Source: PRAIRIE VIEW A&M UNIVERSITY submitted to
CBG - BIOINFORMATICS RESEARCH FOR AGRICULTURE INNOVATIVE STUDENTS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
0230433
Grant No.
2012-38821-19979
Project No.
TEXX-REGISFORD
Proposal No.
2012-02540
Multistate No.
(N/A)
Program Code
EP
Project Start Date
Sep 1, 2012
Project End Date
Aug 31, 2016
Grant Year
2012
Project Director
Regisford, E. G.
Recipient Organization
PRAIRIE VIEW A&M UNIVERSITY
P.O. Box 519, MS 2001
PRAIRIE VIEW,TX 77446
Performing Department
Miscellaneous
Non Technical Summary
Bioinformatics, a novel exciting field of science, can be described as a marriage of computer science and molecular biology. It is used to analyze the vast amount of data generated by the sequencing of numerous organisms, including human, other animals, plants and bacteria. Disappointingly, most undergraduate students at Prairie View A&M University (PVAMU) majoring in Agriculture are unaware of this novel discipline, Bioinformatics, and its related available opportunities and applications to the Food and Agricultural Sciences. Principally, our proposed Capacity Building Grant (CBG) - Bioinformatics Research for Agriculture Innovative Students (BRAINS) at PVAMU program will address the (a) lack of awareness of Bioinformatics among undergraduate Agriculture students and (b) need for more underrepresented minority scientists in the field of Bioinformatics. Therefore, our overall goal is to enhance the infrastructure and culture of the Department of Agriculture using Bioinformatics education and research. We plan to introduce a Bioinformatics module into several Agriculture courses, making these courses more flexible, enjoyable and relevant to the students' lives. To facilitate the incorporation of Bioinformatics into a large number of Agriculture courses, we also propose to train faculty in a three day workshop format. The workshop participants will be trained in the use and applications of Bioinformatics and the ways in which they can integrate Bioinformatics tools and resources into their respective courses. In addition, during the summer, four students will participate in an eight week Bioinformatics research program and will be assigned individual research projects. As a consequence of the experiences afforded by this grant, an increased number of faculty and students in the Department of Agriculture at PVAMU will be trained in Bioinformatics and its applications to the Food and Agricultural Sciences. Approximately 75% of the trained faculty members will integrate and infuse a Bioinformatics project/module into their courses, thus exposing over 250 students/year to Bioinformatics. Furthermore, our CBG-BRAINS program will expand the undergraduate research capacity in Food and Agricultural Sciences and Bioinformatics at PVAMU. It will also serve to retain and carry underrepresented minority students through the high-risk period of the undergraduate college experience and significantly improve the students' professional competitiveness for graduate school and/or the workforce in the Food and Agricultural Sciences. In addition, CBG-BRAINS will lay the foundation for collaborations among faculty in the departments of Agriculture, Biology and Computer Science at PVAMU. Even more collaborations will be formed between faculty of PVAMU and our partnering institution, TAMU. Finally, the collaborations formed will lead to the development of a Bioinformatics course that is cross-referenced between the Departments of Agriculture, Biology and Computer Science; and therefore solidify our future plans to develop a Bioinformatics program at PVAMU.
Animal Health Component
(N/A)
Research Effort Categories
Basic
30%
Applied
(N/A)
Developmental
70%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2012499104010%
2012499208010%
2012499302010%
3043999104010%
3043999208010%
3043999302010%
9032499104010%
9033999104010%
9032499208010%
9033999208010%
Knowledge Area
903 - Communication, Education, and Information Delivery; 201 - Plant Genome, Genetics, and Genetic Mechanisms; 304 - Animal Genome;

Subject Of Investigation
3999 - Animal research, general; 2499 - Plant research, general;

Field Of Science
3020 - Education; 2080 - Mathematics and computer sciences; 1040 - Molecular biology;
Goals / Objectives
The overall goal of our proposed CBG-Bioinformatics Research for Agriculture INnovative Students (BRAINS) is to enhance the infrastructure and culture of the Department of Agriculture using Bioinformatics education and research. The objectives are to (1) improve curriculum and instruction in Agriculture, and (2) engage underrepresented undergraduates in Bioinformatics research. Our activities include the integration of Bioinformatics modules/projects into several Agriculture courses and a summer Bioinformatics-focused research program for four undergraduate students, majoring in Agriculture (2 students); Biology (1 student) and Computer Science (1 student). In addition, more faculty members will be introduced to Bioinformatics tools and resources at a planned workshop during the summer. The aforementioned activities and event will result in an increased number of (i) courses with a Bioinformatics component; (ii) faculty members with basic knowledge in the use of Bioinformatics tools; (iii) undergraduate students engaged in Bioinformatics research; and (iv) students making presentations at local, regional and national science conferences. The accomplishments of our proposed program will be disseminated through the enhanced Agriculture curriculum; professional conferences; a CBG-BRAINS website; and Agricultural and Bioinformatics research and educational journals. In addition, our CBG-BRAINS program will better prepare our students for the next stages of the Food and Agricultural sciences education pathway and ultimately, the workforce.
Project Methods
Objective 1: To improve curriculum and instruction in Agriculture - will be achieved by 1) integrating Bioinformatics into several Agriculture courses and 2) organizing a three day faculty workshop. Drs. Regisford, Lu and Hu will assist faculty members, Drs. Daley, James and Johnson in the integration of Bioinformatics into Agriculture courses during the first year of the grant. During the following years, faculty members, Drs. Daley, James and Johnson, will provide a template for Bioinformatics integration into Agriculture courses and assist CBG-BRAINS senior personnel in reaching other faculty members. The faculty workshop will be organized by Drs. Lu and Hu, with assistance from Dr. Carson, who will work mainly on recruiting faculty from the departments of Agriculture, Biology, Chemistry, Computer Science and Mathematics; and other minority serving institutions in the Texas A&M System. Objective 2: To engage underrepresented undergraduates in Bioinformatics research- will be achieved by selecting four undergraduates from the Departments of Agriculture (2 students); Biology (1 student) and Computer Science (1 student) to participate in our eight-week summer research program. They will be assigned independent Bioinformatics research projects and will present their research findings at local, regional and national research symposiums. Drs. Lu and Hu will each mentor two students. Dr. Carson will coordinate the local research symposium at the end of the summer. Dr. Regisford will work closely with all parties to ensure that the students get a good research experience. The evaluation plan will focus on the assessment of activities; discussing criteria for improvements required to achieve the goals and objectives; transforming the goal and objectives to measurable objectives; and presentation of an evaluation report. Summative Evaluations: Our project will be evaluated based on the following: Number of 1) courses in which the Bioinformatics modules are integrated; 2) students exposed to Bioinformatics; 3) faculty members who incorporate Bioinformatics learning tools into their courses; 4) students who successfully complete the summer Bioinformatics research project in the Food and Agricultural Science fields; 5) students who enter graduate school in Food and Agricultural Science and Bioinformatics fields; and 6) students who go into the workforce in Food and Agricultural Science and Bioinformatics fields. Closed-End Surveys: The evaluator will work with the project management to design surveys to be used in the courses targeted for integrating Bioinformatics modules. Key evaluation questions to be addressed are: 1) How has the Bioinformatics module been implemented in the courses 2) How has the Bioinformatics module deepened students' conceptual understanding 3) How has the Bioinformatics module enhanced students' skills 4) How has the Bioinformatics module increased students' interests in the course and in research 5) How has the Bioinformatics module strengthened students' marketability upon graduation 6) How has the workshop facilitated the ease of integrating an appropriate Bioinformatics module into the faculty's course

