Fredrickson, Jim K.; Konopka, Allan

2012-02-01T23:59:59.000Z

93

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

DOE Green Energy (OSTI)

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

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

2011-05-31T23:59:59.000Z

94

The Role of Chromatin Structure and Histone Modifications in Gene Silencing at the Ribosomal DNA Locus in Saccharomyces cerevisiae  

E-Print Network (OSTI)

One of the fundamental questions in science is how chromatin transitions from actively transcribed euchromatin to silent heterochromatin, and what factors affect this transition. One area of my research has focused on understanding the differences in the chromatin structure of active and silent regions in the ribosomal DNA locus (rDNA), a heterochromatin region in S. cerevisiae. Secondly, I have focused on understanding a histone methyltransferase Set1, which is involved in both euchromatin and heterochromatin regions. To distinguish actively transcribed open regions of chromatin from silent and closed regions of chromatin, we have expressed a DNA methyltransferase M.CviPI in vivo to utilize its accessibility to GpC sites. We have used this technique to study changes in nucleosome positioning within the NTS2 region of the rDNA in two cases: as a result of a silencing defect caused by the loss of Sir2, a histone deacetylase involved in silencing at the rDNA, and as an indicator of active transcription by RNA Pol I. Using this technique, we observed differences between open and closed chromatin structure by changes in nucleosome positioning within NTS2. Additionally, we have observed the presence of bound factors within the 35S rRNA gene promoter that are unique to actively transcribed genes. The second area of my research focused on the protein methyltransferase Set1 that mono-, di-, and trimethylates lysine 4 of histone H3 (H3K4) utilizing the methyl group from S-adenosyl methionine (SAM). Set1 is part of a multi protein complex called COMPASS (Complex associated with Set1), and is associated with both actively transcribed and silent regions. Thirty mutants of Set1 were made within the SET domain to learn more about the catalytic mechanism of Set1. The crystal structures of human SET domain proteins, as well as sequence alignments and a random mutagenesis of yeast Set1, were used to identify conserved amino acids in the SET domain of Set1. Mutants were analyzed for their effect on histone methylation in vivo, silencing of RNA Pol II transcription within the rDNA, suppression of ipl1-2, and COMPASS complex formation. Our results show that trimethylated H3K4 is required for silencing of RNA Pol II transcription at the rDNA. Overall, we have shown the importance of tyrosine residues in SET domain proteins. To summarize, my research has strived to understand chromatin structure and the factors that affect the transition between euchromatin and heterochromatin.

Williamson, Kelly M.

2011-05-01T23:59:59.000Z

95

COMPARATIVE ASSESSMENT OF RADIATION-INDUCED GENE  

NLE Websites -- All DOE Office Websites (Extended Search)

with 0, 50 or 200 cGy gamma-rays and the cells harvested for RNA 48 hours post irradiation. The RNA was hybridized to RAE 230A Affymetrix microarrays and differences in gene...

96

Affymetrix White Paper: GeneChip  

E-Print Network (OSTI)

Affymetrix® White Paper: GeneChip® 3' IVT Express Kit May 14, 2009 P/N WH105 Page 1 of 9 White and optimized reagents that enable lower RNA input and increased ease of use. In this white paper, we describe, and the plastic consumables needed to run the assay. #12;Affymetrix® White Paper: GeneChip® 3' IVT Express Kit May

Wandless, Tom

97

Mutations of the GREAT gene cause cryptorchidism  

E-Print Network (OSTI)

DDBJ/EMBL/GenBank accession no. AF453828 In humans, failure of testicular descent (cryptorchidism) is one of the most frequent congenital malformations, affecting 13 % of newborn boys. The clinical consequences of this abnormality are infertility in adulthood and a significantly increased risk of testicular malignancy. Recently, we described a mouse transgene insertional mutation, crsp, causing high intraabdominal cryptorchidism in homozygous males. A candidate gene Great (G-protein-coupled receptor affecting testis descent), was identified within the transgene integration site. Great encodes a seven-transmembrane receptor with a close similarity to the glycoprotein hormone receptors. The Great gene is highly expressed in the gubernaculum, the ligament that controls testicular movement during development, and therefore may be responsible for mediating hormonal signals that affect testicular descent. Here we show that genetic targeting of the Great gene in mice causes infertile bilateral intraabdominal cryptorchidism. The mutant gubernaculae fail to differentiate, indicating that the Great gene controls their development. Mutation screening of the human GREAT gene was performed using DHPLC analysis of the genomic DNA from 60 cryptorchid patients. Nucleotide variations in GREAT cDNA were found in both the patient and the control populations. A unique missense mutation (T222P) in the ectodomain of the GREAT receptor was identified in one of the patients. This mutant receptor fails to respond to ligand stimulation, implicating the GREAT gene in the etiology in some cases of cryptorchidism in humans.

Ivan P. Gorlov; Aparna Kamat; Natalia V. Bogatcheva; Eric Jones; Dolores J. Lamb; Anne Truong; Colin E. Bishop; Ken Mcelreavey; Er I. Agoulnik

2002-01-01T23:59:59.000Z

98

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

DOE Green Energy (OSTI)

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

Kuchka, M.R.

1992-01-01T23:59:59.000Z

99

GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes  

E-Print Network (OSTI)

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

Pati, Amrita

2012-01-01T23:59:59.000Z

100

Gene for ataxia-telangiectasia complementation group D (ATDC)  

DOE Patents (OSTI)

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

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

1995-03-07T23:59:59.000Z

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


101

Gene for ataxia-telangiectasia complementation group D (ATDC)  

DOE Patents (OSTI)

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

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

1995-03-07T23:59:59.000Z

102

Development and validation of a citrate synthase directed quantitative PCR marker for soil bacterial communities  

SciTech Connect

Molecular innovations in microbial ecology are allowing scientists to correlate microbial community characteristics to a variety of ecosystem functions. However, to date the majority of soil microbial ecology studies target phylogenetic rRNA markers, while a smaller number target functional markers linked to soil processes. We validated a new primer set targeting citrate synthase (gtlA), a central enzyme in the citric acid cycle linked to aerobic respiration. Primers for a 225 bp fragment suitable for qPCR were tested for specificity and assay performance verified on multiple soils. Clone libraries of the PCR-amplified gtlA gene exhibited high diversity and recovered most major groups identified in a previous 16S rRNA gene study. Comparisons among bacterial communities based on gtlA sequencing using UniFrac revealed differences among the experimental soils studied. Conditions for gtlA qPCR were optimized and calibration curves were highly linear (R2 > 0.99) over six orders of magnitude (4.56 10^5 to 4.56 10^11 copies), with high amplification efficiencies (>1.7). We examined the performance of the gtlA qPCR across a variety of soils and ecosystems, spanning forests, old fields and agricultural areas. We were able to amplify gtlA genes in all tested soils, and detected differences in gtlA abundance within and among environments. These results indicate that a fully developed gtlA-targeted qPCR approach may have potential to link microbial community characteristics with changes in soil respiration.

Castro Gonzalez, Hector F [ORNL; Classen, Aimee T [University of Tennessee, Knoxville (UTK); Austin, Emily E [University of Tennessee, Knoxville (UTK); Crawford, Kerri M [Rice University; Schadt, Christopher Warren [ORNL

2012-01-01T23:59:59.000Z

103

Soft computing methods to predict gene regulatory networks: An integrative approach on time-series gene expression data  

Science Conference Proceedings (OSTI)

To unravel the controlling mechanisms of gene regulation, in this paper we present the application of sophisticated soft computing methods applied on an important problem from Bioinformatics-inferring gene regulatory networks (GRN) from time series gene ... Keywords: Automatic model building, Gene regulatory network, LARS, Reverse-engineering, Schizosaccharomyces pombe, Time series microarray data, Yeast

Zeke S. H. Chan; Ilkka Havukkala; Vishal Jain; Yingjie Hu; Nikola Kasabov

2008-06-01T23:59:59.000Z

104

A Rule-Based Framework for Gene Regulation Pathways Discovery  

SciTech Connect

We present novel approach to discover the rules that govern gene regulation mechanisms. The method is based on supervised machine learning and is designed to reveal relationships between transcription factors and gene promoters. As the representation of the gene regulatory circuit we have chosen a special form of IF-THEN rules associating certain features (a generalized idea of a Transcription Factor Binding Site) in gene promoters with specific gene expression profiles.

Wilczynski, B; Hvidsten, T; Kryshtafovych, A; Stubbs, L; Komorowski, J; Fidelis, K

2003-07-21T23:59:59.000Z

105

Pathogenicity island mobility and gene content.  

SciTech Connect

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

106

The mouse angiogenin gene family: Structures of an angiogenin-related protein gene and two pseudogenes  

SciTech Connect

Angiogenin, a homologue of pancreatic ribonuclease, is a potent inducer of blood vessel formation. As an initial step toward investigating the in vivo functional role of this protein via gene disruption, we undertook the isolation of the angiogenin gene (Ang) from the 129 strain mouse, which will be used for generating targeting constructs. Unexpectedly, screening of a genomic library with an Ang gene probe obtained previously from the BALB/c strain yielded two new genes closely similar to Ang rather than Ang itself. One of these encodes a protein with 78% sequence identity to angiogenin and is designated {open_quotes}Angrp{close_quotes} for {open_quotes}angiogenin-related protein.{close_quotes} The ribonucleolytic active site of angiogenin, which is critical for angiogenic activity, is completely conserved in Angrp, whereas a second essential site, thought to bind cellular receptors, is considerably different. Thus, the Angrp product may have a function distinct from that of angiogenin. The second gene obtained by library screening is a pseudogene, designated {open_quotes}Ang-ps1,{close_quotes} that contains a frame shift mutation in the early part of the coding region. Although the Ang gene was not isolated from this library, it was possible to amplify this gene from 129 mouse genomic DNA by the polymerase chain reaction (PCR). Sequence analysis showed that the 129 strain Ang gene is identical to the BALB/c gene throughout the coding region. PCR cloning also yielded a second Ang-like pseudogene, designated {open_quotes}Ang-ps2.{close_quotes} Southern blotting of genomic DNA confirmed the presence of Ang, Angrp, and at least one of the pseudogenes in an individual mouse and suggested that the mouse Ang gene family may contain more than the four members identified here. 31 refs., 4 figs., 1 tab.

Brown, W.E.; Nobile, V.; Shapiro, R. [Harvard Medical School, Boston, MA (United States)] [and others

1995-09-01T23:59:59.000Z

107

(for Gene Recognition Analysis Internet Link),  

NLE Websites -- All DOE Office Websites (Extended Search)

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

108

Regulation of methane genes and genome expression  

DOE Green Energy (OSTI)

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

John N. Reeve

2009-09-09T23:59:59.000Z

109

Gene Expression in the Stallion Testes  

E-Print Network (OSTI)

Understanding the genes that regulate spermatogenesis and steroidogenesis in the testis is critical for enhancement of stallion fertility. Stallion testicular samples were used to identify candidate genes by cDNA microarrays that simultaneously assessed expression levels of 9132 genes. First, gene expression was compared between light (spermatogenically active) and dark (spermatogenically inactive) testis tissue of 1.5-year-old horses (n = 3). Ninety-three genes were differentially expressed (35 light specific, 58 dark specific) in matched paired samples. Second, gene expression was compared between testicular tissue of two mature stallions, one with normal quality semen (fertile) and one with poor quality semen (subfertile). A total of 233 genes were differentially expressed (122 in fertile tissue, 111 in subfertile tissue). Of these, phosphodiesterase 3B (PDE3B), steroidogenic acute regulatory (StAR) protein, and outer dense fiber of sperm tails 2 (ODF2) mRNAs, were localized and quantified by in situ hybridization (ISH) in mature stallions and/or in unilateral cryptorchids. ISH revealed differences (P < 0.05) among mature stallions (n = 10) for PDE3B (localized to seminiferous tubules) and StAR protein (localized to interstitial spaces) mRNAs. A positive correlation coefficient (r = .556, p = .025) was found between StAR protein mRNA and plasma concentration of testosterone. Additionally, both gene products were evaluated in 1-year-old (n = 3) and 3-year-old (n = 3) unilateral cryptorchid stallions. Expression of both PDE3B and StAR protein gene was significantly higher in mature, descended testes compared to mature, retained testes and the descended and retained testes of immature, cryptorchid stallions. StAR protein gene demonstrated significantly higher expression in immature retained testes compared to immature descended testes. A precision-cut tissue slice (PCTS) in vitro culture system was evaluated as a potential tool to study equine testes function. Testes from immature stallions (n = 3) were cut into slices (mean slice weight = 13.85 +/- 0.20 mg; mean slice thickness = 515.00 +/- 2.33 ?m) and exposed to medium containing ovine luteinizing hormone (oLH) at concentrations of 0, 5, 50 and 500 ng/ml for 6 h at 32 degrees C. Medium content of testosterone and estradiol was increased 500% and 120%, respectively, by addition of oLH versus that observed for the testis tissue slices treated with 0 ng oLH (control). An oLH concentration-dependent increase in StAR protein mRNA in tissue slices was detected by in situ hybridization; whereas, differences for PDE3B and ODF2 mRNAs were not observed. Collectively, these results demonstrate that the stallion is an excellent model for studying male fertility due to the initiation of spermatogenesis, frequency of cryptorchidism, and routine castration providing useful tissue to use for studying gene expression.

Laughlin, Andy M.

2010-05-01T23:59:59.000Z

110

The plant mitochondrial mat-r gene/nad1 gene complex. Progress report  

DOE Green Energy (OSTI)

The authors have completed sequencing the segments (totalling 19 kb, both complementary strands) of the maize mtDNA molecule that encode the entire NADH dehydrogenase subunit (nadl) gene. They have identified nucleotides in mature transcripts of the nadl gene that are edited and have generated clones of cDNAs of entire mature (fully spliced) nadl transcripts. They have examined the relative rates of splicing in transcripts of the four nadl gene group II introns and begun examining nadl intron cDNAs to determine the extent and distribution of RNA edits in introns, in order to evaluate the possibility that intron excision and exon splicing might be editing independent.

Wolstenholme, D.R.

1994-06-01T23:59:59.000Z

111

Integrating gene expression profiling and clinical data  

Science Conference Proceedings (OSTI)

We propose a combination of machine learning techniques to integrate predictive profiling from gene expression with clinical and epidemiological data. Starting from BioDCV, a complete software setup for predictive classification and feature ranking without ... Keywords: BioDCV, Biomarkers, Classification, DNA microarray, Feature selection, Functional genomics, SVM, Statistical learning

Silvano Paoli; Giuseppe Jurman; Davide Albanese; Stefano Merler; Cesare Furlanello

2008-01-01T23:59:59.000Z

112

RAS Gene Hot-Spot Mutations in  

E-Print Network (OSTI)

Point mutations in the cellular homologues HRAS, KRAS2, and NRAS of the viral Harvey and Kirsten rat sarcoma virus oncogenes are commonly involved in the onset of malignancies in humans and other species such as dog, mouse, and rat. Most often, three particular hot-spot codons are affected, with one amino acid exchange being sufficient for the induction of tumor growth. While RAS genes have been shown to play an important role in canine tumors such as non-small lung cell carcinomas, data about RAS mutations in canine fibrosarcomas as well as KRAS2 mutations in canine melanomas is sparse. To increase the number of tumors examined, we recently screened 13 canine fibrosarcomas and 11 canine melanomas for point mutations, particularly within the mutational hot spots. The results were compared to the already existing data from other studies about these tumors in dogs. A family of genes often involved in human tumors are the well-characterized RAS genes, which comprise HRAS, KRAS2, and NRAS, coding for closely related, small, 189 amino acid, 21 kDa, membrane-bound, intracellular proteins. The human cellular HRAS and KRAS2 genes were identified to be homologues of the Harvey and Kirsten rat sarcoma

Canine Neoplasias; J. Bullerdiek

2005-01-01T23:59:59.000Z

113

Information Retrieval meets Gene Analysis Hagit Shatkay  

E-Print Network (OSTI)

Information Retrieval meets Gene Analysis Hagit Shatkay Celera Genomics 45 West Gude Drive, based on probabilistic information retrieval, which uses the lit- erature to establish functional-related publications. This wealth of information presents a major data-analysis challenge. An ultimate goal is to under

Shatkay, Hagit

114

Book Review Bayesian Inference for Gene Expression  

E-Print Network (OSTI)

Book Review Bayesian Inference for Gene Expression and Proteomics. Edited by Kim-Anh Do, Peter Mu for a long time. This book is a timely publication entirely devoted to cutting-edge Bayesian methods in their own biological research. Moreover, the book calls for more methodological and theoretical research

Vannucci, Marina

115

Mechanisms of radiation-induced gene responses  

Science Conference Proceedings (OSTI)

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

Woloschak, G.E.; Paunesku, T.

1996-10-01T23:59:59.000Z

116

Molecular Cell Control of Proinflammatory Gene  

E-Print Network (OSTI)

-depen- dent erasure of H4K20me3 is required for effective gene activation and is achieved by NF-kB-depen- dent such as nuclear factor-k B (NF-kB), activator protein 1 (AP1), and interferon regulatory factor (IRFs

Higgins, Darren

117

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

118

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

119

Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression  

E-Print Network (OSTI)

Variable expressivity of mutant phenotypes in genetically identical individuals is a phenomenon widely reported but poorly understood. For example, mutations in the gene encoding the transcription factor ALR-1 in Caenorhabditis ...

Topalidou, Irini

120

Casein genes of Bos taurus. II. Isolation and characterization of the /beta/-casein gene  

SciTech Connect

The expression of the casein genes in the cells of the mammary gland is regulated by peptide and steroid hormones. In order to study the controlling mechanisms we have isolated and characterized the /beta/-casein gene. The gene is 8.6 kb long and exceeds by a factor of 7.8 the length of the corresponding mRNA which is encoded by nine exons. The genomic clones incorporate in addition 8.5 kb and 4.5 kb of the 5/prime/- and 3/prime/-flanking regions. We have determined the sequence of the 5- and 3-terminals of the gene and have performed a comparative analysis of the corresponding regions of the rat /beta/-casein gene. Furthermore we have identified the conversed sequences identical or homologous to the potential sections of binding to the nuclear factor CTF/NF-1 by glucocorticoid and progesterone receptors. The regulatory region of the bovine casein gene contains two variants of the TATA signal, flanking the duplication section in the promoter region.

Gorodetskii, S.I.; Tkach, T.M.; Kapelinskaya, T.V.

1988-11-01T23:59:59.000Z

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.


121

Gene family evolution by duplication, speciation and loss - CECM  

E-Print Network (OSTI)

increase of the lower bound. Let S = {S1,...,Sk} be a set .... (expected number of event by million years) and a gene loss rate of 0.02. We chose a gene gain/loss...

122

Account Request Form | IBM Blue Gene Parallel Supercomputer,...  

NLE Websites -- All DOE Office Websites (Extended Search)

(check all that apply) Please make at least one selection Brookhaven Blue GeneQ Argonne Leadership Computing Facility (based on Blue GeneQ) What is the name of the code? Do you...

123

Cross-regulation and interaction between eukaryotic gene regulatory processes  

E-Print Network (OSTI)

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

Spies, Noah (Noah Walter Benjamin)

2012-01-01T23:59:59.000Z

124

Performance Analysis of Enhanced Clustering Algorithm for Gene Expression Data  

E-Print Network (OSTI)

Microarrays are made it possible to simultaneously monitor the expression profiles of thousands of genes under various experimental conditions. It is used to identify the co-expressed genes in specific cells or tissues that are actively used to make proteins. This method is used to analysis the gene expression, an important task in bioinformatics research. Cluster analysis of gene expression data has proved to be a useful tool for identifying co-expressed genes, biologically relevant groupings of genes and samples. In this paper we applied K-Means with Automatic Generations of Merge Factor for ISODATA- AGMFI. Though AGMFI has been applied for clustering of Gene Expression Data, this proposed Enhanced Automatic Generations of Merge Factor for ISODATA- EAGMFI Algorithms overcome the drawbacks of AGMFI in terms of specifying the optimal number of clusters and initialization of good cluster centroids. Experimental results on Gene Expression Data show that the proposed EAGMFI algorithms could identify compact clus...

Chandrasekhar, T; Elayaraja, E

2011-01-01T23:59:59.000Z

125

Mediator and cohesin connect gene expression and chromatin architecture  

E-Print Network (OSTI)

Transcription factors control cell-specific gene expression programs through interactions with diverse coactivators and the transcription apparatus. Gene activation may involve DNA loop formation between enhancer-bound ...

Kagey, Michael H.

126

Distal chromatin structure influences local nucleosome positions and gene expression  

E-Print Network (OSTI)

The positions of nucleosomes across the genome influence several cellular processes, including gene transcription. However, our understanding of the factors dictating where nucleosomes are located and how this affects gene ...

Jansen, An

127

Ataxia-telangiectasia: mutations in the ATM gene  

DOE Patents (OSTI)

The invention is related to ataxia-telangiectasia, specifically, mutations in the ataxia-telangiectasia mutated gene.

Gatti, Richard A. (3835 Longridge Ave., Sherman Oaks, CA 91243); Concannon, Patrick J. (5335 old Mill Rd. NE., Bainbridge Island, WA 98110)

1999-01-01T23:59:59.000Z

128

Synthetic gene design with a large number of hidden stops  

Science Conference Proceedings (OSTI)

Hidden stops are nucleotide triples TAA, TAG and TGA that appear on the second and third reading frames of a protein coding gene. Recent studies suggested the important role of hidden stops in preventing misread of mRNA. We study the problem of designing ... Keywords: back translation, bioinformatics, codons, gene design, hidden stops, mRNA, protein coding genes, synthetic biology

Vinhthuy Phan; Sudip Saha; Ashutosh Pandey; Tit-Yee Wong

2010-07-01T23:59:59.000Z

129

Functional visualisation of genes using singular value decomposition  

Science Conference Proceedings (OSTI)

Progress in understanding core pathways and processes of cancer requires thorough analysis of many coding regions of the genome. New insights are hampered due to the lack of tools to make sense of large lists of genes identified using high throughput ... Keywords: gene ontology, genes, singular value decomposition, visualisation

Hamid Ghous, Paul J. Kennedy, Nicholas Ho, Daniel R. Catchpoole

2012-12-01T23:59:59.000Z

130

Parametric spectral analysis of malaria gene expression time series data  

Science Conference Proceedings (OSTI)

Spectral analysis of DNA microarray gene expressions time series data is important for understanding the regulation of gene expression and gene function of the Plasmodium falciparum in the intraerythrocytic developmental cycle. In this paper, ... Keywords: autoregressive model, microarray time series analysis, plasmodium falciparum, singular spectrum analysis, spectral estimation

Liping Du; Shuanhu Wu; Alan Wee-Chung Liew; David Keith Smith; Hong Yan

2006-09-01T23:59:59.000Z

131

Classification of co-expressed genes from DNA regulatory regions  

Science Conference Proceedings (OSTI)

The analysis of non-coding DNA regulatory regions is one of the most challenging open problems in computational biology. In this paper we investigate whether we can predict functional information about genes by using information extracted from their ... Keywords: Combinatorial and machine learning methods integration, Gene classification, Gene expression and bio-sequence data integration, Motif extraction and selection

Giulio Pavesi; Giorgio Valentini

2009-07-01T23:59:59.000Z

132

The ribosomal protein genes and Minuteloci of Drosophila melanogaster  

E-Print Network (OSTI)

necessary, D. mela- nogaster genes were named or renamed according to the standard metazoan RP gene nomenclature proposed by Wool and colleagues [5,58,59] and approved by the HUGO Gene Nomenclature Committee [18], whilst still conforming to Fly- Base [60...

Marygold, Steven J; Roote, John; Reuter, Gunter; Lambertsson, Andrew; Ashburner, Michael; Millburn, Gillian; Harrison, Paul; Yu, Zhan; Kenmochi, Naoya; Kaufman, Thomas C; Leevers, Sally J; Cook, Kevin R

2007-10-10T23:59:59.000Z

133

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

SciTech Connect

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

134

The mitochondrial genome of the entomophagous endoparasite Xenosvesparum (Insecta: Strepsiptera)  

SciTech Connect

In this study, the nearly complete sequence (14,519 bp) of the mitochondrial DNA (mtDNA) of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera) is described. All protein coding genes (PCGs) are in the arrangement known to be ancestral for insects, but three tRNA genes (trnA, trnS(gcu), and trnL(uag)) have transposed to derived positions and there are three tandem copies of trnH, each of which is potentially functional. All of these rearrangements except for that of trnL(uag) is within the short span between nad3 and nad4 and there are numerous blocks of unassignable sequence in this region, perhaps as remnants of larger scale predisposing rearrangements. X. vesparum mtDNA nucleotide composition is strongly biased toward As and Ts, as is typical for insect mtDNAs. There is also significant strand skew in the distribution of these nucleotides, with the J-strand being richer in A than T and in C than G, and the N-strand showing an opposite skew for complementary pairs of nucleotides. The hypothetical secondary structure of the 16S rRNA has also been reconstructed, obtaining a structural model similar to that of other insects.

Carapelli, Antonio; Vannini, Laura; Nardi, Francesco; Boore,Jeffrey L.; Beani, Laura; Dallai, Romano; Frati, Francesco

2005-12-01T23:59:59.000Z

135

Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge  

Science Conference Proceedings (OSTI)

To evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted Lucky Strike (37 17'N, 32 16.3'W, depth 1600-1750 m) and the ultramafic-hosted Rainbow (36 13'N, 33 54.1'W, depth 2270-2330 m) vent fields along the Mid-Atlantic Ridge (MAR). Using multiplexed barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA genes, we show statistically significant differences between the archaeal and bacterial communities associated with the different vent fields. Quantitative polymerase chain reaction (qPCR) assays of the functional gene diagnostic for methanogenesis (mcrA), as well as geochemical modelling to predict pore fluid chemistries within the deposits, support the pyrosequencing observations. Collectively, these results show that the less reduced, hydrogen-poor fluids at Lucky Strike limit colonization by strict anaerobes such as methanogens, and allow for hyperthermophilic microaerophiles, like Aeropyrum. In contrast, the hydrogen-rich reducing vent fluids at the ultramafic-influenced Rainbow vent field support the prevalence of methanogens and other hydrogen-oxidizing thermophiles at this site. These results demonstrate that biogeographical patterns of hydrothermal vent microorganisms are shaped in part by large scale geological and geochemical processes.

Flores, Gilberto E [Portland State University; Campbell, James H [ORNL; Kirshtein, Julie D [United States Geological Survey, Reston, VA; Meneghin, Jennifer [Portland State University; Podar, Mircea [ORNL; Steinberg, Joshua [Oregon Episcopal School, Portland, OR; Seewald, Jeffrey S [Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA; Tivey, Margaret Kingston [Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA; Voytek, Mary A [United States Geological Survey & National Aeronautics and Space Administration; Reysenbach, Anna-Louise [Portland State University; Yang, Zamin Koo [ORNL

2011-01-01T23:59:59.000Z

136

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

SciTech Connect

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

137

[Molecular, genetic and physiological analysis of photoinhibition and photosynthetic]. Progress report, June 1991--November 1992  

DOE Green Energy (OSTI)

A major goal of this project is to use a combined molecular genetic, biochemical and physiological approach to understand the relationship between photosynthetic performance and the structure of the multifunctional D1 reaction center protein of Photosystem II encoded by the chloroplast psbA gene. Relative to other chloroplast proteins, turover of D1 is rapid and highly light dependent and de novo synthesis of D1 is required for a plant`s recovery from short term exposure to irradiances which induce photoinhibitory damage. These observations have led to models for a damage/repair cycle of PSII involving the targeted degradation and replacement of photodamaged D1. To investigate the effects of perturbing the D1 cycle on photosynthesis and autotrophic growth under high and low irradiance, we have examined the consequences of site-specific mutations of the psbA and 16S rRNA genes affecting synthesis, maturation and function/stability of the D1 protein introduced into the chloroplast genome of wildtype strain of the green alga Chlamydomonas reinhardtii using biolistic transformation.

Not Available

1992-12-01T23:59:59.000Z

138

[Molecular, genetic and physiological analysis of photoinhibition and photosynthetic  

DOE Green Energy (OSTI)

A major goal of this project is to use a combined molecular genetic, biochemical and physiological approach to understand the relationship between photosynthetic performance and the structure of the multifunctional D1 reaction center protein of Photosystem II encoded by the chloroplast psbA gene. Relative to other chloroplast proteins, turover of D1 is rapid and highly light dependent and de novo synthesis of D1 is required for a plant's recovery from short term exposure to irradiances which induce photoinhibitory damage. These observations have led to models for a damage/repair cycle of PSII involving the targeted degradation and replacement of photodamaged D1. To investigate the effects of perturbing the D1 cycle on photosynthesis and autotrophic growth under high and low irradiance, we have examined the consequences of site-specific mutations of the psbA and 16S rRNA genes affecting synthesis, maturation and function/stability of the D1 protein introduced into the chloroplast genome of wildtype strain of the green alga Chlamydomonas reinhardtii using biolistic transformation.

Not Available

1992-01-01T23:59:59.000Z

139

In vitro circadian ANP secretion by gene transferring cells encapsulated in polycaprolactone tubes: gene chronotherapy  

E-Print Network (OSTI)

A new insofar as chronobiologic therapeutic approach by atrial natriuretic peptide (ANP) for hypertension and/or congestive heart failure (CHF) is based on the release of ANP from ANP cDNA transfected Chinese Hamster Ovary (CHO) cells encapsulated in polycaprolactone (PCL) tubes. ANP secretion was maintained for at least 6 months. The encapsulated cells remained viable during culturing. Control cells without transferred ANP cDNA were negative. ANP secretion is circadian periodic, peaking around 04:18, shifted to around 07:56 by melatonin treatment. The encapsulation technique, based on principles of chronotherapy, may provide a more efficient gene therapy, applicable for eventual human implantation of gene transferred cells.

