good article Image Iron hydroxide precipitate in stream.jpg thumb right Metagenomics allows the study ... mining. Metagenomics is the study of metagenomes , genetics genetic material recovered directly from ... life, metagenomics offers a powerful lens for viewing the microbial world that has the potential ... Etymology The term metagenomics was first used by Jo Handelsman , Jon Clardy, Robert M. Goodman , and others ... of California, Berkeley defined metagenomics as the application of modern genomics techniques ... and archaea l species in a sample. ref name Hugenholz1998 Much of the interest in metagenomics comes ... assembly into contigs and scaffolds. Shotgun metagenomics Advances in bioinformatics , refinements ... other. ref name Allen2005 Shotgun metagenomics also is capable of sequencing nearly complete microbial ... assembly. ref name Charuvaka Bioinformatics The data generated by metagenomics experiments are both ... and a team at Argonne National Laboratory and the University of Chicago released the Metagenomics ... classifications, respectively. ref name mitra2011 Comparative metagenomics Comparative analyses between ... by a community. ref name kiltgord2011 Metatranscriptomics Further Transcriptome Metagenomics ... an environmental sample is through metagenomics. Viral metagenomes also called viromes should thus ... Metagenomics has the potential to advance knowledge in a wide variety of fields. It can also be applied ... communities function is required to control them, and metagenomics is a key tool in their understanding ... Main Bioremediation Metagenomics can improve strategies for monitoring the impact of pollutant s on ecosystem .... ref name simon2011 ref name simon2009a The application of metagenomics has allowed the development ... metagenomics strategies are being used to explore the interactions between plants and microbes through ... ref ref name MarcoD cite book editor Marco, D year 2010 title Metagenomics Theory, Methods and Applications ... editor Marco, D year 2011 title Metagenomics Current Innovations and Future Trends publisher Caister ... 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 doi 10.1099 00207713 45 1 195 issue 1 ref Examples of Candidate Division Bacteria Candidate division TM7 See also Metagenomics Gene cloning Cloning DNA sequencing References reflist 2 Category Bacteriology ... more details
Taxobox color violet virus group i ordo Unassigned familia Unassigned genus Unassigned species Organic Lake virophage Organic Lake virophage is a double stranded DNA virophage a virus that requires the presence of another virus to replicate itself and in so doing limits the other viruses ability to replicate . It was detected Metagenomics metagenomically in samples from Organic Lake , Antarctica . ref Yau S, Lauro FM, Demaere MZ, Brown MV, Thomas T, Raftery MJ, Andrews Pfannkoch C, Lewis M, Hoffman JM, Gibson JA, & Cavicchioli R 2011 . Virophage control of antarctic algal host virus dynamics. Proc Nat Acad Sci USA ref Virology The virus appears to be 100 nanometer s in diameter and to be enveloped. The genome is double stranded DNA and is 26,421 base pairs in length. It encodes 38 protein s. These include the major coat protein, a DNA packaging ATPase , a putative DNA polymerase primase and a N6 adenine specific DNA methyltransferase . References reflist External links Isolation of virus http dx.doi.org 10.1073 pnas.1018221108 Category DNA viruses Category Virophages ... more details
BLP sources date August 2011 Jay Short was CEO, President and Head of Research of Diversa until his departure in 2005. ref cite news url http www.signonsandiego.com uniontrib 20051007 news 1b7diversa.html title Diversa CEO resigns from biotech last Somers first Terri date October 7, 2005 work The San Diego Union Tribune accessdate 12 August 2011 ref 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. References Reflist 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
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
Metaproteomics also Community Proteomics , Environmental Proteomics , or Community Proteogenomics is the study of all protein samples recovered directly from environmental sources. 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, the terms microbial community proteomics and microbial community proteogenomics are sometimes used interchangeably for different types of experiments and results. Proteomics of microbial community The first proteomics experiment was conducted 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, 4007 4021 1974 . ref ref Klose, J. Protein ... 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 Waste treatment technology ar ... more details
Binning may refer to TOCright wiktionary People Surname Bob Binning d.2005 , New Zealand fencer B. C. Binning 1909 1976 , Canadian painter Hugh Binning 1627 1653 , Scottish philosopher Jimmy Binning born 1927 , Scottish soccer player Affix William of Binning , 13th century Cistercian monk and abbott 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 Metagenomic binning Metagenomics is the science to investigate microbial community from the environment directly. Binning is the process to classify reads into different groups or taxonomies. Binning methods can be based on either compositional features or alignment or both of them. Up to date binning algorithms include Phylopythia McHardy et al., 2007 TETRA Teeling et al., 2004 TACOA Diaz et al., 2009 PCAHIER Zheng and Wu, 2010 DiScRIBinATE Ghosh et al., 2010 SPHINX Mohammed et al., 2011 Parallel META Su et al., 2011 PhyloPythiaS Patil et al., 2011 These algorithms provide a global view of how diverse the samples are, and can potentially connect community composition and function in metagenomes. 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 Trout binning , method of fishing Colloquial expression for crashing a motorcycle, usually at speed NZ usage See also Bening disambiguation Benning disambiguation disambiguation surname ... 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 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. It was developed by Daniel Huson and his colleagues at the University of T bingen in Germany . 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 pt Dendroscope ... more details
