Source: UNIVERSITY OF ILLINOIS submitted to
NEW BIOLOGY FELLOWS PROGRAM IN ANIMAL AND PLANT PRODUCTION
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
0227657
Grant No.
2012-38420-30209
Project No.
ILLU-538-632
Proposal No.
2011-03882
Multistate No.
(N/A)
Program Code
KK
Project Start Date
Jan 15, 2012
Project End Date
Jan 14, 2017
Grant Year
2012
Project Director
Rodriguez Zas, S.
Recipient Organization
UNIVERSITY OF ILLINOIS
2001 S. Lincoln Ave.
URBANA,IL 61801
Performing Department
Animal Sciences
Non Technical Summary
There is an urgent need for "new biologists" skilled in systems biology to integrate information and mine large and complex data sets and secure food-producing animal and plants that can adapt, reproduce, and grow sustainably in changing environments. Few scientists possess firm systems biology, informatics, statistics and animal or plant science know-how to translate the new biology into improved U.S. agricultural production. To address this challenge, our overall approach is to establish a New Biology Fellows Program (NBFP) in Animal and Plant Production at the University of Illinois. The overall project goals are to: 1) offer a model graduate education program on the application of systems biology to animal and plant production, and 2) graduate a diverse group of Fellows with core scientific, communication and leadership competencies that will increase the quality and diversity of the workforce. Specific measurable objectives are: I) recruitment with emphasis on underrepresented groups, and graduation of a diverse cadre including 2 M.S. and 2 Ph.D. National Needs Fellows, and II) provide the Fellows with multidisciplinary, systems biology training and hands-on research. The Fellows training includes a) multidisciplinary up-to-date curriculum, b) research with proven and productive Faculty mentors, c) teaching, d) public engagement, and e) fostering professional, communication, decision making, and leadership skills. Rigorous evaluation of the progress of the NBFP and Fellows twice a year includes face-to-face interactions with fellows and mentors, and surveys. The impacts are the enhancement of the diversity and skills on systems biology applied to agriculture of the workforce.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2012499108010%
2022499209010%
2032499208010%
2042499101010%
2112499102010%
3013999104010%
3023999108010%
3033999209010%
3043999208010%
3113999102010%
Goals / Objectives
The overall project goals are to: 1) offer a model graduate education program on the application of systems biology to animal and plant production, and 2) graduate a diverse group of Fellows with core scientific, communication and leadership competencies that will increase the quality and diversity of the workforce. Specific measurable objectives are: I) multi-institutional recruitment with special emphasis on underrepresented groups, and graduation of a diverse cadre including 2 M.S. and 2 Ph.D. National Needs Fellows, and II) provide the Fellows with multidisciplinary experiential learning opportunities. The Fellows' training includes a) multidisciplinary up-to-date curriculum, b) research with proven and productive Faculty mentors, c) teaching, d) fostering professional, communication, decision making and leadership skills, f) monitoring the progress of the program and Fellows through frequent meetings with the Fellows and mentors and surveys. Outcomes include a) four graduate Fellows (2 M.S. and 2 Ph.D.) with expertise on New Biology applied to animal or plant production that will augment the qualification and cultural diversity of the workforce, b) peer-reviewed manuscripts and presentations at annual society meetings by the Fellows, demonstrating the application of systems biology to integrate information, analyze large and complex data sets and uncover relationships influencing animal or plant production (at least one manuscript per M.S. and two per Ph.D.), c) Faculty with experience mentoring a diverse group of students in New Biology, and d) a model program for recruitment, retention and graduation of students, specially from underrepresented groups.
Project Methods
The Steering Committee will proactively recruit gifted students across campuses using a variety of strategies. The program's website will showcase the resources available to the Fellows. Two Fellows will be recruited at the start of the program and two within 18 months. This recruitment timeline maximizes the overlap between Fellows, creating a larger contemporary cohort that will support each other. The recruitment of Fellows from underrepresented groups utilizes three unique resource pillars available at Illinois, our established cooperation with Northeastern Illinois University, the commitment of the Graduate College to accept the Fellows to the Summer Pre-Doctoral Institute if necessary, and the successful minority engagement program at the College of ACES. Successful applicants will have a high GPA, be citizens or nationals of the US, and have demonstrated interest on systems biology applications to animal or plant production. The program will nurture excellence through Hamming's "open doors" concept by encouraging constant and multidisciplinary interactions between Fellows and Faculty and the emergence of integrative approaches to solve problems of paramount, rather than of tangential importance. The multidisciplnary training and combination of research, teaching and public engagement will allow the Fellows to have a "foot in the door" to a second degree if they wish to pursue this opportunity. The Faculty mentor and Steering Committee will direct the Fellows towards jobs, encourage them to apply, prepare them for job interviews and counsel them during negotiations. Retention will be maximized through open door practices and semiannual meetings between the mentor and Fellow and steering committee members. The Fellows will complete all or most of the courses during the initial academic semesters leaving the remainder for thesis research and writing, teaching and other activities. The Fellows will complete the required course-work, pass a preliminary examination (Ph.D. only) and a thesis defense administered by a committee, in fulfillment of departmental requirements. Each Fellow will gain basic and applied competencies on three areas: 1) animal or plant sciences, 2) statistics/computer science/informatics, 3) systems biology/ bioinformatics. In addition, the Fellows will develop communication, leadership, professional and decision-making skills. The Fellows will learn the scientific method, critical thinking and problem solving skills, to work independently and in teams while working on their thesis research at the Faculty mentors' lab. The Fellows will be given the opportunity to help teaching a course directly related to their research project. The Fellows' accomplishments will be showcased on the program's website. Dissemination of the Fellows' research projects will be communicated on relevant media (e.g. peer-reviewed journals) and at meetings. Outcomes and impacts of the NBFP will be communicated to the NNFs Program Officer and to a wider audience of educators, administrators and policy makers at relevant meetings.