Zhengrong Wang A; Liguo Chen A; Chaomin Wan A; Yiqu A; G. Cornlissen B; F. Halberg B

2004-01-01T23:59:59.000Z

140

Molecular characterization of a maize regulatory gene  

DOE Green Energy (OSTI)

Based on initial bombardment studies we have previously concluded that promoter diversity was responsible for the diversity of naturally occurring R alleles. During this period we have found that R is controlled at the level of translation initiation and intron 1 is alternatively spliced. The experiments described in Sections 1 and 2 sought to quantify these effects and to determine whether they contribute to the tissue specific expression of select R alleles. This study was done because very little is understood about the post-transcriptional regulation of plant genes. Section 3 and 4 describe experiments designed to identify important structural components of the R protein.

Wessler, S.R.

1991-12-01T23:59:59.000Z

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.


141

Gene expression in physically impeded maize roots  

E-Print Network (OSTI)

Two approaches were used to search for genes which respond to physical impedance. First, cDNA clones induced by mechanical stress or drought stress of other plant species were hybridized to mRNA from maize root tips. The results showed that only two clones, TCH1 induced by wind stress in Arabidopsis, and LP2 induced by drought stress in pine, had high homology with the RNA in maize root tips, but they did not reveal an inducible pattern of expression in the impeded maize roots tips. Second, a cDNA library was constructed from mMRNA from a 10 min physical impedance treatment of maize roots tips and was differentially screened with radioactive labeled cDNA probes synthesized using mRNA extracted from stressed and non-stressed maize roots tips. Three clones, PIIGI, pIIG2, and pIRG3, were identified as responding to a 10 min physical impedance stress. The first two cDNA clones (PIIGI and pIIG2), whose expressions were induced in a 10 min physical impedance treatment, were characterized further. cDNA PIIGI contains 678 hp with an open reading frame which specifies a polypeptide of 129 amino acid residues which showed 97% similarity at the nucleic acid level to maize root cortical cell delineating protein. Northern analysis with cDNA PIIGI as a probe showed that the expression was strongly induced by the 10 min physical impedance treatment and genomic Southern analysis showed that a relatively conserved gene family exists in maize. The CDNA pIIG2 has a nucleotide sequence of 830 bp with an open reading frame which specifies a polypeptide of 210 amino acid residues, but in a search of the GENBANK database it did not show significant homology with any identified gene of known function. Genomic Southern hybridization using cDNApIIG2 found duplicated loci in maize but single loci in rice. The third cDNA clone pIRG3, 800 bp, whose expression was reduced about 33% by 10 to 30 min physical impedance, is identical to the partial sequence of maize "calreticulin!' gene by GENBANK search.

Huang, Ying-Fei

1996-01-01T23:59:59.000Z

142

Metagenomic gene annotation by a homology-independent approach  

Science Conference Proceedings (OSTI)

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

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

2011-06-02T23:59:59.000Z

143

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

E-Print Network (OSTI)

, Shneiderman B: Visualization and analysis of microarray and gene ontology data with treemaps. BMC Bioinformatics 2004, 5:84. 8. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP...

2012-04-24T23:59:59.000Z

144

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

145

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

146

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

147

Gene Geracao Eolica Do Nordeste | Open Energy Information  

Open Energy Info (EERE)

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

148

Formal models of gene clusters - CECM - Simon Fraser University  

E-Print Network (OSTI)

The detection of conserved gene clusters is a challenge for both the biologi- ..... depending on both the combinatorial nature of the considered data (strings or.

149

Alterations in mitochondrial gene copy numbers following irradiation...  

NLE Websites -- All DOE Office Websites (Extended Search)

Alterations in mitochondrial gene copy numbers following irradiation in radiosensitive mice Sumita Raha Northwestern University Abstract We have developed a quantitative real-time...

150

Alterations in mitochondrial gene copy numbers following irradiation...  

NLE Websites -- All DOE Office Websites (Extended Search)

Alterations in mitochondrial gene copy numbers following irradiation in radiosensitive mice. Sumita Raha, Qiong Wang, Emily Mirkin, M. Beau Wanzer, Tatjana Paunesku and Gayle...

151

Universal Gene Transfer Technology for Gram Positive Bacteria  

research DNA Gene therapy holds great promise to cure cancer, HIV, and other hereditary and contagious diseases Genetic engineering has been widely ...

152

Available Technologies: Library of Plasmids to Control Gene ...  

A scientist wishing to differentially express a set of genes can query the database, choose the most appropriate vectors for the desired expression levels, ...

153

Genomics, Gene Expression and Other Studies in Soybean Rust  

E-Print Network (OSTI)

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

Posada-Buitrago, Martha Lucia

2005-01-01T23:59:59.000Z

154

Regulation of the chitinase gene expression in suspension-cultured ...  

Science Conference Proceedings (OSTI)

Plant Molecular Biology 39: 907914, 1999. 1999 Kluwer Academic Publishers . Printed in the Netherlands. 907. Regulation of the chitinase gene expression...

155

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

Science Conference Proceedings (OSTI)

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

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

2011-04-18T23:59:59.000Z

156

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

DOE Green Energy (OSTI)

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

Kuchka, M.R.

1992-08-01T23:59:59.000Z

157

Evolutionary analyses of nonfamily genes in plants  

NLE Websites -- All DOE Office Websites (Extended Search)

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

158

Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph  

Science Conference Proceedings (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

159

Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph  

Science Conference Proceedings (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

160

Scaling properties of transcription profiles in gene networks  

Science Conference Proceedings (OSTI)

Here we show that the transcriptional noise is an emergent property with scale invariance from genome level to the level of small Transcriptional Regulatory Genetic Networks (TRGN). We show that a small set of 9-12 genes reproduces the geometric ... Keywords: TRGN, behavioural variability, bioinformatics, gene networks, genome size, housekeeping functions, regulatory networks, scale invariance, transcription profiles, transcriptional noise, transcriptional regulatory genetic networks

Renata C. Ferreira; Francisco Bosco; Marcelo R. S. Briones

2009-03-01T23:59:59.000Z

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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

BlueGene/L applications: Parallelism On a Massive Scale  

Science Conference Proceedings (OSTI)

BlueGene/L (BG/L), developed through a partnership between IBM and Lawrence Livermore National Laboratory (LLNL), is currently the world's largest system both in terms of scale, with 131,072 processors, and absolute performance, with a peak rate of ... Keywords: BlueGene/L, application scalability, massively parallel architectures, performance study and optimization

Bronis R. De Supinski; Martin Schulz; Vasily V. Bulatov; William Cabot; Bor Chan; Andrew W. Cook; Erik W. Draeger; James N. Glosli; Jeffrey A. Greenough; Keith Henderson; Alison Kubota; Steve Louis; Brian J. Miller; Mehul V. Patel; Thomas E. Spelce; Frederick H. Streitz; Peter L. Williams; Robert K. Yates; Andy Yoo; George Almasi; Gyan Bhanot; Alan Gara; John A. Gunnels; Manish Gupta; Jose Moreira; James Sexton; Bob Walkup; Charles Archer; Francois Gygi; Timothy C. Germann; Kai Kadau; Peter S. Lomdahl; Charles Rendleman; Michael L. Welcome; William Mclendon; Bruce Hendrickson; Franz Franchetti; Stefan Kral; Jrgen Lorenz; Christoph W. berhuber; Edmond Chow; mit atalyrek

2008-02-01T23:59:59.000Z

162

Early Experience on the Blue Gene/Q Supercomputing System  

Science Conference Proceedings (OSTI)

The Argonne Leadership Computing Facility (ALCF) is home to Mira, a10 PF Blue Gene/Q (BG/Q) system. The BG/Q system is the third generation in Blue Gene architecture from IBM and like its predecessors combines system-on-chip technology with a proprietary ... Keywords: supercomputing, performance, multi-core, scalability, applications

Vitali Morozov, Kalyan Kumaran, Venkatram Vishwanath, Jiayuan Meng, Michael E. Papka

2013-05-01T23:59:59.000Z

163

Petascale Debugging via Allinea DDT for IBM Blue Gene /P  

E-Print Network (OSTI)

@allinea.com> Senior Systems Engineer, Allinea Software Inc. ALCF L2P Workshop, May 23, 2012 #12;Outline ExperienceArchitecture #12;Current Status IBM Blue Gene /P Acceptance testing at ALCF (Allinea DDT 3.1) ­ Scale (Allinea DDT 3.2) ­ Early access for IBM Blue Gene /Q expected July 2012 ALCF requirement ­ Scale for Mira

Kemner, Ken

164

Gene identification in Phytophthora capsici through expressed sequence tags  

Science Conference Proceedings (OSTI)

Expressed Sequence Tags (ESTs) are a rich source of information for gene discovery. In this paper, we describe the annotation of ESTs of Phytophthora capsici whose complete genome is not yet available. P. capsici is an Oomycete plant pathogen ... Keywords: Phytophthora capsici, expressed sequence tags, gene functional annotation

N. Reena; A. Chandrasekar; A. Riju; P. L. Nima; S. J. Eapen; M. Anandaraj

2010-02-01T23:59:59.000Z

165

Parallel volume rendering on the IBM Blue Gene/P  

Science Conference Proceedings (OSTI)

Parallel volume rendering is implemented and tested on an IBM Blue Gene distributed-memory parallel architecture. The goal of studying the cost of parallel rendering on a new class of supercomputers such as the Blue Gene/P is not necessarily to achieve ...

Tom Peterka; Hongfeng Yu; Robert Ross; Kwan-Liu Ma

2008-04-01T23:59:59.000Z

166

Predicting Gene Structures from Multiple RT-PCR Tests  

E-Print Network (OSTI)

Predicting Gene Structures from Multiple RT-PCR Tests (Extended Abstract) Jakub Kov´ac1 , Tom RT-PCR experiments in gene finding. We present hardness results and practical algorithms for several variants of the problem. We also apply our methods to a real RT-PCR data set in the Drosophila genome. We

Vinar, Tomas

167

Detecting reliable gene interactions by a hierarchy of Bayesian network classifiers  

Science Conference Proceedings (OSTI)

The main purpose of a gene interaction network is to map the relationships of the genes that are out of sight when a genomic study is tackled. DNA microarrays allow the measure of gene expression of thousands of genes at the same time. These data constitute ... Keywords: Bayesian network classifiers, DNA microarrays, Gene interactions, Knowledge discovery, Robust arc identification

Rubn Armaanzas; Iaki Inza; Pedro Larraaga

2008-08-01T23:59:59.000Z

168

Text analysis of MEDLINE for discovering functional relationships among genes: evaluation of keyword extraction weighting schemes  

Science Conference Proceedings (OSTI)

One of the key challenges of microarray studies is to derive biological insights from the gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the functional links among genes. However, ... Keywords: BEA-PARTITION, DNA microarray lists, MEDLINE, bioinformatics, clustering analysis, data mining, gene clustering, gene expression patterns, information extraction, keyword association, keyword extraction, keyword weighting, text analysis

Ying Liu; Shamkant B. Navathe; Alex Pivoshenko; Venu G. Dasigi; Ray Dingledine; Brian J. Ciliax

2006-06-01T23:59:59.000Z

169

Prediction of epigenetically regulated genes in breast cancer cell lines  

Science Conference Proceedings (OSTI)

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

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

2010-05-04T23:59:59.000Z

170

BESC Submits 32 Gene Disclosures for Patents | ORNL  

NLE Websites -- All DOE Office Websites (Extended Search)

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

171

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)  

Science Conference Proceedings (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

172

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

SciTech Connect

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

Kappler, Ulrike [University of Queensland, The, Brisbane, Queensland, Australia; Davenport, Karen W. [Los Alamos National Laboratory (LANL); Beatson, Scott [University of Queensland, The, Brisbane, Queensland, Australia; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Berry, Kerrie W. [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

173

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

Science Conference Proceedings (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

174

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

SciTech Connect

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

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

2013-01-01T23:59:59.000Z

175

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

SciTech Connect

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

176

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

177

The synthetic multivulva genes and their suppressors regulate opposing cell fates through chromatin remodeling  

E-Print Network (OSTI)

The synthetic multivulva (synMuv) genes act redundantly to inhibit vulval fates in Caenorhabditis elegans. These genes are grouped into three classes called A, B and C. The class A genes encode putative transcription ...

Andersen, Erik C

2008-01-01T23:59:59.000Z

178

Sorghum bioenergy genotypes, genes and pathways  

E-Print Network (OSTI)

Sorghum (Sorghum bicolor [L.] Moench) is the fifth most economically important cereal grown worldwide and is a source of food, feed, fiber and fuel. Sorghum, a C4 grass and a close relative to sugarcane, is adapted to hot, dry adverse environments and this plant is a potentially important bioenergy crop for Texas. The diversity of the twelve high biomass sorghum genotypes was analyzed using 50 simple sequence repeats (SSR) markers with genome coverage. The accumulation of biomass during sorghum development was studied in BTx623, an elite grain sorghum genotype. Genetic similarity analysis showed that the twelve high biomass genotypes were quite diverse and different from most current grain sorghum genotypes. The ratio of leaf/stem biomass accumulation was higher early in the vegetative phase during rapid canopy development and lower later in this phase when stem growth rate increased. This resulted in an increasing ratio of stem to leaf dry weight during development. Numerous cellulose sythase genes have been putatively identified in the sorghum genome. The relative level of Ces5 RNA in leaves decreased during vegetative phase of development by ~32 fold. There was no change in the relative abundance of Ces5 RNA in stems. Also there was no change in the relative abundance of Ces3 RNA in either stem or leaves during the vegetative stage. The knowledge gained in this study may contribute to the development of sorghum bioenergy hybrids that accumulate more biomass and that are modified in composition to make them more amenable to biofuels production.

Plews, Ian Kenneth

2007-12-01T23:59:59.000Z

179

Transposon-induced nuclear mutations that alter chloroplast gene expression  

DOE Green Energy (OSTI)

The goal of this project is to use mutant phenotypes as a guide to nuclear genes that determine the timing and localization of chloroplast development The immediate goals are to identify nuclear mutants with defects in chloroplast gene expression from maize lines harboring active Mu transposons; characterize their phenotypes to determine the precise defect in gene expression; clone several of the most interesting mutations by exploiting the transposon tag; and use the clones to further define the roles of these genes in modulating chloroplast gene expression. Three mutants were described earlier that had global defects in chloroplast gene expression. We have found that two of these mutations are allelic. Both alleles have global defects in chloroplast translation initiation, as revealed by the failure to assemble chloroplast mRNAs into polysomes. We have isolated and characterized three new mutants from Mu lines that have novel defects in chloroplast RNA metabolism. We are now ready to begin the task of cloning several of these genes, by using the Mu transposon tag.

Barkan, A.

1992-01-01T23:59:59.000Z

180

Gene expression profiles of microdissected pancreatic ductal adenocarcinoma  

E-Print Network (OSTI)

Pancreatic ductal adenocarcinoma (PDAC) remains an important cause of malignancy-related death and is the eighth most common cancer with the lowest overall 5-year relative survival rate. To identify new molecular markers and candidates for new therapeutic regimens, we investigated the gene expression profile of microdissected cells from 11 normal pancreatic ducts, 14 samples of PDAC, and 4 well-characterized pancreatic cancer cell lines using the Affymetrix U133 GeneChip set. RNA was extracted from microdissected samples and cell lines, amplified, and labeled using a repetitive in vitro transcription protocol. Differentially expressed genes were identified using the significance analysis of microarrays program. We found 616 differentially expressed genes. Within these, 140 were also identified in PDAC by others, such as Galectin-1, Galectin-3, and MT-SP2. We validated the differential expression of several genes (e.g., CENPF, MCM2, MCM7, RAMP, IRAK1, and PTTG1) in PDAC by immunohistochemistry and reverse transcription polymerase chain reaction. We present a whole genome expression study of microdissected tissues from PDAC, from microdissected normal ductal pancreatic cells and pancreatic cancer cell lines using highdensity microarrays. Within the panel of genes, we identified novel differentially expressed genes, which have not been associated with the pathogenesis of PDAC before.

Robert Grtzmann; Christian Pilarsky; Ole Ammerpohl Y; Jutta Lttges Z; Bence Sipos Z; Melanie Foerder; Ingo Alldinger; Beatrix Jahnke; Hans Konrad Schackert; Holger Kalthoff Y; Bernd Kremer B; Hans Detlev Saeger

2003-01-01T23:59:59.000Z

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.


181

The human VH3b gene subfamily is highly polymorphic  

SciTech Connect

The authors have previously shown that human antibody (Ab) directed against the capsular polysaccharide of the important bacterial pathogen, Haemophilus influenzae type b (Hib) is encoded by a small group of VH3 gene family members. The majority of anti-Hib PS Ab use members of the smaller VH3b subfamily. To examine directly the available human VH3 repertoire, they have used PCR to amplify and clone candidate germ-line VH3b H chain V region genes from two unrelated subjects from whom anti-Hib polysaccharide mAb had been previously obtained. A single functional VH3b germ-line gene was obtained from one subject. This gene is identical throughout the coding region to the previously identified gene 9.1. Twelve distinct VH3b germ-line sequences, 87.6-99.8% homologous to one another, were obtained from the second subject. One of these genes, LSG1.1, is also identical to the 9.1 germ-line gene, and a second, LSG6.1 is identical to a previously reported cDNA, M85. These germ-line VH3b genes are 82.7-94.1% homologous to rearranged anti-Hib PS VH3b segments obtained from these subjects. These findings further demonstrate that considerable polymorphism of VH segments exists in the human population. Despite the presence of very highly homologous VH elements in the germ line, particular genes are highly conserved within the outbred human population. 52 refs., 4 figs.

Adderson, E.E.; Carroll, W.L. (Univ. of Utah, Salt Lake City, UT (United States)); Azmi, F.H.; Wilson, P.M.; Shackelford, P.G. (Washington Univ., St. Louis, MO (United States))

1993-07-15T23:59:59.000Z

182

Gene network and pathway generation and analysis: Editorial  

Science Conference Proceedings (OSTI)

The past decade has witnessed an exponential growth of biological data including genomic sequences, gene annotations, expression and regulation, and protein-protein interactions. A key aim in the post-genome era is to systematically catalogue gene networks and pathways in a dynamic living cell and apply them to study diseases and phenotypes. To promote the research in systems biology and its application to disease studies, we organized a workshop focusing on the reconstruction and analysis of gene networks and pathways in any organisms from high-throughput data collected through techniques such as microarray analysis and RNA-Seq.

Zhao, Zhongming; Sanfilippo, Antonio P.; Huang, Kun

2011-02-18T23:59:59.000Z

183

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

E-Print Network (OSTI)

The RCg2 promoter was identified in a search for root-specific genes to combat the rice water weevil (RWW) but expressed at low frequency (~10%). Spatial expression of RCg2 was investigated using two reporter constructs YXA (RCg2-gus-ocs) and YXB (RCg2-gus-RCg2) that included 1.6 kb of the RCg2 5' sequence fused to the ?-glucuronidase (gus) coding region. YXB plants were generated via Agrobacterium-mediated transformation but only 8 of 158 plants analyzed showed strong GUS activity despite the presence of an intact construct. Reactivation of RCg2 gene in rice was investigated by treatment of R0 and R1 of YXB transgenic plants with 5-azacytidine. Reactivation of RCg2-gus was observed in some transgenic plants indicating different mechanisms involved in the gene silencing of the YXB lines. DNA methylation analysis, northern blotting, RT-PCR and small RNA analysis supported the conclusion that PTGS and TGS are present in the silenced plants. Promoter analysis in silico and using promoter deletion assays predicted that the RCg2 promoter contains a complex region that includes miRNA homologs, MITEs and repetitive sequences. The high frequency of promoter-related silencing suggests functional interactions of these elements of the transgene and the homologous endogenous gene. To identify key elements contributing to the root-preferential expression of RCg2 and the high frequency of silencing observed in transgenic (YXB) lines, several RCg2 promoter deletion constructs were designed. These include 5' deletions MC1, MC2, MC4, MC7 and MC8 and internal deletions MC5, MC11, MC12 and MC13. The frequency with which silencing was encountered in populations of the deletion mutants was used to characterize the effects of various promoter elements. Deletion of the region from -406 to -208 (compared MC11 to YXB, and MC13 to MC1) revealed that region contains a negative element. Among 36 independent transformants, 33% with MC11 expressed GUS and 85% with MC13 showed GUS expression. Comparing MC7 transgenic plants to MC1 revealed that the region ?888 to ?729 is another negative regulatory element, and comparing MC11 to MC12, the proportion of expression of transgenic plants indicated the region ?729 to ?406 is a positive regulatory element.

Shi, Xiangyu

2009-05-01T23:59:59.000Z

184

Powered by NERSC, A Database of Billions of Genes and Counting...  

NLE Websites -- All DOE Office Websites (Extended Search)

the news" Home News & Publications News Center News Powered by NERSC, a Database of Billions of Genes and Counting Powered by NERSC, a Database of Billions of Genes...

185

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism  

E-Print Network (OSTI)

Cyanophages infecting the marine cyanobacteria Prochlorococcus and Synechococcus encode and express genes for the photosynthetic light reactions. Sequenced cyanophage genomes lack Calvin cycle genes, however, suggesting ...

Thompson, Luke Richard

186

Activation of the human beta interferon gene by the adenovirus type 12 E1B gene  

SciTech Connect

The transcription of endogenous beta interferon mRNA was activated in human embryo kidney (HEK) cells infected with adenovirus 12 (Ad12) but was activated only inefficiently or not at all in HEK cells infected with Ad5 and rc-1 (Ad5 dl312 containing the Ad12 E1A region). The analysis with Ad12 mutants showed that Ad12 E1B products, especially the 19K protein, were important for the expression of the endogenous beta interferon gene and Ad12 E1A products were not involved in the expression. The expression of exogeneously transfected pIFN-CAT (a hybrid plasmid having the human beta interferon promoter fused with the CAT gene) was activated in HEK and chicken embryo fibroblast (CEF) cells infected with either Ad12 or Ad5. The analysis of cotransfection of CEF cells with pIFN-CAT and plasmids containing fragments of Ad12 or Ad5 DNA showed that Ad12 or Ad5 E1B (possibly the 19K protein) was and E1A was not involved in the expression of the exogenous pIFN-CAT.

Shiroki, K.; Toth, M.

1988-01-01T23:59:59.000Z

187

A Model for the Dynamics of Gene Networks  

E-Print Network (OSTI)

In this work we propose a model for gene expression based on the theory of random dynamical systems (RDS) and show that it has a "modularity property" in the following sense: given any collection of genes that are linked in a transcriptional network, if each of them is individually described by a certain class of RDS then there is a natural, and essentially unique, prescription for coupling them together, respecting the network topology, in such a way that the collective system formed by all genes is a RDS as well. Moreover, the class of RDS used to describe the individual genes is flexible enough to account for a wide range of stochastic behaviors within the realm of stationary processes.

Fernando Antoneli; Renata C. Ferreira; Francisco Bosco; Marcelo R. S. Briones

2013-05-14T23:59:59.000Z

188

Single, Key Gene Discovery Could Streamline Production of Biofuels |  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Single, Key Gene Discovery Could Streamline Production of Biofuels Single, Key Gene Discovery Could Streamline Production of Biofuels Single, Key Gene Discovery Could Streamline Production of Biofuels August 11, 2011 - 3:51pm Addthis WASHINGTON, DC -- A team of researchers at the Department of Energy's BioEnergy Science Center (BESC) have pinpointed the exact, single gene that controls ethanol production capacity in a microorganism. This discovery could be the missing link in developing biomass crops that produce higher concentrations of ethanol at lower costs. "The Department of Energy relies on the scientific discoveries of its labs and research centers to improve the production of clean energy sources," said Energy Secretary Steven Chu. "This discovery is an important step in developing biomass crops that could increase yield of

189

New Perspectives on Gene Family Evolution - CECM - Simon Fraser ...  

E-Print Network (OSTI)

PLoS ONE 1, e85 (2006). 12. Doyon, J.-P., Chauve, C., Hamel, S.: Algorithms for exploring the space of gene tree/species tree reconciliations. In: Nelson, C.E....

190

Single-Molecule Approaches to Stochastic Gene Expression  

E-Print Network (OSTI)

Both the transcription of mRNAs from genes and their subsequent translation into proteins are inherently stochastic biochemical events, and this randomness can lead to substantial cell-to-cell variability in mRNA and protein ...

Raj, Arjun

191

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

192

Motif discovery through predictive modeling of gene regulation  

Science Conference Proceedings (OSTI)

We present MEDUSA, an integrative method for learning motif models of transcription factor binding sites PSSMs by incorporating promoter sequence and transcriptome gene expression data. We use a modern large-margin machine learning approach, based on ...

Manuel Middendorf; Anshul Kundaje; Mihir Shah; Yoav Freund; Chris H. Wiggins; Christina Leslie

2005-05-01T23:59:59.000Z

193

Context-specific Bayesian clustering for gene expression data  

Science Conference Proceedings (OSTI)

The recent growth in genomic data and measurement of genome-wide expression patterns allows to examine gene regulation by transcription factors using computational tools. In this work, we present a class of mathematical models that help in understanding ...

Yoseph Barash; Nir Friedman

2001-04-01T23:59:59.000Z

194

Gene and translation initiation site prediction in metagenomic sequences  

Science Conference Proceedings (OSTI)

Motivation: Gene prediction in metagenomic sequences remains a difficult problem. Current sequencing technologies do not achieve sufficient coverage to assemble the individual genomes in a typical sample; consequently, sequencing runs produce ...

Doug Hyatt; Philip F. LoCascio; Loren J. Hauser; Edward C. Uberbacher

2012-09-01T23:59:59.000Z

195

Molecular geomicrobiology: genes and geochemical cycling Jennifer Macalady 1  

E-Print Network (OSTI)

Frontiers Molecular geomicrobiology: genes and geochemical cycling Jennifer Macalady 1 , Jillian F occurs. Yet, the field of molecular geomicrobiology remains in its infancy. In the foreseeable future, merging of modern biogeochemistry with molecularly resolved ecological studies will inspire

Macalady, Jenn

196

Leveraging high-throughput datasets for studies of gene regulation  

E-Print Network (OSTI)

In this thesis, I leveraged computational methods on biological data to better understand gene regulation and development of the human body, as well as of the model organisms mouse and yeast. Firstly, I tackled biological ...

Yen, Angela

2011-01-01T23:59:59.000Z

197

Zebrafish promoter microarrays identify actively transcribed embryonic genes  

E-Print Network (OSTI)

We have designed a zebrafish genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. Using these microarrays, together with chromatin immunoprecipitation ...

Wardle, Fiona C

198

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

199

Deterministic Ensemble Forecasts Using Gene-Expression Programming  

Science Conference Proceedings (OSTI)

A method called gene-expression programming (GEP), which uses symbolic regression to form a nonlinear combination of ensemble NWP forecasts, is introduced. From a population of competing and evolving algorithms (each of which can create a ...

Atoossa Bakhshaii; Roland Stull

2009-10-01T23:59:59.000Z

200

Genome Enabled Discovery of Carbon Sequestration Genes in Poplar  

DOE Green Energy (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

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

Genome-enabled Discovery of Carbon Sequestration Genes  

DOE Green Energy (OSTI)

The fate of carbon below ground is likely to be a major factor determining the success of carbon sequestration strategies involving plants. Despite their importance, molecular processes controlling belowground C allocation and partitioning are poorly understood. This project is leveraging the Populus trichocarpa genome sequence to discover genes important to C sequestration in plants and soils. The focus is on the identification of genes that provide key control points for the flow and chemical transformations of carbon in roots, concentrating on genes that control the synthesis of chemical forms of carbon that result in slower turnover rates of soil organic matter (i.e., increased recalcitrance). We propose to enhance carbon allocation and partitioning to roots by 1) modifying the auxin signaling pathway, and the invertase family, which controls sucrose metabolism, and by 2) increasing root proliferation through transgenesis with genes known to control fine root proliferation (e.g., ANT), 3) increasing the production of recalcitrant C metabolites by identifying genes controlling secondary C metabolism by a major mQTL-based gene discovery effort, and 4) increasing aboveground productivity by enhancing drought tolerance to achieve maximum C sequestration. This broad, integrated approach is aimed at ultimately enhancing root biomass as well as root detritus longevity, providing the best prospects for significant enhancement of belowground C sequestration.

