Source: UNIVERSITY OF DELAWARE submitted to
UNDERGRADUATE EXPERIMENTAL LEARNING IN AGRICULTURE: GENOMICS AND BIOINFORMATICS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
SERD GRANT
Reporting Frequency
Annual
Accession No.
0200294
Grant No.
2004-38411-14734
Project No.
DELE-2004-02755
Proposal No.
2004-02755
Multistate No.
(N/A)
Program Code
ER.B4
Project Start Date
Aug 15, 2004
Project End Date
Aug 14, 2007
Grant Year
2004
Project Director
Schmidt, C. J.
Recipient Organization
UNIVERSITY OF DELAWARE
(N/A)
NEWARK,DE 19717
Performing Department
ANIMAL & FOOD SCIENCE
Non Technical Summary
There is a growing need for preparing students who can understand both computer science in the context of bioinformatics and genomics. The purpose of this project is to provide educational opportunities for advanced undergraduates to conduct reseach that integrates bioinformatics and genomics.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
90360993020100%
Knowledge Area
903 - Communication, Education, and Information Delivery;

Subject Of Investigation
6099 - People and communities, general/other;

Field Of Science
3020 - Education;
Goals / Objectives
To address the need for strong preparation of students in the area of genomics and bioinformatics, we propose to support experimental undergraduate research experiences in laboratories that apply the techniques of genomics and bioinformatics to agriculturally relevant problems. In addition, these students will participate in the evaluation of teaching modules that will be implemented in our Introductory Bioinformatics course. While individual experience will vary for each student as a function of the mentor's research interest, we anticipate students will: Gain experience of the laboratory techniques relevant to genomics, possibly including: 1. Modern recombinant DNA techniques. 2. Mapping genes via classical or molecular biological approaches. 3. The application of high throughput technologies, such as EST sequencing or Massively Parallel Signature Sequencing, to gene discovery. 4. The use of microarrays to characterize gene expression patterns. Increase their understanding of bioinformatics via 1. Supervised use of bioinformatics applications, such as BLAST, multiple alignment programs, chromosomal visualization programs. Mentors will provide instruction in both the execution of programs and the interpretation of output. 2. Participation in module development will provide for a detailed examination of the use of bioinformatics to study homology, ontology development and high throughput expression analysis.
Project Methods
Students will work closely with faculty members whose research incorporate bioinformatics and genomics as applied to agriculturally important problems. The faculty members are not drawn from a single department, but rather from the Animal and Food, Plant and Soil and Computer and Information Sciences departments. The potential mentors for the experimental research experience all have active labs that are addressing problems in bioinformatics and genomics. Hence, students selected for support through this program will be able to select from a variety potential research faculty. When appropriate, students will be encouraged to involve two mentors, one from the life sciences and a second from computer science. The Science and Engineering program provides support for a significant number of students to pursue undergraduate research during the summer between the sophomore and junior year. Because of this, we propose to target students wishing to continue their research experience the summer following their junior year and during winter term of their senior year. This will provide a mechanism for students who have demonstrated interest in pursuing research to continue their efforts. We anticipate supporting approximately five students per years drawn from either life or computer science undergraduates. Course Enhancement: The project director, Carl J. Schmidt, teaches the current introductory Bioinformatics course at the University of Delaware. This course uses a combination of traditional lectures, problem-based learning and student presentations to provide a basic understanding of many different bioinformatics tools. As part of enhancing this course, learning modules will be developed to help students understand concepts that integrate genomics and bioinformatics. In the context of this proposal, a learning module is an Internet accessible package designed to help students understand defined concepts or tools. The intent is to focus upon areas that appear to lack Internet accessible instructional modules. Such modules would include text describing the target concept and exercises making use of Internet databases, such as NCBI, to reinforce the ideas.

Progress 08/15/04 to 08/14/07

Outputs
Suzanne King -- Characterizing Escherichia Coli Isolates of the Delmarva Peninsula Jason Peiffe --Identification of Floral Organ Specific Genes in Arabidopsis Jessica Hall -- Analysis of Hepatic Gene Expression with Hormonally-Induced Lean and Fat Phenotypes. Brian Goldberger - Improved Propagation of Difficult-to-Root Species. Presentations:All students presented posters at the annual Summer Undergraduate Research Symposium at the University of Delaware. Hence, USDA Scholars presented a total of 20 posters in this symposium. In addition , the following students presented posters or papers at national or international meetings: Megan Wolters The Lipase gene of Marek's Disease Virus @ 4th International Workshop on the Molecular Pathogenesis of Marek's Disease Virus. Jason Peiffer: He presented posters with the same title and co-authors at the Mid-Atlantic Plant Molecular Biology Meeting in Laurel, Maryland, and at the Plant and Animal Genome meeting in San Diego (January 2007 Jessica Hall ASBMB Honorable Mention American Society for Biochemistry and Molecular Biology's national undergraduate research poster competition on April 2 in San Francisco Graduate School In addition, the USDA Scholars program played an important role in helping students decide if they wished to attend graduate school. The following students who participated in the Scholars program are currently enrolled in graduate school: Jason Peiffer Cornell University Suzanne King University of Delaware Amanda Kilby University of Delaware Jessica Hall Harvard University Andrea Laycock University of Delaware Teaching Module: Students provided feed back in the development of an annotation module for the our Introductory Bioinformatics class. This module provides an introduction to three important bioinformatics concepts: information retrieval, ontologies, and homology. Project Summaries: 2007 Brittany Jackson Characterization of Hepititis Virus Capsids Vincent Baldanza Cloning of chicken c-Jun Dawn Lenihan Bacterial Artifical Chromosomes of MDV Monica Speier Microarray Analsis of Fat and Lean Lines of Chickens Megan Wolters Gene Expression patterns in Chicken Intestine Danielle Smarsh Validation of a 14K Chicken Integrated Systems Microarray Melissa Schwarmann Identification of chicken IL17 2006 Brian Goldberger Regulation of Macromolecular Trafficking Pathways Jason Peiffer A Spatial Dissection of the Arabidopsis Floral Transcriptome by MPSS Stacey Green Characterization pathogenic E. coli isolates from Delmarva. Jenna Scibilia Population genetics of Mushroom Flies Megan Wolters The Lipase gene of Mareks'Disease Virus Marissa Brown Effect of antimicrobials on Salmonella enterica isolates 2005 Jason Peiffer Spatial Dissection of the Arabidopsis Floral Transcriptome by MPSS Suzanne King Characterization pathogenic E. coli isolates from Delmarva. Amanda Kilby Mutations in the Herpesvirus of Turkeys Lipase Gene Andrea Laycock Non-thermal treatments on Eimeria acervulina Jessica Hall Hepatic gene expression in chickens with hormonally-induced lean and fat phenotypes PRODUCTS: Include presentations and publications in peer reviewed journals. OUTCOMES: Major outcomes of this project include four Senior Theses prepared by students participating in this project; 23 poster presentations and/or talks given by the students at meetings.; 5 students have continued on to graduate school in the life sciences; 1 student is first author on a paper accepted for publiction in BMC Plant Biology DISSEMINATION ACTIVITIES: Students presented posters describing their projects at local, national and international meetings. FUTURE INITIATIVES: The University of Delaware Agriculture Biosciences Center is supporting undergraduate research now that that this USDA project has ended. This is new money devoted to sponsoring undergraduate research at the University of Delaware.

