Genomics Education Partnership Research Articles

Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience.

A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students’ learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our “formative frustration” hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned frustration and struggle, as well as learning and better understanding of the scientific process. Bioinformatics projects are particularly well suited to the process of iteration and refinement because iterations can be performed quickly and are inexpensive in both time and money. Based on these findings, we suggest that a dynamic of “formative frustration” is an important aspect for a successful CURE.

Annotation and Comparison of Drosophila takahashii Genes on the Dot Chromosome

The overall goal for this project is to understand how genes are expressed in a heterochromatic environment. Chromosome four (Dot chromosome; Muller F element) of Drosophila melanogaster is 1.3 Mb long with ~80 genes but is largely heterochromatic. In the Genomics Education Partnership (GEP) project, we are currently annotating a group of species that was diverged from D. melanogaster about 10 million years ago. Our project was to annotate genes on a 70,000 base pair region (contig40) of the D. takahashii Dot chromosome. In order to annotate the genes we used the BLASTX, gene predictors like Gene Scan, RNA‐sequence data, and the results from the Gene Model Checker. According to the gene predictor, Gene Scan, this contig contains five protein‐coding genes. It predicted the genes Slip1, Myo, CG11360, a gene of unknown function (GI25919), and another gene that appears to be a Mex3A‐Slip1 fusion. We annotated the genes Slip1, Myo, CG11360, and GI25919. We are currently annotating the gene Mex3A‐Slip1 fusion gene. The D. takahashii genes that are similar to D. melanogaster are Myo and Slip1. Myo has an identity of 73.1% and a similarity of 81.8%. Slip1 has an identity of 72.3% and a similarity of 82.2%. CG11360 is very different with an identity of 13.1% and a similarity of 26.8%. In contrast to the D. takahashii genes that are present in D. melanogaster, GI25919 is not present at all. It is predicted to be present in several other species including: D. mojavensis, Aedes albopictus, Stomoxys calcitrans, and Musca domestica. We compared GI25919 to D. mojavensis and it has an identity of 39% and a similarity of 55%. In conclusion, some D. takahashii Dot chromosome genes within this region are similar to D. melanogaster, but others are very divergent or missing in D. melanogaster. Our data will be combined with other gene annotations from students in the GEP for a comparative genomics study to identify conserved gene regulatory elements.Support or Funding InformationNSF HRD#1623340NSF IUSE #1431407This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Peer‐Led Team Learning and Course‐based Undergraduate Research Experiences in General Biology and General Chemistry

Lane College is a historically black college with a commitment to educating underserved minority students. Our overall goal for this project is to improve student learning of foundational concepts and retention in Biology and Chemistry through student‐centered activities within our first‐year courses. These approaches include implementation of peer‐led team learning strategies and course‐based undergraduate research experiences (CUREs) within the General Biology and General Chemistry courses. Our peer‐mentors, who serve as supplemental instructors for our General Biology and Chemistry courses are an essential element for the success of the program. They receive leadership training, through a collaboration with the Office of the First Year Experience as well as mentored undergraduate research experiences before working with our first‐year students. We have redesigned our laboratory courses to implement CUREs. Biology projects include comparative genomics in collaboration with the Genomics Education Partnership, environmental surveys of antibiotic resistant bacteria or sequence analysis of GAPC from plants growing on campus. Chemistry projects include development of novel analytical methods to measure chemical components of household products, such as using the iodine‐clock reaction to determine the amount of starch in various foods. We are assessing student learning outcomes related to understanding the scientific method using the Experimental Design Ability Test and the CURE survey developed by the GEP. In addition, we are evaluating student learning outcomes of the process of science, such as development and testing of hypotheses, recording observations within a laboratory notebook, and communication of results through oral presentations and written reports.Support or Funding InformationNSF HRD1623340This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Comparative Genomics and Gene Annotation of a Region of Drosophila eugracilis Chromosome 4

