Multiple issues citation style October 2009 external links October 2009 laundry October 2009 Metagenomics ... year 2010 title Metagenomics Theory, Methods and Applications publisher Caister Academic Press isbn 978 1 904455 54 7 ref ref name MarcoD2011 cite book author Marco, D editor year 2011 title Metagenomics ... 5 issue 3 pages e82 pmid 17355177 pmc 1821061 ref History Origin of the term The term metagenomics ... like nature of the term, has resulted in the broader use of metagenomics to describe any sequencing ... defined metagenomics as the application of modern genomics techniques to the study of communities ... ref Shotgun metagenomics Advances in bioinformatics , refinements of DNA amplification, and proliferation ... cloning the DNA before sequencing, removing one of the main biases in metagenomics. MEGAN In 2007 ... title Metagenomics to paleogenomics large scale sequencing of mammoth DNA. journal Science volume ... Metagenomics RAST server MG RAST a community resource for metagenome data set analysis. ref ..., Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA year 2008 title The metagenomics ... within MG RAST. Applications Metagenomics can improve strategies for monitoring the impact of pollutants .... ref name Georgei cite book author George I et al. year 2010 chapter Application of Metagenomics to Bioremediation title Metagenomics Theory, Methods and Applications publisher Caister Academic Press ... has led to the discovery of new genes, enzymes, and natural products. The impact of metagenomics ... cite book author Wong D year 2010 chapter Applications of Metagenomics for Industrial Bioproducts title Metagenomics Theory, Methods and Applications publisher Caister Academic Press isbn 978 1 904455 ... 2010 chapter Metagenomics and Its Applications to the Study of the Human Microbiome title Metagenomics ... known that the vast majority of microbes have not been cultivated. Functional metagenomics strategies ... chapter The Potential for Investigation of Plant microbe Interactions Using Metagenomics Methods title ... more details
for a list of various candidate divisions Bacterial phyla A candidate division , candidate phylum or candidate division level is a lineage of Prokaryotic organisms for which no Microbiology cultured representatives have been found, but evidence of the existence of the clade has been obtained by 16S rRNA Metagenomics metagenomic analysis of environmental samples. ref name pace cite pmid 9733676 ref The term candidatus in fact means a species which there is insufficient information to call it a new species according to the International Code of Nomenclature of Bacteria ref cite journal title Judicial commission of the international committee on systematic bacteriology Minutes of the meetings, 2 and 6 July 1994, Prague, Czech Republic journal Int. J. Syst. Bacteriol. year 1995 volume 45 pages 195 196 url http ijs.sgmjournals.org cgi reprint 45 1 195.pdf ref See also Metagenomics Gene cloning Cloning DNA sequencing references reflist Category Bacteriology Category Microbiology ... more details
Binning may refer to wiktionary People B. C. Binning , 1909 1976 , Canadian artist Bob Binning , d.2005 , New Zealand fencer Hugh Binning , 1627 1653 , Scottish philosopher and regent of the University of Glasgow Jimmy Binning , b.1927 , Scottish soccer player William of Binning , fl.13th century , Cistercian monk Title of nobility Lord Binning is a subsidiary title of the Earls of Haddington holders include Charles Hamilton, Lord Binning , 1697 1732 , Scottish politician George Baillie Hamilton, Lord Binning , 1856 1917 , British Army officer Other Dumpster diving , sifting through trash bins Data binning , a data pre processing technique Product binning , the sorting of manufactured products or parts based on tested performance Metagenomics SOrt ITEMS algorithm for binning metagenomic sequences Monzoorul et al., 2009 Trout binning , method of fishing Colloquial expression for crashing a motorcycle, usually at speed NZ usage disambig surname ... more details