Impacts
Students contributed significant accomplishments to at least 14 different faculty directed research projects.

Publications

  • Jason A. Peiffer1,4, Shail Kaushik1, Hajime Sakai2, Mario Arteaga-Vazquez3,5, Nidia Sanchez-Leon3, Hassan Ghazal1,6, Jean-Philippe Vielle-Calzada3 , Blake C. Meyers1 (2008) A Spatial Dissection of the Arabidopsis Floral Transcriptome by MPSS BMC Plant Biology in press.


Progress 10/01/04 to 09/30/05

Outputs
The objective was to support five undergraduate students for the period of ten weeks over the summer of 2005. These students, their advisors and their projects are summarized below. STUDENT: Jessica Hall, Junior, Dept. of Animal and Food Science. Mentor: Dr. Larry Cogburn. Project: The goal of my summer research is to identify the major regulatory genes that will be used to functionally map the metabolic pathways responsible for obesity. In order to meet this goal, bioinformatic analysis was on the transcriptional factors present in metabolic tissues (liver, abdominal fat, and breast muscle) of broiler chickens that have been hormonally manipulated to produce lean and fat phenotypes STUDENT: Jason Peiffer, Sophomore, Dept. of Plant and Soil Sciences. Mentor: Dr. Blake Meyers. Project: Massively Parallel Signature Sequencing aids in the discovery of genes by developing signature sequences from mRNA transcripts. This technology was used to uncover genes that are believed to be specific to the floral sex organs in Arabidopsis thaliana. To test these findings at the bench, the promoters of the genes were cloned into vectors containing the gus reporter gene and will be transformed in Arabidopsis. STUDENT: Andrea Laycock Junior Dept. of Animal and Food Sciences. Mentor: Dr. Kali Kniel, Project; Cryptosporidium parvum is a protozoan parasite that is responsible for a life-threatening gastrointestinal illness that has been linked to consumption of contaminated apple cider. In this study, we are using ozone as an alternative to pasteurization of apple cider. Ozone inactivation of the C. parvum oocysts is being analyzed with a cell culture infection assay where C. parvum life stages are detected using PCR. Bioinformatics analysis of C. parvum sequences led to the development of these genomics tools for the detection of this food borne disease. STUDENT: Suzanne King, Junior, Dept. of Animal and Food Sciences. Mentor: Dr. John Dohms. 26 Escherichia coli isolates from various poultry farms around the Delmarva Peninsula were examined for specific virulence factors and antimicrobial susceptibility. After PCR, 65% of the isolates were positive for the increased serum survival (iss) gene, 42% were positive for the temperature sensitive hemagglutinin (tsh) gene, 46% for the iron uptake chelate in the aerobactin system (IucC), 15% for class I integrase (IntI1), and 19% for TraT, which encodes for an outer membrane protein which may play a role in serum resistance. STUDENT: Amanda Kilby Sophomore, Department of Animal and Food Sciences. Mentor: Dr. Carl J. Schmidt. My laboratory has identified several host genes that appear to respond to Meq, a herpesvirus oncogene. By bioinformatic analysis of the chicken genome sequence, I have identified promoter regions for the chicken Interferon gamma and IL6 genes. We have cloned these into a reporter plasmid and are currently determining if the promoters respond to the Meq protein. PRODUCTS: None OUTCOMES: Five students are working in mentored ongoing research projects combining the areas of bioinformatics and genomics. All five students presented a poster describing their work at the University of Delaware Research symposium in August 2005. In addition Ms. Jessica Hall will be presenting her work in a poster at the FASEB meeting in April. DISSEMINATION ACTIVITIES: All five students presented a poster describing their work at the University of Delaware Research symposium in August 2005. In addition Ms. Jessica Hall will be presenting her work at the FASEB meeting in April. FUTURE INITIATIVES: Continuation of the Undergraduate Research Scholarship program.

Impacts
Five undergraduate students have gained significant training in the areas of bioinformatics and genomics. As a consequence of this training, Ms. Jessica Hall has decided to pursue training as a graduate student.

Publications

  • No publications reported this period