Progress 01/15/12 to 01/14/17

Outputs
Target Audience:Institutions of higher education, training programs, and graduate programs. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Unique academic program. A novel program of studies that integrated advanced computational and quantitative biological training (New Biology Program) and University of Illinois graduate program requirements was implemented. Academic training included: a) M.Sc. ≥ 6 full-semester graduate-level courses + seminar + thesis research; b) Ph.D.: M.Sc.+ ≥ 6 full-semester graduate-level courses + seminar + thesis research. Courses included agricultural and biological sciences, statistics, informatics, computer sciences, and molecular biology. Extracurricular training included: a) federal agency (NIH) accepted course in Responsible Conduct of Research developed by the Collaborative Institutional Training Initiative; b) laboratory safety; c) animal care; d) career development workshops offered by the Graduate College; and e) grant writing workshops offered by the Department of Animal Sciences and Graduate College. Post-graduation job placement. All fellows secured positions in federal agencies, industry or academia: a) soil conservationist at USDA National Resources Conservation Services; b) quantitative agronomist and volatility trader at Thresher Capital; c) senior analyst at Abbott; d) research associate at the University of Korea. How have the results been disseminated to communities of interest?Manuscripts, Extension and outreach. The fellows authored or co-authored more than 12 publications and abstracts. Also, the fellow's findings were communicated to a wider audience and stakeholders through a USDA-University of Illinois Extension website and through College of Agriculture, Consumer, and Environmental Sciences reports. Conferences and symposiums that fellows participated and presented their findings include: a) Disciplinary meetings (Midwest Cover Crops Council); b) American Society of Agronomy; Crop Science Society of America; Soil Science Society of America; c) Plant and Animal Genome; d) Conference of Bioinformatics and Computational Biology; e) Illinois Brain Behavior and Immunity; f) Illinois Specialty Crops, Agritourism, and Organic Conference; g) MOSES Organic Farming Conference; and h) Annual Fellows Symposium at the Carl R. Woese Institute for Genomic Biology, University of Illinois. Honors and awards received by the fellows include: a) Achievement Rewards for College Scientists (ARCS) Foundation; b) Graduate College Academic Excellence Award; c) NSF East Asia and Pacific Summer Institutes for U.S. (EAPSI) fellowship; d) Brockson fellowship; e) Graduate College travel awards; and f) Departmental travel awards. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The New Biology Fellows Program in Animal and Plant Production at the University of Illinois aims to increase the workforce that specializes in integrating computer, statistical, and biological sciences. The program trains graduate students in approaches to integrate information and mine large and complex data sets. Fellows receive training and hands-on experiences to improve the performance and health of food-producing animals and plants. Additional matching support from the Departments of Animal Sciences and Crop Sciences at the University of Illinois has enabled additional graduate students to join the program. An innovative strategy key to the success of this USDA NIFA National Needs program (NNF) is the integration of academic requirements with research and public engagement opportunities while addressing workforce needs. Fellows maintained exemplary grade point averages, received intra- and extra-mural awards and communicated research findings at symposiums, national meetings, peer-reviewed publications, and Extension outlets. Recruitment. Complementary outlets were employed to reach out and recruit a diverse pool of applicants including: a) disciplinary societies and mail lists; b) minority serving institutions (e.g. North Eastern Illinois University); and c) scientific minority serving organizations (e.g. HACU; MANRRS). Applicant pool. Applicants to the program came from a variety of sources including: a) direct application to the New Biology Fellows Program via the program website; b) application to the Department of Animal Sciences, Department of Crop Sciences, and Illinois Informatics Institute programs. Diversity of fellows: a) gender: 50% women; b) underrepresented groups (75%); c) program: M.Sc. and Ph.D. graduates; d) disciplines: Departments: Animal Sciences, Crop Sciences, and Informatics. Matching institutional resources from the University of Illinois: Non-USDA New Biology Fellows received support from Department of Animal Sciences, Department of Crop Sciences and Illinois Informatics Institute. Formative and summative assessment of the training program during and at the end of the training program offered evidence of the impact of the USDA NNF New Biology Program. Summative statistics offer evidence of the academic merit of the fellows and hiring success: a) average GPA equal to 3.84; b) graduation on target or before 2 years (Masters) or 3 years (Ph.D.); c) prompt job placement in coveted positions in federal agencies (Soil Conservationist at USDA National Resources Conservation Services), industry (Abbott, Quantitative Agronomist and Volatility Trader, Thresher Capital), and academia (research associate in top livestock bioinformatics program at the University of Korea). Anonymous fellows feedback included: a) "I would like to thank [Mentor's name] for being understanding and supportive during a difficult time, and for guidance during the analysis and writing phase." b) "I'd like to thank the USDA National Needs Fellowship Program for supporting me"; c) "I am gratefulespecially to [Mentors' names] for their amazing support and guidance throughout my program."; d) "The opportunity to work on these projects, much less their completion, are thanks to my advisor", and; e) "Entering into a multi-disciplinary project is a daunting task, with the constant struggle between depth and breadth of knowledge while summarizing appropriately." "[Mentor's name] experience and constant efforts not only gave me the chance to practice, but pushed me to work harder and never accept an answer without understanding it.