BLP unsourced date November 2010 Jay Short was CEO, President and Head of Research of Diversa until his departure on October 6, 2005. While at Diversa, Short invented methods of protein and pathway discovery via metagenomics , in addition to key evolution technologies, Gene Site Saturation MutagenesisTM GSSM and GeneReassemblyTM methods, and was the first to combine these discovery and evolution technologies. He has recently founded the E.O. Wilson Biodiversity Foundation Edward Osborne Wilson Edward Wilson . The Foundation is focused on linking business to life for conservation. External links http www.diversa.com presrele 2005 view release.asp?id 20051006 Diversa press release http www.eowilson.org E Wilson website Persondata Metadata see Wikipedia Persondata . name Short, Jay alternative names short description date of birth place of birth date of death place of death DEFAULTSORT Short, Jay Category American health care businesspeople Category American scientists Category Year of birth missing living people Category Living people US business bio stub ... more details
Metagenomics , links to references follow Metagenomics Medical sciences and biotechnological applications of bodies Metagenomics Extreme environments of extreme environments Metagenomics Marine ecosystems of marine ecosystems Metagenomics Sediments of sediments Microbial ecology Microflora Oral ... more details
Metaproteomics also Community Proteomics , Environmental Proteomics , or Community Proteogenomics is the study of all protein samples recovered directly from environmental samples. Metaproteomics should be used to classify experiments that deal with all the genes and proteins identified from complex communities, where individuals cannot be binned into species or organisms types. The metaproteomics approach is comparable to gene centric environmental genomics, or metagenomics . ref name Dilletal cite book author Dill BD et al. year 2010 chapter Metaproteomics Techniques and Applications title Environmental Molecular Microbiology publisher Caister Academic Press isbn 978 1 904455 52 3 ref ref name MarcoD cite book author Marco, D editor year 2010 title Metagenomics Theory, Methods and Applications publisher Caister Academic Press isbn 978 1 904455 54 7 ref Origin of the term The term metaproteomics was proposed by Francisco Rodr guez Valera to describe the genes and or proteins most abundantly expressed in environmental samples. ref Rodriguez Valera, F. 2004. Environmental genomics, the big picture? FEMS Microbiol. Lett. 231 153 158. ref The term was derived from metagenome. Wilmes and Bond proposed the term metaproteomics for the large scale characterization of the entire protein complement of environmental microbiota at a given point in time. ref Wilmes, P., and P. L. Bond. 2006. Metaproteomics studying functional gene expression in microbial ecosystems. Trends Microbiol. 14 92 97. ref At the same time, terms microbial community proteomics and microbial community proteogenomics are sometimes used interchangeably for different types of experiments and results. Proteomics of microbial community Proteomics is developing rapidly. The first proteomics experiment was conducted 30years ago with the invention of two dimensional polyacrylamide gel electrophoresis 2D PAGE . ref O Farrell, P. H. High resolution two dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4 ... more details
Unreferenced date January 2011 Enhanced biological phosphorus removal EBPR is a wastewater treatment configuration applied to activated sludge systems for the removal of phosphate . The common element in EBPR implementations is the presence of an wikt anaerobic anaerobic tank nitrate and oxygen are absent prior to the aeration tank. Under these conditions a group of heterotroph ic bacteria , called polyphosphate accumulating organisms PAO are selectively enriched in the bacterial community within the activated sludge. These bacteria accumulate large quantities of polyphosphate within their cell biology cell s and the removal of phosphorus is said to be enhanced . Generally speaking, all bacteria contain a fraction 1 2 of phosphorus in their biomass due to the its presence in cellular components, such as Cell membrane membrane phospholipid s and DNA . Therefore as bacteria in a wastewater treatment plant consume nutrients in the wastewater, they grow and phosphorus is incorporated into the bacterial biomass . When PAOs grow they not only consume phosphorus for cellar components but also accumulate large quantities of polyphosphate within their cells. Thus, the phosphorus fraction of phosphorus accumulating biomass is 5 7 . This biomass is then separated from the treated water at end of the process and the phosphorus is thus removed. Thus if PAOs are selectively enriched by the EBPR configuration, considerably more phosphorus is removed, compared to the relatively poor phosphorus removal in conventional activated sludge systems. External links http www.scq.ubc.ca ?p 698 EPBR Metagenomics The Solution to Pollution is Biotechnological Revolution A Review from the Science Creative Quarterly http www.phosphorus recovery.tu darmstadt.de Website of the Technische Universit t Darmstadt and the CEEP about Phosphorus Recovery DEFAULTSORT Enhanced Biological Phosphorus Removal Category Biotechnology Category Microbiology Category Waste treatment technology ar ... more details