The common fruit fly, Drosophilia melanogaster, has around 1,300 genes in its genome. Chromosome 4 is 3.5% of its genome and contains approximately 80 genes within large heterochromatic domains. Interestingly, these genes are expressed at similar levels to genes found in euchromatin. The goal of the Genomics Education Partnership (GEP) project is to understand the gene expression within this heterochromatic environment. For the GEP project, we are identifying conserved DNA regulatory sequences around transcription start sites using the fourth chromosome from other species of Drosophila and D. melanogaster. I annotated genes located within a 35,000 base‐pair section of Drosophilia eugracilis chromosome 4 using BLASTX, Gene predictors, and RNA‐seq evidence within the UCSC Genome Browser. I annotated coding exons and splice sites for 2 genes with 3 isoforms each, Cubitis interruptus (Ci) and Ribosomal protein S3A (RpS3A) and the transcription start sites for each gene. GEP students are annotating many megabases of DNA and their pooled results are furthering an understanding of heterochromatic gene structure and regulation.Support or Funding InformationSupported by NSF IUSE #1431407 and NIH R25GM119157 to Sarah C.R. Elgin (GEP) and NSF HRD#1623340 to MVSThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

The Genomics Education Partnership: Course‐based Research Experiences for Undergraduates

The Genomics Education Partnership (GEP) is a collaboration between faculty from over 100 diverse institutions with the goal of providing authentic course‐based undergraduate research experiences (CUREs) in bioinformatics and genomics for undergraduate students. The GEP faculty have developed curricula for undergraduates at all levels that allow faculty to implement bioinformatics instruction and research within their courses. The research projects have primarily focused on the comparative genomics of the Muller F element (dot chromosome) in several Drosophila species. This chromosome is unusual in that it is largely heterochromatic, but contains ca. 80 genes that are expressed at levels similar to those found in euchromatin. Our students have focused on sequence improvement (finishing), and the annotation of protein‐coding genes and transcription start sites. Through these evolutionary comparisons, we are gaining insights into the regulation of gene expression within this heterochromatic environment. Our most recent paper on the expansion of the Drosophila ananassae F element includes 239 undergraduate students and 31 faculty co‐authors. Our faculty and student surveys, pre/post‐quiz results, and focus groups suggest that students gain the most from CUREs when faculty treat them like members of a research team. They also learn through formative failures — when challenges arise that must be resolved. In addition to research projects, we are developing new curricula, such as the “Understanding Eukaryotic Genes” modules, designed to familiarize beginning students with genome browsers while teaching eukaryotic gene structure, and units on Hidden Markov Models and Dynamic Programming for more advanced students. The GEP is collaborating with Galaxy to create G‐OnRamp (http://gonramp.org), a workflow that constructs UCSC Assembly Hubs and JBrowse genome browsers for newly sequenced eukaryotic genomes. G‐OnRamp enables faculty to engage students in novel annotation projects from a variety of organisms (e.g., Puerto Rican parrot, parasitoid wasps). If interested in participating in a grant‐supported workshop either June 12–15 or July 16–19, 2018 to learn to use G‐OnRamp, contact Sarah Elgin (selgin@wustl.edu).Support or Funding InformationSupported by NSF IUSE #1431407 and NIH R25GM119157 to SCRE.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Annotation of Genes on Contig 31 of the Drosophila eugracilis Chromosome 4

Drosophila melanogaster has a small fourth chromosome, the Muller F element (3.5% of the genome), that has very large heterochromatin domains which are rich in HP1. Our goal for this project is to understand the mechanisms of gene expression in this heterochromatic environment. In the Genomics Education Partnership Project, we are using comparative genomics to identify conserved DNA regulatory sequences, by comparing the D. melanogaster Muller F element to those of other fly species that diverged from D. melanogaster ~10 million years ago, aiming to find regions of homology surrounding the transcription start sites. I have annotated the genes on a 40,000 base‐pair piece from the Drosophila eugracilis chromosome four. Sequence comparisons using BLASTX, gene predictors like Gene Scans, and RNA sequence data were used to annotate coding genes in this region. I identified two genes: myo (3 isoforms) and ey (4 isoforms) and annotated protein coding exons and splice sites for each isoform. The myo amino acid sequence is identical for each isoform in D. eugracilis, with 70.3% amino acid identity compared to the D. melanogaster myo protein. The D. eugracilis ey isoforms are also similar to the D. melanogaster ey protein sequences, with a range from 73% to 78% identity to their corresponding D. melanogaster isoform. Putative Transcription Start Sites for each gene were investigated, including a search for known transcription factor binding sites. By pooling results, GEP students are annotating several megabases of DNA, and contributing to an understanding of heterochromatic genes.Support or Funding InformationSupported by NSF IUSE #1431407 and NIH R25GM119157 to Sarah C.R. Elgin (GEP) and NSF HRD#1623340 to MVSThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