Progress 09/01/12 to 08/31/16

Outputs
Target Audience:Students majoring in Agriculture are our main target audience. We have also recruited students from the Departments of Biology (2) and Computer Science (1) to participate in our summer research program. Changes/Problems:1. Dr. Yi Lu did not fully participate in the 2014 summer Bioinformatics workshop and has since resigned from PVAMU, effective August 31, 2014. 2. The faculty workshop was not held in 2015. For example, a tropical disturbance was predicted to hit Houston and surrounding areas in Texas, such as Prairie View, hence the workshop was postponed to a later date in December, 2015, when all invited speakers and participants would be better able to attend. However, faculty participants were unable to attend. 3. Due to a significant change in our Research Office, that requires our evaluator, Dr. Thomas Landefeld, to take CITI training, instead of using his lifelong NIH, has meant that evaluation has not been done. Dr. Landefeld plans to take CITI training and will evaluate our project both this Fall semester 2015 and in summer 2016. However, Dr. Yoonsong Jung, Research Scientist/Statistician (CAHS) has collected our survey data and has performed statistical analysis. 4. Recruiting students from the Department of Computer Science proved to be difficult because more lucrative programs are at the student's disposal. What opportunities for training and professional development has the project provided?The student participants in our summer research program, 2012 - 2016, were actively engaged in Bioinformatics research. The students, title of their projects and mentors are: John Attia, Genes Associated with Endometrial Cancer, Dr. Regisford; Mirgyea Castleman, Wild and Domesticated Animals Surveyed for Functional Annotations of the TCA Cycle and Apoptosis, Drs. Hu and Regisford; Ardawna Green, Annotations of Genes in Human and Animal Diseases, Drs. Ritter and Regisford; Depresia Grogan, Functional Annotations of the TCA Cycle and DNA Repair in Insects and Plants: A Survey, Drs. Hu and Regisford; Jourdan Kerl, Metagenomic Analysis of Cow Rumen using Galaxy Flow, Dr. Lu; Derrick Marsh, Mitochondrial and Nuclear Gene Associations in Prostate Cancer, Drs. Ritter and Regisford; Diamond Moss, Bioinformatics: Functional Annotations for Agriculturally Important Species in Relation to the Tricarboxylic Acid Cycle, Drs. Hu and Regisford; Aldair Novelo, Genes Associated with Ovarian Cancer, Dr. Regisford; and Cayla Steemer, Gene Ontology of Glycolysis and TCA Cycle in Domesticated Exotic Aninmals, Drs. Hu/Regisford. The students presented their project's progress reports at a weekly science forum, on Thursdays at 12 noon, during the summer and on Friday afternoons during the academic year. All nine students who participated in the CBG-BRAINS summer research program, presented their research at ten (10) local, state and national research symposiums: (i) PVAMU Biology Undergraduate Research symposium; (ii) PVAMU Integrating Research in Student Engagement- Undergraduate Program (iRISE-UP) symposium; (iii) Science, Technology, Engineering, Agriculture, and Math (STEAM) research symposium at PVAMU; (iv) Annual Biomedical Research Conference for Minority Students (ABRCMS); (v) Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS); (vi) American Society for Cell Biology (ASCB) and (vii) The BCM IRACDA Postdoctoral Program Conference; (viii) the TAMUS Pathways Research Symposium; (ix) The Endocrine Society; and (x) 1890 Land Grant Universities 125th Year Celebration. The following students won awards: Depresia Grogan - STEAM 2014; Derrick Marsh - iRISE-UP 2015; Ardawna Green - Biology Research Symposium 2016; and TAMUS Pathways 2016 Cayla Steemer - ASCB 2016 (Honorable mention) How have the results been disseminated to communities of interest?1. Students presented their research at ten (10) local, state and national research symposiums: (i) PVAMU Biology Undergraduate Research symposium; (ii) PVAMU Integrating Research in Student Engagement- Undergraduate Program (iRISE-UP) symposium; (iii) Science, Technology, Engineering, Agriculture, and Math (STEAM) research symposium at PVAMU; (iv) Annual Biomedical Research Conference for Minority Students (ABRCMS); (v) Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS); (vi) American Society for Cell Biology (ASCB) and (vii) The BCM IRACDA Postdoctoral Program Conference; (viii) the TAMUS Pathways Research Symposium; (ix) The Endocrine Society; and (x) 1890 Land Grant Universities 125th Year Celebration. 2. Students of the CBG-BRAINS summer research program presented their research project at the annual Research Symposium for USDA Capacity Building Program participants at the end of the summer research program in August 14, 2013-2016. 3. A facebook page was created last year to record students' activities, such as field trips, research forums, journal club and research symposiums. It is being constantly updated. 4. Dr. Gloria Regisford, PI, gave a talk at the annual meeting for the American Society of Microbiology (ASM) on May 31st, 2015, entitled "Bioinformatics Infusion of Agriculture and Biology Courses". 5. A website, cbgbrains.pvamu.edu, was developed to disseminate information on our program. What do you plan to do during the next reporting period to accomplish the goals?In the next reporting period, in order to accomplish our projects goals and objectives, we plan to do the following: 1. Ensure the maintenance of the Bioinformatics component in all eleven Agriculture courses. 2. Keep Students engaged in Bioinformatics research funded by other funding sources. 3. Have student participants present their research project findings at research conferences, both local, state and national. a. PVAMU Biology Undergraduate Research symposium b. PVAMU Integrating Research in Student Engagement- Undergraduate Program (iRISE-UP) c. Science, Technology, Engineering, Agriculture, and Math (STEAM) d. Annual Biomedical Research Conference for Minority Students (ABRCMS) e. Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS) f. American Society for Cell Biology (ASCB) g. The Endocrine Society h. The BCM IRACDA Postdoctoral Program Conference 4. Maintain the website for dissemination of materials, cbgbrains.pvamu.edu. 5. Publish two papers on the "Integration of Bioinformatics into Agriculture courses at PVAMU, an 1890 institution" and "Engaging Students in Bioinformatics Research at PVAMU". 6. Make more presentations at other National Society conferences.