Tuskan, Gerald A [ORNL; Tschaplinski, Timothy J [ORNL; Kalluri, Udaya C [ORNL; Yin, Tongming [ORNL; Yang, Xiaohan [ORNL; Zhang, Xinye [ORNL; Engle, Nancy L [ORNL; Ranjan, Priya [ORNL; Basu, Manojit M [ORNL; Gunter, Lee E [ORNL; Jawdy, Sara [ORNL; Martin, Madhavi Z [ORNL; Campbell, Alina S [ORNL; DiFazio, Stephen P [ORNL; Davis, John M [University of Florida; Hinchee, Maud [ORNL; Pinnacchio, Christa [U.S. Department of Energy, Joint Genome Institute; Meilan, R [Purdue University; Busov, V. [Michigan Technological University; Strauss, S [Oregon State University

2009-01-01T23:59:59.000Z

202

Stripe Forming Architecture of the Gap Gene System  

E-Print Network (OSTI)

In this report, we show that gap genes encode exactly one set of pair-rule stripes, which occur in the native even-skipped position. The core of this work is a detailed analysis that shows how this conclusion follows from the arrangement of gap domains in the embryo. This analysis shows that: (1) pattern forming information is transmitted from gap to pair-rule genes by means of a nonredundant set of morphogenetic gradients, and (2) the stripe forming capability of the gap genes is constrained by the arrangement of these gradients and by the fact that each gap domain consists of a pair of correlated gradients. We also show that in the blastoderm, the regulatory sign of a transcriptional regulator is unlikely to change in a concentration dependent manner. The principal analytic tool used to establish these results is the gene circuit method. Here, this method is applied to examine hybrid data sets consisting of real gene expression data for four gap genes and hypothetica...

John Reinitz David; David Kosman; Carlos E. Vanario-alonso; David H. Sharp

1998-01-01T23:59:59.000Z

203

Organization and control of genes encoding catabolic enzymes in Rhizobiaceae  

DOE Green Energy (OSTI)

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

Parke, D.; Ornston, L.N.

1993-03-01T23:59:59.000Z

204

GENOME-ENABLED DISCOVERY OF CARBON SEQUESTRATION GENES IN POPLAR  

Science Conference Proceedings (OSTI)

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

DAVIS J M

2007-10-11T23:59:59.000Z

205

Detecting disease genes based on semi-supervised learning and protein-protein interaction networks  

Science Conference Proceedings (OSTI)

Objective: Predicting or prioritizing the human genes that cause disease, or ''disease genes'', is one of the emerging tasks in biomedicine informatics. Research on network-based approach to this problem is carried out upon the key assumption of ''the ... Keywords: Disease gene neighbours, Disease-causing gene prediction, Multiple data resources integration, Protein-protein interaction network, Semi-supervised learning

Thanh-Phuong Nguyen; Tu-Bao Ho

2012-01-01T23:59:59.000Z

206

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

E-Print Network (OSTI)

The largest group of plant disease resistance (R) genes that share similar structures contains a predicted nucleotide-binding site (NBS) domain. NBS domains of this class of R genes show highly conserved amino acid motifs, which makes it possible to isolate resistance gene analogs (RGAs) by PCR with degenerate primers and homology searches from public databases. Multiple combinations of degenerate primers were designed from three conserved motifs (one motif was used for a subgroup-specific primer design) in the NBS regions of R genes of various plants. All combinations of primer pairs were used to amplify genomic DNA from sorghum. TIR-specific primer combinations showed no PCR amplification in sorghum. Homology searches identified many NBS-encoding sequences among the expressed or genomic molecular database entries for sorghum. Motif analysis of the sorghum NBS sequences that were identified in this study revealed eight major conserved motifs plus two additional highly conserved motifs, but no TIR-specific motifs. Phylogenetic analysis of sorghum NBS sequences showed tree topology typical of NBS-LRR genes, including clustered nodes and longbranch lengths. Eleven distinct families of NBS sequences, representing a highly diverse sample, were isolated from Sorghum bicolor. With two exceptions, sorghum RGA families appeared to be closely related in sequence to at least one R-gene cloned from other species. In addition, deduced amino acid sequences of sorghum RGAs showed strong sequence similarity to almost all known non-TIR (Toll/Interleukin 1 Receptor)- type R-genes. Mapping with sorghum RGA markers revealed one linkage group containing four out of ten randomly selected markers, suggesting non-random distribution of NBS sequences in the sorghum genome. Rice sequences homologous to sorghum NBS sequences were found from two-way BLAST searches. Some of them were shown to be orthologs, when determined by using phylogenetic approaches which combined five different evolution models and tree-building methods.

Cho, Jae-Min

2005-05-01T23:59:59.000Z

207

Reconstruction of Gene Networks of Iron Response in Shewanella oneidensis  

Science Conference Proceedings (OSTI)

It is of great interest to study the iron response of the -proteobacterium Shewanella oneidensis since it possesses a high content of iron and is capable of utilizing iron for anaerobic respiration. We report here that the iron response in S. oneidensis is a rapid process. To gain more insights into the bacterial response to iron, temporal gene expression profiles were examined for iron depletion and repletion, resulting in identification of iron-responsive biological pathways in a gene co-expression network. Iron acquisition systems, including genes unique to S. oneidensis, were rapidly and strongly induced by iron depletion, and repressed by iron repletion. Some were required for iron depletion, as exemplified by the mutational analysis of the putative siderophore biosynthesis protein SO3032. Unexpectedly, a number of genes related to anaerobic energy metabolism were repressed by iron depletion and induced by repletion, which might be due to the iron storage potential of their protein products. Other iron-responsive biological pathways include protein degradation, aerobic energy metabolism and protein synthesis. Furthermore, sequence motifs enriched in gene clusters as well as their corresponding DNA-binding proteins (Fur, CRP and RpoH) were identified, resulting in a regulatory network of iron response in S. oneidensis. Together, this work provides an overview of iron response and reveals novel features in S. oneidensis, including Shewanella-specific iron acquisition systems, and suggests the intimate relationship between anaerobic energy metabolism and iron response.

Yang, Yunfeng [ORNL; Harris, Daniel P [ORNL; Luo, Feng [Clemson University; Joachimiak, Marcin [Clemson University; Wu, Liyou [University of Oklahoma; Dehal, Paramvir [Lawrence Berkeley National Laboratory (LBNL); Jacobsen, Janet [Lawrence Berkeley National Laboratory (LBNL); Yang, Zamin Koo [ORNL; Gao, Haichun [University of Oklahoma; Arkin, Adam [Lawrence Berkeley National Laboratory (LBNL); Palumbo, Anthony Vito [ORNL; Zhou, Jizhong [University of Oklahoma

2009-01-01T23:59:59.000Z

208

A functional gene array for detection of bacterial virulence elements  

Science Conference Proceedings (OSTI)

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

Jaing, C

2007-11-01T23:59:59.000Z

209

Low doses of neutrons induce changes in gene expression  

SciTech Connect

Studies were designed to identify genes induced following low-dose neutron but not following {gamma}-ray exposure in fibroblasts. Our past work had shown differences in the expression of {beta}-protein kinase C and c-fos genes, both being induced following {gamma}-ray but not neutron exposure. We have identified two genes that are induced following neutron, but not {gamma}-ray, exposure: Rp-8 (a gene induced by apoptosis) and the long terminal repeat (LTR) of the human immunodeficiency (HIV). Rp-8 mRNA induction was demonstrated in Syrian hamster embryo fibroblasts and was found to be induced in cells exposed to neutrons administered at low (0.5 cGy/min) and at high dose rate (12 cGy/min). The induction of transcription from the LTR of HIV was demonstrated in HeLa cells bearing a transfected construct of the chloramphenicol acetyl transferase (CAT) gene driven by the HIV-LTR promoter. Measures of CAT activity and CAT transcripts following irradiation demonstrated an unresponsiveness to {gamma} rays over a broad range of doses. Twofold induction of the HIV-LTR was detected following neutron exposure (48 cGy) administered at low (0.5 cGy/min) but not high (12 cGy/min) dose rates. Ultraviolet-mediated HIV-LTR induction was inhibited by low-dose-rate neutron exposure.

Woloschak, G.E.; Chang-Liu, C.M. [Argonne National Lab., IL (United States); Panozzo, J.; Libertin, C.R. [Loyola Univ., Maywood, IL (United States)

1993-06-01T23:59:59.000Z

210

Low doses of neutrons induce changes in gene expression  

SciTech Connect

Studies were designed to identify genes induced following low-dose neutron but not following [gamma]-ray exposure in fibroblasts. Our past work had shown differences in the expression of [beta]-protein kinase C and c-fos genes, both being induced following [gamma]-ray but not neutron exposure. We have identified two genes that are induced following neutron, but not [gamma]-ray, exposure: Rp-8 (a gene induced by apoptosis) and the long terminal repeat (LTR) of the human immunodeficiency (HIV). Rp-8 mRNA induction was demonstrated in Syrian hamster embryo fibroblasts and was found to be induced in cells exposed to neutrons administered at low (0.5 cGy/min) and at high dose rate (12 cGy/min). The induction of transcription from the LTR of HIV was demonstrated in HeLa cells bearing a transfected construct of the chloramphenicol acetyl transferase (CAT) gene driven by the HIV-LTR promoter. Measures of CAT activity and CAT transcripts following irradiation demonstrated an unresponsiveness to [gamma] rays over a broad range of doses. Twofold induction of the HIV-LTR was detected following neutron exposure (48 cGy) administered at low (0.5 cGy/min) but not high (12 cGy/min) dose rates. Ultraviolet-mediated HIV-LTR induction was inhibited by low-dose-rate neutron exposure.

Woloschak, G.E.; Chang-Liu, C.M. (Argonne National Lab., IL (United States)); Panozzo, J.; Libertin, C.R. (Loyola Univ., Maywood, IL (United States))

1993-01-01T23:59:59.000Z

211

IMPRINTED GENES & TRANSPOSITIONS: EPIGENOMIC TARGETS FOR LOW DOSE RADIATION EFFECTS  

Science Conference Proceedings (OSTI)

The overall hypothesis of this grant application is that low dose ionizing radiation (LDIR) elicits adaptive responses in part by causing heritable DNA methylation changes in the epigenome. This novel postulate was tested by determining if the level of DNA methylation at the Agouti viable yellow (A{sup vy}) metastable locus is altered, in a dose-dependent manner, by low dose radiation exposure (radiation hormesis, bringing into question the assumption that every dose of radiation is harmful. Our findings not only have significant implications concerning the mechanism of hormesis, but they also emphasize the potential importance of this phenomenon in determining human risk at low radiation doses. Since the epigenetic regulation of genes varies markedly between species, the effect of LDIR on other epigenetically labile genes (e.g. imprinted genes) in animals and humans needs to be defined.

Randy Jirtle

2012-10-11T23:59:59.000Z

212

Low doses of neutrons induce changes in gene expression  

SciTech Connect

Studies were designed to identify genes induced in fibroblasts after exposure to low-dose neutron radiation but not after {gamma} rays. Our past work had shown similar modulation of transcripts for {alpha}-tubulin, {beta}- and {gamma}-actins, ornithine decarboxylase and interleukin 1 after exposure to either neutrons or {gamma} rays. However, differences in the expression of {beta}-protein kinase C and c-fos genes were observed, with both being induced after exposure to {gamma} rays but not neutrons. Recently, we have identified two genes that are induced after exposure to neutrons but not {gamma} rays: Rp-8 (a gene associated with apoptosis) and the long terminal repeat (LTR) of the human immunodeficiency virus (HIV). Induction of Rp-8 mRNA was demonstrated in Syrian hamster embryo (SHE) fibroblasts and was found to be induced in cells exposed to neutrons administered at low (0.005 Gy/min) and high dose rate (0.12 Gy/min). No induction of other genes associated with apoptosis such as Rp-2, bcl-2 and Tcl-30 was observed. The induction of transcription from the LTR of HIV was demonstrated in HeLa cells bearing a transfected construct of the chloramphenicol acetyl transferase (CAT) gene driven by the HIV-LTR promoter. Measurements of CAT activity and CAT transcripts after irradiation demonstrated an unresponsiveness to {gamma} rays over a broad range of doses (0.1-3 Gy). Twofold induction of the HIV-LTR was detected after exposure to neutrons (0.48 Gy) administered at low (0.05 Gy/min) but not high (0.12 Gy/min) dose rates. Ultraviolet-mediated HIV-LTR induction, however, was inhibited by exposure to low-dose-rate neutron irradiation. These results are interesting in light of reports that Rp-8 is induced during apoptosis and that HIV causes apoptosis. 17 refs., 3 figs., 1 tab.

Woloschak, G.E.; Chang-Liu, C.M. [Argonne National Lab., IL (United States); Panozzo, J.; Libertin, C.R. [Loyola Univ. of Chicago, Maywood, IL (United States)

1994-04-01T23:59:59.000Z

213

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks  

SciTech Connect

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

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

2007-07-24T23:59:59.000Z

214

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

215

Identification of a novel gene family that includes the interferon-inducible human genes 616and ISG12  

E-Print Network (OSTI)

Response Elements (ISREs) and the 9 nt GAS elements for type I and type II IFNs, respectively. Most ISGs code for proteins whose biochemical and cellular roles are either well understood (e.g the genes for RNA-dependent protein kinase PKR [6,7], 2... that the ISG12 motif occurs in simple eukary- otes suggests that not all ISG12 genes in higher organisms have necessarily been incorporated into the IFN response. We therefore looked at the number and fidelity of Inter- feron Stimulated Response Elements (ISREs...

Parker, Nadeene; Porter, Andrew C G

2004-01-19T23:59:59.000Z

216

Review: Clustering of high throughput gene expression data  

Science Conference Proceedings (OSTI)

High throughput biological data need to be processed, analyzed, and interpreted to address problems in life sciences. Bioinformatics, computational biology, and systems biology deal with biological problems using computational methods. Clustering is ... Keywords: Bioinformatics, Clustering, Gene expression data, High throughput data, Microarrays

Harun Pirim; Burak Ek?Io?Lu; Andy D. Perkins; Etin YCeer

2012-12-01T23:59:59.000Z

217

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

218

Human Diversity: Our Genes Tell Where we Live  

E-Print Network (OSTI)

Human Diversity: Our Genes Tell Where we Live Dispatch Laurent Excoffier A detailed genetic. The novelty of the recent work of Rosenberg et al. [7] is precisely that they have checked the validity of the analysis of a cell-line panel of 52 worldwide popu- lations [9] managed by the French Center for the Study

Rosenberg, Noah

219

Low Dose Radiation Research Program: Gene Expression Profile...  

NLE Websites -- All DOE Office Websites (Extended Search)

human cDNA clones, we focused on differential gene expression for a low-dose x-ray irradiation at 2cGy and its comparison with high-dose at 4Gy. Four time points were studied at...

220

Overview of the Blue Gene/L system architecture  

Science Conference Proceedings (OSTI)

The Blue Gene/L computer is a massively parallel supercomputer based on IBM system-on-a-chip technology. It is designed to scale to 65,536 dual-processor nodes, with a peak performance of 360 teraflops. This paper describes the project objectives ...

A. Gara; M. A. Blumrich; D. Chen; G. L.-T. Chiu; P. Coteus; M. E. Giampapa; R. A. Haring; P. Heidelberger; D. Hoenicke; G. V. Kopcsay; T. A. Liebsch; M. Ohmacht; B. D. Steinmacher-Burow; T. Takken; P. Vranas

2005-03-01T23:59:59.000Z

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


221

Performance Analysis on Blue Gene Q with HPCToolkit  

E-Print Network (OSTI)

for performance analysis of OpenMP · Next steps · Using HPCToolkit on Blue Gene/Q at ALCF 3 #12;4 Rice University -- within and across nodes 18 #12;HPCToolkit at ALCF · ALCF systems -- /soft/perftools/hpctoolkit/pkgs/hpctoolkit · Man pages -- /soft/perftools/hpctoolkit/pkgs/hpctoolkit/share/man · ALCF guide to HPCToolkit -- http://www.alcf

Kemner, Ken

222

Data mining and genetic algorithm based gene/SNP selection  

Science Conference Proceedings (OSTI)

Objective: Genomic studies provide large volumes of data with the number of single nucleotide polymorphisms (SNPs) ranging into thousands. The analysis of SNPs permits determining relationships between genotypic and phenotypic information as well as ... Keywords: Data mining, Drug effectiveness, Feature selection, Genes, Genetic algorithm, Intersection approach, Single nucleotide polymorphisms (SNPs)

Shital C. Shah; Andrew Kusiak

2004-07-01T23:59:59.000Z

223

Information Retrieval meets Gene Analysis Hagit Shatkay \\Lambda  

E-Print Network (OSTI)

Information Retrieval meets Gene Analysis Hagit Shatkay \\Lambda Celera Genomics 45 West Gude Drive, based on probabilistic information retrieval, which uses the lit­ erature to establish functional­related publications. This wealth of information presents a major data­analysis challenge. An ultimate goal is to under

Shatkay, Hagit

224

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 the structural framework of basement membranes. The glomerular basement membrane (GBM) is a specialized basement membrane involved in the ultrafiltration processes of the kidney. The colIV?1-?5 chains are expressed in the human GBM while the colIV ?1-?6 chains are expressed in the canine GBM. Many inherited diseases of the kidney have been reported and mutations in genes regulating kidney function have been identified. Alport syndrome (AS) is the most common form of human hereditary nephritis (HN). AS is defined as an inherited progressive kidney disorder associated with sensoneural deafness and is characterized by extensive thickening and multilamminar splitting of the GBM when examined by electron microscopy. AS has both X-linked (XLAS) and autosomal (ARAS) modes of inheritance. Mutations in the COLIVA5 gene are responsible for XLAS. A form of HN with characteristic splitting of the GBM with X-linked inheritance has been described in Samoyed dogs. A specific mutation in the COLIVA5 gene has been identified in Samoyed dogs affected with HN. Mutations in the COLIVA3 and COLIVA4 genes are responsible for ARAS. A form of HN has been identified in English cocker spaniel dogs (ECS) that has been described as autosomal in inheritance and includes GBM abnormalities including extensive lammination characteristic of ARAS. Both ARAS and ECS-HN show loss of the colIVA3 and colIVA4 chains in the GBM when examined with monoclonal anitibodies. ECS-HN has been hypothesized to have the same molecular basis of disease as ARAS. As such, we have isolated and characterized canine COLIVA3 and COLIVA4 sequences from normal dogs and ECS dogs affected with HN and compared the coding regions of these candidate genes.

Camacho, Zenaido

2003-12-01T23:59:59.000Z

225

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

DOE Patents (OSTI)

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

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

2011-06-07T23:59:59.000Z

226

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

227

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

E-Print Network (OSTI)

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

Anthes, Emily Kennedy

2006-01-01T23:59:59.000Z

228

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

E-Print Network (OSTI)

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

Zhang, Feng

229

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

230

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

E-Print Network (OSTI)

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

Berdichevsky, Alina

2008-01-01T23:59:59.000Z

231

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

232

APPLYING DATA MINING TECHNIQUES FOR CANCER CLASSIFICATION ON GENE EXPRESSION DATA  

Science Conference Proceedings (OSTI)

Cancer classification through gene expression data analysis has recently emerged as an active area of research. This paper applies Genetic Algorithms (GA) for selecting a group of relevant genes from cancer microarray data. Then, the popular classifiers, ...

Jinn-Yi Yeh

2008-08-01T23:59:59.000Z

233

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

E-Print Network (OSTI)

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

Song, Joe

234

Gene RAD58(XRS4): Mapping to the right arm of chromosome XIII  

Science Conference Proceedings (OSTI)

This report presents the results of mapping of Saccharomyces cerevisiae gene RAD58(XRS4) to the right arm of chromosome XIII at a distance of 48 cM proximal to the gene ADE4. 10 refs., 1 tab.

Kozhin, S.A.; Chepurnaya, O.V.; Korolev, V.G. [Konstantinov Institute of Nuclear Physics, Gatchina (Russian Federation)

1995-02-01T23:59:59.000Z

235

Sumoylation strategies in regulated repression by nuclear receptors and in function of tumor metastasis suppressor genes  

E-Print Network (OSTI)

links gene expression by NF-kB and ?-amyloid precursorinteracts with and inhibits NF-kB in human colon and breastby KAI1. Since KAI1 is a NF-kB target gene, its message

Cai, Ling

2008-01-01T23:59:59.000Z

236

SATB1 packages densely-looped, transciptionally-active chromatin for coordinated expression of cytokine genes  

E-Print Network (OSTI)

T. Loss of silent- chromatin looping and impaired imprintingT. SATB1 targets chromatin remodelling to regulate genesS.T. & Fisher, A.G. Chromatin structure and gene regulation

Cai, Shutao; Lee, Charles C.; Kohwi-Shigematsu, Terumi

2006-01-01T23:59:59.000Z

237

Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus  

Science Conference Proceedings (OSTI)

Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine, Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression, protein motif and intron number were examined. 192, 641 and 109 SS genes were identified in Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers, roots, xylem and cambium or up-regulated by stress. Six conserved motifs in Arabidopsis and Oryza SS proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes. The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research.

Yang, Xiaohan [ORNL; Jawdy, Sara [ORNL; Tschaplinski, Timothy J [ORNL; Tuskan, Gerald A [ORNL

2009-01-01T23:59:59.000Z

238

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

SciTech Connect

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

239

DCGene: a novel predicting approach of the disease related genes on functional annotation  

Science Conference Proceedings (OSTI)

Disease Candidate Genes (DCGene) is an advanced system for predicting the disease related genes, It is a novel computational approach by using the GO annotation information. The performance of the DCGene is evaluated in a set containing 1057 test samples, ...

Yuan Fang; Hui Wang

2009-09-01T23:59:59.000Z

240

Genome of a low-salinity ammoniaoxidizing archaeon determined by single-cell and metagenomic analysis  

E-Print Network (OSTI)

Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles. We sequenced the genome of AOA in an enrichment culture from low-salinity sediments in San Francisco Bay using single-cell and metagenomic genome sequence data. Five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells genomic DNA was amplified by multiple displacement amplification (MDA) in 50 nL volumes and then sequenced by high-throughput DNA pyrosequencing. This microscopy-based approach to single-cell genomics minimizes contamination and allows correlation of high-resolution cell images with genomic sequences. Statistical properties of coverage across the five single cells, in combination with the contrasting properties of the metagenomic dataset allowed the assembly of a high-quality draft genome. The genome of this AOA, which we designate Candidatus Nitrosoarchaeum limnia SFB1, is,1.77 Mb with.2100 genes and a G+C content of 32%. Across the entire genome, the average nucleotide identity to Nitrosopumilus maritimus, the only AOA in pure culture, is,70%, suggesting this AOA represents a new genus of Crenarchaeota. Phylogenetically, the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes of this AOA are most closely related to sequences reported from a wide variety of freshwater ecosystems. Like N. maritimus, the low-salinity AOA genome appears to have an ammonia oxidation pathway distinct from ammonia oxidizing bacteria (AOB). In contrast to other described AOA, these lowsalinity

Paul C. Blainey; Annika C. Mosier; Anastasia Potanina; Christopher A. Francis; Stephen R. Quake

2011-01-01T23:59:59.000Z

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


241

The fission yeast stress MAPK cascade regulates the pmp3+ gene that encodes a highly conserved plasma membrane protein.  

E-Print Network (OSTI)

transcription factor in fission yeast. Genes Dev. Degols, G.stress-activated kinase in fission yeast. Genes Dev. 12,MAP kinase pathway in fission yeast. Genes Dev. 10, 2289-

Wang, Ling-yu; Shiozaki, Kazuhiro

2006-01-01T23:59:59.000Z

242

The fission yeast stress MAPK cascade regulates the pmp3(+) gene that encodes a highly conserved plasma membrane protein  

E-Print Network (OSTI)

transcription factor in fission yeast. Genes Dev. Degols, G.stress-activated kinase in fission yeast. Genes Dev. 12,MAP kinase pathway in fission yeast. Genes Dev. 10, 2289-

Wang, Ling-yu; Shiozaki, Kazuhiro

2006-01-01T23:59:59.000Z

243

Spectral analysis of microarray gene expression time series data of Plasmodium falciparum  

Science Conference Proceedings (OSTI)

We propose a new strategy to analyse the periodicity of gene expression profiles using Singular Spectrum Analysis (SSA) and Autoregressive (AR) model based spectral estimation. By combining the advantages of SSA and AR modelling, more ... Keywords: SSA, autoregressive spectral estimation model, bioinformatics, drug discovery, gene expression profiles, gene target, microarray time series analysis, plasmodium falciparum, singular spectrum analysis

Liping Du; Shuanhu Wu; Alan Wee-Chung Liew; David K. Smith; Hong Yan

2008-07-01T23:59:59.000Z

244

An effective density-based hierarchical clustering technique to identify coherent patterns from gene expression data  

Science Conference Proceedings (OSTI)

We present an effective tree-based clustering technique (Gene ClusTree) for finding clusters over gene expression data. GeneClusTree attempts to find all the clusters over subspaces using a tree-based density approach by scanning the whole database in ... Keywords: coherent patterns, maximal space cluster, p-value, reduced space cluster, z-score

Sauravjyoti Sarmah; Rosy Das Sarmah; Dhruba Kumar Bhattacharyya

2011-05-01T23:59:59.000Z

245

Independent arrays or independent time courses for gene expression time series data analysis  

Science Conference Proceedings (OSTI)

In this paper we apply three different independent component analysis (ICA) methods, including spatial ICA (sICA), temporal ICA (tICA), and spatiotemporal ICA (stICA), to gene expression time series data and compare their performance in clustering genes ... Keywords: DNA microarray, Gene expression data, Independent component analysis, Principal component analysis

Sookjeong Kim; Jong Kyoung Kim; Seungjin Choi

2008-06-01T23:59:59.000Z

246

Analysis of mammary specific gene locus regulation in differentiated cells derived by somatic cell fusion  

Science Conference Proceedings (OSTI)

The transcriptional regulation of a gene is best analysed in the context of its normal chromatin surroundings. However, most somatic cells, in contrast to embryonic stem cells, are refractory to accurate modification by homologous recombination. We show here that it is possible to introduce precise genomic modifications in ES cells and to analyse the phenotypic consequences in differentiated cells by using a combination of gene targeting, site-specific recombination and somatic cell fusion. To provide a proof of principle, we have analysed the regulation of the casein gene locus in mammary gland cells derived from modified murine ES cells by somatic cell fusion. A {beta}-galactosidase reporter gene was inserted in place of the {beta}-casein gene and the modified ES cells, which do not express the reporter gene, were fused with the mouse mammary gland cell line HC11. The resulting cell clones expressed the {beta}-galactosidase gene to a similar extent and with similar hormone responsiveness as the endogenous gene. However, a reporter gene under the control of a minimal {beta}-casein promoter (encompassing the two consensus STAT5 binding sites which mediate the hormone response of the casein genes) was unable to replicate expression levels or hormone responsiveness of the endogenous gene when inserted into the same site of the casein locus. As expected, these results implicate sequences other than the STAT5 sites in the regulation of the {beta}-casein gene.

Robinson, Claire [Molecular Recognition Group, Hannah Research Institute, Ayr KA6 5HL (United Kingdom); Kolb, Andreas F. [Molecular Recognition Group, Hannah Research Institute, Ayr KA6 5HL (United Kingdom)], E-mail: a.kolb@rowett.ac.uk

2009-02-01T23:59:59.000Z

247

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

248

Manipulating Genes with Hidden TALENs | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

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

249

Finding genes in DNA using decision trees and dynamic programming  

E-Print Network (OSTI)

{ salz berg,xchendhndrsn}:~cs.jhu.edu,kewf~gdb.org This study demonstrates the use of decision tree classifiers as the basis for a general gene-finding system. The system uses a dynamic programming algorithm that. finds the optimal segmentation of a DNA sequence into coding and noncoding regions (exons and introits).]he optimality property is dependent oll a separate scoring function that takes a subsequence and assigns to it a score reflecting the probability that the sequence is an exon. In this study, the scoring functions were sets of decision trees and rules that were combined to give the probability estimate. Experimental results on a newly collected database of human DNA sequences are encouraging, and some new observations about the structure of classifiers for tile gene-finding problem have emerged from this study. We also provide descriptions of a new probability chain model that produces very accurate filters to find donor and acceptor sites.

Steven Salzberg; Xin Chen; John Henderson; Kenneth Fasman

1996-01-01T23:59:59.000Z

250

Gene flow and the genealogical history of Heliconius heurippa  

E-Print Network (OSTI)

that H. heurippa is a distinct species and not simply a geographic race of H. cydno; H. heurippa is considerably more differentiated than any other geo- graphic populations of H. melpomene or H. cydno sampled in Panama, Colombia and Venezuela [26... ). It seems likely that there is a hybrid zone between these species somewhere in the Andes between Villavicencio (Colombia) and San Cristobal (Venezuela; Linares Pers. Obs.), which would explain the observed levels of gene flow. Allele networks for nuclear...

Salazar, Camilo; Jiggins, Chris D; Taylor, Jesse E; Kronforst, Marcus R; Linares, Mauricio

2008-05-02T23:59:59.000Z

251

Cloning of the canine glucose-6-phosphatase gene  

SciTech Connect

Two Maltese puppies with massive hepatomegaly and failure to thrive were found to have a markedly reduced Glucose-6-phosphatase (G-6-Pase) activity in the liver and kidney. Deficiency of G-6-Pase activity causes type 1a glycogen storage disease in humans. To further study the mutation responsible for the disease in dog, we cloned G-6-Pase canine cDNA from normal mixed breed dog liver RNA using reverse transcriptase and PCR amplification using primers derived from the published murine G-6-Pase gene sequence. Sequencing revealed an open reading frame of 1071 nucleotides that encodes a predicted 357 amino acid polypeptide in the canine G-6-Pase gene, same as mouse and human. We found more than 90% sequence homology between dog and human G-6-Pase sequence. Hydropathy analysis of the deduced canine G-6-Pase polypeptide shows six transmembrane-spanning segments similar to those seen in human and mouse. Endoplasmic reticulum (ER) localization is similarly predicted by the presence of the ER protein retention signal KK positioned 3 and 4 amino acids from the carboxy terminal. Potential asparagine-linked glycosylation sites are identified at positions 96, 203, and 276. Northern blot analysis revealed increased G-6-Pase mRNA in the deficient dog liver compared to control. This could possibly reflect upregulation of transcription due to the persistent hypoglycemic state. Further studies are directed at the identification of the mutation involved in this deficient dog strain. Characterization of the G-6-Pase gene and protein in the deficient dog model can pave the way for new understanding in the pathophysiology of this disease and for the trials of novel therapeutic approaches including gene therapy.