Gene structure, transcription, translation, and alternative splicing are challenging concepts for many undergraduates studying biology. These topics are typically covered in a traditional lecture environment, but students often fail to master and retain these concepts. To address this problem we have designed a series of six Modules that employ an active learning approach using a bioinformatics tool, the genome browser, to help students understand eukaryotic gene structure and functionality. Students learn how to use a mirror site of the UCSC Genome Browser created by the Genomics Education Partnership while completing the Modules, which focus on gene structure, transcription, splicing, translation, and alternative splicing. The Modules are supplemented with short videos that illustrate key functionalities of the genome browser and fundamental concepts in processing transcripts. These materials have been used successfully to teach gene structure in many different settings, from community colleges to 4-year colleges and universities, encompassing advanced high school students to college seniors. Instructors can easily customize the Modules and/or select a subset for their curriculum. The Modules have helped our students learn about eukaryotic gene structure and expression, simultaneously acquiring skills in the use of a genome browser, and have prepared them to pursue genome annotation projects as independent research. <!--pagebreak-->

The GEP: Crowd-Sourcing Big Data Analysis with Undergraduates

The era of 'big data' is also the era of abundant data, creating new opportunities for student-scientist research partnerships. By coordinating undergraduate efforts, the Genomics Education Partnership produces high-quality annotated data sets and analyses that could not be generated otherwise, leading to scientific publications while providing many students with research experience.

The Genomics Education Partnership: Assessing and Improving a Course‐based Undergraduate Research Experience (CURE)

The Genomics Education Partnership (GEP http://gep.wustl.edu ) started in 2006 with 16 member institutions interested in providing genomics research experiences for their upper division students. Over 10 years, GEP has grown to a consortium of faculty from over 100 colleges and universities that provide a course‐based undergraduate research experience (CURE) in genomics and bioinformatics to students at all levels. The GEP CURE is a cutting edge lab experience that can be implemented at any post‐secondary institution, even at schools that have limited laboratory capabilities. The objectives of the Genomics Education Partnership are four‐fold: 1) provide professional development in genomics for college and university faculty, 2) develop genomics curriculum for a variety of educational settings, from small group seminar courses to large introductory courses, 3) assess student gains in knowledge of genomics and attitudes toward research, and 4) accomplish research into genome structure and evolution. The partnership engages approximately 60 faculty and 1000 students per year in the manual sequence improvement and gene annotation of selected genomic regions from different species of fruit flies (Drosophila spp.). Students are guided by their instructors on how to use genomics databases (e.g., FlyBase, NCBI) and bioinformatics tools (e.g., UCSC Genome Browser, BLAST) while learning about gene structure, chromosome organization, evolution, programming, and other topics, depending on the level and the focus of the course. GEP students have improved the quality of the DNA sequence and annotated the genes and other features of interest (e.g., transposons, non‐coding RNAs) from the euchromatic Muller D element and the heterochromatic Muller F element of several Drosophila species. The results of this comparison reveal that F elements have greater transposon density, and their genes have larger coding spans, more coding exons, larger introns, and lower codon bias than the euchromatic reference regions from the D element (Leung et al. 2015 G3 5: 719 and ongoing research). Regardless of the implementation strategy (i.e. short lab modules, stand‐alone research courses, computer science/biology hybrid courses, or independent research projects) the students participating in the GEP show learning gains on attitude and knowledge assessments; these gains correlate with the amount of time invested in the project. Faculty assessment shows that some barriers to the implementation of a research‐based curriculum (e.g., campus acceptance of this pedagogical approach, availability of IT/computer services, faculty expertise) can be alleviated through a central core facility that provides curriculum materials, computational resources, collaborative pedagogy development, and a supportive community. We are currently focused on developing new curriculum for beginning students, including students at community colleges. Small working groups, alumni workshops and webinars keep the momentum going and sustain this large community. The consortium is actively recruiting faculty interested in developing course‐based research experiences for first and second year students.Support or Funding InformationSupport from HHMI grant 52005780 and NSF grant 1431407 to SCRE and from Washington University in St. Louis