Impacts
What was accomplished under these goals? 1. To improve curriculum and instruction in Agriculture We proposed to achieve this objective by (a) integrating Bioinformatics into several Agriculture courses and (b) organizing a three-day faculty workshop. (a) Integrating Bioinformatics into several Agriculture courses During the academic years, August 2012 to May 2016, eleven (11) Agriculture courses have integrated Bioinformatics (See Table 1). Bioinformatics modules (i) PubMed, (ii) BLAST (iii) OMIM and (iii) OMIA, were used in the courses that were taught by Drs. Daley, James, Johnson, Lewis and Woldesenbet. Specifically, ANSC 3513 Anatomy and Physiology used PuBMed/OMIM/Blast and the instructor of the class was Dr. Barbara Johnson. Crop Production, AGRO 2733 used PubMed/BLAST to study genes associated with crop production and Dr. Annette James was the instructor. Breeding/Genetics (ANSC 4533) used PubMed/OMIA/BLAST to study genes associated with reproduction and the instructor was Dr. Shaye Lewis. Dr. Barbara Johnson was the instructor of Diseases and Sanitation (ANSC 2543); she used PubMed/OMIA/BLAST to study animal diseases. Dr. Milton Daley's course in Dairy Sciences (ANSC 2533) used PubMed/BLAST to study genes associated with milk letdown. Dr. Annette James' course Soil Morphology (AGRO 3623) and Crop Science (AGRO 1703) used PubMed/BLAST to study plant fungi and bacteria; while Dr. Milton Daley's course General Animal Science (ANSC 1513), Animal Nutrition (ANSC 3503), Meat Science (ANSC 4523), Poultry Technology & Marketing (ANSC 2553) used PubMed/OMIA/BLAST to study animal diseases, genes related to animal nutrition, muscle diseases and chicken disease. Dr. Jim Hu (CoPI), Dr. Shaye Lewis Research Scientist at the Cooperative Agriculture Research Center (CARC) in the College of Agriculture and Human Sciences (CAH)); three PVAMU Chemistry graduate students, Deforest Peterson (BS, Agriculture); Donna Gilbert (BS, Biology) and one of our trained students, Depresia Grogan (BS, Agriculture); and one TAMU graduate student (Shabnam Eslamfam, MS) facilitated the dissemination of the Bioinformatics information by working closely with the students enrolled in the class and the faculty. We have achieved one of our main goals, that by the end of the grant period, a total of ten (10) courses would have integrated Bioinformatics. (b) Faculty Workshop The three-day workshop was held in 2013 and 2014. Dr. Shaye Lewis, a newly appointed research scientist in the College of Agriculture and Human Sciences (CAHS), gave lectures on "The Basics of Bioinformatics" and "RNA Sequencing". Dr. Yi Lu, CBG-BRAINS CoPI lectured and provided "hands-on exercises" on "Bioinformatics Tools and Databases". Dr. Hu, CBG-BRAINS CoPI (Texas A&M University, (TAMU)), presented hands-on projects and information on Bioinformatics tools and databases, with emphasis in "Gene Ontology". Dr. Yoonsung Jung, a statistician/research scientist in the College of Agriculture and Human Sciences (CAHS) and a participant in 2013 Bioinformatics workshop, presented a lecture on the "Use of Statistics in Bioinformatics" in the 2014 workshop . Dr. Deborah Ritter, Staff Scientist in Molecular and Clinical Genetics at Baylor College of Medicine, gave presentations on Introduction to Bioinformatics; Bioinformatics Databases and Tools, Using Bioinformatics Databases and Tools; and Examples of Bioinformatics Assignments for Use in the Classroom. Dr. Diedre Vaden, Associate Professor in College of Arts and Sciences here at PVAMU presented seminars on Uploading Bioinformatics Assignments to eCourses and Online Bioinformatics Teaching and Assignments. Over the two years, six faculty members and research scientists from the College of Agriculture and Human Sciences were in attendance. All workshop participants teach at least one course in the College of Agriculture and Human Sciences (CAHS)). Four faculty members from our neighboring Houston Community College System (HCCS) were also in attendance. They planned on integrating Bioinformatics into the courses that they teach at HCCS, which is an institution that provides transfer students to PVAMU. The three-day faculty workshop that was planned for June 16 to June 17, 2015 was cancelled. A tropical disturbance was predicted to hit Houston and surrounding areas in Texas, such as Prairie View, hence the workshop was postponed to a later date in December, 2015, when all invited speakers and participants would be better able to attend. Faculty members and research scientists from the College of Agriculture and Human Sciences, PVAMU; Texas Southern University (TSU); The University of Houston, Downtown; Texas A&M Kingsville; West Texas A&M University, Texas A&M, Kingsville, had all indicated that they would attend. It was therefore difficult to coordinate another set of dates during the summer, hence the proposed dates for the end of the Fall semester. However, the faculty participants were unable to find time to attend the workshop in December, hence a cancellation. An invited Bioinformaticist, Dr. Deborah Ritter, Postdoctoral fellow at Baylor College of Medicine (BCM) planned to present lectures on "Bioinformatics Databases and Tools" using databases such as NCBI, UCSC and Ensembl. Dr. Deirdra Vaden, Associate Professor of Biology, plan to demonstrate mechanisms whereby Bioinformatics assignments and power-point lectures can be uploaded to e-Courses by each professor, so that students have easier access. Dr. Yoonsung Jung, a statistician/research scientist in the College of Agriculture and Human Sciences (CAHS), was scheduled to lecture on the "Use of Statistics in Bioinformatics". Our CBG-BRAINS CoPI from TAMU, Dr. Hu, planned to present more hands-on projects and information on Bioinformatics tools and databases and Gene Ontology. 2. To engage underrepresented undergraduates in Bioinformatics research. Nine underrepresented undergraduates were recruited and selected from the Department of Agriculture (Depresia Grogan, Senior Animal Science concentration; Diamond Moss, Sophomore, Agronomy concentration; Mirygea Castleman, Junior; and Cayla Steemer, Junior Animal Science concentration), Department of Biology (John Attia, Sophomore; Aldair Novelo, Sophomore; Derrick Marsh, Senior; and Ardawna Green, Senior) and the Department of Computer Science (Jourdan Kerl, Sophomore) to be participants in our CBG-BRAINS summer research program. These students were mentored/co-mentored by Dr. Hu, Dr. Lu, Dr. Regisford and Dr. Ritter.

