{"id":387,"date":"2016-06-02T18:15:23","date_gmt":"2016-06-03T01:15:23","guid":{"rendered":"http:\/\/blogs.oregonstate.edu\/wicnews\/?p=387"},"modified":"2016-06-03T16:40:15","modified_gmt":"2016-06-03T23:40:15","slug":"microbiology-wic-students-publish-genome-research","status":"publish","type":"post","link":"https:\/\/blogs.oregonstate.edu\/wicnews\/2016\/06\/02\/microbiology-wic-students-publish-genome-research\/","title":{"rendered":"Microbiology WIC Students Publish Genome Research"},"content":{"rendered":"

<\/a> By WIC<\/em> Team<\/em><\/p>\n

Congratulations to Professor Walt Ream and his Microbiology 311 students for the publication of their article, \u201cDraft Genome Sequence of Erwinia billingiae<\/em> OSU19-1, Isolated from a Pear Tree Canker\u201d in the journal Genome Announcements<\/em>. The students were enrolled in a Molecular Microbiology Lab WIC Course (MB311, winter, 2015).<\/p>\n

Dr. Ream offers the following details on the project:
\n<\/strong><\/p>\n

The first author, Jeannie Klein (a Microbiology major), did her honors thesis research with Virginia Stockwell, who works at the USDA facility in Corvallis. Virginia is well known for her work on biological control of fire blight disease on fruit trees.\u00a0 Jeannie worked on that project for two years.<\/p>\n

Writing Process
\n<\/em>
\n<\/em>Each student in MB311 wrote a proposal to study microbial populations in environmental samples. The students selected the best proposal from each group of twelve. The students selected Jeannie\u2019s proposal to study the bacteria that inhabit fire blight cankers; I agreed with their decision. Jeannie directed the experiment and cultured an organism for genome sequencing.<\/p>\n

The fact that the organism was so interesting was pure luck. This is only the second genome sequence published for this organism. To put that into context, many human pathogens and commensals have been sequenced hundreds of times (or more). The Erwinia billingiae<\/em> type strain was isolated in the 1950s from a fire blight canker on a pear tree in England. \u00a0Despite the great temporal and geographic distances that separate Jeannie\u2019s strain from the type strain, they share many genes in common, including ~40 genes on a plasmid. Because plasmids are not essential for life, they are quickly lost unless they contribute to the fitness of the bacterium. The plasmid genes these two strains share have been conserved for 57 years, which is an eternity for bacteria. So, they must do something important.<\/p>\n

The students and TA (Wei Wei) each contributed to the first draft of the paper, although Jeannie and Rhett Bennett (another student from Stockwell\u2019s group) made the most significant contributions. Logan MacFarland was not part of the original team; his contribution was to show me how to use multiple genome assembly programs in tandem to improve the assembly. I revised the abstract and text so that they met the word limits.<\/p>\n

Jeannie and I struggled with one sentence. We knew the original version was confusing, but neither of us knew how to fix it. We gave the draft to Virginia for review, and she completely misunderstood the sentence, confirming that we had a problem. Here is our solution: OSU19-1 lacks significant similarity to pEB170, but contigs 2 (98,580 bp) and 10 (40,687 bp) share 26,170 bp and 14,490 bp (94 to 96% identity) with different regions of pEB102.\u00a0This is not elegant, but it is more clear than was the original version.<\/p>\n

Virginia also critiqued our interpretation and asked us to cite the original papers by Eve Billing (for whom the species is named). These papers are so old they are not available online, so we made a trip to the library! I find it reassuring that Google does not know everything.<\/p>\n

Jeannie, the lead researcher, has accepted an offer to enter a PhD program at the University of Florida (Gainesville) where she will continue her education in Plant Pathology.<\/p>\n

The library\u2019s Open Access Fund made publication of this article possible. Without their support, we could not have paid the publication costs. This is an important program that supports publication of articles written by OSU students. I hope this fund will continue indefinitely and receive an increased budget. The current level of funding is modest but greatly appreciated. Your support for the Open Access Fund could make a difference.<\/p>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

By WIC Team Congratulations to Professor Walt Ream and his Microbiology 311 students for the publication of their article, \u201cDraft Genome Sequence of Erwinia billingiae OSU19-1, Isolated from a Pear Tree Canker\u201d in the journal Genome Announcements. The students were enrolled in a Molecular Microbiology Lab WIC Course (MB311, winter, 2015). Dr. Ream offers the… Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":7098,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[717009],"tags":[],"class_list":["post-387","post","type-post","status-publish","format-standard","hentry","category-spring-2016"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/blogs.oregonstate.edu\/wicnews\/wp-json\/wp\/v2\/posts\/387","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.oregonstate.edu\/wicnews\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.oregonstate.edu\/wicnews\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/wicnews\/wp-json\/wp\/v2\/users\/7098"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/wicnews\/wp-json\/wp\/v2\/comments?post=387"}],"version-history":[{"count":6,"href":"https:\/\/blogs.oregonstate.edu\/wicnews\/wp-json\/wp\/v2\/posts\/387\/revisions"}],"predecessor-version":[{"id":400,"href":"https:\/\/blogs.oregonstate.edu\/wicnews\/wp-json\/wp\/v2\/posts\/387\/revisions\/400"}],"wp:attachment":[{"href":"https:\/\/blogs.oregonstate.edu\/wicnews\/wp-json\/wp\/v2\/media?parent=387"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/wicnews\/wp-json\/wp\/v2\/categories?post=387"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/wicnews\/wp-json\/wp\/v2\/tags?post=387"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}