Kishnani, P.; Bao, Y. [Duke University Medical Center, Durham, NC (United States); Brix, A.E. [and others

1994-09-01T23:59:59.000Z

252

Ayuda:Imágenes | Open Energy Information  

Open Energy Info (EERE)

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

253

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

254

Probing cell-free gene expression noise in femtoliter volumes  

SciTech Connect

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

255

PHYLOGENOMICS - GUIDED VALIDATION OF FUNCTION FOR CONSERVED UNKNOWN GENES  

SciTech Connect

Identifying functions for all gene products in all sequenced organisms is a central challenge of the post-genomic era. However, at least 30-50% of the proteins encoded by any given genome are of unknown function, or wrongly or vaguely annotated. Many of these 'unknown' proteins are common to prokaryotes and plants. We accordingly set out to predict and experimentally test the functions of such proteins. Our approach to functional prediction is integrative, coupling the extensive post-genomic resources available for plants with comparative genomics based on hundreds of microbial genomes, and functional genomic datasets from model microorganisms. The early phase is computer-assisted; later phases incorporate intellectual input from expert plant and microbial biochemists. The approach thus bridges the gap between automated homology-based annotations and the classical gene discovery efforts of experimentalists, and is much more powerful than purely computational approaches to identifying gene-function associations. Among Arabidopsis genes, we focused on those (2,325 in total) that (i) are unique or belong to families with no more than three members, (ii) are conserved between plants and prokaryotes, and (iii) have unknown or poorly known functions. Computer-assisted selection of promising targets for deeper analysis was based on homology .. independent characteristics associated in the SEED database with the prokaryotic members of each family, specifically gene clustering and phyletic spread, as well as availability of functional genomics data, and publications that could link candidate families to general metabolic areas, or to specific functions. In-depth comparative genomic analysis was then performed for about 500 top candidate families, which connected ~55 of them to general areas of metabolism and led to specific functional predictions for a subset of ~25 more. Twenty predicted functions were experimentally tested in at least one prokaryotic organism via reverse genetics, metabolic profiling, functional complementation, and recombinant protein biochemistry. Our approach predicted and validated functions for 10 formerly uncharacterized protein families common to plants and prokaryotes; none of these functions had previously been correctly predicted by computational methods. The functions of five more are currently being validated. Experimental testing of diverse representatives of these families combined with in silica analysis allowed accurate projection of the annotations to hundreds more sequenced genomes.

V, DE CRECY-LAGARD; D, HANSON A

2012-01-03T23:59:59.000Z

256

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

257

A phylogenomic gene cluster resource: The phylogeneticallyinferred groups (PhlGs) database  

SciTech Connect

We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community.

Dehal, Paramvir S.; Boore, Jeffrey L.

2005-08-25T23:59:59.000Z

258

09/13/2007 08:42 PMTweaking Genes Could Extend ALS Survival Page 1 of 1http://health.usnews.com/usnews/health/healthday/070913/tweaking-genes-could-extend-als-survival.htm  

E-Print Network (OSTI)

09/13/2007 08:42 PMTweaking Genes Could Extend ALS Survival Page 1 of 1http://health.usnews.com/usnews/health/healthday/070913/tweaking-genes-could-extend-als-survival.htm Tweaking Genes Could Extend ALS Survival Mouse study.S. scientists say they've spotted genes that influence survival in mice with amyotrophic lateral sclerosis (ALS

Engelhardt, John F.

259

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 can provide information about these complex traits. We used real-time quantitative polymerase chain reaction (PCR) to detect variations in the expression of 88 disease- and drought-responsive genes within an association population of 354 loblolly pine trees (Pinus taeda L.). Using association genetics approaches, we then linked 3,938 single nucleotide polymorphisms (SNPs) in candidate genes with gene expression phenotypes to identify novel disease- and drought-responsive genes. To further examine differences in gene expression induced by drought, Fusarium circinatum (responsible for pitch canker disease), and drought F. circinatum, the expression of 114 genes identified through comparative and association genetics approaches was analyzed on a subset of 24 loblolly pine trees possessing a range of pitch canker- and drought-resistance phenotypes. Significant differences in the uninduced expression of all 88 genes measured on the association population were observed among loblolly pine trees. Principal component analysis showed that some variation within the association population could be accounted for by population substructure of geographic origin. Hierarchical clustering of genes based on uninduced expression did not consistently group together functionally similar genes probably because expression was collected on unstressed stem tissue. This was supported in the smaller expression study as correlations between expression values of genes in the same functional networks were usually stronger when induced by a treatment compared with correlations between the uninduced expression of genes in the control group. Gene expression frequently changed by up to 4-fold in response to one or more treatments, but PtMYB12 was the only gene that exhibited a statistically significant change in response to treatments. ANOVA analyses of gene expression controlling for pitch canker resistance and for water use efficiency phenotypes identified differentially expressed genes suggesting that they may be contributing to these phenotypes. Finally, association genetics approaches detected 101 significant associations between SNPs in 94 candidate genes potentially involved in stress responses and 27 gene expression phenotypes.

Seeve, Candace Marie

2010-12-01T23:59:59.000Z

260

Imaging gene expression in real-time using aptamers  

Science Conference Proceedings (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 (Frster 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

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

Structural comparison and chromosomal localization of the human and mouse IL-13 genes  

SciTech Connect

The genomic structure of the recently described cytokine IL-13 has been determined for both human and mouse genes. The nucleotide sequence of a 4.6-kb DNA segment of the human gene is described. The human IL-13 gene (IL 13) occurs as a single copy in the haploid genome and maps to human chromosome 5. A 4.3-kb DNA fragment of the mouse IL-13 gene (Il 13) has been sequenced and found to occur as a single copy, mapping to mouse chromosome 11. Intrachromosomal mapping studies revealed that both genes contain four exons and three introns and show a high degree of sequence identify throughout their length. Potential recognition sequences for transcription factors that are present in the 5'-flanking region and are conserved between both genes include IFN-responsive elements, binding sites for AP-1, AP-2, and AP-3, an NF-lL 6 site, and a TATA-like sequence. Both genes map to chromosomal locations adjacent to genes encoding other cytokines, including IL-3, GM-CSF, IL-5, and IL-4 suggesting that IL-13 is another member of this cytokine gene family that may have arisen by gene duplication. 26 refs., 5 figs., 3 tabs.

McKenzie, A.N.J.; Sato, A.; Doyle, E.L.; Zurawski, G. (DNAX Research Institute of Cellular and Molecular Biology, Palo Alto, CA (United States)); Li, X.; Milatovich, A.; Francke, U. (Stanford Univ. Medical School, CA (United States)); Largaespada, D.A.; Copeland, N.G.; Jenkins, N.A. (National Cancer Institute, Frederick, MD (United States))

1993-06-15T23:59:59.000Z

262

(Organization and regulation of the genes for nitrogen fixation in Rhodopseudomonas capsulata)  

DOE Green Energy (OSTI)

In prior support periods we identified, cloned and sequenced three genes involved in the regulation of nif gene expression in Rhodobacter capsulatus. These were called nifRI, nifR2 and nifR4; they turn out to be homologue of the ntrC, ntrB and ntrA genes of enterobacteria. We subsequently found that mutations in an additional gene, nifR5. render R. capsulatus nif genes constitutive with respect to ammonia. The nifR5 gene was shown to be similar to glnB of enteric bacteria, encoding the regulatory protein PII, and furthering the intersection of the glutamine synthetase adenylylation cascade with the control of nif gene transcription. In pursuit of the mechanism of 0{sub 2} control of nif gene expression, we constructed and analyzed the topology of a small plasmid in R. capsulatus as a function of 0{sub 2} concentration. We also cloned and obtained partial sequence data for two genes encoding the B subunit of DNA gyrase. The nucleotide sequence of the rpoB gene encoding RNA polymerase was nearly completed. A method for isolation of genes expressed differentially, developed for cyanobacteria, was applied successfully to R. capsulatus. Several genes that depend on nifR4 for their transcription were isolated. A transcription start site for a nifA gene was identified and the promoter sequence was analyzed. A physical map of the R calsulatus SB1003 chromosome was prepared, based on pulsed-field electrophoresis of XbaI and AseI fragments and hybridization with a gridded cosmid library, using a device that permits 864 cosmids to be hybridized at one time with a labeled chromosomal fragment.

Not Available

1991-01-01T23:59:59.000Z

263

A hierarchy of ECM-mediated signalling tissue-specific gene expression regulates tissue-specific gene expression  

SciTech Connect

A dynamic and reciprocal flow of information between cells and the extracellular matrix contributes significantly to the regulation of form and function in developing systems. Signals generated by the extracellular matrix do not act in isolation. Instead, they are processed within the context of global signalling hierarchies whose constituent inputs and outputs are constantly modulated by all the factors present in the cell's surrounding microenvironment. This is particularly evident in the mammary gland, where the construction and subsequent destruction of such a hierarchy regulates changes in tissue-specific gene expression, morphogenesis and apoptosis during each developmental cycle of pregnancy, lactation and involution.

Roskelley, Calvin D; Srebrow, Anabella; Bissell, Mina J

1995-10-07T23:59:59.000Z

264

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

265

Molecular Assemblies, Genes and Genomics Integrated Efficiently (MAGGIE)  

Science Conference Proceedings (OSTI)

Final report on MAGGIE. We set ambitious goals to model the functions of individual organisms and their community from molecular to systems scale. These scientific goals are driving the development of sophisticated algorithms to analyze large amounts of experimental measurements made using high throughput technologies to explain and predict how the environment influences biological function at multiple scales and how the microbial systems in turn modify the environment. By experimentally evaluating predictions made using these models we will test the degree to which our quantitative multiscale understanding wilt help to rationally steer individual microbes and their communities towards specific tasks. Towards this end we have made substantial progress towards understanding evolution of gene families, transcriptional structures, detailed structures of keystone molecular assemblies (proteins and complexes), protein interactions, biological networks, microbial interactions, and community structure. Using comparative analysis we have tracked the evolutionary history of gene functions to understand how novel functions evolve. One level up, we have used proteomics data, high-resolution genome tiling microarrays, and 5' RNA sequencing to revise genome annotations, discover new genes including ncRNAs, and map dynamically changing operon structures of five model organisms: For Desulfovibrio vulgaris Hildenborough, Pyrococcus furiosis, Sulfolobus solfataricus, Methanococcus maripaludis and Haiobacterium salinarum NROL We have developed machine learning algorithms to accurately identify protein interactions at a near-zero false positive rate from noisy data generated using tagfess complex purification, TAP purification, and analysis of membrane complexes. Combining other genome-scale datasets produced by ENIGMA (in particular, microarray data) and available from literature we have been able to achieve a true positive rate as high as 65% at almost zero false positives when applied to the manually curated training set. Applying this method to the data representing around a quarter of the fraction space for water soluble proteins in D. vulgaris, we obtained 854 reliable pair wise interactions. Further, we have developed algorithms to analyze and assign significance to protein interaction data from bait pull-down experiments and integrate these data with other systems biology data through associative biclustering in a parallel computing environment. We will 'fill-in' missing information in these interaction data using a 'Transitive Closure' algorithm and subsequently use 'Between Commonality Decomposition' algorithm to discover complexes within these large graphs of protein interactions. To characterize the metabolic activities of proteins and their complexes we are developing algorithms to deconvolute pure mass spectra, estimate chemical formula for m/z values, and fit isotopic fine structure to metabolomics data. We have discovered that in comparison to isotopic pattern fitting methods restricting the chemical formula by these two dimensions actually facilitates unique solutions for chemical formula generators. To understand how microbial functions are regulated we have developed complementary algorithms for reconstructing gene regulatory networks (GRNs). Whereas the network inference algorithms cMonkey and Inferelator developed enable de novo reconstruction of predictive models for GRNs from diverse systems biology data, the RegPrecise and RegPredict framework developed uses evolutionary comparisons of genomes from closely related organisms to reconstruct conserved regulons. We have integrated the two complementary algorithms to rapidly generate comprehensive models for gene regulation of understudied organisms. Our preliminary analyses of these reconstructed GRNs have revealed novel regulatory mechanisms and cis-regulatory motifs, as well asothers that are conserved across species. Finally, we are supporting scientific efforts in ENIGMA with data management solutions and by integrating all of the algorithms, software and data into

Nitin S. Baliga

2011-05-26T23:59:59.000Z

266

Molecular Assemblies, Genes and Genomics Integrated Efficiently (MAGGIE)  

SciTech Connect

Final report on MAGGIE. We set ambitious goals to model the functions of individual organisms and their community from molecular to systems scale. These scientific goals are driving the development of sophisticated algorithms to analyze large amounts of experimental measurements made using high throughput technologies to explain and predict how the environment influences biological function at multiple scales and how the microbial systems in turn modify the environment. By experimentally evaluating predictions made using these models we will test the degree to which our quantitative multiscale understanding wilt help to rationally steer individual microbes and their communities towards specific tasks. Towards this end we have made substantial progress towards understanding evolution of gene families, transcriptional structures, detailed structures of keystone molecular assemblies (proteins and complexes), protein interactions, biological networks, microbial interactions, and community structure. Using comparative analysis we have tracked the evolutionary history of gene functions to understand how novel functions evolve. One level up, we have used proteomics data, high-resolution genome tiling microarrays, and 5' RNA sequencing to revise genome annotations, discover new genes including ncRNAs, and map dynamically changing operon structures of five model organisms: For Desulfovibrio vulgaris Hildenborough, Pyrococcus furiosis, Sulfolobus solfataricus, Methanococcus maripaludis and Haiobacterium salinarum NROL We have developed machine learning algorithms to accurately identify protein interactions at a near-zero false positive rate from noisy data generated using tagfess complex purification, TAP purification, and analysis of membrane complexes. Combining other genome-scale datasets produced by ENIGMA (in particular, microarray data) and available from literature we have been able to achieve a true positive rate as high as 65% at almost zero false positives when applied to the manually curated training set. Applying this method to the data representing around a quarter of the fraction space for water soluble proteins in D. vulgaris, we obtained 854 reliable pair wise interactions. Further, we have developed algorithms to analyze and assign significance to protein interaction data from bait pull-down experiments and integrate these data with other systems biology data through associative biclustering in a parallel computing environment. We will 'fill-in' missing information in these interaction data using a 'Transitive Closure' algorithm and subsequently use 'Between Commonality Decomposition' algorithm to discover complexes within these large graphs of protein interactions. To characterize the metabolic activities of proteins and their complexes we are developing algorithms to deconvolute pure mass spectra, estimate chemical formula for m/z values, and fit isotopic fine structure to metabolomics data. We have discovered that in comparison to isotopic pattern fitting methods restricting the chemical formula by these two dimensions actually facilitates unique solutions for chemical formula generators. To understand how microbial functions are regulated we have developed complementary algorithms for reconstructing gene regulatory networks (GRNs). Whereas the network inference algorithms cMonkey and Inferelator developed enable de novo reconstruction of predictive models for GRNs from diverse systems biology data, the RegPrecise and RegPredict framework developed uses evolutionary comparisons of genomes from closely related organisms to reconstruct conserved regulons. We have integrated the two complementary algorithms to rapidly generate comprehensive models for gene regulation of understudied organisms. Our preliminary analyses of these reconstructed GRNs have revealed novel regulatory mechanisms and cis-regulatory motifs, as well asothers that are conserved across species. Finally, we are supporting scientific efforts in ENIGMA with data management solutions and by integrating all of the algorithms, software and data into

Nitin S. Baliga

2011-05-26T23:59:59.000Z

267

Sequence of the dog immunoglobulin alpha and epsilon constant region genes  

SciTech Connect

The immunoglobulin alpha (IGHAC) and epsilon (IGHEC) germline constant region genes were isolated from a dog liver genomic DNA library. Sequence analysis indicates that the dog IGHEC gene is encoded by four exons spread out over 1.7 kilobases (kb). The IGHAC sequence encompasses 1.5 kb and includes all three constant region coding exons. The complete exon/intron sequence of these genes is described. 28 refs., 2 figs., 2 tabs.

Patel, M.; Selinger, D.; Mark, G.E.; Hollis, G.F.; Hickey, G.J. [Merck Research Labs., Rathway, NJ (United States)

1995-03-01T23:59:59.000Z

268

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

269

Gene Brooks and His Contributions to the American Choral Directors Association.  

E-Print Network (OSTI)

?? In his thirty years as Executive Director of ACDA, Dr. Gene Brooks has demonstrated his passion for choral music through his work in the (more)

Zamer, Craig

2007-01-01T23:59:59.000Z

270

Antisense oligodeoxynucleotide inhibition as a potent diagnostic tool for gene function in plant biology  

E-Print Network (OSTI)

for gene function in plant biology Chuanxin Sun 1 , HaileDepartment of Plant Biology & Forest Genetics, UppsalaJansson, Department of Plant Biology & Forest Genetics, The

Sun, Chuanxin

2008-01-01T23:59:59.000Z

271

Gene Repression and Cell Cycle Regulation by PU.1 in Acute Myeloid Leukemia.  

E-Print Network (OSTI)

??Acute myeloid leukemia (AML) is associated with mutations or chromosomal translocations in genes encoding transcription factors. PU.1 is a transcription factor that is required for (more)

Ziliotto, Rachel GH

2013-01-01T23:59:59.000Z

272

Over-expressing a barley ZIP gene doubles grain zinc content in barley (Hordeum vulgare)  

E-Print Network (OSTI)

the ZRT, IRT-related protein (ZIP) family have recently beenover-expressing a barley ZIP gene, HvZIP7 to evaluate its

Tiong, Jingwen; Genc, Yusuf; McDonald, Glenn K; Langridge, Peter; Huang, Chun Y Dr

2009-01-01T23:59:59.000Z

273

An efficient method for exploring the space of gene tree ... - CECM  

E-Print Network (OSTI)

Apr 20, 2011 ... To compute the posterior probability distribution of a subset of .... synthetic gene trees generation process we followed is based on several...

274

Major genes and QTL influencing wool production and quality: a review  

E-Print Network (OSTI)

Abstract The opportunity exists to utilise our knowledge of major genes that influence the economically important traits in wool sheep. Genes with Mendelian inheritance have been identified for many important traits in wool sheep. Of particular importance are genes influencing pigmentation, wool quality and the keratin proteins, the latter of which are important for the morphology of the wool fibre. Gene mapping studies have identified some chromosomal regions associated with variation in wool quality and production traits. The challenge now is to build on this knowledge base in a cost-effective way to deliver molecular tools that facilitate enhanced genetic improvement programs for wool sheep.

Ian William Purvis; Ian Robert Franklin

2004-01-01T23:59:59.000Z

275

The role of sequence, gene orientation, and intergenic distance in chromatin structure and function  

E-Print Network (OSTI)

Bernstein BE (2008) Chromatin state maps: new technologies,histone modifications and chromatin remodeling. Proc Natladdress biases associated with chromatin structure or gene

Langley, Sasha A.

2010-01-01T23:59:59.000Z

276

Antisense oligodeoxynucleotide inhibition as a potent diagnostic tool for gene function in plant biology  

E-Print Network (OSTI)

B, man P, Jansson C. Starch branching enzymes in sorghum (Sorghum bicolor) and barley (Hordeum vulgare): Comparativethe sbeIIb genes in sorghum (Sorghum bicolor) and barley (

Sun, Chuanxin

2008-01-01T23:59:59.000Z

277

Circadian oscillation of starch branching enzyme gene expression in the sorghum endosperm  

E-Print Network (OSTI)

B, Aman P, Jansson C. Starch branching enzymes in sorghum (Sorghum bicolor) and barley (Hordeum vulgare): Comparativethe sbellb genes in sorghum (Sorghum bicolor) and barley (

Mutisya, J.

2010-01-01T23:59:59.000Z

278

Gene copy number studies in archived and fresh mouse tissue samples  

NLE Websites -- All DOE Office Websites (Extended Search)

sections from archived samples were used for DNA isolation and quantitative real time PCR amplification that revealed variations in mitochondrial gene copy numbers in different...

279

Effects of Oilseed Meals and Isothiocyanates (ITCS) on Phymatotrichopsis omnivora (Cotton Root Rot) and Soil Microbial Communities  

E-Print Network (OSTI)

The meals from many oilseed crops contain biocidal chemicals that are known to inhibit the growth and activity of several soil pathogens, though little is known concerning impacts on whole soil microbial communities. We investigated the effect of oilseed meals (SMs) from both brassicaceous plants, including mustard and camelina, as well as non-brassicaceous plants, including jatropha and flax, on P. omnivora (the casual agent of cotton root rot) in Branyon clay soil (at 1 and 5% application rates). We also investigated the effect of SMs from camelina, jatropha, flax, and wheat straw on microbial communities in Weswood loam soil. We also used four types of isothiocyanates (ITCs) including allyl, butyl, phenyl, and benzyl ITC to test their effects on P. omnivora growth on potato dextrose agar (PDA), as well as on soil microbial communities in a microcosm study. Community qPCR assays were used to evaluate relative abundances of soil microbial populations. Soil microbial community composition was determined through tag-pyrosequencing using 454 GS FLX titanium technology, targeting ITS and 16S rRNA gene regions for fungal and bacterial communities, respectively. The results showed that all tested brassicaceous and jatropha SMs were able to inhibit P. omnivora sclerotial germination and hyphal growth, with mustard SM being the most effective. Flax didn't show any inhibitory effects on sclerotial germination. All tested ITCs inhibited P. omnivora OKAlf8 hyphal growth, and the level of inhibition varied with concentration and ITC type. Total soil fungal populations were reduced by ITC addition, and microbial community compositions were changed following SM and ITC application. These changes varied according to the type of SM or ITC added. Our results indicated that SMs of several brassicaceous species as well as jatropha may have potential for reducing cotton root rot as well as some other pathogens. Different SMs releasing varied ITCs may result in differential impacts on soil microorganisms including some pathogens.

Hu, Ping

2012-05-01T23:59:59.000Z

280

Archaeal community composition affects the function of anaerobic co-digesters in response to organic overload  

Science Conference Proceedings (OSTI)

Highlights: Black-Right-Pointing-Pointer Two types of methanogens are necessary to respond successfully to perturbation. Black-Right-Pointing-Pointer Diversity of methanogens correlates with the VFA concentration and methane yield. Black-Right-Pointing-Pointer Aggregates indicate tight spatial relationship between minerals and microorganisms. - Abstract: Microbial community diversity in two thermophilic laboratory-scale and three full-scale anaerobic co-digesters was analysed by genetic profiling based on PCR-amplified partial 16S rRNA genes. In parallel operated laboratory reactors a stepwise increase of the organic loading rate (OLR) resulted in a decrease of methane production and an accumulation of volatile fatty acids (VFAs). However, almost threefold different OLRs were necessary to inhibit the gas production in the reactors. During stable reactor performance, no significant differences in the bacterial community structures were detected, except for in the archaeal communities. Sequencing of archaeal PCR products revealed a dominance of the acetoclastic methanogen Methanosarcina thermophila, while hydrogenotrophic methanogens were of minor importance and differed additionally in their abundance between reactors. As a consequence of the perturbation, changes in bacterial and archaeal populations were observed. After organic overload, hydrogenotrophic methanogens (Methanospirillum hungatei and Methanoculleus receptaculi) became more dominant, especially in the reactor attributed by a higher OLR capacity. In addition, aggregates composed of mineral and organic layers formed during organic overload and indicated tight spatial relationships between minerals and microbial processes that may support de-acidification processes in over-acidified sludge. Comparative analyses of mesophilic stationary phase full-scale reactors additionally indicated a correlation between the diversity of methanogens and the VFA concentration combined with the methane yield. This study demonstrates that the coexistence of two types of methanogens, i.e. hydrogenotrophic and acetoclastic methanogens is necessary to respond successfully to perturbation and leads to stable process performance.

Lerm, S.; Kleyboecker, A. [International Centre for Geothermal Research (ICGR), GFZ German Research Centre for Geosciences, 14473 Potsdam (Germany); Miethling-Graff, R. [International Centre for Geothermal Research (ICGR), GFZ German Research Centre for Geosciences, 14473 Potsdam (Germany); Johann Heinrich von Thuenen Institut, Bundesforschungsinstitut fuer Laendliche Raeume, Wald und Fischerei Institut fuer Biodiversitaet, 38116 Braunschweig (Germany); Alawi, M.; Kasina, M.; Liebrich, M. [International Centre for Geothermal Research (ICGR), GFZ German Research Centre for Geosciences, 14473 Potsdam (Germany); Wuerdemann, H., E-mail: wuerdemann@gfz-potsdam.de [International Centre for Geothermal Research (ICGR), GFZ German Research Centre for Geosciences, 14473 Potsdam (Germany)

2012-03-15T23:59:59.000Z

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


281

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

Science Conference Proceedings (OSTI)

The microbial diversity in subsurface sediments at the Hanford Site's 300 Area in southeastern Washington State was investigated by analyzing 21 samples recovered from depths that ranged from 9 to 52 m. Approximately 8000 non-chimeric Bacterial and Archaeal 16S rRNA gene sequences were analyzed across geological strata that contain 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, defined at the 97% identity level). Microbial community structure and richness varied substantially across the different geological strata. Bacterial OTU richness (based upon 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 transition zone, richness was about 325 and declined to less than 50 in the deeper reduced zones. The Bacterial community in the oxic Hanford and Ringold Formations contained members of 9 major well-recognized phyla as well 30 as unusually high proportions of 3 candidate divisions (GAL15, NC10, and SPAM). The deeper Ringold strata were characterized by low OTU richness and a very high preponderance (ca. 90%) of Proteobacteria. The study has greatly expanded the intralineage phylogenetic diversity within some major divisions. These subsurface sediments have been shown to contain a large number of phylogenetically novel microbes, with substantial heterogeneities between sediment samples from the same geological formation.

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

2012-02-01T23:59:59.000Z

282

Microbial dynamics during intrinsic remediation of oil contaminated coastal wetland sediments (a microcosm study)  

E-Print Network (OSTI)

Arabian medium crude oil was applied to historically exposed estuarine sediments contained in a controlled laboratory environment and intrinsically remediated for 56 days. In situ microbial and petroleum dynamics were monitored via Most Probable Number (MPN) statistical analysis, Gas Chromatography-Mass Spectroscopy (GC-MS) and denaturing gradient gel electrophoresis of polymerase chain reaction-amplified 16S rRNA gene fragments (PCR-DGGE). The microbial community was monitored to determine (i) the extent of intrinsic remediation and (ii) if hydrocarbon contamination caused structural changes to chronically exposed microbial communities. MPN statistical analysis revealed that the addition of oil caused 3-fold increases in both aliphatic and aromatic-degrading bacteria. Petroleum chemistry demonstrated a concomitant decrease of aliphatic and aromatic hydrocarbon fractions. Therefore, an inverse relationship between hydrocarbon-degrading bacterial populations and hydrocarbon concentrations was observed throughout the experiment, illustrating that oil was being intrinsically remediated. Kinetic analysis showed that the aliphatic and aromatic hydrocarbons had a half-life of 18 and 56 days, respectively. While MPN and GC-MS analysis showed that microbial populations were increasing and hydrocarbon concentrations were decreasing, PCR-DGGE analysis revealed that the addition of oil to a complex microbial community had no detectable effect upon the microbial structure. Community changes that occurred in sediments with oil were consistent with those observed in unoiled sediments. Band pattern analysis revealed that microbial community dynamics were independent of oil contamination. Therefore, when historically contaminated sediments are re-exposed to hydrocarbon pollution, the overall structure of the microbial community as detected by PCR-DGGE is negligibly affected, however dominance of specific subpopulations (i.e. aliphatic and aromatic hydrocarbon-degraders) can change significantly.

Thornburg, Nathaniel David

2001-01-01T23:59:59.000Z

283

Mercury and other heavy metals influence bacterial community structure in contaminated Tennessee streams  

Science Conference Proceedings (OSTI)

High concentrations of uranium, inorganic mercury [Hg(II)], and methylmercury (MeHg) have been detected in streams located in the Department of Energy reservation in Oak Ridge, TN. To determine the potential effects of the surface water contamination on the microbial community composition, surface stream sediments were collected 7 times during the year, from 5 contaminated locations and 1 control stream. Fifty-nine samples were analyzed for bacterial community composition and geochemistry. Community characterization was based on GS 454 FLX pyrosequencing with 235 Mb of 16S rRNA gene sequence targeting the V4 region. Sorting and filtering of the raw reads resulted in 588,699 high-quality sequences with lengths of >200 bp. The bacterial community consisted of 23 phyla, including Proteobacteria (ranging from 22.9 to 58.5% per sample), Cyanobacteria (0.2 to 32.0%), Acidobacteria (1.6 to 30.6%), Verrucomicrobia (3.4 to 31.0%), and unclassified bacteria. Redundancy analysis indicated no significant differences in the bacterial community structure between midchannel and near-bank samples. Significant correlations were found between the bacterial community and seasonal as well as geochemical factors. Furthermore, several community members within the Proteobacteria group that includes sulfate-reducing bacteria and within the Verrucomicrobia group appeared to be associated positively with Hg and MeHg. This study is the first to indicate an influence of MeHg on the in situ microbial community and suggests possible roles of these bacteria in the Hg/MeHg cycle.