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Gonzalez-Pena, D., Nixon, S.E., Southey, B.R., Lawson, M.A., McCusker, R.H., Hernandez, A.G., Dantzer, R., Kelley, K.W. and Rodriguez-Zas, S.L. 2016. Differential Transcriptome Networks Between IDO1-Knockout and Wild-Type Mice in Brain Microglia and Macrophages. PLoS One. 2016 Jun 17;11(6):e0157727. doi: 10.1371/journal.pone.0157727. PubMed PMID: 27314674; PubMed Central PMCID: PMC4912085.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Caetano-Anoll�s, K., Rhodes, J.S., Garland, T. Jr., Perez, S.D., Hernandez, A.G., Southey, B.R. and Rodriguez-Zas, S.L. 2016. Cerebellum Transcriptome of Mice Bred for High Voluntary Activity Offers Insights into Locomotor Control and Reward-Dependent Behaviors. PLoS One. 2016 Nov 28;11(11):e0167095. doi: 10.1371/journal.pone.0167095.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Gonzalez-Pena, D., Nixon, S.E., OConnor, J.C., Southey, B.R., Lawson, M.A., McCusker, R.H., Borras, T., Machuca, D., Hernandez, A.G., Dantzer, R., Kelley, K.W. and Rodriguez-Zas, S.L. 2016. Microglia Transcriptome Changes in a Model of Depressive Behavior after Immune Challenge. PLoS One. 2016 Mar 9;11(3):e0150858. doi: 10.1371/journal.pone.0150858. PubMed PMID: 26959683; PubMed Central PMCID: PMC4784788.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Seo, M., Caetano-Anolles, K., Rodriguez-Zas, S., Ka, S., Jeong, J.Y., Park, S., Kim, M.J., Nho, W.G., Cho, S., Kim, H. and Lee, H.J. 2016. Comprehensive Identification of Sexually Dimorphic Genes in Diverse Cattle Tissues Using RNA-seq. BMC Genomics. 2016 Jan 27;17:81. doi: 10.1186/s12864-016-2400-4. PubMed PMID: 26818975; PubMed Central PMCID: PMC4728830.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Aziz, M.F., Caetano-Anoll�s, K. and Caetano-Anoll�s, G. 2016. The Early History and Emergence of Molecular Functions and Modular Scale-Free Network Behavior. Scientific Reports, 6.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Jeong, H., Sung, S., Kwon, T., Seo, M., Caetano-Anoll�s, K., Choi, S.H., Cho, S., Nasir, A. and Kim, H., 2016. HGTree: Database of Horizontally Transferred Genes Determined by Tree Rreconciliation. Nucleic acids research, 44(D1), pp.D610-D619.
  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Kwon, T., Yoon, S.H., Kim, K.W., Caetano-Anolles, K., Cho, S. and Kim, H. 2015. Time-Calibrated Phylogenomics of the Classical Swine Fever Viruses: Genome-Wide Bayesian Coalescent Approach. PloS one, 10(3), e0121578.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Heo, J., Seo, M., Park, H., Lee, W.K., Guan, L.L., Yoon, J., Caetano-Anolles, K., Ahn, H., Kim, S.Y., Kang, Y.M. and Cho, S., 2016. Gut Microbiota Modulated by Probiotics and Garcinia cambogia Extract Correlate with Weight Gain and Adipocyte Sizes in High Fat-Fed Mice. Scientific Reports, 6.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Jeong, Hyeonsoo, Kwondo Kim, Kelsey Caetano-Anoll�s, Heebal Kim, Byung-Ki Kim, Jun-Koo Yi, Jae-Jung Ha, Seoae Cho and Dong Yep Oh. 2016. Whole Genome Sequencing of Gyeongbuk Araucana, A Newly Developed Blue-Egg Laying Chicken Breed, Reveals Its Origin and Genetic Characteristics. Scientific Reports 6.
  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Kim, J., Cho, S., Caetano-Anolles, K., Kim, H. and Ryu, Y.C. 2015. Genome-Wide Detection and Characterization of Positive Selection in Korean Native Black Pig from Jeju Island. BMC genetics, 16(1), p.1.
  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Jeong, H., Song, K.D., Seo, M., Caetano-Anoll�s, K., Kim, J., Kwak, W., Oh, J.D., Kim, E., Jeong, D.K., Cho, S. and Kim, H. 2015. Exploring Evidence of Positive Selection Reveals Genetic Basis of Meat Quality Traits in Berkshire Pigs Through Whole Genome Sequencing. BMC genetics, 16(1), p.1.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Ahn, S., Chung, H.Y., Lim, S., Kim, K., Kim, S., Na, E.J., Caetano-Anolles, K., Lee, J.H., Ryu, S., Choi, S.H. and Kim, H.,2016. Complete Genome of Vibrio Parahaemolyticus FORC014 Isolated From the Toothfish. Gut Pathogens, 8(1), p.59.
  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Kim, H., Caetano-Anolles, K., Seo, M., Kwon, Y.J., Cho, S., Seo, K. and Kim, H., 2015. Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds. Genomics & informatics, 13(4), pp.137-145.


Progress 01/15/15 to 01/14/16

Outputs
Target Audience:The New Biology Fellows Program in Animal and Plant Production at the University of Illinois aims to increase the workforce that specializes in integrating computer, statistic, and biological sciences. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Thesis research, attendance of workshops, attendance of courses, seminar presentations, presentations at conferences, peer-reviewed manuscripts, limited teaching assistant responsibilities, nomination to awards, responsible conduct of research training. How have the results been disseminated to communities of interest?Manuscripts, abstracts, posters, and Extension communications. What do you plan to do during the next reporting period to accomplish the goals?Continue offering training opportunities to theNNF fellows including research and academic training experiences.

Impacts
What was accomplished under these goals? The overall project goals are to: 1. Offer a model graduate education program on the application of systems biology to animal and plant production, and 2. Graduate a diverse group of Fellows with core scientific, communication and leadership competencies that will increase the quality and diversity of the workforce. Among the initiatives encompassed in Objective 1, the program trains graduate students in approaches to integrate information and mine large and complex data sets. Fellows receive training and hands-on experiences to improve the performance and health of food-producing animals and plants. Among the initiatives encompassed in Objective 2, the program recruited 50% women and 75% students from underrepresented groups.