In molecular biology a pan genome or supra genome describes the full complement of genes in a species typically applied to bacteria and archaea , 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 pan genome 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 . See also Quasispecies , a similar concept defined by John Maynard Smith . References references Category Evolutionary biology Category Genomics fr Pang nome ... 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
orphan date 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 10.1128 AEM.71.12.8228 8235.2005 ref Research methods 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 to create references using ref ref tags which wil ... 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 coord missing South Africa Category Research institutes in South Africa ... more details
Taxobox color violet name Sea turtle tornovirus 1 virus group ii familia genus subdivision ranks Species subdivision Sea turtle tornovirus 1 Sea turtle tornovirus 1 is a single stranded DNA virus that was isolated from a turtle with fibropapillomatosis in 2009. ref name Ng2009 Ng TF, Manire C, Borrowman K, Langer T, Ehrhart L, Breitbart M 2009 Discovery of a novel single stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics. J Virol 83 6 2500 2509 ref Virology The genome is circular and 1.8 kilobases in length with a G C content of 50 . It has at least three open reading frames ORF 1, 2, 3 and two others ORF 4 and 5 may also be present. The genome is of negative polarity. ORF 1 possesses a putative nuclear localization signal at its N terminal. ORF 2 has some homology to the viral protein 2 of chicken anaemia virus. ORF 3 has no homology to any known protein. Similarly neither ORF 4 or 5 have any homology with any known protein. The functions of these proteins is not known. A TATA box sequence TATAAA and a poly adenosine signal sequence AATAAA are present in the genome. Taxonomy The final classification of this virus has yet to be decided. It has a low level of homology to the Circovirus chicken anemia virus . Clinical The virus can be isolated from the blood and all the major organs as well as the fibropapiloma. Genome sequences Listing http www.ncbi.nlm.nih.gov nuccore?term EU867816 EU867824 pacc References reflist Category DNA viruses ... more details
IMG M system is an extension of the IMG system providing a comparative analysis context of Metagenomics ... of all publicly available genomes in IMG. See also Genomics Metagenomics References Reflist External ... more details
or Ensembl . Metagenomics Main MetagenomicsMetagenomics is the study of metagenomes , genetics genetic ... life, metagenomics offers a powerful lens for viewing the microbial world that has the potential ... year 2010 title Metagenomics Theory, Methods and Applications publisher Caister Academic Press isbn 978 1 904455 54 7 ref ref name MarcoD2011 cite book editor Marco, D year 2011 title Metagenomics Current ... Genomics of domestication Immunomics Metagenomics Nitrogenomics Personal genomics Proteomics Psychogenomics ... more details
MarcoD cite book author Marco, D editor year 2010 title Metagenomics Theory, Methods and Applications ... Marco, D editor year 2011 title Metagenomics Current Innovations and Future Trends publisher Caister ... Networks publisher Caister Academic Press isbn 978 1 908230 03 4 ref Metagenomics and Other Molecular Techniques Metagenomics is the culture independent analysis of the collective genomes of microbes ... technologies have greatly facilitated metagenomics research. ref name MarcoD2011 cite book author Marco, D editor year 2011 title Metagenomics Current Innovations and Future Trends publisher Caister ... 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 RF01826 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 ... more details
Multiple issues BLP sources February 2012 citation style February 2012 Image JGI EMRubin.jpg thumb 300px DOE Joint Genome Institute Director Eddy Rubin. Edward M. Eddy Rubin is an internationally known geneticist and medical researcher at the Lawrence Berkeley National Laboratory in Berkeley, California and has served as the director of the United States Department of Energy Department of Energy s Joint Genome Institute since 2002. In addition to his research, Rubin has trained more than 50 scientists who have moved on from his laboratory to serve as faculty at leading institutions. He is on the editorial boards of several journals and scientific advisory boards, including the Board of Reviewing Editors for the journal Science, and has played key roles in directing genomic research at the DOE and the U.S. National Institutes of Health. Rubin oversaw the DOE JGI s involvement in the Human Genome Project, during which time the DOE JGI worked on chromosomes 5, 13 and 16. After that project, he reoriented the DOE JGI toward applying genomics to studies related to bioenergy and the environment, sequencing and analyzing the genetic codes of hundreds of plants, fungi and microbes. Rubin s early scientific work centered on the functional exploration of the human genome, harnessing sequence comparisons between species for the discovery of genes and non coding sequences of pivotal evolutionary and biomedical importance. Among his projects is work involving http www.lbl.gov Science Articles Archive Genomics Neanderthal.html sequencing DNA from Neanderthal bones , though he was not involved in the http www.sciencemag.org cgi content full 328 5979 710 May 2010 publication of a draft Neanderthal genome. Rubin has published more than 200 peer reviewed publications, primarily focused on the development of methods to study genomes. More recently, he has been on the forefront of the new science of metagenomics , deriving important insights from his http www.scivee.tv node 11256 inves ... more details
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