Comparative Genomic Analysis of Euchromatic and Heterochromatic Chromosomal regions of two species of Drosophila

Comparative genomic analyses can yield important information about the structure and function of genomes. The public availability of DNA sequence data from genome sequencing projects provides opportunities for undergraduate and high school students to do genomics research. The Genomics Education Partnership (GEP, see www.gep.wustl.edu) is a scientific and educational collaboration centered at Washington University in St. Louis (WUSTL), which provides a variety of tools for comparative genome analysis of several Drosophila species. The goal of the current GEP project is to compare sequences of chromosome four (also called the ‘dot' chromosome) from D. melanogaster with homologous regions from other species. The dot chromosome has interesting features of heterochromatin and euchromatin, and is therefore a good choice for studying the evolution of these two types of sequences. Here we describe the analysis of a euchromatic region from D. biarmipes that is homologous to chromosome 3L of D. melanogaster. This analysis serves as an important control comparison in our larger project. We analyzed 40,000 base pairs of DNA from contig 6 of the D. biarmipes genome. Initial analysis suggested there are nine predicted genes in this region. We used several analysis tools available from the GEP and other sources to generate precise gene models for these genes. Our results will contribute to the completion of the full genomic map of D. biarmipes and will be compiled along with other student data to analyze the evolution of the structure and function of heterochromatin as compared to euchromatin. *The Genomics Education Partnership is funded by HHMI (Professors grant #52007051 to SCR Elgin) and by Washington University in St. Louis (WUSTL).

Using Comparative Genomics to Study DNA Sequences of the Muller F Element from Drosophila biarmipes

The Genomics Education Partnership* (GEP) is a scientific and educational partnership using comparative genomics to characterize the Muller F element, a distinct chromosomal domain, from the genomes of several Drosophila species (see www.gep.wustl.edu). In Drosophila melanogaster, the F element corresponds to the fourth chromosome (or “dot” chromosome), which appears to be heterochromatic by many criteria, but has a relatively high gene density. Our goal is to study the evolution of these sequences to further our understanding of the function of heterochromatin. As part of an advanced genetics course at Albion College, we used several web-based tools to annotate a 50,000 base pair contiguous sequence from the genome of Drosophila biarmipes. The annotation process involved using the corresponding genomic region of the Drosophila melanogaster fourth chromosome as a reference sequence. Using BLAST we estimated the positions of each exon, then using a variety of evidence tracks from the UCSC genome browser, we precisely localized start codons, donor and acceptor splice sites, and stop codons for each isoform. Gene models were verified using the Gene Model Checker program and by generating final sequence alignments and dot plots using BLAST. Our analysis resulted in the annotation of five distinct genes in this contig. The genes ranged in complexity from 2-7 splice variants, with individual isoforms ranging in size from 4 to 12 exons each. Our analysis will be combined with data from other student members of the partnership to help answer questions about the organization and function of the Muller F element in several different species. *The Genomics Education Partnership is funded by HHMI (Professors grant #52007051 to SCR Elgin) and by Washington University in St. Louis (WUSTL).

A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics.

In their 2012 report, the President's Council of Advisors on Science and Technology advocated "replacing standard science laboratory courses with discovery-based research courses"-a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates.