Publications

  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Welch, Rachel Yoso. 2015. Using cover crops to alleviate compaction in organic grain farms. University of Illinois Urbana-Champaign.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Febrer, Daniel. 2015. Nitrogen recommendation systems, weather effects on nitrogen response, and the prediction of nitrogen response in Illinois. University of Illinois Urbana-Champaign.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Nixon, S. 2015. Study of phenotypic and gene expression response to bacterial challenge. University of Illinois Urbana-Champaign.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Nixon, S.E., Gonz�lez-Pe�a, D., Lawson, M.A., McCusker, R.H., Hernandez, A.G., O'Connor, J.C., Dantzer, R., Kelley, K.W. and Rodriguez-Zas, S.L. 2015. Analytical workflow profiling gene expression in murine macrophages. J. Bioinform. Comput. Biol. 2015 Jan 14:1550010. [Epub ahead of print] PMID: 25708305.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Rodriguez-Zas, S.L. 2015. National Needs New Biology Fellows Program: Success through workforce preparation. USDA Multicultural Scholars Program and NNF Project Directors Meeting August 26-27, 2015 Washington, DC.
  • Type: Other Status: Published Year Published: 2015 Citation: http://web.extension.illinois.edu/state/newsdetail.cfm?NewsID=32416 [Genes and physical activity support muscle growth and strengthening].
  • Type: Other Status: Published Year Published: 2015 Citation: http://web.extension.illinois.edu/state/newsdetail.cfm?NewsID=32445 [Cover crops in organic grain production systems].
  • Type: Other Status: Published Year Published: 2015 Citation: http://web.extension.illinois.edu/state/newsdetail.cfm?NewsID=32446 [Improving the prediction of nitrogen response in corn].
  • Type: Other Status: Published Year Published: 2015 Citation: http://web.extension.illinois.edu/state/newsdetail.cfm?NewsID=32369 [Understanding infection, inflammation, and chronic behavior].
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Caetano-Anolles, K., Mishra S. and S.L. Rodriguez-Zas. 2015. Synergistic and antagonistic interplay between the myostatin gene and physical activity on global gene expression patterns. PLoS One. 2015 Feb 24;10(2):e0116828. doi: 10.1371/journal.pone.0116828. PMID: 25710176.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Caetano-Anolles, K., Seo, M., Rodriguez-Zas, S., Oh, J.D., Han, J.Y., Lee, K., Park, T.S., Shin, S., Jiao Jiao, Z., Ghosh, M., Jeong, D.K., Cho, S., Kim, H., Song, K.D. and Lee, H.K. 2015. Comprehensive identification of sexual dimorphism-associated differentially expressed genes in two-way factorial designed RNA-seq data on Japanese quail (Coturnix coturnix japonica). PLoS One. 2015 Sep 29;10(9):e0139324. doi: 10.1371/journal.pone.0139324. eCollection 2015. PubMed PMID: 26418419.


Progress 01/15/14 to 01/14/15

Outputs
Target Audience: Scientists integrating quantitative and biological data to improve performance, health, and behavior of food andbiomedical animals and humans. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Allfellows have taken courses at the University of Illinois, conducted research, prepared manuscripts,and presented their findings at meetings and seminars. Some of the fellows have applied for travel awards and fellowships. One fellow spent part of Summer 2014 in South Korea learning techniques and writing a manuscript. Fellows are encouraged to attend meetings tointegrate themselves intoprofessional networks. Fellows are encouraged to attend additional workshops offered by the Graduate College on career development. How have the results been disseminated to communities of interest? Manuscripts, proceedings, abstracts, and presentations at meetings and seminars. What do you plan to do during the next reporting period to accomplish the goals? Continue mentoring and advising fellows on academics, research and career opportunities.

Impacts
What was accomplished under these goals? The project goals were accomplished. The New Biology program continues to offer a model of graduate education on the application of systems biology to animal and plant production. A diverse cradle of fellows is receiving academic and hands-on training on science and research ethics, conducting state-of-the-art research, communicating findings at meetings and developing profesional career skills. The fellows include 50% women and50% from underrepresented minority groups. The first fellow graduated with a M.Sc. in Crop Sciences. All fellows completed training on research ethics offered by the CITI program on responsible conduct of research (www.citiprogram.org). The rest of the fellows are on track to graduate in a timely manner.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Rodriguez-Zas, S., Nixon, S., Lawson, M., McCusker, R., Southey, B., O'Connor, J., Dantzer, R. and Kelley, K. Advancing the understanding of behaviors associated with Bacille Calmette Gu�rin infection using multivariate analysis. Brain Behav. Immun. Oct 7. pii: S0889-1591(14)00471-1. doi: 10.1016/j.bbi.2014.09.018. PMID: 25300921.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Gonzalez-Pe�a, D., Nixon, S., Southey, B., Lawson, M., McCusker, R., Dantzer, R., Kelley, K. and Rodriguez-Zas, S. Impact of the increase in the biological samples and alternatives vs. defaults in setting in the transcripts analysis. 6th International Conference on Bioinformatics and Computational Biology (BICoB). March, Las Vegas, NV. http://www.cs.umb.edu/bicob/.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Nixon, S., Gonzalez-Pe�a, D., Lawson, M., McCusker, R., OConnor, J., Dantzer, R., Kelley, K. and Rodriguez-Zas, S.L. Transcriptomic analysis by rna-seq and gene enrichment analysis. 6th International Conference on Bioinformatics and Computational Biology (BICoB). March, Las Vegas, NV. http://www.cs.umb.edu/bicob/.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Zavala, C., Nixon, S., Wu, C., Southey, B., Romanova, E., Sweedler, J. and Rodriguez-Zas, S. Understanding the impact of fractionation and dynamic exclusion on proteomics. 6th International Conference on Bioinformatics and Computational Biology (BICoB). March Las Vegas, NV. http://www.cs.umb.edu/bicob/. 4p.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Caetano-Anolles, K., Nixon, S. and Rodriguez-Zas, S. Advanced statistical analysis of RNA-seq differential gene expression profiles of animal gene-environment interactions. 6th International Conference on Bioinformatics and Computational Biology (BICoB). March Las Vegas, NV. http://www.cs.umb.edu/bicob/. 4p.
  • Type: Other Status: Published Year Published: 2014 Citation: Gonzalez-Pe�a, D., Nixon, S., Southey, B., Lawson, M., McCusker, R., Dantzer, R., Kelley, K. and Rodriguez-Zas, S. Characterization of the microglia transcriptome in IDO1 knockout and wild-type mice. Plant and Animal Genome. January. San Diego, CA. https://pag.confex.com/pag/xxii/webprogram/POSTER.html.
  • Type: Other Status: Published Year Published: 2014 Citation: Nixon, S., Gonzalez-Pe�a, D., Lawson, M., McCusker, R., OConnor, J., Dantzer, R., Kelley, K. and Rodriguez-Zas, S. Modifications in the gene expression of Microglia following peripheral Mycobacterium challenge. Plant and Animal Genome. January. San Diego, CA. https://pag.confex.com/pag/xxii/webprogram/POSTER.html.
  • Type: Other Status: Published Year Published: 2014 Citation: Gonzalez-Pe�a, D., Caetano-Anoll�s, K., Wheeler, M. and Rodriguez-Zas, S. Characterization of the endometrial transcriptome in pregnant and non-pregnant sows. 2014 Midwest American Society of Animal Science. March, IA. https://www.asas.org/membership-services/asas-sections/midwest-section/meetings.
  • Type: Theses/Dissertations Status: Awaiting Publication Year Published: 2014 Citation: Febrer, D. Nitrogen recommendation systems, weather effects on nitrogen response, and the prediction of nitrogen response in Illinois.
  • Type: Other Status: Published Year Published: 2013 Citation: Febrer, D., Nafziger, E.D. and Villamil, M.B. Improving nitrogen rate recommendations with weather and N-carryover variables. Agronomy, Crop Science, and Soil Science Societies Annual Meetings. ASA, CSSA and SSSA International Annual Meeting. Tampa, FL. Nov 3-6.
  • Type: Other Status: Published Year Published: 2014 Citation: Villamil, M.B., Williams, A. and Welch, R. Alleviation of soil compaction with cover crops in organic farms: A participatory experience. 2014 Illinois Specialty Crops, Agritourism, and Organic Conference. Springfield, IL. Jan 10-12, 2014.
  • Type: Other Status: Published Year Published: 2014 Citation: Villamil, M.B., Welch, R. and Masiunas, J. Evaluation of soil compaction and cover crops in organic farms: A participatory approach. Workshop held at the 2014 MOSES Organic Farming Conference, La Crosse, Wisconsin. Feb 27-Mar 1, 2014.
  • Type: Other Status: Published Year Published: 2014 Citation: Welch, R., Behnke, G.D., Masiunas, J., Anderson, D. and Villamil, M.B. Improving weed suppression with cover crops in organic grain production. ASA, CSSA and SSSA International Annual Meeting. Long Beach, CA. Nov 2-6. 2014.