Publications


    Progress 09/01/14 to 08/31/15

    Outputs
    Target Audience:Students majoring in Agriculture are our main target audience. We have also recruited students from the Departments of Biology (2) and Computer Science (1) to participate in our summer research program. Changes/Problems:1. A tropical disturbance was predicted to hit Houston and surrounding areas in Texas, such as Prairie View, hence the workshop was postponed to a later date in December, 2015, when all invited speakers and participants would be better able to attend. 2. Due to a significant change in our Research Office, that requires our evaluator, Dr. Thomas Landefeld, to take CITI training, instead of using his lifelong NIH training, has meant that evaluation has not been done. Dr. Landefeld plans to take CITI training and will evaluate our project both this Fall semester 2015 and in summer 2016. 3. Recruiting students from the Department of Computer Science has proven difficult because more lucrative programs are at the student's disposal. What opportunities for training and professional development has the project provided?All three students who participated in the CBG-BRAINS summer research program last summer, Depresia Grogan, Mirygea Castleman and Derrick Marsh, presented their research at both local and national research symposiums: (i) PVAMU Biology Undergraduate Research symposium; (ii) Annual Biomedical Research Conference for Minority Students (ABRCMS); (iii) Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS); (iv) American Society for Cell Biology (ASCB) and (v) The BCM IRACDA Postdoctoral Program Conference; (vi) The Endocrine Society and (vii) 1890 Land Grant Universities 125th Year Celebration. 1. The student participants in our summer research program, 2015, were actively engaged in Bioinformatics research (Table 4). Table 4: Projects and Mentors of Participants in CBG-BRAINS Summer Bioinformatics Research Program Participant Name: Depresia Grogan Project Title: Functional Annotations of TCA Cycle and DNA Repair in Insects and Plants: A Survey Mentor: Jim Hu, PhD Participant Name: Cayla Steemer Project Title: Gene Ontology of Glycolysis and TCA Cycle in Domesticated Exotic Animals Mentor: Jim Hu, PhD Participant Name: Aldair Novelo Project Title: Genes Associated with Ovarian Cancer Mentor: Gloria Regisford, PhD The students presented their project's progress reports at a weekly science forum, on Thursdays at 12 noon, during the summer and on Friday afternoons during the academic year. How have the results been disseminated to communities of interest?1. Depresia Grogan, Mirygea Castleman, Aldair Novelo and Derrick Marsh who participated in the CBG-BRAINS summer research program last summer, presented their research at both local and national research symposiums: (i) PVAMU Biology Undergraduate Research symposium (October 2014); (ii) Annual Biomedical Research Conference for Minority Students (ABRCMS, November 2014); (iii) American Society for Cell Biology (ASCB, December 2014); (iv) 1890 Land Grant Universities 125th Year Celebration (March, 2015); (v) BCM IRACDA Postdoctoral Program Conference (May, 2015). 2. Depresia Grogan and Cayla Steemer students of the CBG-BRAINS summer research program, 2015, presented their research project at our Research Symposium for USDA Capacity Building Program participants on Friday, August 14, 2015. In addition, the facebook page that was created last year, to record their activities, such as field trips, research forums, journal club and research symposiums, is being constantly updated. 3. Dr. Gloria Regisford, PI, gave a talk at the annual meeting for the American Society of Microbiology (ASM) on May 31st, 2015, entitled "Bioinformatics Infusion of Agriculture and Biology Courses". 4. A website was developed, cbgbrains.pvamu.edu to disseminate information on our program. What do you plan to do during the next reporting period to accomplish the goals?In the next reporting period, in order to accomplish our projects goals and objectives, we plan to do the following: 1. Integrate Bioinformatics into four additional courses, so that a total of fourteen Agriculture courses will have a Bioinformatics component. 2. Have student participants present their research project findings at research conferences, both local and national. PVAMU Biology Undergraduate Research symposium Annual Biomedical Research Conference for Minority Students (ABRCMS) Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS) American Society for Cell Biology (ASCB) The Endocrine Society The BCM IRACDA Postdoctoral Program Conference 3. Recruit and select three more students from the Department of Agriculture (1 student); Biology (1 student) and Computer Science (1 student) to be participants in our CBG-BRAINS summer research program, June 1 to August 31, 2016. 4. Continue to work on the website for dissemination of materials, cbgbrains.pvamu.edu. 5. Have our evaluator, Dr. Thomas Landefeld, evaluate the progress and success of the activities of our project. 6. Publish two papers on the "Integration of Bioinformatics into Agriculture courses at PVAMU, an 1890 institution" and "Engaging Students in Bioinformatics Research at PVAMU". 7. Make more presentations at other National Society conferences.