Infobox Software name Dendroscope logo screenshot Image DendroscopeScreenCaptures.png 220px caption Dendroscope a circular cladogram, b radial phylogram, c rectangular phylogram, and d slanted cladogram. Image by Huson et al. developer Daniel Huson et al. latest release version 2.3 latest release date 2009 latest preview version latest preview date operating system Windows, Linux, Mac OS X platform genre Bioinformatics license free use, but not open source website http www.dendroscope.org Dendroscope is an interactive software computer software program written in Java programming language Java for Information graphics viewing Phylogenetic tree s. ref cite journal last Huson first Daniel H. authorlink coauthors Daniel C. Richter, Christian Rausch, Tobias Dezulian, Markus Franz, and Regula Rupp title Dendroscope An interactive viewer for large phylogenetic trees journal BMC Bioinformatics volume 8 460 publisher BioMedCentral location United Kingdom date 2007 11 22 url http www.biomedcentral.com content pdf 1471 2105 8 460.pdf paper doi 10.1186 1471 2105 8 460 accessdate 2008 04 03 pages 460 pmid 18034891 pmc 2216043 ref This program is designed to view trees of all sizes and is very useful for creating figures. Dendroscope can be used for a variety of Cladistics analyses of Molecule molecular data sets but is particularly designed for metagenomics or analyses of uncultured Natural environment environmental samples. space See also Phylogenetic tree viewers SplitsTree MEGAN References reflist External links http www.dendroscope.org Dendroscope homepage http evolution.genetics.washington.edu phylip software.html List of phylogeny software , hosted at the University of Washington space genomics footer Category Bioinformatics Category Bioinformatics software Category Computational phylogenetics ... more details
primarysources date December 2008 The http www.nmpdr.org National Microbial Pathogen Data Resource was one of the eight Bioinformatics Resource Centers funded by the National Institutes of Allergy and Infectious Diseases, NIAID a component of the National Institutes of Health NIH , which is an agency of the United States Department of Health and Human Services . The NMPDR was funded for five years from 2004 through a grant to co PI s Rick Stevens from the Computation Institute at the University of Chicago, and Ross Overbeek at the http www.thefig.info Fellowship for the Interpretation of Genomes . The NMPDR was initially tasked with annotating and curating the genomes of five pathogenic species of Bacteria , Campylobacter , Listeria , Staphylococcus , Streptococcus , and Vibrio . However, after four years, the team were asked to also oversee the curation and annotation of the genomes of seven additional bacterial species Chlamydia bacterium Chlamydia , Chlamydophila , Haemophilus , Mycoplasma , Neisseria , Treponema , and Ureaplasma . The flagship website, the http www.nmpdr.org National Microbial Pathogen Data Resource provides curated annotations in an environment for comparative analysis of genomes and biological subsystems. In addition, the NMPDR team have also developed the http rast.nmpdr.org Rapid Annotation using Subsystems Technology Server RAST for annotating and curating complete microbial genomes and the http metagenomics.nmpdr.org Metagenomics RAST for annotating metagenomes. Note to NMPDR Users As of January 2010, the bacterial organism originally covered by NMPDR under the BRC program have been transferred to PATRIC the Pathosystems Resource Integration Center. Category Biology organizations ... more details
Giant, Ornate, Lake and Lactobacillales Derived GOLLD RNA is a conserved RNA structure present in bacteria . GOLLD RNAs were originally detected based on metagenomics metagenome sequences of DNA isolated from Lake Gatun in Panama. ref name zasha cite journal author Weinberg Z, Perreault J, Meyer MM, Breaker RR title Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis journal Nature volume 462 issue 7273 pages 656 9 year 2009 month December pmid 19956260 doi 10.1038 nature08586 url ref However, they are known to be present in at least eight strains of cultivated bacteria. GOLLD RNAs are extraordinarily large compared to other RNAs with a conserved, complex secondary structure , and average roughly 