Progress 01/15/13 to 01/14/14

Outputs
Target Audience: Graduate and undergraduate training programs in STEM disciplines. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The followingtraining opportunities are the result from the activities supporting the three goals of the project: First, the New Biology Graduate Fellows Program (NBGFP) continues to grow. The program has now 16 fellow students working on animal and plant production and health research projects. The program’s comprehensive and up-to-date website includes a list of the fellow students and projects and additional resources (http://ansci.illinois.edu/labs/bioinformatics/new-biology-fellows-program). Second, the program is centered on supporting and advancing a cohort of 16 graduate fellows offering academic, research and outreach opportunities. Third, two of the fellows are receiving National Needs Fellowships and are working towards a M. Sc. and two towards a Ph. D. degree. Fourth, the 16 NBGFP fellows are learning and performing research on state-of-the-art applications of systems biology including: 1) Scott Nixon (study of inflammatory response to infection using next-generation sequencing technology), 2) Daniel Febrer (study of nitrogen inputs in cropping systems), 3) Dianelys González-Peña (study of insemination technique and semen preparation in the genetic progress and financial indicators of pig production systems), 4) Kristin Delfino (study of microRNA-target gene networks influencing survival and disease progression), 5) M. Nadeem Akhtar (study of computational proteomic approaches to detect neuropeptides), 6) Zeeshan Fazal (study of gene expression patterns associated with changes in the environment), 7) Luciano Pinheiro da Silva (study of genetic improvement for growth and reproductive traits in poultry), 8) Brad Daigneault (study of the impact of indicators of boar fertility in frozen-thawed boar sperm, 9) M. Jawad Khan (study of molecular adaptations in liver of dairy cows in response to nutrition), 10) Caroline Gonzalez Vega (study of calcium digestibility, metabolism, and requirements in pigs), 11) Yiwen Xiang (study of the response of soybean genotypes to sudden death syndrome), 12) Elizabeth Blissett (study of the role of maize root architecture in plant performance), 13) Sungyul Chang (study of the genes underlying resistance to the fungal pathogen in a wild perennial species related to cultivated soybean that has limited resistance), 14) Kelsey Caetano-Anolles (study of gene by environment interactions using next generation sequencing technology), 15) Cynthia Zavala (study of the peptidome changes in response to inflammation), and 16) Rachel Welch (study of deep rooted cover crops alone and in mixtures to alleviate soil compaction and suppress weeds in organic grain farms). Fifth, as demonstrated by the 16 projects, all NBGF are receiving training and hands-on research experiences in systems biology approaches to integrate information and mine large complex data in support of animal and plant production and health. The research projects of both the Ph. D. and M. Sc., fellows are advancing at steady pace. All the students receiving graduate studies fellowships are taking graduate-level courses in biology, statistics, informatics and computer sciences. How have the results been disseminated to communities of interest? The New Biology program website and resources are models for other graduate training projects. The impact of the New Biology program in the recruitment and retention of Science, Technology, Engineering and Mathematics (STEM) graduate students has resulted in PI Rodriguez-Zas becoming member of the steering committee of the National Science Foundation (NSF) Integrative Graduate Education and Research Traineeship (IGERT) program Vertically Integrated Training with Genomics. Similarly, PI Rodriguez-Zas also became member of the College of Agricultural, Consumer and Environmental Sciences (ACES) 2013-2014 Graduate Education Policy committee. What do you plan to do during the next reporting period to accomplish the goals? During the next reporting period the program will continue to offer learning opportunities to the graduate student fellows including courses, research experiences, and presentations at meetings. Program assessment including graduation rate, retention rate, presentation at meetings, and manuscripts authored by the graduate program fellows and progress towards their graduation will continue.