Vishnivetskaya, Tatiana A [ORNL; Mosher, Jennifer J [ORNL; Palumbo, Anthony Vito [ORNL; Yang, Zamin [ORNL; Podar, Mircea [ORNL; Brown, Steven D [ORNL; Brooks, Scott C [ORNL; Gu, Baohua [ORNL; Southworth, George R [ORNL; Drake, Meghan M [ORNL; Brandt, Craig C [ORNL; Elias, Dwayne A [ORNL

2011-01-01T23:59:59.000Z

284

Insights into the Structure and Metabolic Function of Microbes That Shape Pelagic Iron-Rich Aggregates ( Iron Snow )  

SciTech Connect

Metaproteomics combined with total nucleic acid-based methods aided in deciphering the roles of microorganisms in the formation and transformation of iron-rich macroscopic aggregates (iron snow) formed in the redoxcline of an acidic lignite mine lake. Iron snow had high total bacterial 16S rRNA gene copies, with 2 x 109 copies g (dry wt)-1 in the acidic (pH 3.5) central lake basin and 4 x 1010 copies g (dry wt)-1 in the less acidic (pH 5.5) northern lake basin. Active microbial communities in the central basin were dominated by Alphaproteobacteria (36.6%) and Actinobacteria (21.4%), and by Betaproteobacteria (36.2%) in the northern basin. Microbial Fe-cycling appeared to be the dominant metabolism in the schwertmannite-rich iron snow, because cloning and qPCR assigned up to 61% of active bacteria as Fe-cycling bacteria (FeB). Metaproteomics revealed 70 unique proteins from central basin iron snow and 283 unique proteins from 43 genera from northern basin. Protein identification provided a glimpse into in situ processes, such as primary production, motility, metabolism of acidophilic FeB, and survival strategies of neutrophilic FeB. Expression of carboxysome shell proteins and RubisCO indicated active CO2 fixation by Fe(II) oxidizers. Flagellar proteins from heterotrophs indicated their activity to reach and attach surfaces. Gas vesicle proteins related to CO2-fixing Chlorobium suggested that microbes could influence iron snow sinking. We suggest that iron snow formed by autotrophs in the redoxcline acts as a microbial parachute, since it is colonized by motile heterotrophs during sinking which start to dissolve schwertmannite.

Lu, S [Friedrich Schiller University Jena, Jena Germany; Chourey, Karuna [ORNL; REICHE, M [Friedrich Schiller University Jena, Jena Germany; Nietzsche, S [Friedrich Schiller University Jena, Jena Germany; Shah, Manesh B [ORNL; Hettich, Robert {Bob} L [ORNL; Kusel, K [Friedrich Schiller University Jena, Jena Germany

2013-01-01T23:59:59.000Z

285

Microsoft PowerPoint - gene_kight_panelist_presentation  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Fossil Energy R&D Fossil Energy R&D American Recovery & Reinvestment Act Projects 10 th Annual U.S. Department of Energy Small Business Conference Small Businesses Leading the Way to Recovery and Reinvestment Gene Kight Director, Finance and Procurement Office of Fossil Energy August 12, 2009 2 Small Businesses Leading the Way to Recovery and Reinvestment Expand and Extend Clean Coal Power Initiative (CCPI) Round 3 (Additional available CCPI funds total >$600 million) Industrial Carbon Capture and Storage Geologic Sequestration Site Characterization Geologic Sequestration Training & Research Carbon Capture and Storage (FutureGen Re-start) FE Program Direction $800 million $1.52 billion $50.0 million $20.0 million $1.0 billion

286

A2 Processor User's Manual for Blue Gene/Q  

NLE Websites -- All DOE Office Websites (Extended Search)

A2 Processor A2 Processor User's Manual for Blue Gene/Q Note: This document and the information it contains are provided on an as-is basis. There is no plan for providing for future updates and corrections to this document. October 23, 2012 Version 1.3 Title Page ® Copyright and Disclaimer © Copyright International Business Machines Corporation 2010, 2012 Printed in the United States of America October 2012 IBM, the IBM logo, and ibm.com are trademarks or registered trademarks of International Business Machines Corp., registered in many jurisdictions worldwide. Other product and service names might be trademarks of IBM or other compa- nies. A current list of IBM trademarks is available on the Web at "Copyright and trademark information" at www.ibm.com/legal/copytrade.shtml.

287

Cold, Salty and Promiscuous-Gene-shuffling Microbes Dominate  

NLE Websites -- All DOE Office Websites (Extended Search)

September 30, 2013 September 30, 2013 Cold, Salty and Promiscuous—Gene-shuffling Microbes Dominate Antarctica’s Deep Lake Sequestered in Antarctica's Vestfold Hills, Deep Lake became isolated from the ocean 3,500 years ago by the Antarctic continent rising, resulting in a saltwater ecosystem that remains liquid in extreme cold, and providing researchers a unique niche for studying the evolution of the microbes that now thrive under such conditions. Deep Lake's microscopic inhabitants are dominated by haloarchaea, microbes that require high salt concentrations to grow and are naturally adapted to conditions - at minus 20°C - that would prove lethally cold to other organisms. In a detailed analysis published online the week of September 30, 2013 in the journal Proceedings

288

Performance Evaluation of Gene Expression Programming for Hydraulic Data Mining  

E-Print Network (OSTI)

Abstract: Predication is one of the fundamental tasks of data mining. In recent years, Artificial Intelligence techniques are widely being used in data mining applications where conventional statistical methods were used such as Regression and classification. The aim of this work is to show the applicability of Gene Expression Programming (GEP), a recently developed AI technique, for hydraulic data prediction and to evaluate its performance by comparing it with Multiple Linear Regression (MLR). Both GEP and MLR were used to model the hydraulic jump over a roughened bed using very large series of experimental data that contain all the important flow and roughness parameters such as the initial Froude number, the height of roughness ratio, the length of roughness ratio, the initial length ratio (from the gate) and the roughness density. The results show that GEP is a promising AI approach for hydraulic data prediction.

Khalid Eldr; Abdel-azim Negm

2006-01-01T23:59:59.000Z

289

Identification of human gene core promoters in silico  

E-Print Network (OSTI)

Identification of the 5-end of human genes requires identification of functional promoter elements. In silico identification of those elements is difficult because of the hierarchical and modular nature of promoter architecture. To address this problem, I propose a new stepwise strategy based on initial localization of a functional promoter into a 1-2 kb (extended-promoter) region from within a large genomic DNA sequence of 100 kb or larger, and further localization of a Transcriptional Start Site (TSS) into a 50-100 bp (core-promoter) region. Using positional dependent 5-tuple measures, a Quadratic Discriminant Analysis (QDA) method has been implemented in a new program- CorePromoter. Our experiments indicate that when given a 1-2 kb extended promoter, CorePromoter will correctly localize the TSS to a 100 bp interval approximately 60 % of the time.

Michael Q. Zhang

1998-01-01T23:59:59.000Z

290

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

291

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

292

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

293

Identification of candidate genes in Populus cell wall biosynthesis using text-mining, co-expression network and comparative genomics  

SciTech Connect

Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of ethanol from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidences supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. The 694 Arabidopsis genes were computationally divided into 22 clusters. Queries of the Populus genome using the Arabidopsis genes revealed 817 Populus orthologs. Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional genomics in relation to cell wall biosynthesis.

Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Bisaria, Anjali [ORNL; Tuskan, Gerald A [ORNL; Kalluri, Udaya C [ORNL

2011-01-01T23:59:59.000Z

294

Complete Genome Sequence of the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aurantiacus  

Science Conference Proceedings (OSTI)

Chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. According to 16S rRNA analysis, Chloroflexi species are the earliest branching bacteria capable of photosynthesis, and Cfl. aurantiacus has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. Cfl. aurantiacus contains a chimeric photosystem that comprises some characters of green sulfur bacteria and purple photosynthetic bacteria, and also has some unique electron transport proteins compared to other photosynthetic bacteria.

Tang, Kuo-Hsiang [Washington University, St. Louis; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Honchak, Barbara M [Washington University, St. Louis; Karbach, Lauren E [Washington University, St. Louis; Land, Miriam L [ORNL; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Larimer, Frank W [ORNL; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Pierson, Beverly K [University of Puget Sound, Tacoma, WA

2011-01-01T23:59:59.000Z

295

A heuristic for gene selection and visual prediction of sample type  

Science Conference Proceedings (OSTI)

In this paper, we introduce a heuristic method for gene selection. We target this method, coupled with RadViz visualisation, to the visual prediction of tissue samples which may exist in normal and disease states. As a result of this coupling, the gene ...

Jianping Zhou; Georges Grinstein; Kenneth Marx

2011-07-01T23:59:59.000Z

296

Plasimids containing the gene for DNA polymerase I from Streptococcus pneumoniae  

DOE Patents (OSTI)

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

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

1991-01-01T23:59:59.000Z

297

Blue Gene/L compute chip: control, test, and bring-up infrastructure  

Science Conference Proceedings (OSTI)

The Blue Gene/L compute (BLC) and Blue Gene/L link (BLL) chips have extensive facilities for control, bring-up, self-test, debug, and nonintrusive performance monitoring built on a serial interface compliant with IEEE Standard 1149.1. Both the ...

R. A. Haring; R. Bellofatto; A. A. Bright; P. G. Crumley; M. B. Dombrowa; S. M. Douskey; M. R. Ellavsky; B. Gopalsamy; D. Hoenicke; T. A. Liebsch; J. A. Marcella; M. Ohmacht

2005-03-01T23:59:59.000Z

298

A novel approach to determine normal variation in gene expression data  

Science Conference Proceedings (OSTI)

Animal models for human diseases are of crucial importance for studying gene expression and regulation. In the last decade the development of mouse models for cancer, diabetes, neuro-degenerative and many other diseases has been on steady rise. Microarray ... Keywords: gene expression, hypertension, immune response, mouse models, normal variance, principal component analysis, replicates

Vinay Nadimpally; Mohammed J. Zaki

2003-12-01T23:59:59.000Z

299

An integrated algorithm for gene selection and classification applied to microarray data of ovarian cancer  

Science Conference Proceedings (OSTI)

Objective: The type of data in microarray provides unprecedented amount of data. A typical microarray data of ovarian cancer consists of the expressions of tens of thousands of genes on a genomic scale, and there is no systematic procedure to analyze ... Keywords: Gene selection, Genetic algorithm, Microarray data, Ovarian cancer, Particle swarm optimization, Support vector machine

Zne-Jung Lee

2008-01-01T23:59:59.000Z

300

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis  

E-Print Network (OSTI)

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively in an algorithm that allows us to bypass the gene trees and compute species tree likelihoods directly from

Rosenberg, Noah

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

An ant colony optimization based algorithm for identifying gene regulatory elements  

Science Conference Proceedings (OSTI)

It is one of the most important tasks in bioinformatics to identify the regulatory elements in gene sequences. Most of the existing algorithms for identifying regulatory elements are inclined to converge into a local optimum, and have high time complexity. ... Keywords: Ant colony optimization, Gene regulatory elements, Motif identification

Wei Liu, Hanwu Chen, Ling Chen

2013-08-01T23:59:59.000Z

302

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.

303

Genomic analysis of 12-oxo-phytodienoic acid reductase genes of Zea mays  

E-Print Network (OSTI)

The 12-oxo-phytodienoic acid reductases (OPRs) are enzymes of the octadecanoid pathway which converts linolenic acid to a phytohormone, jasmonic acid. Bioinformatics analysis of ESTs and genomic sequences from available private and public databases revealed that the maize genome encodes eight different OPR genes. This number of maize OPR genes has been independently confirmed by Southern blot analysis and by mapping of individual OPR genes to maize chromosomes using oat maize chromosome addition lines. Survey of massively parallel signature sequencing (MPSS) assays revealed that transcripts of each OPR gene accumulate differentially in diverse organs of maize plants. This data suggested that individual OPR genes may have a distinct function in development. Similarly, RNA blot analysis revealed that distinct OPR genes are differentially regulated in response to stress hormones, wounding or pathogen infection. ZmOPR1 and ZmOPR2 appear to have important functions in defense responses to pathogens because they are transiently induced by salicylic acid (SA), chitooligosaccharides and by infection with Cochliobolus carbonum, Bipolaris maydis and Fusarium verticillioides and not by wounding. In contrast to these two genes, ZmOPR6 and ZmOPR7/8 are highly induced by wounding and treatments with wound-associated signaling molecules jasmonic acid, ethylene and abscisic acid. ZmOPR6 and ZmOPR7/8 are not induced by SA treatments or pathogen infections suggesting their specific involvement in wound-induced defense responses. Possible functions of specific OPR genes are discussed.

Zhang, Jinglan

2004-12-01T23:59:59.000Z

304

A database-centric approach to system managemant in the blue gene/L supercomputer  

Science Conference Proceedings (OSTI)

In designing the management system for Blue Gene/L, we adopted a database-centric approach, All configuration and operational data for a particular Blue Gene/L system are stored in a relational database that is kept in the system's service node. The ...

Ralf Bellofatto; Paul G. Crumley; David Darrington; Brant knudson; Mark Megerian; Jos E. Moreira; Alda S. Ohmacht; John Orbeck; Don Reed; Greg Stewart

2006-04-01T23:59:59.000Z

305

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

E-Print Network (OSTI)

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

Church, George M.

306

The improvement of breast cancer prognosis accuracy from integrated gene expression and clinical data  

Science Conference Proceedings (OSTI)

Predicting the accurate prognosis of breast cancer from high throughput microarray data is often a challenging task. Although many statistical methods and machine learning techniques were applied to diagnose the prognosis outcome of breast cancer, they ... Keywords: Breast cancer prognosis, Cancer classification, Clinical data, Gene expression, Gene selection, Genetic algorithm, Support vector machine

Austin H. Chen; Chenyin Yang

2012-04-01T23:59:59.000Z

307

Plasmids containing the gene for DNA polymerase I from Streptococcus pneumoniae  

DOE Patents (OSTI)

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

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

1987-08-28T23:59:59.000Z

308

Population Structure and Gene Flow of the Yellow Anaconda (Eunectes notaeus) in Northern Argentina  

E-Print Network (OSTI)

Population Structure and Gene Flow of the Yellow Anaconda (Eunectes notaeus) in Northern Argentina States of America Abstract Yellow anacondas (Eunectes notaeus) are large, semiaquatic boid snakes found anaconda population structure (IBD), and important for gene flow, although genetic distances were

Shaffer, H. Bradley

309

Independent component analysis: Mining microarray data for fundamental human gene expression modules  

Science Conference Proceedings (OSTI)

As public microarray repositories rapidly accumulate gene expression data, these resources contain increasingly valuable information about cellular processes in human biology. This presents a unique opportunity for intelligent data mining methods to ... Keywords: Data mining, Gene modules, Independent component analysis, Microarrays, Parthenolide

Jesse M. Engreitz; Bernie J. Daigle, Jr.; Jonathan J. Marshall; Russ B. Altman

2010-12-01T23:59:59.000Z

310

Ah receptor represses acute-phase response gene expression without binding to its cognate response  

E-Print Network (OSTI)

Repression of the nuclear factor-kB (NF-kB) pathway has been extensively researched because of its pivotal NF-kB regulated-gene expression, especially acute-phase genes, such as serum amyloid A (Saa). Using of transcription factors, such as nuclear factor-kB (NF-kB), signal transducer and activator of transcription-3

Perdew, Gary

311

Scaling physics and material science applications on a massively parallel Blue Gene/L system  

Science Conference Proceedings (OSTI)

Blue Gene/L represents a new way to build supercomputers, using a large number of low power processors, together with multiple integrated interconnection networks. Whether real applications can scale to tens of thousands of processors (on a machine like ... Keywords: Blue Gene/L, MPI, applications, scalability, supercomputers

George Almasi; Gyan Bhanot; Alan Gara; Manish Gupta; James Sexton; Bob Walkup; Vasily V. Bulatov; Andrew W. Cook; Bronis R. de Supinski; James N. Glosli; Jeffrey A. Greenough; Francois Gygi; Alison Kubota; Steve Louis; Thomas E. Spelce; Frederick H. Streitz; Peter L. Williams; Robert K. Yates; Charles Archer; Jose Moreira; Charles Rendleman

2005-06-01T23:59:59.000Z

312

Selective gene silencing in activated leukocytes by targeting siRNAs to the integrin lymphocyte  

E-Print Network (OSTI)

to suppress gene expression and cell proliferation only in activated lymphocytes. The siRNA-fusion proteinSelective gene silencing in activated leukocytes by targeting siRNAs to the integrin lymphocyte are resistant to lipid-based transfection in vitro and are difficult to target in vivo. We show here

Lieberman, Judy

313

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

SciTech Connect

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

314

Regulation of adenovirus transcription by an Ela gene in microinjected Xenopus laevis oocytes  

SciTech Connect

The regulation of adenovirus type 5 gene expression by the E1a gene product was examined in microinjected Xenopus laevis oocytes. Chimeric genes were constructed which included the promoter region of early adenovirus type 5 gene 3 and the structural sequence which codes for the bacterial enzyme chloramphenicol-3-O-acetyltransferase (CAT). A plasmid containing this chimeric gene as well as plasmids containing the E1a gene were coinjected into oocyte nuclei. The presence of the E1a gene was shown to increase CAT activity by up to 8.5-fold over basal levels. Synthesis of the functional product from the E1a gene requires the removal of intron sequences by RNA splicing. The E1a gene and a derivative that precisely lacks the intron were equally effective in increasing CAT activity, suggesting that splicing of the primary E1a transcript is efficiently accomplished in the oocyte nucleus. This was confirmed by directly examining the E1a mRNAs by the S1 mapping procedure. A protein extract from adenovirus type 5-infected HeLa cells enriched for the E1a protein may supplant the E1a plasmid in enhancing CAT activity. Synthesis of the CAT enzyme after gene injection is invariant in oocytes from the same frog, but oocytes from different frogs show a high degree of variability in their ability to synthesize the CAT enzyme. Microinjected X. laevis oocytes appear to be an extremely useful system to study the effects of protein elements on transcription.

Jones, N.C.; Richter, J.D.; Weeks, D.L.; Smith, L.D.

1983-12-01T23:59:59.000Z

315

Rice Transformation as a Means to Study Gene Expression  

E-Print Network (OSTI)

An exceptionally effective transformation procedure has been established by using class I embryo-derived rice callus. Every treated callus clump yielded multiple independently transformed plants (average 40 plantlets). Analysis of genomic DNA blots and pollen expressing green fluorescent protein (GFP) from T0 plants revealed that 64% bore a single locus T-DNA insertion in which half had one T-DNA copy. Additive transgene expression was observed fromT0 plants with GFP driven by mUbi1 promoter. Transgenic plants could be rapidly characterized by analyzing GFP pollen from T0 plants without the need for further generations or genomic DNA blot analysis. Agrobacterium tumefaciens-mediated transformation of microspore-derived callus for generating large numbers of T-DNA haploid and doubled haploid(DH) plants has also been investigated. The established transformation procedure resulted in 100% transformation frequency for class I microspore-derived rice callus. Each callus typically yields multiple independent transgenic plants. Genomic DNA blot analysis suggested 98% of the transgenic plants are independent events. About half of the transgenic plants were identified as haploid plants, whereas half are DH hemizygous or homozygous transgenic plants. DH homozygous transgenic plants were obtained from T0plants and confirmed by pollen GFP expression and genomic blot analysis in T0transgenic DH plants. In this study, about 60% ofT0transgenic DH plants had a single locus T-DNA insertion of which 45% bore one T-DNA copy. Furthermore, in a population of over 2,000 haploid and doubled haploid T-DNA plants , about 25% showed phenotypic differences from non-transformed haploid plants. Approximately 5% were seriously phenotypically abnormal including lethal or semi-lethal mutants. This highly efficient transformation procedure using microspore-derived callus could be valuable in speeding up plant breeding and in new gene discovery. Diversification of the mUbi1 promoter led to a minimal promoter that has a similar function as the original mUbi1. Transient and stable transformation as measured from gene expression driven by the minimal promoter suggested that it has a similar function as the original wild type promoter.

Jiang, Yiming

2009-08-01T23:59:59.000Z

316

Implementation of genomics and bioinformatics approaches for identification and characterization of tomato ripening-related genes  

E-Print Network (OSTI)

Initial activities were focused on isolation and characterization of fruit ripening-related genes from tomato. Screening of four tomato cDNA libraries at low stringency with 10 fruit development and ripening-related genes yielded ~3000 positives clones. Microarray expression analysis of half of these positives in mature green and breaker stage fruits resulted in eight ripening-induced genes. RNA gel-blot analysis and previously published data confirmed expression for seven of the eight. One novel gene, designated LeEREBP1, was chosen for further characterization. LeEREBP1 encodes an AP2/ERF-domain transcription factor and is ethylene inducible. The expression profiles of LeEREBP1 parallel previously characterized ripening-related genes from tomato. Transgenic plants with increased and decreased expression of LeEREBP1 were generated and are currently being characterized to define the function of LeEREBP1. A large public tomato EST dataset was mined to gain insight into the tomato transcriptome. By clustering genes according to the respective expression profiles of individual tissues, tissue and developmental expression patterns were generated and genes with similar functions grouped together. Tissues effectively clustered for relatedness according to their profiles confirming the integrity of the approach used to calculate gene expression. Statistical analysis of EST prevalence in fruit and pathogenesis-related libraries resulted in 333 genes being classified as fruit ripening-induced, 185 as fruit ripening-repressed, and 169 as pathogenesis-related. We performed a parallel analysis on public EST data for grape and compared the results for ripening-induced genes to tomato to identify similar and distinct ripening factors in addition to candidates for conserved regulators of fruit ripening. An online interactive database for tomato gene expression data - Tomato Expression Database (TED) was implemented. TED contains normalized expression data for approximately 12,000 ESTs over ten time points during fruit development. It also contains comprehensive annotation of each EST. Through TED, we provide multiple approaches to pursue analysis of specific genes of interest and/or access the larger microarray dataset to identify sets of genes that may behave in a pattern of interest. In addition, a set of useful data mining and data visualization tools were developed and are under continuing expansion.

Fei, Zhangjun

2003-12-01T23:59:59.000Z

317

Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network  

E-Print Network (OSTI)

Contemporary high-throughput technologies permit the rapid identification of transcription factor (TF) target genes on a genome-wide scale, yet the functional significance of TFs requires knowledge of target gene expression ...

Busser, Brian W.

318

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

319

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

320

Rb pathway and chromatin remodeling genes that antagonize let-60 Ras signaling during C. elegans vulval development  

E-Print Network (OSTI)

The synthetic multivulva (synMuv) class A and class B genes act redundantly to regulate Ras-mediated vulval cell fate specification in the nematode Caenorhabditis elegans. The class B synMuv gene lin-35 encodes a protein ...

Ceol, Craig J. (Craig Joseph), 1971-

2003-01-01T23:59:59.000Z

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.


321

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

322

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

DOE Green Energy (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

323

EarlyExperienceOnBlueGeneQ.pptx  

NLE Websites -- All DOE Office Websites (Extended Search)

and Performance Engineering Team Early Experience on the Blue Gene/Q Supercomputing System Mira P erformance B oot C amp Argonne, M ay 2 1, 2 013 Argonne L eadership C ompuDng F acility Argonne N aDonal L aboratory, A rgonne, I L 2 Outline  Introduc+on - Argonne L eadership C ompu+ng F acility - From B G/P t o B G/Q  BG/Q S ystem C haracteris+cs - Memory S ubsystem - Computa+on C apabili+es - Interconnect a nd C ommunica+on P roper+es - Power C onsump+on a nd E fficiency  BG/Q S pecific F eatures - QPX --- 4 ---way S IMD V ector U nit - Prefetching U nit a nd L ist P refetching  Applica+on S tudies - GTC, G FMC, D NS3D ALCF @ Argonne 3 Produc'on S ystems: Mira - B G/Q s ystem - 49,152 nodes / 786,432 cores - 786 TB of memory - Peak fl op r ate: 1 0 P F - Linpack fl op r ate: 8 .1 P F Intrepid

324

Barbara McClintock, Jumping Genes, and Transposition  

NLE Websites -- All DOE Office Websites (Extended Search)

Barbara McClintock and Transposable Genetic Elements McClintock Honored · Woman of Science · Educational Material · Resources with Additional Information Barbara McClintock's remarkable life spanned the history of genetics in the twentieth century. ... [T]he science of genetics, to which McClintock made seminal contributions both experimental and conceptual, has come to dominate all of the biological sciences, from molecular biology, through cell and developmental biology, to medicine and agriculture. ... Barbara McClintock Courtesy of the Cold Spring Harbor Laboratory Archives McClintock made her first significant contribution as a graduate student, developing cytological techniques that allowed her to identify each of the ten maize chromosomes. These early experiments laid the groundwork for a remarkable series of cytogenetic discoveries ... [for which] McClintock was the intellectual driving force ... . These include identification of maize linkage groups with individual chromosomes, the well-known cytological proof of genetic crossing-over, evidence of chromatid crossing-over, cytological determination of the physical location of genes within chromosomes, identification of the genetic consequences of nonhomologous pairing, establishment of the causal relationship between the instability of ring-shaped chromosomes and phenotypic variegation, discovery that the centromere is divisible, and identification of a chromosomal site essential for the formation of the nucleolus. ...

325

Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus  

DOE Green Energy (OSTI)

Quantitative trait locus (QTL) studies are an integral part of plant research and are used to characterize the genetic basis of phenotypic variation observed in structured populations and inform marker-assisted breeding efforts. These QTL intervals can span large physical regions on a chromosome comprising hundreds of genes, thereby hampering candidate gene identification. Genome history, evolution, and expression evidence can be used to narrow the genes in the interval to a smaller list that is manageable for detailed downstream functional genomics characterization. Our primary motivation for the present study was to address the need for a research methodology that identifies candidate genes within a broad QTL interval. Here we present a bioinformatics-based approach for subdividing candidate genes within QTL intervals into alternate groups of high probability candidates. Application of this approach in the context of studying cell wall traits, specifically lignin content and S/G ratios of stem and root in Populus plants, resulted in manageable sets of genes of both known and putative cell wall biosynthetic function. These results provide a roadmap for future experimental work leading to identification of new genes controlling cell wall recalcitrance and, ultimately, in the utility of plant biomass as an energy feedstock.

Ranjan, Priya [ORNL; Yin, Tongming [ORNL; Zhang, Xinye [ORNL; Kalluri, Udaya C [ORNL; Yang, Xiaohan [ORNL; Jawdy, Sara [ORNL; Tuskan, Gerald A [ORNL

2009-11-01T23:59:59.000Z

326

Self-assembled pentablock copolymers for selective and sustained gene delivery  

SciTech Connect

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

327

Organization and transfer of heterologous chloramphenicol and tetracycline resistance genes in pneumococcus  

SciTech Connect

The cat and tet genes of chloramphenicol- and tetracycline-resistant clinical isolates of Streptococcus pneumuoniae from Paris and Japan were shown to be contained in adjacent heterologous insertions into the chromosome. The two insertions transformed laboratory strains at frequencies that were low, unequal, and, for tet, very sensitive to the length of the donor deoxyribonucleic acid strand. In contrast, the transforming activity of cat was relatively stable. There was an unusual asymmetric cotransfer, in that a majority of the tet transformants also acquired cat, whereas only a few of the cat transformants also acquired tet. The evidence for chromosomal insertion came from genetic data showing linkage of cat to a chromosomal gene and from cosedimentation of cat with chromosomal markers in both velocity and dye-buoyancy experiments. Genes on a known plasmid introduced into pneumococcus from Streptococcus faecalis showed very different physical behavior. Most of the transformation properties of these genes can be readily accounted for by analogy to transformation of deletions of normal genes. Whether transposition contributes any of the transfers remains to be determined. The presence of one of the genes in the recipient promoted the integration of the other, demonstrating enhanced accumulation of heterologous genes by a process that did not involve plasmids in the species of concern.

Shoemaker, N.B.; Smith, M.D.; Guild, W.R.

1979-08-01T23:59:59.000Z

328

Multistage Gene Normalization and SVM-Based Ranking for Protein Interactor Extraction in Full-Text Articles  

Science Conference Proceedings (OSTI)

The interactor normalization task (INT) is to identify genes that play the interactor role in protein-protein interactions (PPIs), to map these genes to unique IDs, and to rank them according to their normalized confidence. INT has two subtasks: gene ... Keywords: Data mining, feature evaluation and selection, mining methods and algorithms, text mining, scientific databases.

Hong-Jie Dai; Po-Ting Lai; Richard Tzong-Han Tsai

2010-07-01T23:59:59.000Z

329

Molecular dissection of the roles of the SOD genes in mammalian response to low dose irradiation  

SciTech Connect

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

330

Mutations of the Apc gene in experimental colorectal carcinogenesis induced by azoxymethane in F344 rats  

E-Print Network (OSTI)

Summary We investigated in the rat the role of the Apc gene, which is mutated in familial adenomatous polyposis and sporadic colon cancer in the process leading from normal colonic mucosa to aberrant crypt foci (ACF) and finally to adenomas and adenocarcinomas. We analysed mutations in exon 15 of the rat Apc gene using in vitro synthesized protein assay in 66 ACF and in 28 colon tumours induced by azoxymethane. No Apc mutations were found in ACF, whereas five mutations were found in the tumours. The data suggest that mutations of the Apc gene are associated with the transition from ACF to adenoma and adenocarcinoma and not from normal mucosa to ACF.

