The Genomic Standards Consortium GSC is an initiative working towards richer descriptions of our collection of genomes, Metagenomics metagenomes and marker genes. Established in September 2005, this international community includes representatives from a range of major DNA sequencing sequencing and bioinformatics centres including National Center for Biotechnology Information NCBI , EMBL , DDBJ , J. Craig Venter Institute JCVI , Joint Genome Institute JGI , European Bioinformatics Institute EBI , Wellcome Trust Sanger Institute Sanger , FIG and research institutions. The goal of the GSC is to promote mechanisms for standardizing the description of meta genomes, including the exchange and integration of meta genomic data. The number and pace of genomic and metagenomic sequencing projects will only increase as the use of ultra high throughput methods becomes common place and standards are vital to scientific progress and data sharing. Mission Community driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large scale comparative genomic analyses, and those with experience of building community based standards. The mission of the GSC is to work with the wider community towards the implementation of a new genomic standards methods of capturing and exchanging metadata harmonization of metadata collection and analysis efforts across the wider genomics community MIGS MIMS MIMARKS and other projects The GSC has published a Minimum Information about a Meta Genome Sequence specification and has now completed a Minimum Information about an ENvironmental Sequence specification. MIGS MIMS MIMARKS provides an extension of the minimum information already captured by the primary nucleotide sequence archives http www.insdc.org INSDC or DDBJ ENA GenBank . The development of any checklist must be an open and itera ... 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
Orphan date January 2012 BLP sources date January 2012 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. ref http coralreefsystems.org content forest rohwer ref His particular interests include coral reef microbial ecology and virus es 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 blo ... more details
No footnotes date September 2011 The Microbial Culture Collection , in Pune , is India s microbial culture collection centre, recognized by World Federation for Culture Collections WFCC and has a status of International Depositary Authority IDA . The Microbial Culture Collection is a national facility funded by the Department of Biotechnology DBT , Government of India . The MCC is affiliated to National Centre for Cell Science NCCS , Pune , India . It is an affiliate member of the World Federation for Culture Collections WFCC and is registered with the World Data Centre for Microorganisms WDCM, registeration number 773 . The main objectives of MCC are to act as a national depository, to supply authentic microbial cultures and to provide related services to the scientific community working in research institutions, universities and industries. The MCC was recognized by the World Intellectual Property Organization WIPO , Geneva , Switzerland as an International Depository Authority IDA on April, 2011. The deposit of microorganisms under the Budapest Treaty is recognized to fulfill the requirement of patent procedure in 55 member countries. The MCC scientists are actively involved in the research programmes relating to microbial diversity , metagenomics , ecology and taxonomy using both classical and molecular approaches. Objectives The centre focuses on basic research in the areas of microbial diversity , microbial taxonomy , microbial genomics and proteomics etc. Isolation and Identification of microorganisms from various environmental niches. Preservation of microbial biodiversity from niche areas as metagenomic libraries. Development of new strategies for isolation of uncultivable microbes . To provide consultation services for patent deposits, preservation, propagation,biodeterioration, Industrial problems, biosystematics and microbial biodiversity issues etc. To serve as National facility for microbial culture collection, deposit and the supply of authentic micro ... more details
in the new disciplines of metagenomics and metatranscriptonomics , along with massive databases ... ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA title Gene centric metagenomics ... shotgun metagenomics metagenomic studies. The former focuses on specific known marker genes ... sequencing Metagenomics is also used extensively for studying microbial communities. ref name ... genome. ref name Kucz2012 Despite the fact that metagenomics is limited by the availability of reference sequences, one significant advantage of metagenomics over targeted amplicon sequencing is that metagenomics ... project Metagenomics Multigenomic organism Skin flora External links http www.systemsbiology.net symposium ... more details
Agrophysics is a branch of science bordering on agronomy and physics , whose objects of study are the agroecosystem the biological Physical body object s, biotope and biocoenosis affected by human task activity , studied and described using the methods of physical science s. Agrophysics is closely related to biophysics , but is restricted to the biology of the plant s, animal s, soil and an atmosphere involved in Agriculture agricultural activities and biodiversity . It is different from biophysics in having the necessity of taking into account the specific features of biotope and biocoenosis , which involves the knowledge of Nutrition nutritional science and agroecology , Agricultural Science agricultural technology , biotechnology , genetics etc. Principles of history The needs of agriculture, concerning the past experience study of the local complex soil and next plant atmosphere systems, lay at the root of the emergnece of new branch agrophysics dealing this with experimental physics. The scope of the branch starting from soil science physics and originally limited to the study of relations within the soil environment, expanded over time onto influencing the properties of agricultural crops and produce as foods and Postharvest raw postharvest materials, and onto the issues of quality, safety and labeling concerns, considered distinct from the field of nutrition for application in food science. A research centre that is focused on the development of the Science is the Institute of Agrophysics, Polish Academy of Sciences in Lublin . cyt Agrophysics, utilizing the achievements of Exact Sciences for solving major problems of Agriculture, is involved in study of materials and processes occurring in the production and processing of agricultural crops, with particular emphasis on the condition of the environment and the quality of farming materials and food productions. See also Agriculture Agroecology Genomics Metagenomics Metabolomics Nitrogenomics Physics Aristotle ... more details