Impacts
What was accomplished under these goals? The project has three goals: 1) build and sustain a recognized graduate program that trains and graduates Fellows in New Biology to enter into the workforce and meet the needs of the agricultural system; 2) promote diversity among the trainees; and 3) act as model for other training programs. In its second year, the project continues to deliver outputs on all three goals that address the urgent need for new biologists skilled in systems biology approaches to integrate information and mine large and complex data sets to secure food-producing animals and plants. Addressing the first goal, the New Biology Graduate Fellows Program (NBGFP) at the University of Illinois started on February 2012. The Program has grown to a cohort of 16 graduate students, four of whom receive USDA-NIFA National Needs graduate studies fellowships (NNF). The rest of the graduate students received travel awards to present their research on New Biology topics at national meetings. All 16 New Biology Graduate Fellows, their program of studies and their New Biology projects are listed in the program’s website (http://ansci.illinois.edu/labs/bioinformatics/new-biology-fellows-program). The New Biology program’s website has served as aneffective tool to recruit and promote this successful program. Recruitment included advertisement of the program in various venues including American Society of Animal Sciences Graduate Bulletin (http://blog.asas.org/GraduateBulletin/), SACNAS (http://sacnas.org/), recruitment at national meetings (e.g. American Society of Animal Sciences, American Society of Dairy Science, 4th International Conference in Proteomics and Bioinformatics), various email lists (including AGDG-LIST and the NRSP-8 National Animal Genome Research Program AnGenMap), undergraduate seminars at the University of Illinois, and through the NSF-sponsored undergraduate research mentoring fellows program. From the recruitment efforts, 8 students applied and the top two students were selected by the steering committee to receive fellowships. The fellows supported by this project have been full-time students at the University of Illinois attending graduate-level courses, conducting research, participating in seminars and presenting research at national meetings. Addressing the second goal, 50% of the fellows supported by New Biology program are from under-represented (URM) groups and 50% are females. Recruitment included advertisement in SACNAS and at Hispanic Serving Institutions such as North Eastern Illinois University. The PI promoted the program among students invited to visit campus as part of the Community of Scholars and ASPIRE programs that target URM students. Also, the PI participated in the 2013 Illinois Partners for Diversity retreat that established links between the University of Illinois and U.S. minority serving institutions. The impact of the New Biology program in the recruitment and retention of graduate URM students has resulted in PI Rodriguez-Zas becoming a member of the Graduate College 2013 Council on Equity and Access. Addressing the third goal, the New Biology program website and resources are models for other graduate training projects. The impact of the New Biology program in the recruitment and retention of Science, Technology, Engineering and Mathematics (STEM) graduate students has resulted in PI Rodriguez-Zas becoming a member of the steering committee of the National Science Foundation (NSF) Integrative Graduate Education and Research Traineeship (IGERT) program Vertically Integrated Training with Genomics. Similarly, PI Rodriguez-Zas also became member of the College of Agricultural, Consumer and Environmental Sciences (ACES) 2013-2014 Graduate Education Policy committee.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Nixon S. E., Lawson M. A., McCusker R. H., Gonzalez-Pe�a D., OConnor J. C., Dantzer R., Kelley K. W., Rodriguez-Zas S. L. Sickness and Behavioral Changes Associated with Infection. 2013 IGB Fellows Symposium. May 2, 2013, Urbana, IL. #43. http://conferences.igb.illinois.edu/fellows/.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Ferber, D., Nafziger, E. D., and Villamil, M. B. Examining Variability in Corn Nitrogen Response and Economic Return. American Society of Agronomy (ASA), Crop Science Society of America (CSSA), and Soil Science Society of America (SSSA) International Annual Meeting Nov 3-6, 2013. Poster #2110.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Gonzalez-Pena, D., N. V. L. Ser�o, J. E. Beever, D. B. Faulkner, and S. L. Rodriguez-Zas. Genetic parameters and single nucleotide polymorphism of feed utilization in beef cattle. J. Anim. Sci. Vol. 91, E-Suppl. 1/J. Dairy Sci. Vol. 96, E-Suppl. 1/Poult. Sci. Vol. 91, E-Suppl. 1, T203. http://www.jtmtg.org/2013/pdf/2013-JAM-Program_SciPortion_DRAFT.pdf?v=20120508.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Zavala, C., N. V. L. Ser�o, D. Gonz�lez-Pe�a, and S. L. Rodriguez-Zas. Genomic variants and genetic parameters of feed efficiency from univariate and multivariate analyses. J. Anim. Sci. Vol. 91, E-Suppl. 1/J. Dairy Sci. Vol. 96, E-Suppl. 1/Poult. Sci. Vol. 91, E-Suppl. 1. T204. http://www.jtmtg.org/2013/pdf/2013-JAM-Program_SciPortion_DRAFT.pdf?v=20120508.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Gonzalez-Pena, D., N. V. L. Ser�o, J. Pettigrew, R. Knox, and S. L. Rodriguez-Zas. Effect of pig insemination technique and semen preparation on profitability. J. Anim. Sci. Vol. 91, E-Suppl. 1/J. Dairy Sci. Vol. 96, E-Suppl. 1/Poult. Sci. Vol. 91, E-Suppl. 1. 120. http://www.jtmtg.org/2013/pdf/2013-JAM-Program_SciPortion_DRAFT.pdf?v=20120508.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Gonzalez-Pena, D., N. V. L. Ser�o, R. Knox, and S. L. Rodriguez-Zas. Understanding the impact of frozen semen on swine production systems. J. Anim. Sci. Vol. 91, E-Suppl. 1/J. Dairy Sci. Vol. 96, E-Suppl. 1/Poult. Sci. Vol. 91, E-Suppl. 1, W197. http://www.jtmtg.org/2013/pdf/2013-JAM-Program_SciPortion_DRAFT.pdf?v=20120508.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Silva, L., D. Gonz�lez-Pena, J. Ribeiro, A. Crispim, S. L. Rodriguez-Zas, and R. Torres. Genetic parameters of body weight at multiple ages in meat-type quails. J. Anim. Sci. Vol. 91, E-Suppl. 1/J. Dairy Sci. Vol. 96, E-Suppl. 1/Poult. Sci. Vol. 91, E-Suppl. 1, W204. http://www.jtmtg.org/2013/pdf/2013-JAM-Program_SciPortion_DRAFT.pdf?v=20120508.