800 nucleotides. Such large, complex RNAs are often ribozyme s, although the biochemical function of GOLLD RNAs remains unknown. The discovery of large RNAs like GOLLD RNAs among bacteria that are mostly uncultivated under laboratory conditions suggests that many other unusually large RNAs might be found in bacteria that have not yet been studied. ref name zasha ref name scidaily cite web url http www.sciencedaily.com releases 2009 12 091202131618.htm title Newly Explored Bacteria Reveal Some Huge RNA Surprises author ScienceDaily date 7th Dec 2009 work Science News publisher accessdate 8 July 2010 ref The GOLLD RNA in Lactobacillus brevis ATCC 367 was studied experimentally. ref name zasha This GOLLD RNA is apparently encoded by a prophage , and its transcription is increased during the phage lytic cycle . Therefore, this GOLLD RNA presumably serves a function that is useful to the phage during this process. GOLLD RNAs are often located near transfer RNA s tRNAs , and in some cases a tRNA is predicted to be inside the GOLLD RNA structure itself. However, the biological reason underlying this association is not understood. ref name zasha ref name scidaily The Rfam model of GOLLD RNA uses only the 3 half of GOLLD, as this region of the full RNA is ... more details
File IMES 3.svg right frame Consensus secondary structure of IMES 3 RNAs. This figure is adapted from supplementary data of a previous publication. ref name Weinberg2009 The IMES 3 RNA motif is a conserved RNA structure that was identified based on metagenomics and bioinformatics , ref name Weinberg2009 cite journal author Weinberg Z, Perreault J, Meyer MM, Breaker RR title Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis journal Nature volume 462 issue 7273 pages 656 9 year 2009 month December pmid 19956260 doi 10.1038 nature08586 url ref and the underlying RNA sequences were identified independently by an earlier study. ref name Shi2009 cite journal author Shi Y, Tyson GW, DeLong EF title Metatranscriptomics reveals unique microbial small RNAs in the ocean s water column journal Nature volume 459 issue 7244 pages 266 9 year 2009 month May pmid 19444216 doi 10.1038 nature08055 url ref These RNAs are RNAs present in environmental samples present in environmental sequences , and as of 2009 are not known to be present in any cultivated species . IMES 3 RNAs are abundant in comparison to ribosome s ref name Weinberg2009 in RNAs sampled from the Pacific Ocean . ref cite journal author Frias Lopez J, Shi Y, Tyson GW, et al. title Microbial community gene expression in ocean surface waters journal Proc. Natl. Acad. Sci. U.S.A. volume 105 issue 10 pages 3805 10 year 2008 month March pmid 18316740 pmc 2268829 doi 10.1073 pnas.0708897105 url ref ref name Shi2009 References reflist colwidth 30em Category Non coding RNA ... more details
File IMES 4.svg right frame Consensus secondary structure of IMES 4 RNAs. This figure is adapted from supplementary data of a previous publication. ref name Weinberg2009 The IMES 4 RNA motif is a conserved RNA structure that was identified in marine environmental sequences by metagenomics and bioinformatics . ref name Weinberg2009 cite journal author Weinberg Z, Perreault J, Meyer MM, Breaker RR title Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis journal Nature volume 462 issue 7273 pages 656 9 year 2009 month December pmid 19956260 doi 10.1038 nature08586 url ref These RNAs are RNAs present in environmental samples present in environmental sequences , and as of 2009 are not known to be present in any cultivated species . IMES 4 RNAs are fairly abundant in comparison to ribosome s ref name Weinberg2009 in RNAs sampled from the Pacific Ocean . ref cite journal author Frias Lopez J, Shi Y, Tyson GW, et al. title Microbial community gene expression in ocean surface waters journal Proc. Natl. Acad. Sci. U.S.A. volume 105 issue 10 pages 3805 10 year 2008 month March pmid 18316740 pmc 2268829 doi 10.1073 pnas.0708897105 url ref ref name Shi2009 cite journal author Shi Y, Tyson GW, DeLong EF title Metatranscriptomics reveals unique microbial small RNAs in the ocean s water column journal Nature volume 459 issue 7244 pages 266 9 year 2009 month May pmid 19444216 doi 10.1038 nature08055 url ref References reflist colwidth 30em Category Non coding RNA ... more details