    Impacts
    What was accomplished under these goals? 1. To improve curriculum and instruction in Agriculture We proposed to achieve this objective by (a) integrating Bioinformatics into several Agriculture courses and (b) organizing a three day faculty workshop. During the academic year, August 25 to May 8, ten (10) Agriculture courses have integrated Bioinformatics, two additional courses from the previous academic year of 2013-2014. (See Table 1; new courses with infused Bioinformatics are in blue). Bioinformatics modules (i) PubMed, (ii) BLAST (iii) OMIM and (iii) OMIA, were used in the courses that were taught by Drs. Daley, James, Johnson, Lewis and Woldesenbet (Table 1). Dr. Jim Hu (CoPI), Dr. Shaye Lewis (newly hired research scientist at the Cooperative Agriculture Research Center (CARC) in the College of Human Sciences); a PVAMU Chemistry graduate student, Deforest Peterson (BS, Biology) and one of our trained students, Depresia Grogan, facilitated the dissemination of the Bioinformatics information by working closely with the students enrolled in the class and the faculty. We have achieved one of our main goals, that by the end of the grant period, a total of ten (10) courses would have integrated Bioinformatics. Table 1: Infusion of Bioinformatics in Agriculture Courses Course: Anatomy and Physiology - ANSC 3513 Databases and Tools: PubMed/OMIM/BLAST Subject: Anatomy and Physiology Instructor: Barbara Johnson Course: Crop Production - AGRO 2733 Databases and Tools: PubMed/BLAST Subject: Genes Associated with Crop Production Instructor: Annette James Course: Diseases and Sanitation - ANSC 2543 Databases and Tools: PubMed/OMIA/BLAST Subject: Animal Diseases Instructor: Barbara Johnson Course: Dairy Science - ANSC 2533 Databases and Tools: PubMed/BLAST Subject: Genes associated with milk letdown Instructor: Milton Daley Course: Soil Morphology - AGRO 3623 Databases and Tools: PubMed/BLAST Subject: Plant fungi and Bacteria Instructor: Annette James Course: General Animal Science - ANSC 1513 Databases and Tools: PubMed/OMIA/BLAST Subject: Animal diseases Instructor: Milton Daley Course: Animal Nutrition - ANSC 3503 Databases and Tools: PubMed/OMIA/BLAST Subject: Animal diseases Instructor: Milton Daley Course: Crop Science - AGRO 1703 Databases and Tools: PubMed/BLAST Subject: Plant fungi and Bacteria Instructor: Annette James Course: Poultry Technology and Marketing - ANSC 2553 Databases and Tools: PubMed/OMIA/BLAST Subject: Chicken diseases Instructor: Milton Daley Course: Breeding/Genetics ANSC 4533 Databases and Tools: PubMed/OMIA/BLAST Subject: Genes associated with production Instructor: Shaye Lewis, Sela Woldesenbet The three day faculty workshop was planned for June 16 to June 17, 2015. However, a tropical disturbance was predicted to hit Houston and surrounding areas in Texas, such as Prairie View, hence the workshop was postponed to a later date in December, 2015, when all invited speakers and participants would be better able to attend. An invited Bioinformaticist, Dr. Deborah Ritter, Postdoctoral fellow at Baylor College of Medicine (BCM) plan to present lectures on "Bioinformatics Databases and Tools" using databases such as NCBI, UCSC and Ensembl. Dr. Deirdra Vaden, Associate Professor of Biology, plan to demonstrate mechanisms whereby Bioinformatics assignments and power-point lectures can be uploaded to e-Courses by each professor, so that students have easier access. Dr. Yoonsung Jung, a statistician/research scientist in the College of Agriculture and Human Sciences (CAHS), was scheduled to lecture on the "Use of Statistics in Bioinformatics". Our CBG-BRAINS CoPI from TAMU, Dr. Hu, plans to present more hands-on projects and information on Bioinformatics tools and databases and Gene Ontology (Table 2). Table 2: Proposed Speakers and their Topics for Postponed Faculty Bioinformatics Workshop Speakers Name: Deborah Ritter, PhD Position/ (College/Institution): Postdoctoral Fellow (BCM) Title of Talk: Introduction to Bioinformatics; Bioinformatics Databases and Tools; Using Bioinformatics, Databases and Tools; Examples of Bioinformatics Assignments for use in the Classroom Speakers Name: Yoosung Jung, PhD Position/ (College/Institution): Research Scientist- Statistician (CAHS/ PVAMU) Title of Talk: Bioinformatics and Statistics Speakers Name: Deirdra Vaden, Phd Position/ (College/Institution): Associate Professor (College of Arts and Sciences/ PVAMU) Title of Talk: Uploading Bioinformatics Assignments to ecourses; "Online Bioinformatics teaching and assignments" Speakers Name: Jim Hu Position/ (College/Institution): Professor, CoPI (Biochemistry and Biophysics/ TAMU) Title of Talk: More Bioinformatics Databases and Tools; Gene Ontology Faculty members and research scientists from the College of Agriculture and Human Sciences, PVAMU; Texas Southern University (TSU); The University of Houston, Downtown; Texas A&M Kingsville; West Texas A&M University, Texas A&M, Kingsville, had all indicated that they would attend. It was therefore difficult to coordinate another set of dates during the summer, hence the proposed dates for the end of the Fall semester. 2. To engage underrepresented undergraduates in Bioinformatics research. Three underrepresented undergraduates were recruited and selected from the Department of Agriculture (2 students) to be participants in our CBG-BRAINS summer research program (Table 3). Table 3: Participants in CBG-BRAINS Summer Bioinformatics Research Program Participant Name: Depresia Grogan Classification: Senior Major: Agriculture (Animal Science) Mentor: Jim Hu, PhD Participant Name: Cayla Steemer Classification: Rising Junior Major: Agriculture (Animal Science) Mentor: Jim Hu, PhD Participant Name: Aldair Novelo Classification: Rising Sophomore Major: Pre-Nursing/ Biology Mentor: Gloria Regisford, PhD