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Silva, L., D. Gonz�lez-Pena, G. Caetano, R. Pacheco, S. L. Rodriguez-Zas, and R. Torres. Genetic relationships between cloacal gland area and fertility traits in meat quality. J. Anim. Sci. Vol. 91, E-Suppl. 1/J. Dairy Sci. Vol. 96, E-Suppl. 1/Poult. Sci. Vol. 91, E-Suppl. 1, W205. http://www.jtmtg.org/2013/pdf/2013-JAM-Program_SciPortion_DRAFT.pdf?v=20120508.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Delfino K. R. and Rodriguez-Zas S. L. Transcription factor-microRNA-target gene networks associated with ovarian cancer survival and recurrence. PLoS One. 2013;8(3):e58608. doi: 10.1371/journal.pone.0058608. Epub 2013 Mar 12.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Daigneault, B.W., McNamara, K.A., Purdy, P.H., Knox, R.V., Krisher, R.L., and Miller, D.J. Post-thaw motility of frozen boar sperm does not predict success with in vitro fertilization. Society for the Study of Reproduction, Montreal, Quebec, Canada, July 22-26, 2013. http://www.canalpoint.sugarcane.usda.gov/research/publications/Publications.htm?seq_no_115=292507.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Fazal Z, Southey BR, Sweedler JV, and Rodriguez-Zas SL. Multifactorial Understanding of Ion Abundance in Tandem Mass Spectrometry Experiments. J Proteomics Bioinform. 2013 Jan 29;6(2):23-29.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Khan, M. J., D. E. Graugnard, S. L. Rodriguez-Zas, and J. J. Loor. Polymorphonuclear leukocyte transcriptomics in transition Holstein cows fed two levels of dietary energy prepartum. J. Anim. Sci. Vol. 91, E-Suppl. 1/J. Dairy Sci. Vol. 96, E-Suppl. 1/Poult. Sci. Vol. 91, E-Suppl. 1, 374.http://www.jtmtg.org/2013/pdf/2013-JAM-Program_SciPortion_DRAFT.pdf?v=20120508.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Khan M. J., Trevisi E., Graugnard D. E., Bertoni G., and Loor J. J. Inflammation and endoplasmic reticulum (ER) stress gene network expression in liver of peripartal Holstein cows fed two levels of dietary energy prepartum. J. Anim. Sci. Vol. 91, E-Suppl. 1/J. Dairy Sci. Vol. 96, E-Suppl. 1/Poult. Sci. Vol. 91, E-Suppl. 1, 234. http://www.jtmtg.org/2013/pdf/2013-JAM-Program_SciPortion_DRAFT.pdf?v=20120508.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Khan M. J., Welge M., Bushell C., Berry M., Gatzke L., and Loor J. J. Visual analytics of bovine nutriphysiogenomics datasets. J. Anim. Sci. Vol. 91, E-Suppl. 1/J. Dairy Sci. Vol. 96, E-Suppl. 1/Poult. Sci. Vol. 91, E-Suppl. 1, T352. http://www.jtmtg.org/2013/pdf/2013-JAM-Program_SciPortion_DRAFT.pdf?v=20120508.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Moyes K. M., Graugnard D. E., Drackley J. K., Khan M. J., Bionaz M. and Loor J. J. Neutrophil (PMN) expression of extracellular trap formation and immunometabolic genes in response to prepartal energy intake and postpartal intramammary lipopolysaccharide challenge in postpartal dairy cows. J. Anim. Sci. Vol. 91, E-Suppl. 1/J. Dairy Sci. Vol. 96, E-Suppl. 1/Poult. Sci. Vol. 91, E-Suppl. 1, W139. http://www.jtmtg.org/2013/pdf/2013-JAM-Program_SciPortion_DRAFT.pdf?v=20120508.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Kadegowda A. K., Khan M. J., Piperova L. S., Teter B. B., Rodriguez-Zas S. L., Erdman R. A., and Loor J. J. Trans-10, is 12-Conjugated Linoleic Acid-Induced Milk Fat Depression Is Associated with Inhibition of PPAR? Signaling and Inflammation in Murine Mammary Tissue. J Lipids. 2013;2013:890343. doi: 10.1155/2013/890343. Epub 2013 May 14. PMID: 23762566.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Bionaz M., Chen S., Khan M. J. and Loor J. J. Functional Role of PPARs in Ruminants: Potential Targets for Fine-Tuning Metabolism during Growth and Lactation. PPAR Res. 2013;2013:684159. doi: 10.1155/2013/684159. Epub 2013 Apr 29. PMID: 23737762.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Khan M. J., Hosseini A., Burrell S., Rocco S. M., McNamara J. P. and Loor J. J. Change in subcutaneous adipose tissue metabolism and gene network expression during the transition period in dairy cows, including differences due to sire genetic merit. J Dairy Sci. 2013 Apr;96(4):2171-82. doi: 10.3168/jds.2012-5794. Epub 2013 Feb 15. PMID: 23415532.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Graugnard D. E., Moyes K. M., Trevisi E., Khan M. J., Keisler D., Drackley J. K., Bertoni G. and Loor J. J. Liver lipid content and inflammometabolic indices in peripartal dairy cows are altered in response to prepartal energy intake and postpartal intramammary inflammatory challenge. J Dairy Sci. 2013 Feb;96(2):918-35. doi: 10.3168/jds.2012-5676. Epub 2012 Dec 20.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Jaworski N. W., Gonzalez-Vega J. C. and Stein H. H. Growth performance of weanling pigs fed diets containing copra meal, palm kernel expellers, or palm kernel meal. J. Anim. Sci. Vol. 91, E-Suppl. 1/J. Dairy Sci. Vol. 96, E-Suppl. 1/Poult. Sci. Vol. 91, E-Suppl. 1, 780. http://www.jtmtg.org/2013/pdf/2013-JAM-Program_SciPortion_DRAFT.pdf?v=20120508.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Gonz�lez-Vega J. C., Walk C. L., Liu Y. and Stein H. H. Endogenous intestinal losses of calcium and true total tract digestibility of calcium in canola meal fed to growing pigs. J Anim Sci. 2013 Oct;91(10):4807-16. doi: 10.2527/jas.2013-6410. Epub 2013 Aug 13.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Welch R., Behnke G., Suarez Tapia A. and Villamil M.B. Multifunctional Cover Crops in Organic Grain Production Systems. American Society of Agronomy (ASA), Crop Science Society of America (CSSA), and Soil Science Society of America (SSSA) International Annual Meeting Nov 3-6, 2013. Poster #1003.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Xiang Y. and Hartman G. L. Comparison of Fusarium virguliforme and F. tucumaniae isolates on selected soybean genotypes from Argentina and the United States. American Phytopathological Society (APS) and The Mycological Society of America (MSA) Joint Meeting, August 10-14, 2013 Austing, TX. Poster # 274.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Chang S. Construction of Genetic Maps for Glycine latifolia by High-Throughput Sequencing. Plant and Animal Genome XXI, January 12-16, 2013, San Diego, CA. P0341. https://pag.confex.com/pag/xxi/webprogram/Paper7194.html.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Chang S., Hartman, G. L., Singh, R. J., Lambert, K. N., Hobbs H. A. and Domier, L. L. Identification of high-quality single-nucleotide polymorphisms in Glycine latifolia using a heterologous reference genome sequence. Theor. Appl. Genet. Volume 126, Issue 6, pp 1627-1638 doi 10.1007/s00122-013-2079-8.