, re sequencing of whole genomes and target DNA regions, metagenomics and RNA analysis. Full ... nucleotide polymorphism SNP , insertion deletion and splice variant discovery. MetagenomicsMetagenomics ... within a specific environment. Metagenomics samples are found nearly everywhere, including several microenvironments ... more details
Jo Handelsman is a Howard Hughes Medical Institute professor of molecular, cellular and developmental biology at Yale University . ref name yale page cite web url http bbs.yale.edu people jo handelsman.profile title Jo Handelsman, PhD publisher Yale School of Medicine accessdate 10 September 2010 ref She is editor in chief of the academic journal DNA and Cell Biology and author of books on Scientific teaching scientific education , most notably Scientific Teaching . ref name yale profile cite web url http bbs.yale.edu people jo handelsman 2.profile title Jo Handelsman, PhD Profile publisher Yale School of Medicine accessdate 10 September 2010 ref ref name hhmi cite web url http www.hhmi.org grants professors handelsman bio.html title Jo Handelsman, Ph.D. publisher Howard Hughes Medical Institute accessdate 10 September 2010 ref Education Handelsman earned her B.S. degree in agronomy from Cornell University in 1979 and her Ph.D. in molecular biology from the University of Wisconsin Madison in 1984. ref name CV cite web url http www.unh.edu news docs handelsmancv.pdf title Curriculum vitae publisher The University of New Hampshire accessdate 10 September 2010 ref Career Handelsman secured a faculty position in plant pathology at the University of Wisconsin Madison in 1985. She remained at Wisconsin until 2009, and then took a position at the Yale School of Medicine in 2010. ref name yale profile ref name hhmi ref name Gellman cite web url http www.yaledailynews.com news 2010 feb 01 prof to push diversity title Prof. to push diversity last Gellman first Lindsay date February 1, 2010 publisher Yale Daily News accessdate 10 September 2010 ref Her research involves the study of microorganism s present in soil and insect gut anatomy gut , and she has contributed to the field of functional metagenomics . ref name yale profile She has published books and held work shops on scientific teaching, for which she is recognized nationally. ref name hhmi She is an active researcher ... more details
sequencing shotgun metagenomics have been developed or are under development. ref name EMPprotocols ... is called shotgun metagenomics, in which all the DNA in the sample is sheared and the random ... reflist 2 See also Microbiome Human microbiome project Metagenomics Skin flora External links http ... more details
Image Cyanophages.png thumb 300px right Electron micrograph of negative stained Prochlorococcus myoviruses Marine bacteriophages or marine phages are virus es that live as Obligate parasite obligate parasitism parasitic agents in Marine ocean marine bacteria such as cyanobacteria . ref name Mann cite journal last Mann first NH title The Third Age of Phage journal PloS Biol volume 3 issue 5 pages 753 755 publisher Public Library of Science location United States date 2005 05 17 url 7885 3 5 pdf 10.1371 journal.pbio.0030182 S.pdf doi 10.1371 journal.pbio.0030182 accessdate 2008 03 31 pmid 15884981 pmc 1110918 ref Their existence was discovered through Transmission electron microscopy electron microscopy and epifluorescence microscopy of ecological water samples, and later through Metagenomics metagenomic sampling of uncultured viral samples. ref name Mann ref name Wommack1996 cite journal last Wommack first K. Eric coauthors Russell T. Hill, Terri A. Muller, and Rita R. Colwell title Effects of sunlight on bacteriophage viability and structure journal Applied and Environmental Microbiology volume 62 issue 4 pages 1336 1341 publisher American Society for Microbiology location United States of America date April 1996 accessdate pmid 8919794 pmc 167899 ref The Caudovirales tailed bacteriophages appear to dominate marine ecosystems in number and diversity of organisms. ref name Mann Bacteriophages, viruses that are parasitic on bacteria, were first discovered in the early twentieth century. Scientists today consider that their importance in ecosystems , particularly marine ecosystems , has been underestimated, leading to these infectious agents being poorly investigated and their numbers and species biodiversity being greatly under reported. ref name Kellogg1995 cite journal last Kellogg first CA coauthors JB Rose, SC Jiang, and JM Thurmond, and JH Paul title Genetic diversity of related vibriophages isolated from marine environments around Florida and Hawaii, USA journal ... more details
A wide variety of non coding RNA s have been identified in various species of organisms known to science. However, RNAs have also been identified in metagenomics sequences derived from samples of DNA or RNA extracted from the environment, which contain unknown species. Initial work in this area detected homology biology homolog s of known bacteria l RNAs in such metagenome samples. ref cite journal author Kazanov MD, Vitreschak AG, Gelfand MS title Abundance and functional diversity of riboswitches in microbial communities journal BMC Genomics volume 8 issue pages 347 year 2007 pmid 17908319 pmc 2211319 doi 10.1186 1471 2164 8 347 url ref ref cite journal author Barrick JE, Breaker RR title The distributions, mechanisms, and structures of metabolite binding riboswitches journal Genome Biol. volume 8 issue 11 pages R239 year 2007 pmid 17997835 pmc 2258182 doi 10.1186 gb 2007 8 11 r239 url ref Many of these RNA sequences were distinct from sequences within cultivated bacteria, and provide the potential for additional information on the RNA classes to which they belong. The distinct environmental sequences were exploited to detect previously unknown RNAs in the marine bacterium Pelagibacter ubique . P. ubique is extremely common in marine sequences. So sequences of DNA extracted from ocean s, many of which are inevitably derived from species related to P. ubique , were exploited to facilitate the analysis of possible secondary structure s of RNAs predicted in this species. ref 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 ref Subsequent studies identified novel RNAs exclusively using sequences extracted from environmental samples. The first study determined the sequences of RNAs directly extracted from microbial biomass in the Pacific Ocean . ... more details
developed for Metagenomics metagenomic and environmental data . ref name pmid18045787 cite pmid ... from known species, data arising from metagenomics studies is from environmental i.e. uncultured ... more details
metagenomics approaches suggest existence of many more phyla based on the deep lineages of 16S rRNA gene sequences recovered. ref name MarcoD cite book author Marco, D editor year 2010 title Metagenomics ... more details
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