G Caderni; M Bazzicalupo; C Briani; A Giannini; M Fazi; P Dolaral

1998-01-01T23:59:59.000Z

331

The effects of transcription factor competition on gene regulation  

E-Print Network (OSTI)

Transcription factor (TF) molecules translocate by facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA). Despite the attention this mechanism received in the last 40 years, only a few studies investigated the influence of the cellular environment on the facilitated diffusion mechanism and, in particular, the influence of `other' DNA binding proteins competing with the TF molecules for DNA space. Molecular crowding on the DNA is likely to influence the association rate of TFs to their target site and the steady state occupancy of those sites, but it is still not clear how it influences the search in a genome-wide context, when the model includes biologically relevant parameters (such as: TF abundance, TF affinity for DNA and TF dynamics on the DNA). We performed stochastic simulations of TFs performing the facilitated diffusion mechanism, and considered various abundances of cognate and non-cognate TFs. We show that, for both obstacles that move on the DNA and obstacles that are fixed on the DNA, changes in search time are not statistically significant in case of biologically relevant crowding levels on the DNA. In the case of non-cognate proteins that slide on the DNA, molecular crowding on the DNA always leads to statistically significant lower levels of occupancy, which may confer a general mechanism to control gene activity levels globally. When the `other' molecules are immobile on the DNA, we found a completely different behaviour, namely: the occupancy of the target site is always increased by higher molecular crowding on the DNA. Finally, we show that crowding on the DNA may increase transcriptional noise through increased variability of the occupancy time of the target sites.

Nicolae Radu Zabet; Boris Adryan

2013-03-27T23:59:59.000Z

332

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

333

Rewriting game theory as a foundation for state-based models of gene regulation  

Science Conference Proceedings (OSTI)

We present a game-theoretic foundation for gene regulatory analysis based on the recent formalism of rewriting game theory. Rewriting game theory is discrete and comes with a graph-based framework for understanding compromises and interactions ...

Chafika Chettaoui; Franck Delaplace; Pierre Lescanne; Mundelanji Vestergaard; Ren Vestergaard

2006-10-01T23:59:59.000Z

334

Powered by NERSC, A Database of Billions of Genes and Counting!  

NLE Websites -- All DOE Office Websites (Extended Search)

Powered by NERSC, a Powered by NERSC, a Database of Billions of Genes and Counting! Powered by NERSC, a Database of Billions of Genes and Counting! With More than a Billion Microbial genes, IMG/M Breaks a Record January 26, 2012 | Tags: Joint Genome Institute Linda Vu, lvu@lbl.gov, +1 510 495 2402 IMG/M team celebrates the recording of 1 billionth gene. Microbes are microscopic organisms that live in every nook and cranny of our planet. Without them, plants wouldn't grow, garbage wouldn't decay, humans wouldn't digest food, and there would literally be no life on Earth, or at least as we know it. By examining the genetic makeup of these "bugs," scientists hope to understand how they work, and how they can be used to solve a variety of important problems like identifying new

335

Computational prediction of RNA-based gene regulatory mechanisms in human and Tetrahymena  

E-Print Network (OSTI)

The diversity and profound impact of gene regulation mediated by small RNAs (sRNAs) is just beginning to come into focus. RNA interference (RNAi) pathways have been shown to mediate processes such as genomic rearrangement ...

Kitzman, Jacob O

2006-01-01T23:59:59.000Z

336

miRNAminer: a tool for homologous microRNA gene search  

E-Print Network (OSTI)

Background MicroRNAs (miRNAs), present in most metazoans, are small non-coding RNAs that control gene expression by negatively regulating translation through binding to the 3'UTR of mRNA transcripts. Previously, experimental ...

Artzi, Shay

337

A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland  

Science Conference Proceedings (OSTI)

Motivation: The identification of functional cis-acting DNA regulatory elements is a crucial step towards understanding gene regulation. Ab initio motif detection algorithms have been extensively used in search of regulatory elements. ...

Shahar Alon; Eli Eisenberg; Jasmine Jacob-Hirsch; Gideon Rechavi; Gad Vatine; Reiko Toyama; Steven L. Coon; David C. Klein; Yoav Gothilf

2009-03-01T23:59:59.000Z

338

Biomedical data retrieval utilizing textual data in a gene expression database by Richard Lu, MD.  

E-Print Network (OSTI)

Background: The commoditization of high-throughput gene expression sequencing and microarrays has led to a proliferation in both the amount of genomic and clinical data that is available. Descriptive textual information ...

Lu, Richard, M.D

2010-01-01T23:59:59.000Z

339

Endogenous control of stochastic gene expression in the development of Caenorhabditis elegans  

E-Print Network (OSTI)

Studies in the past decade have established gene expression as an inherently variable process. Accompanying this exciting finding is a fundamental question: how do physiological events, such as cell fate specification, ...

Ji, Ni, Ph. D. Massachusetts Institute of Technology

2013-01-01T23:59:59.000Z

340

MOLECULAR THERAPY Vol. 4, No. 2, August 2001 Copyright The American Society of Gene Therapy  

E-Print Network (OSTI)

that a plasmid car- rying the full SERPINA1 on a 19-kb genomic fragment and the EBV gene EBNA1 and its family] and Liu [5] have developed a simple hydro- dynamic procedure for efficient transfection of liver cells

Ford, James

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

Differential Gene Expression Pre-processing: from CEL files to ExpressionSet  

E-Print Network (OSTI)

different between mutants and wild types Install Libraries and Load Data > source-processing: from CEL files to ExpressionSet Gene Annotation Visualize Expression Profile using Heatmap Produce

Qiu, Weigang

342

A role for the Spemann organizer gene, Goosecoid, in tumor metastasis  

E-Print Network (OSTI)

The process of invasion and metastasis during tumor progression is often reminiscent of cell migration events occurring during embryonic development. I hypothesized that genes controlling cellular changes in the Spemann ...

Hartwell, Kimberly A. (Kimberly Ann)

2007-01-01T23:59:59.000Z

343

Analysis of metazoan DNA replication initiation using Drosophila gene amplification as a model system  

E-Print Network (OSTI)

Gene amplification in Drosophila follicle cells is an excellent model to study origin specification and developmental regulation of DNA replication in vivo. We mapped all follicle cell amplicons using a comparative genomic ...

Kim, Jane Christina

2011-01-01T23:59:59.000Z

344

BMP7 Gene Transfer via Gold Nanoparticles into Stroma Inhibits Corneal Fibrosis In Vivo  

E-Print Network (OSTI)

This study examined the effects of BMP7 gene transfer on corneal wound healing and fibrosis inhibition in vivo using a rabbit model. Corneal haze in rabbits was produced with the excimer laser performing -9 diopters ...

Tandon, Ashish

345

Coevolution of languages and genes on the island of Sumba, eastern Indonesia  

E-Print Network (OSTI)

Coevolution of languages and genes on the island of Sumba, eastern Indonesia J. Stephen Lansing Angeles, CA 90095; and Eijkman Institute for Molecular Biology, Diponegoro 69, Jakarta 10430, Indonesia

Watkins, Joseph C.

346

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

E-Print Network (OSTI)

In Nature, pp. 661-665. Grenier, J. K. , and Carroll, S.101, 577-580. Carroll, S. , Grenier, J. and Weatherbee, S. (sets of target genes (Grenier and Carroll, 2000). Moreover,

Hsia, Cheryl Chih-Jui

2007-01-01T23:59:59.000Z

347

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

Science Conference Proceedings (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

2010-03-25T23:59:59.000Z

348

The Antioxidant Vitamins C & EChapter 15 Vitamin E and Selenium Effects on Differential Gene  

Science Conference Proceedings (OSTI)

The Antioxidant Vitamins C & E Chapter 15 Vitamin E and Selenium Effects on Differential Gene Health Nutrition Biochemistry eChapters Health - Nutrition - Biochemistry Press Downloadable pdf of Chapter 15 Vitam

349

An Efficient Method for Exploring the Space of Gene Tree/Species ...  

E-Print Network (OSTI)

Jan 19, 2010 ... If one is interested in the posterior probability distribution of a subset of .... loss rates along each branch of S, the generation of a gene tree starts.

350

Polylipid Nanoparticle, a Novel Lipid-Based Vector for Liver Gene Transfer  

E-Print Network (OSTI)

for Liver Gene Transfer Yahan Fan and Jian Wu Additionalapplicable for in vivo 2013 Fan and Wu; licensee InTech.Award (321 Plan). Yahan Fan is the recipient of China

Fan, Yahan; Wu, Jian

2013-01-01T23:59:59.000Z

351

Molecular Biology, Pathobiology, and Genetics Intrinsic Gene Expression Profiles of Gliomas Are a Better  

E-Print Network (OSTI)

Molecular Biology, Pathobiology, and Genetics Intrinsic Gene Expression Profiles of Gliomas distinct molecular subgroups that correlate with survival. These include two favorable prognostic subgroups with poor prognosis (median survival, molecular subtypes

352

Drug-loaded nanoparticles induce gene expression in human pluripotent stem cell derivatives  

E-Print Network (OSTI)

typically contain few functional groups for further chemical modification. Doxycycline (DXC), a potent small complex spatiotemporal control of gene expression and cell transitions.8 Doxycycline (DXC) is a small

Saha, Krishanu

353

Effects of melatonin and age on gene expression in mouseCNS using microarray analysis  

E-Print Network (OSTI)

gene contains an activation site for NF-kB (Cowland et al. ,and levels of activated NF-kB increase in murine cortex withThus, increased levels of NF-kB activation in the aged brain

Bondy, Stephen Bondy C

2007-01-01T23:59:59.000Z

354

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression  

E-Print Network (OSTI)

We recently showed that the mammalian genome encodes >1,000 large intergenic noncoding (linc)RNAs that are clearly conserved across mammals and, thus, functional. Gene expression patterns have implicated these lincRNAs in ...

Presser, Aviva

355

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)

356

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

SciTech Connect

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

357

Modified cellulose synthase gene from Arabidopsis thaliana confers herbicide resistance to plants  

DOE Patents (OSTI)

Cellulose synthase ("CS"), a key enzyme in the biosynthesis of cellulose in plants is inhibited by herbicides comprising thiazolidinones such as 5-tert-butyl-carbamoyloxy-3-(3-trifluromethyl)phenyl-4-thiazolidinone (TZ), isoxaben and 2,6-dichlorobenzonitrile (DCB). Two mutant genes encoding isoxaben and TZ-resistant cellulose synthase have been isolated from isoxaben and TZ-resistant Arabidopsis thaliana mutants. When compared with the gene coding for isoxaben or TZ-sensitive cellulose synthase, one of the resistant CS genes contains a point mutation, wherein glycine residue 998 is replaced by an aspartic acid. The other resistant mutation is due to a threonine to isoleucine change at amino acid residue 942. The mutant CS gene can be used to impart herbicide resistance to a plant; thereby permitting the utilization of the herbicide as a single application at a concentration which ensures the complete or substantially complete killing of weeds, while leaving the transgenic crop plant essentially undamaged.

Somerville, Chris R. (Portola Valley, CA); Scheible, Wolf (Golm, DE)

2007-07-10T23:59:59.000Z

358

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 ...

Alemn, Lourdes Maria

2008-01-01T23:59:59.000Z

359

Assignment of the cysteinyl-tRNA synthetase gene (CARS) to 11p15. 5  

SciTech Connect

The attachment of each of the 20 naturally occurring amino acids to their cognate tRNA isoaccepting families is catalyzed by a specific aminoacyl-tRNA synthetase. The structural genes encoding 10 of these enzymes have been assigned to specific human chromosomes. The HARS, LARS, RARS, and TARS genes, encoding histidyl-, leucyl-, arginyl-, and threonyl-tRNA synthetases, respectively, are all located on chromosome 5( 1, 5, 7, 9, 14). The MARS (methionyl-tRNA synthetase), NARS (asparaginyl-tRNA synthetase), VARS (valyl-tRNA synthetase), and WARS (tryptophanyl-tRNA synthetase) genes have been assigned to chromosomes 12, 18, 6, and 14, respectively (3, 4, 6, 8). A gene originally identified as encoding glutaminyl-tRNA synthetase was mapped to chromosome 1q32-q42 (10). However, a recent study suggests that the product of this gene is, in fact, a multifunctional enzyme with both glutamyl- and prolyl-tRNA synthetase activities (2). The fact that 4 of the 10 aminoacyl-tRNA synthetase genes already mapped are located on chromosome 5 may be fortuitous but might also indicate an evolutionary or regulatory relatedness. It is therefore, of interest to map genes encoding other aminoacyl-tRNA synthetases to determine if additional examples of synteny exist. The recent isolation of cDNA and genomic DNA clones for human cysteinyl-tRNA synthetase has now enabled us to map the CARS gene to segment p15.5 on chromosome 11 by fluorescence in situ hybridization.

Cruzen, M.E.; Bengtsson, U.; McMahon, J.; Wasmuth, J.J.; Arfin, S.M. (Univ. of California, Irvine (United States))

1993-03-01T23:59:59.000Z

360

Snapshot of iron response in Shewanella oneidensis by gene network reconstruction  

Science Conference Proceedings (OSTI)

Background: Iron homeostasis of Shewanella oneidensis, a gamma-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, we integrate physiological, transcriptomics and genetic approaches to delineate the iron response of S. oneidensis. Results: We show that the iron response in S. oneidensis is a rapid process. Temporal gene expression profiles were examined for iron depletion and repletion, and a gene co-expression network was reconstructed. Modules of iron acquisition systems, anaerobic energy metabolism and protein degradation were the most noteworthy in the gene network. Bioinformatics analyses suggested that genes in each of the modules might be regulated by DNA-binding proteins Fur, CRP and RpoH, respectively. Closer inspection of these modules revealed a transcriptional regulator (SO2426) involved in iron acquisition and ten transcriptional factors involved in anaerobic energy metabolism. Selected genes in the network were analyzed by genetic studies. Disruption of genes encoding a putative alcaligin biosynthesis protein (SO3032) and a gene previously implicated in protein degradation (SO2017) led to severe growth deficiency under iron depletion conditions. Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways. Conclusions: Using a reconstructed gene network, we identified major biological pathways that were differentially expressed during iron depletion and repletion. Genetic studies not only demonstrated the importance of iron acquisition and protein degradation for iron depletion, but also characterized a novel transcriptional factor (SO1415) with a role in anaerobic energy metabolism.

Yang, Yunfeng; Harris, Daniel P.; Luo, Feng; Xiong, Wenlu; Joachimiak, Marcin; Wu, Liyou; Dehal, Paramvir; Jacobsen, Janet; Yang, Zamin; Palumbo, Anthony V.; Arkin, Adam P.; Zhou, Jizhong

2008-10-09T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
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they are not comprehensive nor are they the most current set.
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361

A comparative method for identification of gene structures and alternatively spliced variants  

E-Print Network (OSTI)

Motivation: Alternative splicing (AS) serves as a mechanism to create diversity of functional proteins. Increasing evidence indicates that a large portion of genes have AS forms. Hence AS variants should be considered while analyzing gene structures. Results: A new cross-species gene identification and AS analysis system, PSEP, has been developed. The system is based on EST-to-genome and genome-to-genome comparisons and is implemented in two steps: sequence alignment and a series of post-alignment processes, including progressive signal extracting and patching. For gene identification, these post-alignment processes serve as noise filters and enable PSEP to eliminate approximately 88 % of potential overprediction. The overall accuracy of PSEP is better or comparable to that of other well-known cross-species gene prediction programs, including the ROSETTA program, TWINSCAN, SGP-1/-2, and SLAM, when tested on three benchmark data sets (the ELN gene region, the HoxA cluster, and the ROSETTA set). In addition, 76.2 % and 76.0 % of multiple-exon genes in the ROSETTA data set and human chromosome 20, respectively, are found to have AS forms. Approximately 23 % of the 210 elementary alternatives identified in the ROSETTA data set are not conserved between the human and mouse genomes, and all of the 210 transcripts are not found in the RefSeq annotation. With its dual functions in cross-species conserved sequence analysis and AS analysis, PSEP is highly suitable for studying the evolution of AS patterns and for finding unidentified gene expression features. Availability: The programs of PESP as well as the visualization tool required to build the proposed annotation scheme is available at

Trees-juen Chuang; Feng-chi Chen; Meng-yuan Chou

2004-01-01T23:59:59.000Z

362

Status of clinical gene sequencing data reporting and associated risks for information loss  

Science Conference Proceedings (OSTI)

Clinical gene sequencing is growing in importance and cost-effectiveness. In the past two years, the number of genes associated with disease has grown by roughly 25%. Knowledge of genetic variations will soon guide drug selection and dosages, predict ... Keywords: Algorithms, Automatic data processing, Computational biology, Computer-assisted, DNA/Analysis, Diagnosis, Diagnostic use, Genetics, Genome, Human, Information storage and retrieval, Variation (genetics)

Douglas R. Mitchell; Joyce A. Mitchell

2007-02-01T23:59:59.000Z

363

Risk haplotype pattern discovery for gene mapping by recursive partitioning method based on weighted classification trees  

Science Conference Proceedings (OSTI)

In this paper, we present a combinatorial approach based on recursive weighted longest prefix trees (RWLPT) for mining a massive genetic marker data. Given a case and a control chromosome dataset, we develop a fast recursive permutation algorithm ... Keywords: combinatorial optimisation, disease susceptibility genes, gene mapping, genetic markers, haplotype clusters, haplotype-disease association, multilocus SNP analysis, non-numerical algorithms, recursive partitioning, risk haplotype pattern discovery, weighted classification trees

Tran Trang; Hoang Ngoc Minh

2010-02-01T23:59:59.000Z

364

Organization and control of genes encoding catabolic enzymes in Rhizobiaceae. Progress report, March 1993  

DOE Green Energy (OSTI)

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

Parke, D.; Ornston, L.N.

1993-03-01T23:59:59.000Z

365

The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE)  

SciTech Connect

The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE) will be held June 8-12, 2005 at the University of Texas at Austin. Exciting new and ongoing discoveries show significant regulation of gene expression occurs after transcription. These post-transcriptional control events in plants range from subtle regulation of transcribed genes and phosphorylation, to the processes of gene regulation through small RNAs. This meeting will focus on the regulatory role of RNA, from transcription, through translation and finally degradation. The cross-disciplinary design of this meeting is necessary to encourage interactions between researchers that have a common interest in post-transcriptional gene expression in plants. By bringing together a diverse group of plant molecular biologist and biochemists at all careers stages from across the world, this meeting will bring about more rapid progress in understanding how plant genomes work and how genes are finely regulated by post-transcriptional processes to ultimately regulate cells.

Karen S. Browning; Marie Petrocek; Bonnie Bartel

2006-06-01T23:59:59.000Z

366

Analysis of the human [alpha]-globin gene cluster in transgenic mice  

SciTech Connect

A 350-bp segment of DNA associated with an erythroid-specific DNase I-hypersensitive site (HS -40), upstream of the [alpha]-globin gene cluster, has been identified as the major tissue-specific regulator of the [alpha]-globin genes. However, this element does not direct copy number-dependent or developmentally stable expression of the human genes in transgenic mice. To determine whether additional upstream hypersensitive sites could provide more complete regulation of [alpha] gene expression, the authors have studied 17 lines of transgenic mice bearing various DNA fragments containing HSs -33, -10, -8, and -4, in addition to HS -40. Position-independent, high-level expression of the human [zeta]- and [alpha]-globin genes was consistently observed in embryonic erythroid cells. However, the additional HSs did not confer copy-number dependence, alter the level of expression, or prevent the variable down-regulation of expression in adults. These results suggest that the region upstream of the human [alpha]-globin genes is not equivalent to that upstream of the [beta] locus and that although the two clusters are coordinately expressed, there may be differences in their regulation.

Sharpe, J.A.; Vyas, P.; Higgs, D.R.; Wood, W.G. (Univ. of Oxford, Oxford (United Kingdom)); Wells, D.J. (Royal Veterinary College, Royal College Street, London (United Kingdom)); Whitelaw, E. (Univ. of Sydney, Sydney (Australia))

1993-11-15T23:59:59.000Z

367

Mathematical modeling and information theoretical analysis of DevR regulated genes in Mycobacterium tuberculosis  

E-Print Network (OSTI)

The DevR-DevS two component system of Mycobacterium tuberculosis is responsible for its dormancy in host and becomes operative under hypoxic condition. It is experimentally known that phosphorylated DevR controls the expression of several downstream genes in a complex manner. In the present work we have developed a mathematical model to show the role of binding sites in the DevR mediated gene expression. Through modeling it has been shown the individual and collective role of the binding sites in regulating the DevR mediated gene expression. The objective of the present work is two fold. First, to describe qualitatively the temporal dynamics of wild type genes and their known mutants. Based on these results we propose that DevR controlled gene expression follows a specific pattern which is efficient in describing other DevR mediated gene expression. Second, to analyze the behavior of the system from the information theoretical point of view. Using the tools of information theory we have calculated the molecular efficiency of the system and have shown that it is close to the maximum limit of isothermal efficiency.

Arnab Bandyopadhyay; Soumi Biswas; Alok Kumar Maity; Suman K Banik

2013-09-03T23:59:59.000Z

368

Repression of the Drosophila proliferating-cell nuclear antigen gene promoter by zerknuellt protein  

SciTech Connect

A 631-bp fragment containing the 5{prime}-flanking region of the Drosophila melanogaster proliferating-cell nuclear antigen (PCNA) gene was placed upstream of the chloramphenicol acetyltransferase (CAT) gene of a CAT vector. A transient expression assay of CAT activity in Drosophila Kc cells transfected with this plasmid and a set of 5{prime}-deletion derivatives revealed that the promoter function resided within a 192-bp region. Cotransfection with a zerknuellt (zen)-expressing plasmid specifically repressed CAT expression. However, cotransfection with expression plasmids for a nonfunctional zen mutation, even skipped, or bicoid showed no significant effect on CAT expression. RNase protection analysis revealed that the repression by zen was at the transcription step. The target sequence of zen was mapped within the 34-bp region of the PCNA gene promoter, even though it lacked zen protein-binding sites. Transgenic flies carrying the PCNA gene regulatory region fused with lacZ were established. These results indicate that zen indirectly represses PCNA gene expression, probably by regulating the expression of some transcription factor(s) that binds to the PCNA gene promoter.

Yamaguchi, Masamitsu; Hirose, Fumiko; Nishida, Yasuyoshi; Matsukage, Akio (Aichi Cancer Center Research Inst., Nagoya (Japan))

1991-10-01T23:59:59.000Z

369

SATB1 tethers multiple gene loci to reprogram expression profiledriving breast cancer metastasis  

SciTech Connect

Global changes in gene expression occur during tumor progression, as indicated by expression profiling of metastatic tumors. How this occurs is poorly understood. SATB1 functions as a genome organizer by folding chromatin via tethering multiple genomic loci and recruiting chromatin remodeling enzymes to regulate chromatin structure and expression of a large number of genes. Here we show that SATB1 is expressed at high levels in aggressive breast cancer cells, and is undetectable in non-malignant breast epithelial cells. Importantly, RNAi-mediated removal of SATB1 from highly-aggressive MDA-MB-231 cells altered the expression levels of over 1200 genes, restored breast-like acinar polarity in three-dimensional cultures, and prevented the metastastic phenotype in vivo. Conversely, overexpression of SATB1 in the less-aggressive breast cancer cell line Hs578T altered the gene expression profile and increased metastasis dramatically in vivo. Thus, SATB1 is a global regulator of gene expression in breast cancer cells, directly regulating crucial metastasis-associated genes, including ERRB2 (HER2/NEU), TGF-{beta}1, matrix metalloproteinase 3, and metastasin. The identification of SATB1 as a protein that re-programs chromatin organization and transcription profiles to promote breast cancer metastasis suggests a new model for metastasis and may provide means of therapeutic intervention.

Han, Hye-Jung; Kohwi, Yoshinori; Kohwi-Shigematsu, Terumi

2006-07-13T23:59:59.000Z

370

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

E-Print Network (OSTI)

Intraspecific relationships among the anchialine cave shrimp Typhlatya mitchelli were examined by sequencing a total of 1505 bp from portions of three mitochondrial DNA genes. Cytochrome b, cytochrome oxidase I, and 16S rRNA were partially sequenced and analyzed for specimens from six different cenotes (water-filled caves) across the Yucatan Peninsula, Mexico. The conspecific Typhlatya pearsei that is sympatric with T. mitchelli was also sequenced and used as the outgroup. Comparisons among specimens of T. mitchelli yielded low sequence divergence values (0-1.7%), with the majority being less than 0.4%. Phylogenetic tree topologies reconstructed with neighbor-joining, maximum likelihood, and maximum parsimony were in agreement in regards of the resolution of deep branches. Also, there was no obvious geographic differentiation among the majority of T. mitchelli samples, with the exception of specimens from Cenote San Antonio Chiich (Yokdzonot, Yucatan, Mexico) which all clustered into an extremely well supported monophyletic group. The level of differentiation of this group, together with the nearly total absence of differentiation among T. mitchelli from distant cave systems, suggests that this is an Evolutionary Significant Unit (ESU), which may correspond to a new species. This unidentified Typhlatya from Cenote San Antonio Chiich was helpful in establishing a period in which the epigean ancestor colonized the cenotes. Based on pairwise distance data and previously published shrimp molecular clocks (Baldwin et al., 1998), T. mitchelli and the putative new Typhlatya species last shared a common ancestor between 3-5 million years ago (mya), during the mid-Pliocene era, while T. mitchelli and T. pearsei was approximately 7-10 mya (middle to late Miocene). The ancestor to T. mitchelli and the unidentified Typhlatya species abandoned its shallow coastal water existence in the early Pliocene and eventually expanded its range across the peninsula. Approximately 4 mya, Cenote San Antonio Chiich became isolated from the remaining gene pool thereby halting gene flow. As the regional water table fluctuated in response to the rise and fall of Pleistocene sea levels, T. mitchelli actively colonized the peninsula. The discovery of a single, continuous subterranean freshwater system provides for a better understanding of anchialine biogeography within the Yucatan Peninsula.

Webb, Michael Scott

2003-05-01T23:59:59.000Z

371

Organization and regulation of the genes for nitrogen fixation in Rhodopseudomonas capsulata: Progress report for the period June 5, 1986-June 4, 1987  

DOE Green Energy (OSTI)

This document describes research conducted between June 1986 and June 1987. Results dealing with the organization and regulation of genes in the photosynthetic bacterium Rhodobacter capsulatus includes cloning, sequencing, and demonstrating characterizing the products of genes that regulate expression of nitrogen fixation genes; the connection between DNA supercoiling mediated by DNA gyrase and nif gene expression; and mapping the entire chromosome of R. capsulatus.

Haselkorn, R.

1987-03-01T23:59:59.000Z

372

A molecular genetic analysis of carotenoid biosynthesis and the effects of carotenoid mutations on other photosynthetic genes in Rhodobacter capsulatus  

DOE Green Energy (OSTI)

The nine known R. capsulatus carotenoid genes are contained within the 46 kilobase (kb) photosynthesis gene cluster. An 11 kb subcluster containing eight of these genes has been cloned and its nucleotide sequence determined. A new gene, crtK, has been located in the middle of the subcluster. The carotenoid gene cluster contains sequences homologous to Escherichia coli ..omega../sup 70/ promoters, rho-independent transcription terminators, and prokaryotic transcriptional factor binding sites. The phenotypes and genotypes of ten transposon Tn5.7 insertion mutations within the carotenoid gene cluster have been analyzed, by characterization of the carotenoids accumulated and high resolution mapping of the Tn5.7 insertions. The enzymatic blockages in previously uncharacterized early carotenoid mutants have been determined using a new in vitro synthesis system, suggesting specific roles for the CrtB and CrtE gene products. The expression of six of the eight carotenoid genes in the cluster is induced upon the shift from dark chemoheterotrophic to anaerobic photosynthetic growth. The magnitude of the induction is equivalent to that of genes encoding structural photosynthesis polypeptides, although the carotenoid genes are induced earlier after the growth shift. Different means of regulating photosynthesis genes in R. capsulatus are discussed, and a rationale for the temporal pattern of expression of the carotenoid genes during photosynthetic adaptation is presented. Comparison of the deduced amino acid sequences of the two dehydrogenases of the R. capsulatus carotenoid biosynthesis pathway reveals two regions of strong similarity. The effect of carotenoid mutations on the photosynthetic phenotype has been studied by examining growth rates, pigments, pigment-protein complexes and gene expression for a complete set of carotenoid mutants. 161 refs.

Armstrong, G.A.

1989-04-01T23:59:59.000Z

373

[Organization and regulation of the genes for nitrogen fixation in Rhodopseudomonas capsulata]. Progress report, [June 5, 1989--June 4, 1991  

DOE Green Energy (OSTI)

In prior support periods we identified, cloned and sequenced three genes involved in the regulation of nif gene expression in Rhodobacter capsulatus. These were called nifRI, nifR2 and nifR4; they turn out to be homologue of the ntrC, ntrB and ntrA genes of enterobacteria. We subsequently found that mutations in an additional gene, nifR5. render R. capsulatus nif genes constitutive with respect to ammonia. The nifR5 gene was shown to be similar to glnB of enteric bacteria, encoding the regulatory protein PII, and furthering the intersection of the glutamine synthetase adenylylation cascade with the control of nif gene transcription. In pursuit of the mechanism of 0{sub 2} control of nif gene expression, we constructed and analyzed the topology of a small plasmid in R. capsulatus as a function of 0{sub 2} concentration. We also cloned and obtained partial sequence data for two genes encoding the B subunit of DNA gyrase. The nucleotide sequence of the rpoB gene encoding RNA polymerase was nearly completed. A method for isolation of genes expressed differentially, developed for cyanobacteria, was applied successfully to R. capsulatus. Several genes that depend on nifR4 for their transcription were isolated. A transcription start site for a nifA gene was identified and the promoter sequence was analyzed. A physical map of the R calsulatus SB1003 chromosome was prepared, based on pulsed-field electrophoresis of XbaI and AseI fragments and hybridization with a gridded cosmid library, using a device that permits 864 cosmids to be hybridized at one time with a labeled chromosomal fragment.

