Progress 08/15/23 to 08/14/24
Outputs
Target Audience:Between 8/15/23and 8/14/24, the target audience for this portion of the training project included threegraduate students. Initially, two graduate students were hired. Both Tyler Weide and Kathryn Heffernan completedthree 8-week rotations as part of the interdisciplinary genetics program. Both students identified a permanent advisor. However, Kathryn Heffernan experienced personal issues that caused her to leave the program. We were able to replace Kathryn with Leonara James, who was in her first semester as a Ph.D. student in the Department of Animal Science and fit the criteria for funding by the grant. Each of the students have gained knowledge and skills across disciplines that contribute to the Genetics and Genomics of Disease. They have gained skills in laboratory and data analytics. Both students have participated in dissemination of their research results through peer-reviewed abstracts and publications. Therefore, the secondary audience for this training project is the conference and journal article participants and subscribers. Changes/Problems:Initially, we hired Mr. Tyler Weide and Ms. Kathryn Heffenan as Ph.D. fellows under the USDA NIFA National Needs Training Grant. However, in the spring of 2024, Kathryn experienced some personal issues that caused her to leave the program. We were allowed to replace Kathryn with another student as long as their research was related to the overarching theme of genetics and genomics of disease and the student was within their first semester of their Ph.D. program. As it turned out, Ms. Leonara Jamesjust completed a master of science degree in fall 2023 and began her Ph.D. program in January of 2024. We are very fortunate and grateful to be able to use these funds for Leonara's program. What opportunities for training and professional development has the project provided?Leonara James attended the Interdisciplinary Biological Science Symposium (April 3-4, 2024, Ames, IA) and the Advances in Genome Biolpug and Technology meetings (April 15-17, Phoenix, AZ). How have the results been disseminated to communities of interest?Both students have submitted papers to peer-reviewed journals. In addition, Leonara has presented her research at two conferences. What do you plan to do during the next reporting period to accomplish the goals?1. Research training: Each graduate student has chosen a permanent laboratory. Tyler will continue to investigate porcine spermatozoa and diseases related to fertility. Leonara will continue to investigate the relationship between fecal and oral microbiomes and animal health and efficiency. Both students will continue the dissemination of the results through conferences and peer-reviewed journal articles. 2. We will conduct two SOTL projects, beginning in the fall of 2024 (Leonara). The second project will begin in 2025, as described above.
Impacts
What was accomplished under these goals?
1. Research training: a. Tyler Weide. From the period of 8/15/2023 to 8/14/2024, Tyler Weide has developed a number of new skills in image-based flow cytometry, cell sorting, utilization of high-performance computing, data handling, and data analysis. Tyler has learned to code in R and Julia computing languages. Hehas also received training in the following statistical methods that include but are not limited to, K-meansclustering, GWAS, QTL mapping, and Bayesian analysis. He has used these skills while participating in a variety of projects, including multi-omic research on porcine spermatozoa fertility, nuclear and mitochondrial genome interaction studies, and biomarker analysis on porcine spermatozoa. b. Leonara James: From the period of 3/1/24 (when Ms. James replaced Ms. Katheryn Heffernan as a National Needs Fellow) to 8/14/24 Leonara James has conducted trials related to the fecal and oral microbiomes role in dairy cattle health and feed efficiency. Leonara has developed data analytics skills in both R and Nova platforms. She has used partial least squares, random forest, stepwise regression, and genomic prediction methods to analyze her data sets. 2. Teaching and SOTL training: a. Tyler Weide's SOTL project will take place in 2025. He is planning to investigate the effectiveness of a new AI tool that will be used in our undergraduate Animal Anatomy and Physiology course. The AI tool is currently being developed and will be introduced to the course in the spring semester of 2025. Data collection will include exam and quiz scores as well as student feedback surveys to gauge the usefulness of the tool. b. Leonara James will participate in her SOTL project beginning in the fall of 2024. Initially, she will analyze existing pre-quiz data from our quantitative genetics course. This quiz allows us to measure students' prior knowledge in the field of genetics and determine which prerequisites were most effective at preparing students for the ANS 3520 course (Genetic Improvement of Domestic Animals).
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2024
Citation:
Weide T., Shofner I., Breitzmann M., Mills K., Kerns K. Metabolic shift in porcine spermatozoa during sperm capacitation induced zinc flux. Submitted and awaiting review June 2024.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2024
Citation:
James L.M., Mayes M.S., Cooper C.J., Steibel J.P., Pe�agaricano F., Koltes J.E., (2024), Milk fatty acids inferred from spectral data are predictive of feed intake in lactating Holstein dairy cattle. Proceedings of the Second Annual Interdisciplinary Biological Sciences Symposium. Ames, IA. Selected for a poster presentation.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2024
Citation:
James L.M., Mayes M.S., Cooper C.J., Breitzman M.W., Pe�agaricano F., Koltes J.E., (2024), Milk metabolites are associated with feed efficiency traits and predictive of feed intake in lactating Holsten dairy cattle. Proceedings of the Advances in Genome Biology and Technology Agriculture 24. Pheonix, AZ. Selected for a poster presentation.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2024
Citation:
James, L.J., Mayes, M.S., Siberski-Cooper, C.J., Breitzman, M.W., Vandehaar, M.J., and J.E. Koltes. (2024) Association of milk metabolites with feed intake and traits impacting feed efficiency in lactating Holstein dairy cows. Accepted 5/26/2024 at Frontiers in Animal Science.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2024
Citation:
Davison C, Harzman H, Nicholson J, Entriken S, Mobley K, Krull A, Singhal M, Skow C, Matthews N, Kopp L, Gillette B, Weide TJ, Hukvari JR, Stumpf SCP, Feldmann OM, McGrail M, Srivastava R, Essner JJ. Tagging the tjp1a Gene in Zebrafish with Monomeric Red Fluorescent Protein Using Biotin Homology Arms. Zebrafish. 2024 Apr;21(2):191-197. doi: 10.1089/zeb.2023.0096. PMID: 38621205; PMCID: PMC11035848.
