Becoming a GEP Member
The Genomics Education Partnership is supported by NSF through 2017. We are seeking new members, particularly faculty interested in working with beginning students, including those at community colleges.
We are looking for faculty who teach genetics, molecular biology, bioinformatics, etc. who are interested in strengthening the work in genomics and in providing their students with a research experience. The advent of genomic and other high-throughput technologies has changed the way we do research in biology, and hence is changing the way we teach. At Washington University, an upper level lab course, Bio 4342, Research Explorations in Genomics, allows students to participate in a collaborative genome sequencing project, each student taking responsibility for sequencing and annotating a segment of DNA. A new freshman seminar, Bio 193, Investigating Eukaryotic Genomes, teaches basic eukaryotic gene structure to enable these beginning students to participate in the genomics research project. The purpose of the Genomics Education Partnership (GEP) is to make this opportunity available to students on other campuses, building a national network of participating faculty and students.
The GEP at present is a consortium of over 100 colleges and universities, with ~70 schools contributing actively in any given year. You can view the membership list and learn more about the GEP at our website, http://gep.wustl.edu. The GEP was initially funded by the Howard Hughes Medical Institute, and is currently supported by an IUSE grant from NSF. Grant funding supports two annual workshops for faculty who wish to join the GEP, and Alumni Workshops that bring GEP faculty together in the summer to work on curriculum, assessment, publications, etc., as well as computer staff to help manage data and communications.
Three Levels of Participation
Interested faculty with a major focus on teaching undergraduates are invited to join with us to share teaching materials that 1) use genomics data in problem solving, 2) engage students in sequence improvement, potentially including wet lab, or 3) engage students in annotating sequence data. Students who participate in a collaborative project at levels 2 and 3 can become co-authors on a resulting manuscript (see Leung et al. 2015 for an example).
Genomes are assembled from sequencing "reads" ranging in size from ~100 bp to kilobases, depending on the sequencing platform used. Errors can occur both in assigning the appropriate nucleotide, and in assembling the fragments. For a region we are investigating, the raw sequencing data (taken from public databases) will be posted on the GEP server in student-sized packages, along with instructional materials, training exercises, and computer tools to allow students to take ownership of a segment of DNA. Students will find that they can correct many mistakes using the data available, but in some instances will need to recommend that additional sequencing be done to resolve a particular region. We have found that each student can complete a ~100 kb project in 2-3 weeks in a lab course meeting 8 hr/wk. (Note that the software we use in sequence improvement, Consed, is designed for unix-based computers, including Mac OS X; a free license is available for GEP members.) Instructors who wish to schedule a wet lab as part of their course can have their students design primers to carry out PCR reactions to generate the fragments needed for additional sequencing. Otherwise, segments needing additional sequencing are reported, along with the improved sequence, to the central GEP for work during the summer. Participating in sequence enhancement is very satisfying for students, as they are contributing new knowledge for use by scientists and students alike.
Our second challenge is to annotate a 40 kb segment of a fly genome, using BLAST and other tools to identify genes (assembling defendable gene models), repetitious sequences, and other features. Students may also use Clustalw to create multiple alignments; carry out various evolutionary comparisons; use FlyBase to investigate the pattern of gene expression, and possible gene functions; etc. You can choose to participate in annotation without participating in sequence improvement. Because annotation is entirely computer-based, and relies on tools and databases available on the web, it is easy to incorporate annotation projects into a variety of teaching schedules. Annotating eukaryotic genes is one of the best ways to develop an appreciation for the complexities of eukaryotic genomes!
We understand that not every curriculum can afford a full course dedicated to eukaryotic genes and genomes. Therefore, we have developed several less time consuming alternatives. Ready-to-go data sets are available in our "Sandbox", and can be claimed for practice analysis at any time, using the same teaching tools posted for all GEP students for sequence improvement and annotation. Alternatively, faculty can claim a small number of annotation research projects and divide the work up among several students, so that students can experience real problems in genome annotation within the context of a more general advanced lab course, spending a few weeks rather than the whole semester on the project. (Note, however, that to qualify for co-authorship, a team working on one project can have no more than 3 students.) Versions of the GEP materials designed to be used in a beginning genetics lab requiring ~10 hr of class time are available on the web site, along with curriculum designed for a course devoted to genomics. Sample introductory student labs based on generating and using DNA sequence information are posted on the GEP web site, along with materials designed to help beginning students learn about eukaryotic genes through use of a genome browser.
Growing Experience with Undergraduate Genome Sequencing
Our current projects center on the distal ~1.3 Mb domain of the small dot chromosome (F element) of various Drosophila species. The biological interest in this domain comes from the fact that the small dot chromosome appears to be heterochromatic in D. melanogaster by many criteria, yet this distal portion has ~80 genes, a gene density similar to that seen in the euchromatic arms of the other chromosomes. We have been interested in analyzing the evolution of this unique domain, following both the characteristics of the chromosome (size, organization, etc.) and the characteristics of the genes that live in this heterochromatic domain. Careful annotation of the genes by our students has created a high-quality resource for a variety of studies. Our goal is to engage the students in publishable work, and our first published papers can be seen at Genetics:
Leung W, Shaffer CD, Cordonnier T, Wong J, Itano MS, Slawson Tempel EE, Kellmann E, Desruisseau DM, Cain C, Carrasquillo R, Chusak TM, Falkowska K, Grim KD, Guan R, Honeybourne J, Khan S, Lo L, McGaha R, Plunkett J, Richner JM, Richt R, Sabin L, Shah A, Sharma A, Singhal S, Song F, Swope C, Wilen CB, Buhler J, Mardis ER, Elgin SCR. (2010) Evolution of a distinct genomic domain in Drosophila: Comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis. Genetics 185: 1519-1534.