Not Available

1991-12-31T23:59:59.000Z

374

Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus  

DOE Green Energy (OSTI)

Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight ``bch`` genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

Burke-Agueero, D.H.

1992-08-01T23:59:59.000Z

375

Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus  

DOE Green Energy (OSTI)

Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight bch'' genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

Burke-Agueero, D.H.

1992-08-01T23:59:59.000Z

376

6982.full.pdf  

NLE Websites -- All DOE Office Websites (Extended Search)

of a circular chromosome of 4,613,747 bp (37.26% GC content), which includes 4,025 cod- ing genes, 61 tRNAs, and 8 rRNA operons. A total of 3,012 coding genes (73.16% of the...

377

Role of Morphological Growth State and Gene Expression in Desulfovibrio africanus strain Walvis Bay Mercury Methylation  

Science Conference Proceedings (OSTI)

The biogeochemical transformations of mercury are a complex process, with the production of methylmercury, a potent human neurotoxin, repeatedly demonstrated in sulfate- and Fe(III)- reducing as well as methanogenic bacteria. However, little is known regarding the morphology, genes or proteins involved in methylmercury generation. Desulfovibrio africanus strain Walvis Bay is a Hg-methylating -proteobacterium with a sequenced genome and has unusual pleomorphic forms. In this study, a relationship between the pleomorphism and Hg methylation was investigated. Proportional increases in the sigmoidal (regular) cell form corresponded with increased net MeHg production, but decreased when the pinched cocci (persister) form became the major morphotype. D. africanus microarrays indicated that the ferrous iron transport genes (feoAB), as well as ribosomal genes and several genes whose products are predicted to have metal binding domains (CxxC), were up-regulated during exposure to Hg in the exponential phase. While no specific methylation pathways were identified, the finding that Hg may interfere with iron transport and the correlation of growth-phase dependent morphology with MeHg production are notable. The identification of these relationships between differential gene expression, morphology, and the growth phase dependence of Hg transformations suggests that actively growing cells are primarily responsible for methylation, and so areas with ample carbon and electron-acceptor concentrations may also generate a higher proportion of methylmercury than more oligotrophic environments. The observation of increased iron transporter expression also suggests that Hg methylation may interfere with iron biogeochemical cycles.

Moberly, James G [ORNL; Miller, Carrie L [ORNL; Brown, Steven D [ORNL; Biswas, Abir [ORNL; Brandt, Craig C [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

2012-01-01T23:59:59.000Z

378

Gene Expression of ANP, BNP and ET-1 in the Heart of Rats during Pulmonary Embolism  

E-Print Network (OSTI)

Aims: Atrial natriuretic petide (ANP), brain natriuretic peptide (BNP) and endothelin-1 (ET-1) may reflect the severity of right ventricular dysfunction (RVD) in patients with pulmonary embolism (PE). The exact nature and source of BNP, ANP and ET-1 expression and secretion following PE has not previously been studied. Methods and Results: Polystyrene microparticles were injected to induce PE in rats. Gene expression of BNP, ANP and ET-1 were determined in the 4 cardiac chambers by quantitative real time polymerase chain reaction (QPCR). Plasma levels of ANP, BNP, ET-1 and cardiac troponin I (TNI) were measured in plasma. PE dose-dependently increased gene expression of ANP and BNP in the right ventricle (RV) and increased gene expression of ANP in the right atrium (RA). In contrast PE dosedependently decreased BNP gene expression in both the left ventricle (LV) and the left atrium (LA). Plasma levels of BNP, TNI and ET-1 levels dose-dependently increased with the degree of PE. Conclusion: We found a close correlation between PE degree and gene-expression of ANP, and BNP in the cardiac chambers with a selective increase in the right chambers of the heart. The present data supports the idea of natriuretic peptides as

Henrik Gutte; Jytte Oxbl; Ulrik Sloth Kristoffersen; Jann Mortensen; Andreas Kjr

2010-01-01T23:59:59.000Z

379

Regulation of hepatic PPAR{gamma}2 and lipogenic gene expression by melanocortin  

SciTech Connect

The central melanocortin system regulates hepatic lipid metabolism. Hepatic lipogenic gene expression is regulated by transcription factors including sterol regulatory element-binding protein 1c (SREBP-1c), carbohydrate responsive element-binding protein (ChREBP), and peroxisome proliferator-activated receptor {gamma}2 (PPAR{gamma}2). However, it is unclear if central melanocortin signaling regulates hepatic lipogenic gene expression through the activation of these transcription factors. To delineate the molecular mechanisms by which the melanocortin system regulates hepatic lipid metabolism, we examined the effect of intracerebroventricular injection of SHU9119, a melanocortin receptor antagonist, on hepatic expression levels of genes involved in lipid metabolism in mice. SHU9119 treatment increased hepatic triglyceride content and mRNA levels of lipogenic genes, SREBP-1c, and PPAR{gamma}2, whereas it did not cause any changes in hepatic ChREBP mRNA levels. These findings suggest that reduced central melanocortin signaling increases hepatic lipid deposition by stimulating hepatic lipogenic gene expression at least partly through the activation of SREBP-1c and PPAR{gamma}2.

Poritsanos, Nicole J.; Wong, Davie [Department of Physiology, University of Manitoba, 730 William Avenue, Winnipeg, MB, R3E 3J7 (Canada); Vrontakis, Maria E. [Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB, R3E 3J7 (Canada); Mizuno, Tooru M. [Department of Physiology, University of Manitoba, 730 William Avenue, Winnipeg, MB, R3E 3J7 (Canada)], E-mail: mizunot@cc.umanitoba.ca

2008-11-14T23:59:59.000Z

380

Activation of endothelial-leukocyte adhesion molecule 1 (ELAM-1) gene transcription  

SciTech Connect

Leukocyte adherence to endothelium is in part mediated by the transient expression of endothelial-leukocyte adhesion molecule 1 (ELAM-1) on endothelial surfaces stimulated by tumor necrosis factor {alpha} (TNF), interleukin (IL) 1, or bacterial lipopolysaccharide (LPS). The intracellular factors controlling induction of ELAM-1 mRNA and protein are unknown. In nuclear runoff experiments with cultured human umbilical vein endothelial cells (HUVEC), the authors demonstrate that transcriptional activation of the ELAM-1 gene occurs following stimulation with TNF. Sequence analysis of the 5{prime} flanking region of the ELAM-1 gene reveals consensus DNA-binding sequences for two known transcription factors, NF-{kappa}B and AP-1. Gel mobility shift assays demonstrate that TNF, IL-1, or LPS induces activation of NF-{kappa}B-like DNA binding activity in HUVEC. Phorbol 12-myristate 13-acetate, a known activator of protein kinase C (PKC), weakly induces NF-{kappa}B-like activity, ELAM-1 mRNA, and ELAM-1 surface expression in HUVEC. However, TNF, IL-1, and LPS do not activate PKC in HUVEC at doses that strongly induce NF-{kappa}B-like protein activation and ELAM-1 gene expression. PKC blockade with H7 does not inhibit activation of these NF-kB-like proteins but does inhibit ELAM-1 gene transcription. They conclude that PKC-independent activation of NF-{kappa}B in HUVEC with TNF, IL-1, or LPS is associated with, but not sufficient for, activation of ELAM-1 gene transcription.

Montgomery, K.F.; Tarr, P.I.; Bomsztyk, K.; Harlan, J.M.; Pohlman, T.H. (Univ. of Washington, Seattle (United States)); Osborn, L.; Hession, C.; Tizard, R.; Goff, D.; Vassallo, C.; Lobb, R. (Biogen, Inc., Cambridge, MA (United States))

1991-08-01T23:59:59.000Z

Note: This page contains sample records for the topic "16s rrna gene" from the National Library of EnergyBeta (NLEBeta).
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381

In silico analysis of motifs in promoters of Differentially Expressed Genes in rice (Oryza sativa L.) under anoxia  

Science Conference Proceedings (OSTI)

The aim of this study was to characterise the molecular mechanisms of transcriptional regulation of Differentially Expressed Genes (DEGs) in rice coleoptiles under anoxia by identifying motifs that are common in the promoter region of co-regulated ... Keywords: AREs, DEGs, Oryza sativa, anaerobic response elements, anoxia, bioinformatics, consensus promoter motif, differentially expressed genes, eukaryotic promoters, gene promoters, in silico motifs, in-silico motifs, microarrays, molecular mechanisms, motif detection, promoter motifs, rice, transcriptional regulation

Ashutosh Kumar; Shuchi Smita; Neeti Sahu; Vivekanand Sharma; Shankaracharya; Ambarish S. Vidyarthi; Dev Mani Pandey

2009-09-01T23:59:59.000Z

382

DFCI Gene Index Project: Genomic Databases for Plants, Animals, Protist, and Fungi from the Dana-Farber Cancer Institute  

DOE Data Explorer (OSTI)

The DFCI Gene Index Project creates databases for specific organisms. The goal for these databases is to provide an analysis of publicly available Expressed Sequence Transcripts (ESTs). ESTs are fragments of genes that were, at some time, copied from DNA to RNA. and gene sequence data to identify transcrips. The databases are in zipped files and free for download. The website also provides software and tools for use with the data, along with instructions from the website on how to link to background resources. The Gene Indices are organized into four categories: Animals, Plants, Protist, and Fungi.

383

Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency  

NLE Websites -- All DOE Office Websites (Extended Search)

Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency Qin Ma, Ying Xu PII: S1672-0229(13)00008-9 DOI: http://dx.doi.org/10.1016/j.gpb.2013.01.004 Reference: GPB 52 To appear in: Please cite this article as: Q. Ma, Y. Xu, Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency, (2013), doi: http://dx.doi.org/10.1016/j.gpb.2013.01.004 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process

384

Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon  

NLE Websites -- All DOE Office Websites (Extended Search)

Annotation Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon Ludmila Tyler 1,2 , Jennifer N Bragg 1† , Jiajie Wu 1,3† , Xiaohan Yang 4 , Gerald A Tuskan 4 , John P Vogel 1* Abstract Background: Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast- growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally

385

Ionizing radiation downregulates ASPM, a gene responsible for microcephaly in humans  

SciTech Connect

Microcephaly is a malformation associated with in utero exposed atomic bomb survivors and can be induced in mice by fetal exposure to ionizing radiation (IR). The pathogenesis of IR-induced microcephaly, however, has not been fully understood. Our analyses of high-coverage expression profiling (HiCEP) demonstrated that the abnormal spindle-like microcephaly associated gene (ASPM) was down-regulated in irradiated human diploid fibroblasts. ASPM was recently reported as the causative gene for MCPH-5, the most common type of congenital microcephaly in humans. Here, we show that the expression of the Aspm gene was significantly reduced by IR in various human and murine cells. Additionally, Aspm was found downregulated in the irradiated fetal mouse brain, particularly in the ventricular zones. A similar suppression was observed in the irradiated neurosphere cultures. This is the first report suggesting that the suppression of Aspm by IR could be the initial molecular target leading to the future microcephaly formation.

Fujimori, Akira [Cellular and Molecular Biology Team, National Institute of Radiological Sciences, Heavy-Ion Radiobiology Research Group, Research Center for Charged Particle Therapy, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan)], E-mail: fujimora@nirs.go.jp; Yaoi, Takeshi; Ogi, Hiroshi [Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine, Graduate School of Medical Sciences, Kawaramachi Hirokoji, Kamigyo-ku, Kyoto 602-8566 (Japan); Wang Bing [National Institute of Radiological Sciences, Heavy-Ion Radiology Research Group, Research Center for Charged Particle Therapy, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan); Suetomi, Katsutoshi; Sekine, Emiko; Yu Dong; Kato, Takamitsu [Cellular and Molecular Biology Team, National Institute of Radiological Sciences, Heavy-Ion Radiobiology Research Group, Research Center for Charged Particle Therapy, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan); Takahashi, Sentaro [National Institute of Radiological Sciences, Heavy-Ion Radiology Research Group, Research Center for Charged Particle Therapy, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan); Okayasu, Ryuichi [Cellular and Molecular Biology Team, National Institute of Radiological Sciences, Heavy-Ion Radiobiology Research Group, Research Center for Charged Particle Therapy, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan); Itoh, Kyoko; Fushiki, Shinji [Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine, Graduate School of Medical Sciences, Kawaramachi Hirokoji, Kamigyo-ku, Kyoto 602-8566 (Japan)

2008-05-09T23:59:59.000Z

386

Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data  

SciTech Connect

Three-dimensional gene expression PointCloud data generated by the Berkeley Drosophila Transcription Network Project (BDTNP) provides quantitative information about the spatial and temporal expression of genes in early Drosophila embryos at cellular resolution. The BDTNP team visualizes and analyzes Point-Cloud data using the software application PointCloudXplore (PCX). To maximize the impact of novel, complex data sets, such as PointClouds, the data needs to be accessible to biologists and comprehensible to developers of analysis functions. We address this challenge by linking PCX and Matlab via a dedicated interface, thereby providing biologists seamless access to advanced data analysis functions and giving bioinformatics researchers the opportunity to integrate their analysis directly into the visualization application. To demonstrate the usefulness of this approach, we computationally model parts of the expression pattern of the gene even skipped using a genetic algorithm implemented in Matlab and integrated into PCX via our Matlab interface.

Ruebel, Oliver; Keranen, Soile V.E.; Biggin, Mark; Knowles, David W.; Weber, Gunther H.; Hagen, Hans; Hamann, Bernd; Bethel, E. Wes

2011-03-30T23:59:59.000Z

387

Porting Charm++/NAMD to IBM Blue Gene/Q Wei Jiang Argonne Leadership Computing Facility  

NLE Websites -- All DOE Office Websites (Extended Search)

Porting Charm++/NAMD to IBM Blue Gene/Q Porting Charm++/NAMD to IBM Blue Gene/Q Wei Jiang Argonne Leadership Computing Facility 7 th , March NAMD_esp NAMD - Parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems Portable to all popular supercomputing platforms Great scalability based on Charm++ parallel objects Scientific aims on Blue Gene/Q Ensemble run that launches large number of replicas concurrently - mainly for energetic simulation High throughput simulation for large scale systems ~100M atoms Requirements for charm++ New communication layer that supports parallel/parallel runs Enable charm++ programming paradigm on Parallel Active Messaging Interface (PAMI) Parallel Structure of NAMD Hybrid force/spatial decomposition Adaptive Overlap of Communication and Computation

388

Gene H. McCall, 1988 | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

Gene H. McCall, 1988 Gene H. McCall, 1988 The Ernest Orlando Lawrence Award Lawrence Award Home Nomination & Selection Guidelines Award Laureates 2000's 1990's 1980's 1970's 1960's Ceremony The Life of Ernest Orlando Lawrence Contact Information The Ernest Orlando Lawrence Award U.S. Department of Energy SC-2/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-9395 E: lawrence.award@science.doe.gov 1980's Gene H. McCall, 1988 Print Text Size: A A A RSS Feeds FeedbackShare Page National Security: For his pioneering work in the field of laser-driven inertial fusion and its application to nuclear weapon design and diagnostics, for his early, independent work on laser-plasma interactions and the role of electron heating, and for his work on hypervelocity particles and shockless acceleration to enable development of a new class

389

Easy preparation of a large-size random gene mutagenesis library in Escherichia coli  

NLE Websites -- All DOE Office Websites (Extended Search)

Easy preparation of a large-size random gene mutagenesis library in Easy preparation of a large-size random gene mutagenesis library in Escherichia coli Chun You, Y.-H. Percival Zhang PII: S0003-2697(12)00291-6 DOI: http://dx.doi.org/10.1016/j.ab.2012.05.022 Reference: YABIO 10976 To appear in: Analytical Biochemistry Received Date: 27 April 2012 Revised Date: 21 May 2012 Accepted Date: 22 May 2012 Please cite this article as: C. You, Y.-H. Percival Zhang, Easy preparation of a large-size random gene mutagenesis library in Escherichia coli, Analytical Biochemistry (2012), doi: http://dx.doi.org/10.1016/j.ab.2012.05.022 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and

390

Murine chromosomal location of five bHLH-Zip transcription factor genes  

Science Conference Proceedings (OSTI)

The genes for the bHLH-Zip transcription factors Tfap4, Mxi1, Tcfeb, Usf1, and Usf2 have been mapped in mouse by interspecific backcross analysis. Mxi1, Usf1, and Usf2 have been mapped previously by in situ hybridization, but their positions on the meiotic linkage map had not been determined. The other two genes have not previously been mapped in mouse. These transcription factors belong to a growing family of transcriptional regulators, some of which are known to form a complex network of interacting proteins that control cell proliferation and apoptosis. As expected, based on mapping studies of other bHLH-Zip genes, these loci were well distributed among mouse chromosomes. In addition, some of the probes used in this study detected multiple, independently segregating loci, suggesting the possible existence of additional family members or species-specific pseudogenes. 34 refs., 1 fig., 1 tab.

Steingrimsson, E.; Gilbert, D.J.; Copeland, N.G.; Jenkins, N.A. [Univ. of Texas, Houston, TX (United States)] [and others

1995-07-20T23:59:59.000Z

391

Cloning and expression of the gene for bacteriophage T7 RNA polymerase  

DOE Patents (OSTI)

This application describes a means to clone a functional gene for bacteriophage T7 RNA polymerase. Active T7 RNA polymerase is produced from the cloned gene, and a plasmid has been constructed that can produce the active enzyme in large amounts. T7 RNA polymerase transcribes DNA very efficiently and is highly selective for a relatively long promoter sequence. This enzyme is useful for synthesizing large amounts of RNA in vivo or in vitro, and is capable of producing a single RNA selectively from a complex mixture of DNAs. The procedure used to obtain a clone of the T7 RNA polymerase gene can be applied to other T7-like phages to obtain clones that produce RNA polymerases having different promoter specificities, different bacterial hosts, or other desirable properties. T7 RNA polymerase is also used in a system for selective, high-level synthesis of RNAs and proteins in suitable host cells.

Studier, F. William (Stony Brook, NY); Davanloo, Parichehre (Basel, CH); Rosenberg, Alan H. (Setauket, NY); Moffatt, Barbara A. (East Lansing, MI); Dunn, John J. (Bellport, NY)

1990-01-01T23:59:59.000Z

392

Cloning and expression of the gene for bacteriophage T7 RNA polymerase  

DOE Patents (OSTI)

This application describes a means to clone a functional gene for bacteriophage T7 RNA polymerase. Active T7 RNA polymerase is produced from the cloned gene, and a plasmid has been constructed that can produce the active enzyme in large amounts. T7 RNA polymerase transcribes DNA very efficiently and is highly selective for a relatively long promoter sequence. This enzyme is useful for synthesizing large amounts of RNA in vivo or in vitro, and is capable of producing a single RNA selectively from a complex mixture of DNAs. The procedure used to obtain a clone of the R7 RNA polymerase gene can be applied to other T7-like phages to obtain clones that produce RNA polymerases having different promoter specificities, different bacterial hosts, or other desirable properties. T7 RNA polymerase is also used in a system for selective, high-level synthesis of RNAs and proteins in suitable host cells.

Studier, F. William (Stony Brook, NY); Davanloo, Parichehre (Basel, CH); Rosenberg, Alan H. (Setauket, NY); Moffatt, Barbara A. (Waterloo, CA); Dunn, John J. (Bellport, NY)

1997-12-02T23:59:59.000Z

393

Cloning and expression of the gene for bacteriophage T7 RNA polymerase  

DOE Patents (OSTI)

This application describes a means to clone a functional gene for bacteriophage T7 RNA polymerase. Active T7 RNA polymerase is produced from the cloned gene, and a plasmid has been constructed that can produce the active enzyme in large amounts. T7 RNA polymerase transcribes DNA very efficiently and is highly selective for a relatively long promoter sequence. This enzyme is useful for synthesizing large amounts of RNA in vivo or in vitro, and is capable of producing a single RNA selectively from a complex mixture of DNAs. The procedure used to obtain a clone of the R7 RNA polymerase gene can be applied to other T7-like phages to obtain clones that produce RNA polymerases having different promoter specificities, different bacterial hosts, or other desirable properties. T7 RNA polymerase is also used in a system for selective, high-level synthesis of RNAs and proteins in suitable host cells.

Studier, F. William (Stony Brook, NY); Davanloo, Parichehre (Basel, CH); Rosenberg, Alan H. (Setauket, NY); Moffatt, Barbara A. (Waterloo, CA); Dunn, John J. (Bellport, NY)

1999-02-09T23:59:59.000Z

394

Variation in Telangiectasia Predisposing Genes Is Associated With Overall Radiation Toxicity  

SciTech Connect

Purpose: In patients receiving radiotherapy for breast cancer where the heart is within the radiation field, cutaneous telangiectasiae could be a marker of potential radiation-induced heart disease. We hypothesized that single nucleotide polymorphisms (SNPs) in genes known to cause heritable telangiectasia-associated disorders could predispose to such late, normal tissue vascular damage. Methods and Materials: The relationship between cutaneous telangiectasia as a late normal tissue radiation injury phenotype in 633 breast cancer patients treated with radiotherapy was examined. Patients were clinically assessed for the presence of cutaneous telangiectasia and genotyped at nine SNPs in three candidate genes. Candidate SNPs were within the endoglin (ENG) and activin A receptor, type II-like 1 (ACVRL1) genes, mutations in which cause hereditary hemorrhagic telangiectasia and the ataxia-telangiectasia mutated (ATM) gene associated with ataxia-telangiectasia. Results: A total of 121 (19.1%) patients exhibited a degree of cutaneous telangiectasiae on clinical examination. Regression was used to examine the associations between the presence of telangiectasiae in patients who underwent breast-conserving surgery, controlling for the effects of boost and known brassiere size (n=388), and individual geno- or haplotypes. Inheritance of ACVRL1 SNPs marginally contributed to the risk of cutaneous telangiectasiae. Haplotypic analysis revealed a stronger association between inheritance of a ATM haplotype and the presence of cutaneous telangiectasiae, fibrosis and overall toxicity. No significant association was observed between telangiectasiae and the coinheritance of the candidate ENG SNPs. Conclusions: Genetic variation in the ATM gene influences reaction to radiotherapy through both vascular damage and increased fibrosis. The predisposing variation in the ATM gene will need to be better defined to optimize it as a predictive marker for assessing radiotherapy late effects.

Tanteles, George A. [Department of Genetics, University of Leicester, Leicester (United Kingdom) [Department of Genetics, University of Leicester, Leicester (United Kingdom); Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom); Murray, Robert J.S. [Department of Genetics, University of Leicester, Leicester (United Kingdom)] [Department of Genetics, University of Leicester, Leicester (United Kingdom); Mills, Jamie [Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom)] [Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom); Barwell, Julian [Department of Genetics, University of Leicester, Leicester (United Kingdom) [Department of Genetics, University of Leicester, Leicester (United Kingdom); Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom); Chakraborti, Prabir [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom)] [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom); Chan, Steve [Department of Clinical Oncology, Nottingham University Hospitals NHS Trust, Nottingham (United Kingdom)] [Department of Clinical Oncology, Nottingham University Hospitals NHS Trust, Nottingham (United Kingdom); Cheung, Kwok-Leung [Division of Breast Surgery, University of Nottingham, Nottingham (United Kingdom)] [Division of Breast Surgery, University of Nottingham, Nottingham (United Kingdom); Ennis, Dawn [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom)] [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom); Khurshid, Nazish [Department of Genetics, University of Leicester, Leicester (United Kingdom)] [Department of Genetics, University of Leicester, Leicester (United Kingdom); Lambert, Kelly [Department of Breast Surgery, University Hospitals of Leicester, Glenfield Hospital, Leicester (United Kingdom)] [Department of Breast Surgery, University Hospitals of Leicester, Glenfield Hospital, Leicester (United Kingdom); Machhar, Rohan; Meisuria, Mitul [Department of Genetics, University of Leicester, Leicester (United Kingdom)] [Department of Genetics, University of Leicester, Leicester (United Kingdom); Osman, Ahmed; Peat, Irene [Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom)] [Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom); Sahota, Harjinder [Department of Genetics, University of Leicester, Leicester (United Kingdom)] [Department of Genetics, University of Leicester, Leicester (United Kingdom); Woodings, Pamela [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom)] [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom); Talbot, Christopher J., E-mail: cjt14@le.ac.uk [Department of Genetics, University of Leicester, Leicester (United Kingdom); and others

2012-11-15T23:59:59.000Z

395

Genomic structure of the choroideremia (CHM) gene and mutation analysis in CHM patients  

Science Conference Proceedings (OSTI)

We have isolated the complete open reading frame (ORF) of the choroideremia (CHM) gene and elucidated its exon-intron structure. The ORF of the CHM gene is located on 15 exons and encodes a protein of 653 amino acids. Among 75 CHM patients investigated for large structural abnormalities, 15 (20%) showed deletions of one or more exons of the gene. The deletions vary in size from a few kb spanning one exon to more than 10 megabases encompassing a large part of Xq21. In addition, we have positioned the X-chromosomal breakpoint in a CHM female with an X;7 translocation between exons 3 and 4. Fine mapping of the deletions indicates that there is no clustering of deletion breakpoints. Moreover, only 2 deletions are located entirely within the CHM gene, indicating that most deletions can be detected by PCR amplification of exons 1 and 15. From within the CHM gene we identified two microsatellite markers, a (CA){sub n}- and a [(TA){sub 4-12}C]{sub n}-like repeat, which should be very valuable for CHM diagnostics in clear-cut CHM families. In patients in which the diagnosis of choroideremia is less obvious, mutation analysis can be performed by PCR-SSCP analysis and direct sequencing. The feasibility of this approach was illustrated by the finding of 10 causative mutations in 12 Danish CHM families investigated. Interestingly, all CHM gene mutations detected thus far give rise to the introduction of a premature stop codon. Missense mutations thus far have not been found.

Bokhoven, H. van; Hurk, J. van den; Bogerd, L. [Univ. Hospital Nijmegen (Netherlands)] [and others

1994-09-01T23:59:59.000Z

396

Chromosomal localization of the gene encoding the human DNA helicase RECQL and its mouse homologue  

Science Conference Proceedings (OSTI)

We have determined the chromosomal location of the human and mouse genes encoding the RECQL protein, a putative DNA helicase homologous to the bacterial DNA helicase, RecQ. RECQL was localized to human chromosome 12 by analysis of human-rodent somatic cell hybrid DNA, fine mapping of RECQL by fluorescence in situ hybridization revealed its chromosomal location to be 12p11-p12. The corresponding mouse gene, Recql, was mapped to the telomeric end of mouse chromosome 6 by analysis of DNA from an interspecific cross. 19 refs., 2 figs.

Puranam, K.L.; Kennington, E.; Blackshear, P.J. [Duke Univ., Durham, NC (United States)] [and others

1995-04-10T23:59:59.000Z

397

Temperature, acetosyringone, virulence genes and wounding effects on Agrobacterium-mediated transformation efficiency  

E-Print Network (OSTI)

Several conditions were evaluated to determine their impact on Agrobacterium-mediated transformation efficiency. Temperature and acetosyringone (AS) effects were first studied in tobacco, as a plant model system and then applied to cotton transformation. In tobacco, AS significantly increased transformation rates that resulted in stable transformed plants. Four temperatures were evaluated during the cc-cultivation period to determine the most appropriate temperature for T-DNA transfer and integration into the plant genome. Even though 19C was reported in the literature as the optimal temperature for Agrobacterium-mediated gene transfer, 25C was statistically significantly different as compared to 15C, 19C or 32C and produced the highest number of transgenic tobacco plants. The superior treatments established in tobacco transformation were applied to Agrobacterium-mediated transformation of the cotton shoot apex. Explant survival rates in selection medium were recorded and used to compare two temperatures (19C and 25C) and the effects of AS to induce the vir genes. After approximately 6-7 wk in selection medium, the percentage of surviving exhalants established that 25C was the best temperature for cotton transformation, either with or without AS. Two wounding methods and the addition of a super-virulent plasmid were tested in cotton shoot apex transformation experiments. Their effects were evaluated using the green fluorescent protein (GFP) as an in vivo reporter gene to determine the early transformation patterns. Both removal of a leaf primordial and sanitation were examined. Transient GFP expression did not reveal any major benefit of the treatments on the transformation pattern. In contrast, when additional copies of virG and virE genes were inserted into Agrobacterium, a considerable increase in the number of fluorescence spots per exploit was evident. This was the first time GFP gene was used in cotton. Its expression was reliable, and the system was successfully established. Since GFP has several advantages as a reporter gene over the traditional GUS gene and herbicide resistance genes, it would allow the development of a more accurate selection process and therefore it would speed up the optimization of the shoot apex method.