    Publications

    • Type: Websites Status: Other Year Published: 2015 Citation: Website: cbgbrains.pvamu.edu is in the developmental stage. Depresia Grogan is working with Dr. Paul Johnson, Research Scientist at PVAMU.
    • Type: Websites Status: Accepted Year Published: 2015 Citation: A facebook page for our Bioinformatics Group at PVAMU was created and is maintained by one of our student participants, Depresia Grogan. Abstracts for the student participants in our summer research program have been published in the proceedings of the research conferences for ABRCMS and ASCB.


    Progress 09/01/13 to 08/31/14

    Outputs
    Target Audience: Students majoring in Agriculture are our main target audience. We have also recruited students from the Departments of Biology (2) and Computer Science (1) to participate in our summer research program. Changes/Problems: Last year, 2012-2013, we encountered one problem that affects the dissemination of our projects activities and accomplishments to a small degree. Creating a website has proven to require more time than expected, as one has to work on the timetable of the IT department at PVAMU. We had planned to resolve this issue by creating a page for CBG-BRAINS at PVAMU on the website for the Department of Computer Science in the Fall semester, 2013. However, due to unforeseen challenges and problems encountered by Dr. Lu, CoPI, the person assigned with building the website, we have yet to achieve this objective. Plans are to recruit a student who will work with Dr. Paul Johnson to create a CBG-BRAINS website. Dr. Yi Lu did not fully participate in the summer Bioinformatics workshop and has since resigned from PVAMU, effective August 31. Dr. Deborah Ritter, a postdoctoral fellow in Bioinformatics at Baylor College of Medicine, filled in for him and did an excellent job in providing information and valuable lessons on Bioinformatics tools and databases. Due to a significant change in our Research Office, that requires our evaluator, Dr. Thomas Landefeld, to take CITI training, instead of using his lifelong NIH, has meant that evaluation has not been done. Dr. Landefeld plans to take CITI training and will evaluate our project both this Fall semester 2014 and in summer 2015. Recruiting students from the Department of Computer Science has proven difficult because more lucrative programs are at their disposal. In addition, Jourdan Kerl-Henderson, a Computer Science major, who was a participant in our summer research program, 2013, decided not to participate in research conferences. Another student, Diamond Moss, decided not return to college for his final year. We were more selective in our recruitment efforts this year and so far all three summer research students have promised to participate in research conferences and journal clubs. What opportunities for training and professional development has the project provided? 1) At the faculty workshop this summer, participants from the CAHS at PVAMU were trained in using Bioinformatics tools and databases. They were also provided materials and project assignments that would facilitate the integration of Bioinformatics into their courses. 2) Another faculty workshop was held on September 26-27, 2013 in collaboration with Jason Williams, iPlant collaborative, DNA Learning Center, Cold Springs Harbor at PVAMU. Faculty members and students from the College of Agriculture, the Departments of Biology and Computer Science were in attendance. 3) Two students, John Attia and Depresia Grogan, who participated in the CBG-BRAINS summer research program last summer, presented their research at both local and national research symposiums: (i) PVAMU Biology Undergraduate Research symposium; (ii) PVAMU Science Technology Engineering Agriculture and Mathematics (STEAM) Research Symposium; (iii) Annual Biomedical Research Conference for Minority Students (ABRCMS); (iv) Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS); (v) American Society for Cell Biology (ASCB). 4) The student participants in our summer research program, 2014, were actively engaged in Bioinformatics research. The project, project title and mentor are: Mirygea Castleman, Wild and Domesticated Animals Surveyed for Functional Annotations of the TCA Cycle and Apoptosis, Hu/Eslamfam; Depresia Grogan, Survey of Functional Annotation for TCA Cycle and DNA Repair in Insects and Plants, Hu/Eslamfam; and Derrick Marsh, Mitochondrial and Nuclear Gene Associations in Prostate Cancer, Regisford/Ritter The students presented their project’s progress reports at a weekly science forum, on Thursdays at 12 noon. They also attended journal club that is an event held in the department of Biology and cohosted by the postdoctoral organization at Baylor College of Medicine. Drs. Deborah Ritter, Karienn Montgomery and Danielle Goodspeed presented their published research findings and also provided the students with advice on Graduate school. Students also participated in 3 field trips. (1) Texas A&M University Department of Biochemistry/Biophysics, (Dr. Jim Hu, CoPI, and mentor Dr. Larry Dangott in a Protein Chemistry Lab, and Dr. Tatyana Igumenova in a NMR Lab) all who are part of the Texas Agri-Life Research Center. Students also visited the Genome Exhibit at the Bush Library in College Station, TX (2) Baylor College of Medicine Human Genome Sequencing Center where they were given a guided tour of the sequencing center, by Dr. Steve Scherer, Associate Professor and Co-Director of the Human Genome Sequencing Center. How have the results been disseminated to communities of interest? Two students, John Attia and Depresia Grogan, who participated in the CBG-BRAINS summer research program last summer, presented their research at both local and national research symposiums: (i) PVAMU Biology Undergraduate Research symposium; (ii) PVAMU Science Technology Engineering Agriculture and Mathematics (STEAM) Research Symposium; (iii) Annual Biomedical Research Conference for Minority Students (ABRCMS); (iv) Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS); (v) American Society for Cell Biology (ASCB). Depresia Grogan won an award at the STEAM Research Symposium, March, 2014. All three students of the CBG-BRAINS summer research program, 2014, presented their research project at our Research Symposium for USDA Capacity Building Program participants on Monday, August 9, 2014. In addition, the Facebook page that was created last year, to record their activities, such as field trips, research forums, journal club and research symposiums, is being constantly updated. What do you plan to do during the next reporting period to accomplish the goals? In the next reporting period, in order to accomplish our projects goals and objectives, we plan to do the following: 1) Integrate Bioinformatics into four additional courses, so that a total of twelve Agriculture courses will have a bioinformatics component. 2) Have student participants present their research project findings at research conferences, both local and national. a. PVAMU Biology Undergraduate Research symposium b. PVAMU Science Technology Engineering Agriculture and Mathematics (STEAM) Research Symposium c. Annual Biomedical Research Conference for Minority Students (ABRCMS) d. Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS) e. American Society for Cell Biology (ASCB) 3) Recruit and select three more students from the Department of Agriculture (1 student); Biology (1 student) and Computer Science (1 student) to be participants in our CBG-BRAINS summer research program, June 1 to July 31, 2015. 4) Build a website for dissemination of materials. 5) Have our evaluator, Dr. Thomas Landefeld, evaluate the progress and success of the activities of our project. 6) Publish two papers on the “Integration of Bioinformatics into Agriculture courses at PVAMU, an 1890 institution” and “Engaging Students in Bioinformatics Research at PVAMU”