Multiple issues wikify October 2010 orphan October 2010 UniFrac is a method to calculate a distance measure between bacterial communities using phylogenetic information, and is widely used in metagenomics . The method was devised by Catherine Lozupone and Rob Knight of the University of Colorado at Boulder in 2005. ref Cite journal last Lozupone first C coauthors Rob Knight title UniFrac a New Phylogenetic Method for Comparing Microbial Communities journal APPLIED AND ENVIRONMENTAL MICROBIOLOGY volume 71 issue 12 pages 8228 8235 year 2005 pmid 16332807 doi http aem.asm.org cgi content full 71 12 8228?view long&pmid 16332807 ref The distance is calculated between pairs of samples each sample represents a bacterial community . All taxa found in one or both samples are placed on a phylogenetic tree. A branch leading to taxa from both samples is marked as shared and branches leading to taxa which appears only in one sample are marked as unshared . The distance between the two samples is then calculated as the sum of shared branch lengths the sum of all tree branches shared unshared , i.e. the fraction of shared branch length. This definition satisfies the requirements of a distance metric , being non negative, zero only when entities are identical, transitive, and conformant to the triangle inequality . If there are several different samples, a distance matrix can be created, by making a tree for each pair of samples and calculating their UniFrac measure. Later, standard multivariate statistical, methods such as data clustering and principal co ordinates analysis can be used. Unifrac also enables to determine if two samples differ significantly, by using Monte Carlo simulation s. Namely, randomizing the sample classification of each taxa on the tree leaving the branch structure unchanged and creating a distribution of UniFrac distance values. Having a distribution of UniFrac values, a p value can be given to the actual distance. References See Wikipedia Footnotes on how ... more details
Infobox organization name Technology Innovation Agency bgcolor fgcolor image Technology innovation agency logo.gif image border size alt caption map msize malt mcaption abbreviation motto formation extinction type status purpose headquarters Pretoria , South Africa location region served membership language leader title leader name main organ parent organization affiliations num staff num volunteers budget website http www.amts.co.za remarks The Technology Innovation Agency TIA is an organization which reviews and promotes government funded science projects in South Africa . History The TIA was created by an act of parliament on 24 November 2008. ref cite web url http www.amts.co.za docs tia act.pdf title No. 26 of 2008 Technology Innovation Agency Act, 2008 author date 24 November 2008 work Government Gazette of South Africa Government Gazette publisher accessdate 29 March 2011 ref Projects The TIA was a coordinating agency in the following projects ref cite web url http www.amts.co.za ?q node 49 title Projects author date work publisher Technology Innovation Agency accessdate 29 March 2011 ref CAPRISA 004 , a clinical trial to measure the efficacy of an HIV preventative gel Adept Engine, an aerospace design project Citrogold & Biogold, intellectual property developers and holders who work in horticulture Metagenomics Platform, a software interface to sort genetics data References reflist External links http www.amts.co.za Technology Innovation Agency Category Research institutes in South Africa ... more details
Infobox rfam Name SAM V image SAM V SScon.png width caption Conserved secondary structure of the SAM V riboswitch. Symbol SAM V AltSymbols Rfam RNA type Cis regulatory element Cis reg Riboswitch Tax domain Metagenomics Marine metagenome SAM V riboswitch is the fifth known riboswitch to bind S adenosyl methionine SAM . It was first discovered in the marine organism Pelagibacter ubique Candidatus Pelagibacter ubique and can also be found in marine metagenomics metagenomes . ref name Mey09 cite journal author Meyer MM, Ames TD, Smith DP, et al. title Identification of candidate structured RNAs in the marine organism Candidatus Pelagibacter ubique journal BMC Genomics volume 10 issue pages 268 year 2009 pmid 19531245 pmc 2704228 doi 10.1186 1471 2164 10 268 url http www.biomedcentral.com 1471 2164 10 268 accessdate 2010 08 20 ref SAM V features a similar consensus sequence and secondary structure as the binding site of SAM II riboswitch , but bioinformatics scans cluster the two aptamer aptamers independently. These similar binding pockets suggest that the two riboswitches have undergone convergent evolution . ref name Poi09 cite journal author Poiata E, Meyer MM, Ames TD, Breaker RR title A variant riboswitch aptamer class for S adenosylmethionine common in marine