Genomics Education Partnership: a research‐based approach to undergraduate teaching utilizing a centralized support system (618.39)

The Genomics Education Partnership (GEP) is a consortium of educators with common research and educational goals in genomics, and is comprised of 100+ faculty members instructing 1000+ students annually. Our focus is 1) undergraduate education via research in comparative genomics and 2) assessment of pedagogy within diverse student populations. To examine the evolution of the Drosophila “dot” chromosome, students in GEP courses improved over 7 Mb of genomic sequence and generated over 1000 manually curated gene models. To assess pedagogy, we evaluated student learning gains in both the cognitive domain (pre‐ and post‐course knowledge quiz) and the affective domain (pre‐and post‐course CURE survey). We find that institutional characteristics have little impact on student outcomes, while the instructional time spent on the GEP projects has a significant impact on student experience. Cognitive learning gains are observed in both short and long implementation formats, and across a wide range of cognitive skill levels. However, only longer time investments show student benefits commensurate with those reported for students conducting summer research. A survey of faculty participants reveals that a centralized support system is critical for sustaining GEP. In summary, our data suggest that a research‐based curriculum with centralized support is a successful approach in STEM education.Grant Funding Source: Supported by grant #52007051 from the HHMI to SCRE and by the Washington University in St. Louis

Genomic Annotation of Drosophila biarmipes Dot Chromosome Contig 19 (LB531)

Comparative analysis of the genome of Drosophila melanogaster with other Drosophila species at various evolutionary distances can reveal information about differences in euchromatic and heterochromatic gene structure, and how evolutionary processes have changed the expression of genes located in these regions. The goal of this project, performed in conjunction with the Genomics Education Partnership at Washington University, was to annotate all the major features of Drosophila biarmipes dot chromosome Contig 19 ‐ including genes, pseudogenes, and repetitive sequences ‐ to generate a high quality section of the genome of this species. Basic Local Alignment Search Tool (BLAST) was used along with Gene Record Finder to compare the protein sequence of D. melanogaster exons to the D. biarmipes contig in order to locate the placement of the homologous exons in the latter species. Gene predicting programs were used to examine regions of the genome not immediately shown to contain genes. This information was entered into Gene Model Checker to compile a comprehensive map of the contig. Contig 19 is on the fourth (dot) chromosome of Drosophila biarmipes and it contains three genes, Syt7, Rad23 and Zip102B. Both the Syt7 and Rad23 genes showed high sequence conservation with their orthologs in D. melanogaster and are present in the same orientation. The Zip102B gene showed evidence of greater sequence divergence. Consistent RNAseq data and agreement between gene prediction programs led to the conclusion that this sequence divergence was due to the accumulation of point mutations relative to a common ancestral species. The contig displayed a repetitive element percentage of 40.32 percent, which is consistent with a heterochromatic DNA classification. No pseudogenes were identified in this contig.Grant Funding Source: Supported by HHMI grant # 52005780 to SCR Elgin at Washington University (St. Louis).

Interdisciplinary collaborative project‐based instruction: students in two distinct courses teach each other by building software to solve biological problems (618.38)

We developed and piloted a novel approach to interdisciplinary instruction; this approach relies on well‐defined interdependent roles for biology (BIO) and computer science (CS) students in a project‐based laboratory accompanied by two distinct discipline‐specific lecture courses. Student interactions are structured around software development process: (1) BIO students are presented with a biological question, (2) they figure out what data is required and write program requirements, (3) CS partners write a program, (4) BIO and CS students collaborate on testing the program, (5) BIO students use the program to answer the original question. We applied this workflow to five increasingly complex assignments relevant to the genome analysis project conducted by the Genomics Education Partnership (GEP, www.gep.wustl.edu). We tested this approach during two 10‐week quarters (Spring 2012 and 2013) with 65 CS students and 47 BIO students. We assessed cognitive learning gains (skills and knowledge) by evaluating course artifacts and student gains in the affective domain (attitudes and self‐efficacy) using confidential surveys. Assessment data indicate that students appreciate and mutually benefit from interdisciplinary interactions. Students from both disciplines improve communication skills and reinforce mastery of their own discipline by acting as experts and teachers in their field.Grant Funding Source: Supported by NSF TUES # 1140828.