    Impacts
    What was accomplished under these goals? (1) To improve curriculum and instruction in Agriculture We proposed to achieve this objective by (a) integrating Bioinformatics into several Agriculture courses and (b) organizing a three day faculty workshop. During the academic year, August 26 to May 10, eight Agriculture courses have integrated Bioinformatics. The Bioinformatics modules created by Dr. Lu, (i) PubMed, (ii) BLAST and (iii) OMIA, were used in the courses that are taught by Drs. Daley, James, Johnson, Lewis and Woldesenbet. Specifically, the courses, databases, subject and instructor are as follows: Disease and Sanitation (ANSC 2543), PubMed/OMIA/BLAST, Animal Diseases, Barbara Johnson; Dairy Science (ANSC 2533), PubMed/BLAST, Genes associated with milk letdown, Milton Daley; Soil Morphology (AGRO 3623), Crop Science (AGRO 1703) PubMed/BLAST, Plant fungi and bacteria, Annette James; General Animal Science (ANSC 1513), Animal Nutrition (ANSC 3503) PubMed/OMIA/BLAST, Animal Disease, Milton Daley; Poultry Technology and Marketing (ANSC 2553), PubMed/OMIA/BLAST, chicken diseases, Milton Daley; Breeding/Genetics (ANSC 4533), PubMed/OMIA/BLAST, chicken diseases, Drs. Shaye Lewis and Sela Woldesenbet. Dr. Jim Hu’s graduate student, Shabnam Eslamfam and one of our trained students, Depresia Grogan, facilitated the dissemination of the Bioinformatics information by working closely with the students enrolled in the class. By the end of the grant period, a total of ten courses would have integrated Bioinformatics. The three day faculty workshop was organized on July 15 to July 17, 2014. Our CBG-BRAINS CoPI from TAMU, Dr. Hu, presented hands-on projects and information on Bioinformatics tools and databases. Dr. Yoonsung Jung, a statistician/research scientist in the College of Agriculture and Human Sciences (CAHS) and a participant in last year’s Bioinformatics workshop, presented a lecture on the “Use of Statistics in Bioinformatics”. Five faculty members and research scientists from the College of Agriculture and Human Sciences were in attendance. All workshop participants teach at least one course in the CAHS. Specifically, Milton Daley, Adjunct Professor; Annette James, Assistant Professor; Paul Johnson and Yoonsung Jung, both Research Scientist; and Selamawit Woldesenbet, Research Specialist. Two faculty members, Vimlarani Chopra, and Idowu Famuyiwa, both Adjunct Professor from our neighboring Houston Community College System (HCCS) were also in attendance. They plan on integrating Bioinformatics into the courses that they teach at HCCS, which is an institution that provides transfer students to our institution here at PVAMU. (2) To engage underrepresented undergraduates in Bioinformatics research. Three underrepresented undergraduates were recruited and selected from the Department of Agriculture (2 students – Mirygea Castleman and Depresia Grogan, both Seniors) and Biology (Derrick Marsh, rising Junior) to be participants in our CBG-BRAINS summer research program.