Progress 01/15/12 to 01/14/13

Outputs
OUTPUTS: The project has three goals: 1) build and sustain a recognized graduate program that trains and graduates Fellows in New Biology to enter into the workforce and meet the needs of the agricultural system; 2) promote diversity among the trainees; and 3) to be a model for other training programs. The project already has outputs on all three goals that address the urgent need for new biologists skilled in systems biology approaches to integrate information and mine large and complex data sets to secure food-producing animal and plants. Addressing the first goal, the New Biology Graduate Fellows Program (NBGFP) at the University of Illinois started on February 2012. The Program already accommodates 10 graduate students, two of whom receive USDA NIFA National Needs fellowships (NNF). The NNF supports two graduate students that were admitted to the graduate program of studies and started on August 2012. One student is pursuing a M. Sc. in Crop Sciences and the other is pursuing a Ph. D. in bioInformatics. All 10 New Biology Graduate Fellows and their New Biology projects are listed in the program's website (http://ansci.illinois.edu/labs/bioinformatics/new-biology-fellows-pr ogram). The program's website has served as effective tool to recruit and promote this successful program. Recruitment included advertisement of the program in various venues including American Society of Animal Sciences Graduate BULLetin (http://blog.asas.org/GraduateBulletin/); SACNAS (http://sacnas.org/); email lists (AGDG-LIST; NRSP8 National Animal Genome Research Program angenmap); undergraduate seminars at the University of Illinois; NSF undergraduate research mentored fellows). From the recruitment efforts, 8 students applied and the top two students were selected by the steering committee to receive fellowships. Both fellows supported by the project have been full-time students at the University of Illinois attending courses, conducting research and participating in seminars. Addressing the second goal, half of the fellows supported by NNF are from under-represented (URM) groups. Recruitment included advertisement in SACNAS and at Hispanic Serving Institution. Addressing the third goal, the PI has offered support in the submission of an application to the USDA NNF program by another unit. The NBGFP website and resources are a model for other NNF projects. PARTICIPANTS: Daniel Febrer. Graduate student receiving a fellowship. Scott Nixon. Graduate student receiving a fellowship. TARGET AUDIENCES: Target audiences are other training programs, academic institutions, industry and federal agencies that aim at having a diverse population knowledgeable on the application of informatics, statistics and computer sciences to enhance animal and plant production PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
Six outcomes are the result from the activities supporting the three goals of the project. First, a New Biology Graduate Fellows Program was created. A comprehensive web-site including a list of fellows and projects, a site for program applications and additional resources was created (http://ansci.illinois.edu/labs/bioinformatics/new-biology-fellows-pr ogram). Second, the program is centered on a cohort of 10 New Biology Graduate Fellows (NBGF). Third, two of the fellows are receiving National Needs Fellowships and are working towards a M. Sc. and a Ph. D. degree. Fourth, the 10 NBGFP fellows are learning and performing research on state-of-the-art applications of systems biology including genetic flow and net profit in swine cross-breeding systems, application of proteomics to identify neuropeptides with importance in growth, reproduction and behavior, identification of microRNAs, transcription factors and target genes associated with survival and disease recurrence, characterization of mass spectra used to identify peptides, efficacy of frozen semen, inference of growth curves and study of fertility and survival in poultry, and transcriptome adaptations in liver of dairy cows in response to nutrition around the time of calving. Fifth, all NBGF are receiving training and hands-on research experiences in systems biology approaches to integrate information and mine large complex data in support of animal and plant production and health. The NNF-funded Ph. D. fellow's new biology project centers on transcriptome and alternative splicing profiles associated with infection challenge and subsequent inflammatory response across two genetic lines. The Ph. D. fellow has taken the following graduate level courses: CPSC 541 Regression Analysis, KIN 557 Stress Immunology, ANSC 545 Statistical Genomics, ANSC 542 Applied Bioinformatics, workshop on RNA-Seq analysis, workshop on Unix platforms. The NNF-funded M. Sc. fellow's new biology project focuses on complex modeling nitrogen response using climactic and soil taxonomic data to improve the accuracy of maximum response to nitrogen calculation in support of farmers fertilizing decisions. This M. Sc. fellow has taken the following graduate level courses: CPSC 437 Principles of Agroecology, HORT 447 Horticultural Plant Breeding, CPSC 448 Soil Fertility and Fertilizers, CPSC 545 Statistical Genomics, CPSC 540 Applied Statistical Methods II. Fifth, 50% of the fellows supported by NNF are from under-represented (URM) groups, 2 NBGF are women, and two NBGF are from URM groups. The NBGFP continues to offer high-quality, learning-centered and outcomes-based graduate training that addresses the NNF charge to 1) support graduate training to resolve the TESA, 2) increase graduation in agricultural sciences, and 3) develop intellectual capital on Science, Technology, Engineering and Mathematics (STEM) to ensure the preeminence of U.S. food and agricultural systems.

Publications

  • No publications reported this period