Salas Fernandez, Maria Guadalupe

1999-01-01T23:59:59.000Z

398

GWAS Meets Microarray: Are the Results of Genome- Wide Association Studies and Gene-Expression Profiling Consistent? Prostate Cancer as an Example  

E-Print Network (OSTI)

Background: Genome-wide association studies (GWASs) and global profiling of gene expression (microarrays) are two major technological breakthroughs that allow hypothesis-free identification of candidate genes associated with tumorigenesis. It is not obvious whether there is a consistency between the candidate genes identified by GWAS (GWAS genes) and those identified by profiling gene expression (microarray genes). Methodology/Principal Findings: We used the Cancer Genetic Markers Susceptibility database to retrieve single nucleotide polymorphisms from candidate genes for prostate cancer. In addition, we conducted a large meta-analysis of gene expression data in normal prostate and prostate tumor tissue. We identified 13,905 genes that were interrogated by both GWASs and microarrays. On the basis of P values from GWASs, we selected 1,649 most significantly associated genes for functional annotation by the Database for Annotation, Visualization and Integrated Discovery. We also conducted functional annotation analysis using same number of the top genes identified in the meta-analysis of the gene expression data. We found that genes involved in cell adhesion were overrepresented among both the GWAS and microarray genes. Conclusions/Significance: We conclude that the results of these analyses suggest that combining GWAS and microarray data would be a more effective approach than analyzing individual datasets and can help to refine the identification of

Ivan P. Gorlov; Gary E. Gallick; Olga Y. Gorlova; Christopher Amos; Christopher J. Logothetis

2009-01-01T23:59:59.000Z

399

Genetic analysis of mycobacterium avium subspecies paratuberculosis reveals sequence and epigenetic variation among field isolates  

E-Print Network (OSTI)

Previous research performed in 1999 by Harris et al. has shown that many varieties of ruminants serve as the host species for Mycobacterium avium subspecies paratuberculosis (MparaTb) infections. Gene sequencing has supported the contention that organisms isolated from different hosts harbor different gene sequences; this has been exemplified by Amonsin et al. in 2004 with the sequencing of the mfd (transcription-repair coupling factor) and by Motiwala et al. in 2005 through sequence analysis of phosphatidylethanolaminebinding proteins which reveal a host-specific correlation of isolates. Some contradicting reports from Bannantine et al. from 2003 have further claimed that MparaTb is a monogenic organism based upon sequence data from regions flanking the origin of replication and the 16s rRNA. One of the drawbacks to the techniques implemented in these reports is the extremely restricted region of the bacterial genome that was analyzed; furthermore, only a select number of isolates were analyzed. In the present studies, amplified fragment length polymorphism (AFLP) was used as a tool for a genome scale comparison of MparaTb isolates from differing isolation types as well as a comparison of MparaTb isolates to the genetically similar yet avirulent Mycobacterium avium subspecies avium isolates. AFLP data reveals the MparaTb genome to be much more plastic and polymorphic than previously thought. These polymorphic regions were identified and characterized and are shown to be unique to the organism when compared to an array of Mycobacterial isolates of differing species. These polymorphic regions were also utilized in polymerase chain reaction (PCR) based diagnostic as well as epidemiologic tests. Furthermore, AFLP comparative analysis of intracellular and fecal MparaTb isolates reveals polymorphic regions unique to each isolate type. While these genomic differences are not based upon differences in the genetic code, they are based upon epigenetic modifications such as DNA methylation. These DNA methylation patterns are unique to intracellular MparaTb isolates as opposed to isolates from fecal material. Furthermore, AFLP comparisons of fecal MparaTb isolates that were passaged through the bovine ileum revealed banding pattern differences as compared to the original inoculum.

O'Shea, Brian James

2007-12-01T23:59:59.000Z

400

Engineering PFLOTRAN for Scalable Performance on Cray XT and IBM BlueGene Architectures  

E-Print Network (OSTI)

Engineering PFLOTRAN for Scalable Performance on Cray XT and IBM BlueGene Architectures Richard University, Raleigh, NC 27695-8206 3 Department of Civil, Construction, and Environmental Engineering, North the release of a hypothetical uranium plume at the Hanford 300 Area in southeastern Washington state

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

Diverse RNA processing pathways important for post-transcriptional gene regulation  

E-Print Network (OSTI)

Cis-acting elements in 3' untranslated regions (UTRs) of mRNAs are crucial to the regulation of gene expression. Animal microRNAs (miRNAs) each target hundreds of mRNAs, which are recognized by pairing to nucleotides 2-7 ...

Jan, Calvin H

2010-01-01T23:59:59.000Z

402

Discovering genes-diseases associations from specialized literature using the grid  

Science Conference Proceedings (OSTI)

This paper proposes a novel method for text mining on the Grid, aimed at pointing out hidden relationships for hypothesis generation and suitable for semi-interactive querying. The method is based on unsupervised clustering and the outputs are visualized ... Keywords: Grid, genes-diseases association, knowledge discovery, text mining, unsupervised clustering

Alberto Faro; Daniela Giordano; Francesco Maiorana; Concetto Spampinato

2009-07-01T23:59:59.000Z

403

Using feedback to regulate gene expression in a developmental control architecture  

Science Conference Proceedings (OSTI)

We present what we believe is the first attempt to physically reconstruct the exploratory mechanism of genetic regulatory networks. Feedback plays a crucial role during developmental processes and its mechanisms have recently become much clearer due ... Keywords: adaptation/self-adaptation, developmental processes, evolvable hardware, gene regulatory networks, signal processing

Kester Clegg; Susan Stepney; Tim Clarke

2007-07-01T23:59:59.000Z

404

Dynamic and collective analysis of membrane protein interaction network based on gene regulatory network model  

Science Conference Proceedings (OSTI)

Membrane protein interactions are vitally important for every process in a living cell. Information about these interactions can improve our understanding of diseases and provide the basis to revolutionize therapeutic treatments. However, current experimental ... Keywords: Bio-network, Dynamic and collective control, Gene regulatory network, Membrane protein interaction network, Robustness, Scale free distributing, Small-world network

Yong-Sheng Ding; Yi-Zhen Shen; Li-Hong Ren; Li-Jun Cheng

2012-12-01T23:59:59.000Z

405

Neuroinformatics for Genome-Wide 3-D Gene Expression Mapping in the Mouse Brain  

Science Conference Proceedings (OSTI)

Large scale gene expression studies in the mammalian brain offer the promise of understanding the topology, networks and ultimately the function of its complex anatomy, opening previously unexplored avenues in neuroscience. High-throughput methods permit ... Keywords: Bioinformatics (genome or protein) databases, Data mining, Registration, Segmentation, Information Visualization

Lydia Ng; Sayan Pathak; Chihchau Kuan; Chris Lau; Hong-wei Dong; Andrew Sodt; Chinh Dang; Brian Avants; Paul Yushkevich; James Gee; David Haynor; Ed Lein; Allan Jones; Mike Hawrylycz

2007-07-01T23:59:59.000Z

406

Blue Gene/L compute chip: synthesis, timing, and physical design  

Science Conference Proceedings (OSTI)

As one of the most highly integrated system-on-a-chip application-specific integrated circuits (ASICs) to date, the Blue Gene/L compute chip presented unique challenges that required extensions of the standard ASIC synthesis, timing, and physical ...

A. A. Bright; R. A. Haring; M. B. Dombrowa; M. Ohmacht; D. Hoenicke; S. Singh; J. A. Marcella; R. F. Lembach; S. M. Douskey; M. R. Ellavsky; C. G. Zoellin; A. Gara

2005-03-01T23:59:59.000Z

407

Investigating the Efficacy of Nonlinear Dimensionality Reduction Schemes in Classifying Gene and Protein Expression Studies  

Science Conference Proceedings (OSTI)

The recent explosion in procurement and availability of high-dimensional gene- and protein-expression profile datasets for cancer diagnostics has necessitated the development of sophisticated machine learning tools with which to analyze them. A major ... Keywords: Bioinformatics (genome or protein) databases, Clustering, classification, and association rules, Data and knowledge visualization, Data mining, Feature extraction or construction

George Lee; Carlos Rodriguez; Anant Madabhushi

2008-07-01T23:59:59.000Z

408

Shrinkage-based regularization tests for high-dimensional data with application to gene set analysis  

Science Conference Proceedings (OSTI)

Traditional multivariate tests such as Hotelling's test or Wilk's test are designed for classical problems, where the number of observations is much larger than the dimension of the variables. For high-dimensional data, however, this assumption cannot ... Keywords: Feature selection, Gene set analysis, High dimensionality, MANOVA, Power, Regularization

Yanfeng Shen; Zhengyan Lin; Jun Zhu

2011-07-01T23:59:59.000Z

409

In silico analysis of mycobacteriophage Che12 genome: Characterization of genes required to lysogenise Mycobacterium tuberculosis  

Science Conference Proceedings (OSTI)

Che12 is a temperate Chennai phage infecting Mycobacterium tuberculosis. The nucleotide sequence of the 52,047bp linear double stranded DNA genome has a GC content of 62.9% with 70 putative ORFs identified. Functions are assigned to 24 genes based on ... Keywords: Bioinformatics, Mycobacterium tuberculosis, Temperate mycobacteriophage

N. S. Gomathi; H. Sameer; Vanaja Kumar; S. Balaji; V.N. Azger Dustackeer; P. R. Narayanan

2007-04-01T23:59:59.000Z

410

Classical and dominance-based rough sets in the search for genes under balancing selection  

Science Conference Proceedings (OSTI)

Since the time of Kimuras theory of neutral evolution at molecular level the search for genes under natural selection is one of the crucial problems in population genetics. There exists quite a number of statistical tests designed for it, however, ... Keywords: ATM, BLM, RECQL, WRN, balancing selection, classical rough sets approach, dominance-based rough sets approach, natural selection, neutrality tests

Krzysztof A. Cyran

2010-01-01T23:59:59.000Z

411

Intrinsic and extrinsic regulation of type III secretion gene expression in Pseudomonas aeruginosa  

E-Print Network (OSTI)

Pseudomonas aeruginosa is an opportunistic pathogen that is particularly problematic in the healthcare setting where it is a frequent cause of pneumonia, bloodstream, and urinary tract infections. An important determinant of P. aeruginosa virulence is a type III secretion system (T3SS). T3SS-dependent intoxication is a complex process that minimally requires binding of P. aeruginosa to host cells, injection of the cytotoxic effector proteins through the host cell plasma membrane, and induction of T3SS gene expression. The latter process, referred to as contact-dependent expression, involves a well-characterized regulatory cascade that activates T3SS gene expression in response to host cell contact. Although host cell contact is a primary activating signal for T3SS gene expression, the involvement of multiple membrane-bound regulatory systems indicates that additional environmental signals also play a role in controlling expression of the T3SS. These regulatory systems coordinate T3SS gene expression with many other cellular activities including motility, mucoidy, polysaccharide production, and biofilm formation. The signals to which the organism responds are poorly understood but many seem to be coupled to the metabolic state of the cell and integrated within a master circuit that assimilates informational signals from endogenous and exogenous sources. Herein we review

Manisha R. Diaz; Jessica M. King; Timothy L. Yahr; Jrgen Heesemann; Max Von; Matthew C. Wolfgang; Timothy L. Yahr; Department Of

2011-01-01T23:59:59.000Z

412

Prokaryotic Gene Finding Based on Physicochemical Characteristics of Codons Calculated from Molecular Dynamics Simulations  

E-Print Network (OSTI)

calculated solvation energies and flexibility of codon sequences as well as codon usage in genes and amino are typically very small in prokaryotic genomes. Usage of a genome-specific plane as opposed to a common energy, the base pair stacking energy, and an index of the propensity of a codon for protein-nucleic acid

Jayaram, Bhyravabotla

413

Software Note: Using probe secondary structure information to enhance Affymetrix GeneChip background estimates  

Science Conference Proceedings (OSTI)

High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed ... Keywords: Background correction, DNA microarray, Probe secondary structure

Raad Z. Gharaibeh; Anthony A. Fodor; Cynthia J. Gibas

2007-04-01T23:59:59.000Z

414

GeneBox: Interactive Visualization of Microarray Data Sets Nameeta Shah  

E-Print Network (OSTI)

led biologists to ask complex questions, which the existing, fully automated analyses are often and Differential Ex- pression Calculation of differential expression of a gene requires one to compare fluorescence phosphate conditions (low Pi) vs. high Pi; on the blue axis we show the differential expression of DBY7286

California at Davis, University of

415

Designing a highly-scalable operating system: the Blue Gene/L story  

Science Conference Proceedings (OSTI)

Blue Gene/L is currently the world's fastest and most scalable supercomputer. It has demonstrated essentially linear scaling all the way to 131,072 processors in several benchmarks and real applications. The operating systems for the compute and I/O ...

Jos Moreira; Michael Brutman; Jos Castaos; Thomas Engelsiepen; Mark Giampapa; Tom Gooding; Roger Haskin; Todd Inglett; Derek Lieber; Pat McCarthy; Mike Mundy; Jeff Parker; Brian Wallenfelt

2006-11-01T23:59:59.000Z

416

Astronomical real-time streaming signal processing on a Blue Gene/L supercomputer  

Science Conference Proceedings (OSTI)

LOFAR is the first of a new generation of radio telescopes, that combines the signals from many thousands of simple, fixed antennas, rather than from expensive dishes. Its revolutionary design and unprecedented size enables observations in a frequency ... Keywords: Blue Gene/L, LOFAR, correlator, filtering

John W. Romein; P. Chris Broekema; Ellen van Meijeren; Kjeld van der Schaaf; Walther H. Zwart

2006-07-01T23:59:59.000Z

417

Massively parallel genomic sequence search on the Blue Gene/P architecture  

Science Conference Proceedings (OSTI)

This paper presents our first experiences in mapping and optimizing genomic sequence search onto the massively parallel IBM Blue Gene/P (BG/P) platform. Specifically, we performed our work on mpiBLAST, a parallel sequence-search code that has been optimized ...

Heshan Lin; Pavan Balaji; Ruth Poole; Carlos Sosa; Xiaosong Ma; Wu-chun Feng

2008-11-01T23:59:59.000Z

418

Genetic Background Modulates Gene Expression Profile Induced by Skin Irradiation in Ptch1 Mice  

Science Conference Proceedings (OSTI)

Purpose: Ptch1 germ-line mutations in mice predispose to radiation-induced basal cell carcinoma of the skin, with tumor incidence modulated by the genetic background. Here, we examined the possible mechanisms underlying skin response to radiation in F1 progeny of Ptch1{sup neo67/+} mice crossed with either skin tumor-susceptible (Car-S) or -resistant (Car-R) mice and X-irradiated (3 Gy) at 2 days of age or left untreated. Methods and Materials: We conducted a gene expression profile analysis in mRNA samples extracted from the skin of irradiated or control mice, using Affymetrix whole mouse genome expression array. Confirmation of the results was done using real-time reverse-transcriptase polymerase chain reaction. Results: Analysis of the gene expression profile of normal skin of F1 mice at 4 weeks of age revealed a similar basal profile in the nonirradiated mice, but alterations in levels of 71 transcripts in irradiated Ptch1{sup neo67/+} mice of the Car-R cross and modulation of only eight genes in irradiated Ptch1{sup neo67/+} mice of the Car-S cross. Conclusions: These results indicate that neonatal irradiation causes a persistent change in the gene expression profile of the skin. The tendency of mice genetically resistant to skin tumorigenesis to show a more complex pattern of transcriptional response to radiation than do genetically susceptible mice suggests a role for this response in genetic resistance to basal cell tumorigenesis.

Galvan, Antonella; Noci, Sara [Department of Experimental Oncology and Laboratories, Fondazione IRCCS Istituto Nazionale Tumori, Milan (Italy); Mancuso, Mariateresa; Pazzaglia, Simonetta; Saran, Anna [ENEA Laboratories, Rome (Italy); Dragani, Tommaso A. [Department of Experimental Oncology and Laboratories, Fondazione IRCCS Istituto Nazionale Tumori, Milan (Italy)], E-mail: tommaso.dragani@istitutotumori.mi.it

2008-12-01T23:59:59.000Z

419

Ethanol production by Escherichia coli strains co-expressing Zymomonas PDC and ADH genes  

DOE Patents (OSTI)

A novel operon and plasmids comprising genes which code for the alcohol dehydrogenase and pyruvate decarboxylase activities of Zymomonas mobilis are described. Also disclosed are methods for increasing the growth of microorganisms or eukaryotic cells and methods for reducing the accumulation of undesirable metabolic products in the growth medium of microorganisms or cells.

Ingram, Lonnie O. (Gainesville, FL); Conway, Tyrrell (Lincoln, NE); Alterthum, Flavio (Gainesville, FL)

1991-01-01T23:59:59.000Z

420

A light-weight virtual machine monitor for Blue Gene/P  

Science Conference Proceedings (OSTI)

In this paper, we present a light-weight, micro--kernel-based virtual machine monitor (VMM) for the Blue Gene/P Supercomputer. Our VMM comprises a small ?-kernel with virtualization capabilities and, atop, a user-level VMM component that manages virtual ...

Jan Stoess; Jonathan Appavoo; Udo Steinberg; Amos Waterland; Volkmar Uhlig; Jens Kehne

2011-05-01T23:59:59.000Z

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.


421

Design and implementation of message-passing services for the Blue Gene/L supercomputer  

Science Conference Proceedings (OSTI)

The Blue Gene/L (BG/L) supercomputer, with 65,536 dual-processor compute nodes, was designed from the ground up to support efficient execution of massively parallel message-passing programs. Part of this support is an optimized implementation of ...

G. Almsi; C. Archer; J. G. Castaos; J. A. Gunnels; C. C. Erway; P. Heidelberger; X. Martorell; J. E. Moreira; K. Pinnow; J. Ratterman; B. D. Steinmacher-Burow; W. Gropp; B. Toonen

2005-03-01T23:59:59.000Z

422

Mining time-shifting co-regulation patterns from gene expression data  

Science Conference Proceedings (OSTI)

Previous work for finding patterns only focuses on grouping objects under the same subset of dimensions. Thus, an important bio-interesting pattern, i.e. time-shifting, will be ignored during the analysis of time series gene expression data. In this ...

Ying Yin; Yuhai Zhao; Bin Zhang; Guoren Wang

2007-06-01T23:59:59.000Z

423

Discrete Dynamical System Modeling for Gene Regulatory Networks of HMF Tolerance for  

E-Print Network (OSTI)

Saccharomyces cerevisiae in response to 5-hydroxymethylfurfural, a bioethanol conversion inhibitor. The modeling) In the bioethanol conversion process, this system equation describes the ideal behavior of yeast gene expression in yeast during biomass conversion to ethanol. The Verhulst equation, a single- variable DDS model

Song, Joe

424

Isolation and Characterization of Flowering Genes in Ryegrass (Lolium perenne L.)  

E-Print Network (OSTI)

ryegrass. In L. temulentum LD conditions also induces the LtCO expression peak with light and activates GAs with a concomitant production of GA20 floral bio-active GA5. In Arabidopsis CO activates FLOWERING LOCUS T (FT), which in turn activates the transcription of the floral meristem identity genes. FT belongs to a group

425

Functional analysis of the microRNA genes of C. elegans  

E-Print Network (OSTI)

MicroRNAs (miRNAs) were discovered in C. elegans during studies of the control of developmental timing. MicroRNAs are a large class of short non-coding RNAs found in many viruses, plants and animals that regulate gene ...

Alvarez-Saavedra, Ezequiel (Ezequiel Andrs)

2008-01-01T23:59:59.000Z

426

Effects of soil type and farm management on soil ecological functional genes and microbial activities  

Science Conference Proceedings (OSTI)

Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes.

Reeve, Jennifer [Washington State University; Schadt, Christopher Warren [ORNL; Carpenter-Boggs, Lynne [Washington State University; Kang, S. [University of Oklahoma; Zhou, Jizhong [University of Oklahoma, Norman; Reganold, John P. [Washington State University

2010-01-01T23:59:59.000Z

427

Towards isolation of the gene for X-linked retinitis pigmentosa (RP3)  

Science Conference Proceedings (OSTI)

Until recently the region of interest containing the gene for X-linked retinitis pigmentosa (RP3) was thought to lie between CYBB (Xp21.1) and the proximal end of the deletion in patient BB (JBBprox). This region was thought to span 100-150 kb. Here we present new mapping data to show that the distance between the 5{prime} (most proximal) end of CYBB and JBBprox is only 50 kb. Recently Roux et al. (1994) have described the isolation of a gene within this region but this showed no disease-associated changes. Further evidence from mapping the deletion in patient NF (who suffered from McLead`s syndrome and CGD but not RP) and from linkage analysis of our RP3 families with a new dinucleotide repeat suggests that the gene must extend proximally from JBBprox. In order to extend the region of search we have constructed a YAC contig spanning 800 kb to OTC. We are continuing our search for the RP3 gene using a variety of strategies including exon trapping and cDNA enrichment as well as direct screening of cDNA libraries with subclones from this region.

Dry, K.L.; Aldred, M.A.; Hardwick, L.J. [MRC Human Genetics Unit, Scotland (United Kingdom)] [and others

1994-09-01T23:59:59.000Z

428

Control of Stochastic Gene Expression by Host Factors at the HIV Promoter  

E-Print Network (OSTI)

promoter contains cis- acting Sp1 and NF-kB elements that regulate gene expression via the recruitment lentivirus variants with mutations introduced in the Sp1 and NF-kB elements, we employed flow cytometry, m and reduction in the regulation of histone acetylation and deacetylation. Furthermore, the NF-kB sites exhibit

Schaffer, David V.

429

Gene Regulation in M Cell Lineages: In Vitro and In Vivo  

E-Print Network (OSTI)

LTbR agonist (Fig 2-1C). The NF-kB gene relB (Relb) has alsoof relB is regulated by NF-kB activation, and the LT?R andreceptors all signal through NF-kB activation, this finding

Wang, Jing

2011-01-01T23:59:59.000Z

430

Global Control of Motor Neuron Topography Mediated by the Repressive Actions of a Single Hox Gene  

E-Print Network (OSTI)

Global Control of Motor Neuron Topography Mediated by the Repressive Actions of a Single Hox Gene transcription factors are critical in controlling motor neuron fates along the rostrocaudal axis, exemplified by the precise pattern of limb innervation by more than fifty Hox-dependent motor pools. The mechanisms by which

Gifford, David K.

431

Sp1 and CREB regulate basal transcription of the human SNF2L gene  

Science Conference Proceedings (OSTI)

Imitation Switch (ISWI) is a member of the SWI2/SNF2 superfamily of ATP-dependent chromatin remodelers, which are involved in multiple nuclear functions, including transcriptional regulation, replication, and chromatin assembly. Mammalian genomes encode two ISWI orthologs, SNF2H and SNF2L. In order to clarify the molecular mechanisms governing the expression of human SNF2L gene, we functionally examined the transcriptional regulation of human SNF2L promoter. Reporter gene assays demonstrated that the minimal SNF2L promoter was located between positions -152 to -86 relative to the transcription start site. In this region we have identified a cAMP-response element (CRE) located at -99 to -92 and a Sp1-binding site at -145 to -135 that play a critical role in regulating basal activity of human SNF2L gene, which were proven by deletion and mutation of specific binding sites, EMSA, and down-regulating Sp1 and CREB via RNAi. This study provides the first insight into the mechanisms that control basal expression of human SNF2L gene.

Xia Yu; Jiang Baichun; Zou Yongxin; Gao Guimin; Shang Linshan; Chen Bingxi; Liu Qiji [Key Laboratory for Experimental Teratology of the Ministry of Education and Institute of Medical Genetics, Shandong University School of Medicine, Jinan, Shandong 250012 (China); Gong Yaoqin [Key Laboratory for Experimental Teratology of the Ministry of Education and Institute of Medical Genetics, Shandong University School of Medicine, Jinan, Shandong 250012 (China)], E-mail: yxg8@sdu.edu.cn

2008-04-04T23:59:59.000Z

432

SATB1 packages densely-looped, transciptionally-active chromatinfor coordinated expression of cytokine genes  

SciTech Connect

SATB1 is an important regulator of nuclear architecture that anchors specialized DNA sequences onto its cage-like network and recruits chromatin remodeling/modifying factors to control gene transcription. We studied the role of SATB1 in regulating the coordinated expression of Il5, Il4, and Il13 from the 200kb cytokine gene cluster region of mouse chromosome 11 during T-helper 2 (Th2)-cell activation. We show that upon cell activation, SATB1 is rapidly induced to form a unique transcriptionally-active chromatin structure that includes the cytokine gene region. Chromatin is folded into numerous small loops all anchored by SATB1, is histone H3 acetylated at lysine 9/14, and associated with Th2-specific factors, GATA3, STAT6, c-Maf, the chromatin-remodeling enzyme Brg-1, and RNA polymerase II across the 200kb region. Before activation, the chromatin displays some of these features, such as association with GATA3 and STAT6, but these were insufficient for cytokine gene expression. Using RNA interference (RNAi), we show that upon cell activation, SATB1 is not only required for chromatin folding into dense loops, but also for c-Maf induction and subsequently for Il4, Il5, and Il13 transcription. Our results show that SATB1 is an important determinant for chromatin architecture that constitutes a novel higher-order, transcriptionally-active chromatin structure upon Th2-cell activation.

Cai, Shutao; Lee, Charles C.; Kohwi-Shigematsu, Terumi

2006-05-23T23:59:59.000Z

433

VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data  

E-Print Network (OSTI)

the increased computational load. Since all of these transactions are stored in the VAMPIRE database, no dataVAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data of analysis, collectively known as variance-modeled posterior inference with regional exponentials (VAMPIRE

434

In silico analysis of putative miRNAs and their target genes in sorghum Sorghum bicolor  

Science Conference Proceedings (OSTI)

MicroRNAs miRNAs are small endogenous genes regulators which regulate different processes underlying plant adaptation to abiotic stresses. To gain a deep understanding of role of miRNAs in plants, in the present study, we computationally analyzed different ...

Gobind Ram; Arun Dev Sharma

2013-06-01T23:59:59.000Z

435

Validating candidate gene-mutation relations in MEDLINE abstracts via crowdsourcing  

Science Conference Proceedings (OSTI)

We describe an experiment to elicit judgments on the validity of gene-mutation relations in MEDLINE abstracts via crowdsourcing. The biomedical literature contains rich information on such relations, but the correct pairings are difficult to extract ... Keywords: annotation, crowdsourcing, mutations, text mining

John D. Burger; Emily Doughty; Sam Bayer; David Tresner-Kirsch; Ben Wellner; John Aberdeen; Kyungjoon Lee; Maricel G. Kann; Lynette Hirschman

2012-06-01T23:59:59.000Z

436

Unsupervised gene/protein named entity normalization using automatically extracted dictionaries  

Science Conference Proceedings (OSTI)

Gene and protein named-entity recognition (NER) and normalization is often treated as a two-step process. While the first step, NER, has received considerable attention over the last few years, normalization has received much less attention. We have ...

Aaron M. Cohen

2005-06-01T23:59:59.000Z

437

Discovery of Mineralization Predication Classification Rules by Using Gene Expression Programming Based on PCA  

Science Conference Proceedings (OSTI)

Classification is one of the fundamental tasks in geology field. In this paper, we propose an evolutionary approach for discovering classification rules of mineralization predication from distinct combinations of geochemistry elements by using gene expression ... Keywords: GEP, Principal Component Analysis, mineralization predication

Dongmei Zhang; Yue Huang; Jing Zhi

2009-08-01T23:59:59.000Z

438

Modified cellulose synthase gene from 'Arabidopsis thaliana' confers herbicide resistance to plants  

DOE Patents (OSTI)

Cellulose synthase ('CS'), a key enzyme in the biosynthesis of cellulose in plants is inhibited by herbicides comprising thiazolidinones such as 5-tert-butyl-carbamoyloxy-3-(3-trifluromethyl) phenyl-4-thiazolidinone (TZ), isoxaben and 2,6-dichlorobenzonitrile (DCB). Two mutant genes encoding isoxaben and TZ-resistant cellulose synthase have been isolated from isoxaben and TZ-resistant Arabidopsis thaliana mutants. When compared with the gene coding for isoxaben or TZ-sensitive cellulose synthase, one of the resistant CS genes contains a point mutation, wherein glycine residue 998 is replaced by an aspartic acid. The other resistant mutation is due to a threonine to isoleucine change at amino acid residue 942. The mutant CS gene can be used to impart herbicide resistance to a plant; thereby permitting the utilization of the herbicide as a single application at a concentration which ensures the complete or substantially complete killing of weeds, while leaving the transgenic crop plant essentially undamaged.

Somerville, Chris R.; Scieble, Wolf

2000-10-11T23:59:59.000Z

439

Polymorphisms and haplotypes in folate-metabolizing genes and risk of non-Hodgkin lymphoma  

E-Print Network (OSTI)

) in the promoter region of the thymidylate synthase gene (TYMS 3R 3 2R) and variant alleles in the cytosolic serine in the development of lymphoma.8,9 For example, in agreement with our previous findings in adultALL, the TYMS 3R

California at Berkeley, University of

440

Candidate genes for chromosomes 6 and 10 quantitative trait loci for age-related retinal degeneration in mice  

E-Print Network (OSTI)

), complement factor B (CFB), and complement component 2 (C2), Chemokine (C-X3-C motif) receptor 1 (CX3CR1), Age to permanent exposure to reactive oxygen species generated by the absorption of light. Genes involved in gene expression should reflect an adjustment of blood flow for the oxygen requirement of the retina

Dahlquist, Kam D.

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