{"id":158,"date":"2014-06-18T15:43:30","date_gmt":"2014-06-18T15:43:30","guid":{"rendered":"http:\/\/wpdev.acsu.buffalo.edu\/wnygirp\/?page_id=158"},"modified":"2014-09-09T20:45:38","modified_gmt":"2014-09-09T20:45:38","slug":"project-details","status":"publish","type":"page","link":"http:\/\/ubwp.buffalo.edu\/wnygirp\/project-details\/","title":{"rendered":"Project Details"},"content":{"rendered":"<div class=\"wider\">\n<div>The innovative technology experience for students and teachers used in this project\u00a0involves a \u201chands-on\u201d cyber-learning approach, known as <a href=\"http:\/\/www.geni-act.com\/\">GENI-ACT<\/a>, that will involve participants in a current and global research project while learning basic concepts of biology.<\/div>\n<div><\/div>\n<p>&nbsp;<\/p>\n<div>The GENI-ACT\u00a0consists of nine independent modules:<\/div>\n<div style=\"padding-left: 30px\"><\/div>\n<div style=\"padding-left: 30px\">\n<ol style=\"padding-left: 30px\">\n<li>Basic Information (DNA coordinates, DNA sequence, Protein Sequence, Isoelectric point)<\/li>\n<li>Sequence-based Similarity Data (BLAST, CDD, T-Coffee, WebLogo)<\/li>\n<li>Cellular Localization Data (Gram Stain, TMHMM, SignalP, PSORT-B, Phobius)<\/li>\n<li>Alternative Open Reading Frame<\/li>\n<li>Structure-based Evidence (TIGRfam, Pfam, PDB)<\/li>\n<li>Enzymatic Function (KEGG, MetaCyc, E.C. Number)<\/li>\n<li>Gene DuplicationGene Degradation (Paralog and Psuedogene Determination)<\/li>\n<li>Evidence for Horizontal Gene Transfer (Phylogenetic Tree, Gene Context, GC Heat Map)<\/li>\n<li>RNA Information (Rfam)<\/li>\n<\/ol>\n<\/div>\n<div><\/div>\n<div>Use of the modules encourages participants to:<\/div>\n<div><\/div>\n<div>\n<ul>\n<ul>\n<ul>\n<li style=\"text-align: left\">Use and master multiple database analysis software packages related to <a href=\"http:\/\/en.wikipedia.org\/wiki\/Bioinformatics\" rel=\"nofollow\"><span style=\"color: #0000ff\">bioinformatics<\/span><\/a>.<\/li>\n<li style=\"text-align: left\">Strengthen library and web-search skills<\/li>\n<li style=\"text-align: left\">Develop skills in making hypotheses and the design of experiments to test them<\/li>\n<li style=\"text-align: left\">Sharpen skills in analysis, synthesis and in the presentation and interpretation of results<\/li>\n<li style=\"text-align: left\">Experience the collaborative nature of science.<\/li>\n<\/ul>\n<\/ul>\n<\/ul>\n<\/div>\n<div style=\"font-weight: bold\"><\/div>\n<\/div>\n<div class=\"wider\">The project will use the genome of the bacterium <i>Kytoccocus sedentarius<\/i>\u00a0as the source of material for analysis. \u00a0<i>Kytococcus<\/i>\u00a0is one of the Genomic Encyclopedia of Bacteria and Archea (<a href=\"http:\/\/www.nature.com\/nature\/journal\/v462\/n7276\/full\/nature08656.html\" rel=\"nofollow\"><span style=\"color: #0000ff\">GEBA<\/span><\/a>) organisms. \u00a0GEBA organisms have had their genomes sequenced to help fill in gaps in the tree of life that exist due to the fact that sequencing had previously been done only for those organisms that were easy to grow or which had clinical significance. \u00a0A basic summary of the importance of sequencing and annotating GEBA genomes can be found <a href=\"http:\/\/bytesizebio.net\/2009\/12\/23\/filling-in-the-evolutionary-blanks-genome-by-genome\/\" rel=\"nofollow\"><span style=\"color: #0000ff\">here<\/span><\/a>.<\/div>\n<div><\/div>\n<p>&nbsp;<\/p>\n<div class=\"wider\">The image below is a scanning electron micrograph showing the characteristic cuboidal appearance of <i>Kytococcus \u00a0sedentarius <\/i>\u00a0in culture. \u00a0Each one of the sphere-like structures in the micrograph is a single bacterium. \u00a0Students and teachers participating in the project will help to annotate the genomic sequence of this microbe and, in addition to gaining experience in basic bioinformatic analysis, will contribute to the basic understanding of its biology.