Incorporating genome annotation with the Genomics Education Partnership (GEP) in an undergraduate biochemistry course

A computer‐based lab was developed to accompany the second semester of a year‐long biochemistry sequence. The goal for this lab was to emphasize the importance of computers in modern biochemical research. Lecture covered signaling, metabolic pathways, and genome structure and organization. Students began by using the bioinformatics programs BLAST, OMIM, and KEGG, to analyze the impact of a DNA mutation on protein structure and function in a biochemical pathway. In the second module students learned about microarrays through research articles and online curriculum from GCAT (www.bio.davidson.edu/gcat) then worked with a microarray data set. The third module on genome annotation spans the final eight weeks of the laboratory. This module used curriculum generated by the GEP (www.gep.wustl.edu) and included three weeks of introduction to the UCSC Genome Browser and FlyBase followed by four weeks of annotating raw sequence data from Drosophila and a week of project presentations. During this module, students received data and had access to tools from the GEP. Assessment results indicate that students had a better understanding of how computers are used in biochemical research, gained understanding of genome organization, and enjoyed the collaborative nature of the genome annotation research project.

Vision and Change in Biology Undergraduate Education, A Call for Action—Initial Responses

The executive summary provides an overview of some of V&C's key recommendations regarding next steps in the effort to mobilize the biology community. It is, in essence, a call for national service. A publication discussing these recommendations and action items in more depth will be available later this year. Meanwhile, we highly recommend reading the Executive Summary of V&C, the NAS report (NAS, 2010), and a seminal article by Labov et al. (2010) summarizing the synergy created by these several reports on the changing nature of studies in biology and concomitant need to change biology education. Then, take action! Our hope is to see the formation of a community of biologists, similar to that forming in geology (Manduca et al., 2010): one that will advance biology undergraduate education so it truly reflects the discipline it serves.

Promoting undergraduate research through the Genomics Education Partnership

Rapid increases in DNA sequence information now permit comparative examination of genes and genome organization. The goal of the Genomics Education Partnership (GEP) is to provide undergraduate students with an opportunity to participate in a large‐scale genome sequencing and annotation project to achieve the integrated goals of enhancing student learning in bioinformatics and related fields while making a contribution to new knowledge. The current focus of the GEP is on the dot chromosomes of several Drosophila species. This unique domain warrants further study because it has properties of both euchromatin, including normal gene density, and heterochromatin, including a high density of repetitive elements. Students take ownership of stretches of sequence and work to improve the posted sequence data and generate carefully annotated gene models; their work is supported by the central resources of the GEP. The assembled data permits analysis of the chromosome organization among different Drosophila species, resulting in publication and the development of new research questions. Surveys have indicated student learning gains in knowledge of genes and genomes and also demonstrate that GEP student personal gains are similar to those of students involved in a full‐time summer research experience. This project is funded by HHMI and NIH.

The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.

Community Outreach through Genomics Education Partnership

AbstractThe J Craig Venter Institute (JCVI) has recently partnered with undergraduate university faculty to expand the scope of education and outreach program as part of the NIAID’s BRC initiative, by joining forces with faculty members participating in the Genomics Education Partnership (GEP). The goal of the GEP is to provide opportunities for undergraduate students to participate in genomics research and gain hands on experience. Faculty members trained on annotation methodologies and tools during the Prokaryotic Annotation Workshop conducted at JCVI, impart their knowledge in the classroom as part of the semester course. As a pilot project, we are currently collaborating with 3 groups lead by a faculty member, spread across 3 universities in the community curation of bacterial genomes. Each participating undergraduate group collectively annotates a specific bacterial genome that was sequenced at JCVI and run through the automatic annotation pipeline. Remote access to genome sequence data, pre-computed gene predictions, search results, automatic annotation and bioinformatics analysis is provided through our web-based manual annotation tool, MANATEE. The students log into JCVI genome databases with user specific ids and password and learn to annotate single genes, entire metabolic pathways leading to analysis of a question that may be unique to the genome being analyzed. Users of the genome data receive dedicated support and guidance from our in house annotation experts on the usage of JCVI’s tools and annotation methodologies. Through this exercise, the undergraduate students are introduced to concepts of genomics and bioinformatics and gain deeper understanding of the concepts of cellular metabolism and disease pathology, which may lead them to making scientific research their career path. Some groups are focusing on genome specific pathways and plan to conduct wet lab experiments to understand unique genome features. We are highly encouraged that this model of web based, remote access, community annotation has been successful and propose to leverage the community of annotators to update annotations of pathogen genomes in Pathema-BRC.