Recently we completed sequence improvement and annotation of the F element, and a comparison euchromatic domain from the D element, from three species covering 40 million years of evolutions, D. grimshawi, D. mojavensis, and D. erecta for comparison with D. melanogaster. This study shows that the F element genes have maintained a unique set of characteristics, being larger (due to larger introns, with more repeat sequences), showing generally less codon bias, and a lower melting temperature than D element genes. We were also able to identify a "hot spot" for gene insertions of the F element. For more details, see:
Leung, W. … [940 students, 72 faculty] … Elgin, SCR (2015) The Drosophila Muller F elements maintain a distinct set of genomics properties over 40 million years of evolution. G3: GENES, GENOMES, GENETICS 5: 719-740.
This paper received considerable social commentary because of the high number of undergraduate co-authors; see http://gep.wustl.edu/community/four_genomes_paper for a summary.
Our current project involves sequence improvement and annotation of a group of species that diverged from D. melanogaster about 10 million years ago. We want to use phylogenetic footprinting to see if we can identify motifs specific to the F element, and this evolutionary distance represents the "sweet spot" for identifying such elements based on conservation. A second project is investigation of a small number of species that have a greatly expanded F element, creating a domain that is 80% repeats — while maintaining gene function!
Members of the GEP are currently developing opportunities to collaborate with scientists working on gut bacteria and on the Puerto Rican parrot. Our project with Galaxy will make it easier to create good genome browser pages for annotation of any sequenced genome. In the long run, we anticipate developing a website that can connect our members to annotation projects in a wide range of eukaryotes.
The easiest way for you to learn more about the GEP is to browse the web site at http://gep.wustl.edu. The site includes curriculum materials we have used in our workshops and with our students, a video tour of the McDonnell Genome Institute emphasizing Sanger sequencing, and a new one on "next generation" sequencing, examples of student work, student assessment surveys and a section (Workshops) that includes the draft schedule and logistics for the June "new faculty" workshop. A bulletin board and wiki are also accessed through the web site. The wiki includes examples of syllabi from current members, along with comments on implementation. We have been very impressed with what the students have been able to accomplish, as shown by their final reports and our quality control checks. Our assessments indicate that our students gain considerable understanding of how new knowledge is created in the field, and end the course with a real sense of accomplishment (see papers by Shaffer et al., 2010, 2014).
Grant Funding Covers Faculty and TA Training plus Core IT Support
The current NSF grant provides funds to bring faculty from a range of undergraduate institutions to Washington University for a workshop that introduces current teaching materials, allows faculty to gain facility with the computer tools that we use, and allows for joint discussion, sharing, and planning. Air travel up to $400 and local costs are covered. Funds are budgeted for two people from each campus. This allows each faculty member to bring a student, staff member, or colleague to the workshop in June or January. Students who become peer instructors by this route can earn a $500 honorarium by working with you as you implement new materials in genomics into your teaching, and filing beginning and end of the semester reports. Note that the one item that will not be covered by present or proposed grants at WU will be your student computers; it is necessary to run the course in a setting where each student can use a computer with web access.
We hope that this project will continue to attract faculty interested in joining us in this new venture. Becoming a partner commits you to introducing new material in genomics into one or more of your courses, at any of the levels of participation described above (Level 1, working with prepared genome sequence data and worksheets; 2) engaging students in sequence improvement, potentially including wet lab, or 3) engaging students in annotating sequence data. Students participating in levels 2 and 3 can be eligible to be co-authors on the resulting publication. We ask that your students participate in a pre-course / post-course on-line survey and quiz; this requires you to get local IRB approval. (Note that TA support from the grant is provided for the first year implementation only — be sure to recruit some bright students who can TA the following year!) Implementation can involve a large lab class, or in the first instance can be done with just a few students in a special topics course. At WU, Bio 4342 typically enrolls 12-16 juniors and seniors. One current emphasis is on designing courses for beginning students. Examples of different implementation strategies used at different schools can be seen on the GEP Wiki "Table of Faculty."
If you are interested in joining the GEP, now or in the future, please let me know! If you have a colleague whom you think would be interested, please forward this email/website. The Faculty/TA workshops are divided into two segments, with annotation being the focus from Sunday evening through noon Wednesday, and sequence improvement (finishing) being the focus from noon Wednesday to Thursday evening. A draft agenda can be seen on the "Workshop Information" page on the GEP web site. Washington University student alumni serve as TAs at the workshops, and will share their experiences. Workshops are capped at 16 participants. Let me know your interests, and any questions or concerns you might have. Email is best to start with, generally followed by a telephone or Skype (preferred) chat. And then the workshop!
Viktor Hamburger Professor of Arts & Sciences
Washington University in St.Louis