    Publications


      Progress 09/01/12 to 08/31/13

      Outputs
      Target Audience: Students majoring in Agriculture are our main target audience. Changes/Problems: We have encountered one problem that affects the dissemination of our projects activities and accomplishments to a small degree. Creating a website has proven to require more time than expected, as one has to work on the timetable of the IT department at PVAMU. However, this problem will be resolved as we are currently working on a website, which will be accessible this Fall semester, 2013. What opportunities for training and professional development has the project provided? At the faculty workshop, participants from the CAHS at PVAMU were trained in using Bioinformatics tools and databases. They were also provided materials and project assignments that would facilitate the integration of Bioinformatics into their courses. The student participants in our summer research program were actively engaged in Bioinformatics research.Participant Names, Project Title, and Mentor names are as follow: John Attia, A Search for Genes Involved in Endometrial Cancer, Regisford; Deprecia Grogan, Functional Annotation for Selected Pathways for Agriculturally Important Species, Hu; Jourdan Kerl-Henderson, Genomic Analysis of the Cow Rumen using Galaxy Workflow, Hu; and Diamond Moss, Bioinformatics: Functional Annotation for Selected Pathways for Agriculturally Important Species in Relation to the Tricarboxylic Acid Cycle, Lu. The students presented their project’s progress reports at a weekly science forum, on Thursdays at 12 noon. They also attended journal club that is an event held in the department of Biology and cohosted by the postdoctoral organization at Baylor College of Medicine. Drs. Melissa Parsons and Jennifer McGehee presented their published research findings and also provided the students with advice on Graduate school. Dr. Danielle Harris, Assistant Dean for Student Success in the College of Agriculture & Life Sciences at Texas A&M University talked with the participants about the pros and cons of attending graduate school and how to select a graduate school. Students also participated in 3 field trips. 1. Texas A&M University Department of Biochemistry/Biophysics, (Dr. Jim Hu, CoPI, and mentor Dr. Larry Dangott in a Protein Chemistry Lab, and Dr. Tatyana Igumenova in a NMR Lab) all who are part of the Texas Agri-Life Research Center. Students also visited the Genome Exhibit at the Bush Library in College Station, TX 2. Baylor College of Medicine Human Genome Sequencing Center where they were given a guided tour of the sequencing center, by Dr. Debra Murray, Director of Minority Programs in the Human Genome Sequencing Center. 3. Dr. Michael Hume at USDA ARS in College Station, where he discussed his career as a research scientist at USDA. The students then visited with faculty at TAMU who both teach and do research in Genomics and Bioinformatics. Dr. Jason Gill spoke to our students about his research on the Genomics and Bioinformatics of Bacteriophages. Dr. Rodolfo Aramayo discussed his research on Fungal Genomics and Bioinformatics and further enlightened the students about the future of Genomics and Bioinformatics. How have the results been disseminated to communities of interest? All four students presented their research project at our Research Symposium for USDA Capacity Building Program participants on Monday, August 5, 2013. In addition, a facebook page was created to record their activities, such as field trips, research forums, journal club and research symposiums. What do you plan to do during the next reporting period to accomplish the goals? In the next reporting period, in order to accomplish our projects goals and objectives, we plan to do the following: 1. Integrate Bioinformatics in six Agriculture courses. 2. Organize two faculty workshops, (i) September 26-27, 2013 in collaboration with Jason Williams, iplant collaborative, DNA Learning Center, Cold Springs Harbor, and (ii) June 16-18, 2014. 3. Have student participants present their research project findings at research conferences, both local and national. a. PVAMU Biology Undergraduate Research symposium b. PVAMU Science Technology Engineering Agriculture and Mathematics (STEAM) Research Symposium c. Annual Biomedical Research Conference for Minority Students (ABRCMS) d. Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS) e. American Society for Cell Biology (ASCB) 4. Recruit and select three more students from the Department of Agriculture (1 student); Biology (1 student) and Computer Science (1 student) to be participants in our CBG-BRAINS summer research program, June 1 to July 31, 2014. 5. Build a website for dissemination of materials. 6. Have our evaluator, Dr. Thomas Landefeld, evaluate the progress and success of the activities of our project. 7.Publish one paper on the “Integration of Bioinformatics into Agriculture courses at PVAMU, and 1890 institution”.

      Impacts
      What was accomplished under these goals? 1. To improve curriculum and instruction in Agriculture We proposed to achieve this objective by (a) integrating Bioinformatics into several Agriculture courses and (b) organizing a three day faculty workshop. To date, no Agriculture courses have integrated Bioinformatics. However, Dr. Lu, CoPI, has developed modules for the following Bioinformatics tools and databases (i) PubMed, (ii) BLAST and (iii) OMIA. These modules will be integrated in at least six Agriculture courses in the second year of the grant. By the end of the grant period, ten would have integrated Bioinformatics.The three day faculty workshop was organized on June 17 to June 19, 2013. Our CBG-BRAINS CoPIs, Drs. Lu and Hu, presented hands-on Bioinformatics projects and information on Bioinformatics tools and databases. Dr. Shaye Lewis, a newly employed research scientist was our guest speaker and he lectured on the “DNA Basics and the Central Dogma”. Six faculty members and research scientists from the College of Agriculture and Human Sciences were in attendance. All workshop participants teach at least one course in the College of Agriculture and Human Sciences (CAHS). Participant Names and Titles are as follow: a) Milton Daley, Adjunct Faculty; b) Richard Griffin, Professor; c) Annette James, Assistant Professor; d) Barbara Johnson, Assistant Professor; e) Paul Johnson, Research Specialist; f) Yoonsong Jung, Research Scientists-Statistician; and g) Selamawit Woldesenbet, Research Specialist. 2. To engage underrepresented undergraduates in Bioinformatics research. Four underrepresented undergraduates were recruited and selected from the Department of Agriculture (2 students); Biology (1 student) and Computer Science (1 student) to be participants in our CBG-BRAINS summer research program. Participant Names, Classification, Major, and Mentor names are as follow: a)John Attia, Rising Sophomore, Biology, Regisford; b)Deprecia Grogan, Rising Senior, Agriculture (Animal Science), Hu; c)Jourdan Kerl-Henderson, Rising Sophomore, Computer Science, Lu; and d)Diamond Moss, Rising Senior, Agriculture (Soil and Plant Science), Hu.

      Publications