bacteria journal RNA volume 15 issue 11 pages 2046 56 year 2009 month November pmid 19776155 pmc 2764483 doi 10.1261 rna.1824209 url http rnajournal.cshlp.org cgi pmidlookup?view long&pmid 19776155 accessdate 2010 08 20 ref SAM binding was confirmed using equilibrium dialysis . The riboswitch has been characterised as a tandem riboswitch it is able to regulate both translation genetics translation and transcription genetics transcription . When SAM is present in high concentration, SAM II will bind its ligand and form a terminator genetics terminator stem to halt transcription. If SAM exists in lower concentrations, SAM V will be transcribed and, if SAM concentration should then increase, it can bind SAM and ... more details
hypothesis in Metagenomics of the human body . ref cite journal last Proal first Amy coauthors Albert, Paul Marshall, Trevor title Autoimmune disease and the human metagenome journal Metagenomics ... ref name PMID 21278764 cite pmid 21278764 ref and a detailed hypothesis in Metagenomics of the human ... Autoimmune disease and the human metagenome journal Metagenomics of the human body year 2010 pages ... more details
pangenome describes the full complement of genes in a species typically applied to prokaryotes, which can have large variation in gene content among closely related strains . It is a superset of all the genes in all the strain biology strains of a species ref name medini2005 cite journal author Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R title The microbial pan genome journal Curr. Opin. Genet. Dev. volume 15 issue 6 pages 589 94 year 2005 month December pmid 16185861 doi 10.1016 j.gde.2005.09.006 ref . The significance of the pangenome arises in an evolutionary context, especially with relevance to metagenomics ref cite journal author Reno ML, Held NL, Fields CJ, Burke PV, Whitaker RJ title Biogeography of the Sulfolobus islandicus pan genome journal Proc. Natl. Acad. Sci. U.S.A. volume 106 issue 21 pages 8605 10 year 2009 month May pmid 19435847 doi 10.1073 pnas.0808945106 pmc 2689034 ref , but is also used in a broader genomics context ref cite journal author Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL title De novo assembly using low coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae journal Genome Res. volume 19 issue 2 pages 294 305 year 2009 month February pmid 19015323 pmc 2652211 doi 10.1101 gr.083311.108 ref . The pangenome includes the core genome containing genes present in all strains, a dispensable genome containing genes present in two or more strains, and finally unique genes specific to single strains ref name medini2005 . The pan genome is very important in designing vaccine for specific strain in species of micro organisms especially Pathogens . Like Streptococcus agalactiae has many strains all of these strains contain core genome found across all strains and dispensable genome found in two or more in strains of one species , and unigue genes specific for a strain in species so universal vaccine were designed against GBS Group B Streptococcus using such pan genome as an ess ... more details
File IMES 1.svg right frame Consensus secondary structure of IMES 1 RNAs. This figure is adapted from supplementary data of a previous publication. ref name Weinberg2009 The indicated transcription terminator is predicted as a Intrinsic termination Rho independent transcription terminator . The IMES 1 RNA motif is a conserved RNA structure that was identified in marine environmental sequences by two studies based on metagenomics and bioinformatics , the first analyzing metatranscriptome RNA data ref name Shi2009 cite journal author Shi Y, Tyson GW, DeLong EF title Metatranscriptomics reveals unique microbial small RNAs in the ocean s water column journal Nature volume 459 issue 7244 pages 266 9 year 2009 month May pmid 19444216 doi 10.1038 nature08055 url ref and the second using metagenome DNA data. ref name Weinberg2009 cite journal author Weinberg Z, Perreault J, Meyer MM, Breaker RR title Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis journal Nature volume 462 issue 7273 pages 656 9 year 2009 month December pmid 19956260 doi 10.1038 nature08586 url ref These RNAs are RNAs present in environmental samples present in environmental sequences , and as of 2009 are not known to be present in any cultivated species . However, the species that use these RNAs are most closely related to known alphaproteobacteria and gammaproteobacteria . ref name Shi2009 IMES 1 RNAs make up a significant portion of marine RNA transcripts ref name Shi2009 and are exceptionally abundant in that over five times as many IMES 1 RNAs were found as ribosome s ref name Weinberg2009 in RNAs sampled from the Pacific Ocean . ref name Shi2009 ref cite journal author Frias Lopez J, Shi Y, Tyson GW, et al. title Microbial community gene expression in ocean surface waters journal Proc. Natl. Acad. Sci. U.S.A. volume 105 issue 10 pages 3805 10 year 2008 month March pmid 18316740 pmc 2268829 doi 10.1073 pnas.0708897105 url ref Only two bacterial RNAs are known 6S RNA and ... more details