\u00a0<img loading=\"lazy\" decoding=\"async\" class=\"aligncenter\" src=\"https:\/\/sites.google.com\/site\/ubbclsgenomeannotation\/_\/rsrc\/1399649988742\/project-introduction\/Kytococcus.png?height=251&amp;width=320\" alt=\"http:\/\/www.standardsingenomics.org\/index.php\/sigen\/article\/view\/sigs.761\/51\" width=\"320\" height=\"251\" border=\"0\" \/><\/div>\n<div class=\"wider\">Image taken from: <span style=\"color: #0000ff\"><a href=\"http:\/\/www.standardsingenomics.org\/index.php\/sigen\/article\/view\/sigs.761\/51\" rel=\"nofollow\">http:\/\/www.standardsingenomics.org\/index.php\/sigen\/article\/view\/sigs.761\/51<\/a><\/span><\/div>\n<div><\/div>\n<p>&nbsp;<\/p>\n<div>\n<div class=\"wider\">Examples of work on the genome annotation project performed by high school students and MS level students at the university at Buffalo can be seen in the <a href=\"http:\/\/wpdev.acsu.buffalo.edu\/wnygirp\/in-the-news\/\" target=\"_blank\"><span style=\"color: #0000ff\">In the news&#8230;.<\/span><\/a> page of this website.<\/div>\n<p>&nbsp;<\/p>\n<p><span style=\"font-weight: bold;color: #0000ff;font-size: medium\"><a href=\"http:\/\/www.nsf.gov\/awardsearch\/showAward?AWD_ID=1311902&amp;HistoricalAwards=false\" rel=\"nofollow\"><span style=\"color: #0000ff\">Link to the the NSF project description page<\/span>.<\/a><\/span><\/p>\n<div class=\"wider\">\n<div><b><a href=\"http:\/\/www.genome.jp\/dbget-bin\/www_bget?gn:T00974\" rel=\"nofollow\"><span style=\"color: #0000ff;font-size: medium\">Summary of information about <i>Kytococcus sedentarius<\/i> and the sequencing of its genome.<\/span><\/a><\/b><\/div>\n<div><\/div>\n<p>&nbsp;<\/p>\n<div><\/div>\n<\/div>\n<\/div>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The innovative technology experience for students and teachers used in this project\u00a0involves a \u201chands-on\u201d cyber-learning approach, known as GENI-ACT, that will involve participants in a current and global research project &hellip; <a href=\"http:\/\/ubwp.buffalo.edu\/wnygirp\/project-details\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Project Details<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":10,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_bbp_topic_count":0,"_bbp_reply_count":0,"_bbp_total_topic_count":0,"_bbp_total_reply_count":0,"_bbp_voice_count":0,"_bbp_anonymous_reply_count":0,"_bbp_topic_count_hidden":0,"_bbp_reply_count_hidden":0,"_bbp_forum_subforum_count":0,"footnotes":""},"class_list":["post-158","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/ubwp.buffalo.edu\/wnygirp\/wp-json\/wp\/v2\/pages\/158","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/ubwp.buffalo.edu\/wnygirp\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/ubwp.buffalo.edu\/wnygirp\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/ubwp.buffalo.edu\/wnygirp\/wp-json\/wp\/v2\/users\/10"}],"replies":[{"embeddable":true,"href":"http:\/\/ubwp.buffalo.edu\/wnygirp\/wp-json\/wp\/v2\/comments?post=158"}],"version-history":[{"count":3,"href":"http:\/\/ubwp.buffalo.edu\/wnygirp\/wp-json\/wp\/v2\/pages\/158\/revisions"}],"predecessor-version":[{"id":336,"href":"http:\/\/ubwp.buffalo.edu\/wnygirp\/wp-json\/wp\/v2\/pages\/158\/revisions\/336"}],"wp:attachment":[{"href":"http:\/\/ubwp.buffalo.edu\/wnygirp\/wp-json\/wp\/v2\/media?parent=158"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}