File IMES 2 consensus.svg right frame Consensus secondary structure of IMES 2 RNAs. This figure is adapted from supplementary data of a previous publication. ref name Weinberg2009 File IMES 2 oneseq.svg left frame Predicted IMES 2 RNA secondary structure in alphaproteobacterium HIMB114. Nucleotides are numbered starting at the 5 end. Lines labeled 0 nt do not contain any nucleotides. The IMES 2 RNA motif is a conserved RNA structure that was identified by a study based on metagenomics and bioinformatics , ref name Weinberg2009 cite journal author Weinberg Z, Perreault J, Meyer MM, Breaker RR title Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis journal Nature volume 462 issue 7273 pages 656 9 year 2009 month December pmid 19956260 doi 10.1038 nature08586 url ref and the underlying RNA sequences were identified independently by a similar earlier study. ref name Shi2009 cite journal author Shi Y, Tyson GW, DeLong EF title Metatranscriptomics reveals unique microbial small RNAs in the ocean s water column journal Nature volume 459 issue 7244 pages 266 9 year 2009 month May pmid 19444216 doi 10.1038 nature08055 url ref These RNAs are RNAs present in environmental samples present in environmental sequences , and when discovered were not known to be present in any cultivated species . However, an IMES 2 RNA has been detected in alphaproteobacteria alphaproteobacterium HIMB114, which is classified in the SAR11 clade of marine bacteria. This finding fits with earlier predictions that species that use IMES 2 RNAs are most closely related to alphaproteobacteria . ref name Shi2009 IMES 2 RNAs are exceptionally abundant, as twice as many IMES 2 RNAs were found as ribosome s ref name Weinberg2009 in RNAs sampled from the Pacific Ocean . ref name Shi2009 ref cite journal author Frias Lopez J, Shi Y, Tyson GW, et al. title Microbial community gene expression in ocean surface waters journal Proc. Natl. Acad. Sci. U.S.A. volume 105 issue 10 pages 3805 ... more details
Image Forest Rohwer.JPG thumb 150px alt Forest Rohwer Microbial ecologist Forest Rohwer. Forest Rohwer born 1969 is an USA American microbial ecologist and Professor of Biology at San Diego State University. His particular interests include coral reef microbial ecology and Virus viruses as both evolutionary agents and opportunistic pathogens in various environments. Education and career Rohwer holds bachelor degrees in biology, chemistry, and history from the College of Idaho and earned his doctorate in molecular biology from the University of California, San Diego San Diego State University Joint Doctoral Program. Work He has authored more than 90 scientific papers and book chapters, as well as one popular science book, Coral Reefs in the Microbial Seas , published in 2010. He pioneered the use of metagenomics as a means to characterize previously inscrutable viral and microbial communities, such as those associated with coral reefs. His field work with colleagues includes expeditions to the Northern Line Islands in 2005 and 2010, and to the Southern Line Islands in 2009. Awards Rohwer has been named a Fellow of both the American Association for the Advancement of Science AAAS and the Canadian Institute for Advanced Research CIFAR . In 2008, he received the Young Investigators Award from the International Society of Microbial Ecology ISME . Personal life Growing up in Idaho , Rohwer learned scuba diving in a frigid glacial lake. Later he took that skill to tropical waters where, for more than twenty years, he has been diving and doing research on coral reefs around the world. He lives in University Heights, San Diego, CA, with microbial geneticist Anca Segall, and their daughter Willow. External links http phage.sdsu.edu The Rohwer Lab at San Diego State University http www.coralreefsystems.org Coral Reef Systems website including documentary videos and the blog of the 2010 research expedition to the Line Islands Persondata Metadata see Wikipedia Persondata . NAME ... more details
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