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Progress 08/15/22 to 08/14/23
Outputs
Target Audience:Between 8/15/22 and 8/14/23, the target audience for this portion of the project was the two graduate students that we have hired. Per the grant proposal, these students must complete three 8-week rotations as part of the interdisciplinary genetics program to identify a permanent advisor. Both students are wrapping up their third rotation, and declaration of their permanent mentor will occur after the start of the fall semester. Each of the students have gained knowledge and skills across disciplines that contribute to the Genetics and Genomics of Disease. One of the students (Tyler Weide) presented a poster at the Society for Study of Reproduction, which created a secondary target audience in the researchers and attendees of that meeting. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?As described above, both graduate students that are funded under this project have worked in three different research labs. This has offered the opportunity to learn a variety of research approaches as it relates to the genetics and genomics of disease. Additionally, students have participated in departmental seminars and one student has attended a scientific conference. How have the results been disseminated to communities of interest?The projects completed under each rotation are small and do not achieve the overarching goal of this grant. However, they have exposed the students to a variety of research methods from which to approach the project. Tyler Weide was able to publish an abstract (poster) at the SSR meeting this past summer. What do you plan to do during the next reporting period to accomplish the goals?1. Research Training Each graduate student will choose a permanent research lab and begin work on a project directly related to the genetics and genomics of disease. Results from these studies will be disseminated at professional conferences and through peer-reviewed publications. 2. Teaching and SOTL Training Each graduate student will be expected to serve as a teaching assistant for an undergraduate course in genetics or genomics. Additionally, each graduate student will begin a SOTL based project in 2024 (topics to be determined by major professor once major professor is identified).
Impacts
What was accomplished under these goals?
1. Research Training: Tyler Weide (graduate student) has participated in three rotations with different researchers to gain experience in molecular and quantitative labs. In his first rotation with Dr. Karl Kerns, Tyler learned about imaging mammalian sperm cells and comparing the metabolism of capacitated vs. non-capacitated spermatozoa in boar. This work was presented at SSR in July. During the second rotation with Dr. Juan Steibel, Tyler learned how to manage, manipulate, and analyze large and complex data sets pertaining to heat stress in pigs. This was Tyler's first experience with programming and statistical analysis in R. In the third rotation, Tyler worked with Dr. Aileen Keating doing High-Resolution Microscopy training with a Stellaris confocal-STED at VetMed. This rotation is currently winding down, anda formal mentor will be identified after the start of the fall semester. Kathryn Heffernan (graduate student) has participated in three rotations with different researchers to gain experience in quantitative labs. During the first rotation, Kathryn worked alongside Dr. Juan Steibel with a focus on Deep and Federated Learning, as well as Computer Vision. We discussed these concepts each week alongside recommended papers by Funkhouser that studied genomic data for selection candidates and popular methods for test matings. She also worked with 50K genotypes of purebred Large White, Landrace, Duroc, and Pietran swine breeds, as well as a three-way crossbred animal of Pietran, Large White, and Landrace, analyzing correlations between all lines and allelic frequencies of each. In the second rotation under Dr. Jack Dekkers, Kathryn focused on disease resilience and associations of candidate genes on host response within swine. Naturally occurring SNPs in genes such as CD163 and GBP5 were discussed. Kathryn also worked with autosomal and sex genotypes in generation of a G-matrix to analyze relationships within the data. For the third and final rotation, she is working alongside Dr. James Koltes. Between discussions of common genetic analyses done within the dairy industry, Kathryn is currently working with cattle sensor data to validate its readings. This rotation is currently winding down, anda formal mentor will be identified after the start of the fall semester. In both cases, Tyler and Kathryn have had a variety of research exposure to disciplines related to the genetics and genomics of disease. 2. Teaching and SOTL training: Once Tyler and Kathryn identify their permanent mentors, efforts will be made to place them into teaching assistant roles within undergraduate courses. At that time, we can also identify research projects in the Scholarship of Teaching and Learning (SOTL) for each of them to work on. Permanent mentors will be identified in the fall of 2023, and SOTL work will begin in spring 2023.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Weide, T., I. Shofner, A. Keller, M. Breitzmann, K. Kerns. 2023 Metabolism of Mammalian Sperm Capacitation. Proceedings of the Society for the Study of Reproduction, July11-14, Ottawa, CA.
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Progress 08/15/21 to 08/14/22
Outputs
Target Audience:This award was awarded in August of 2021 and at that time, the PD was Dr. Nick Serao. After Dr. Serao left the university early in 2022, I (Jennifer Bundy) took over as PD of the grant. Therefore, my efforts during this reporting period have focused on recruitment of qualified graduate students to fill the two available Ph.D. fellowship positions. Announcements of the open positions were sent to: ANGENMAP listserve AGDG listserve internal advertisement through the Interdepartmental Genetics and Genomics Faculty Meeting internal advertisement on the Interdepartmental Genetics and Genomics website internal advertisement through the Bioinformatics and Computational Biology Faculty Meeting e-newsletter through Association of 1890 Research Directors (Alton Thompson) job announcement through MANRRS (Ebony Weber) listserve announcement to Tribal Colleges and Schools (Dr. Cory Welch) listserve announcement to Society for Advancement of Hispanic, Chicano, and Native Americans in the Sciences (SACNAS - Dr. Gustavo Macintosh) North Carolina A&M - Contact made by Dr. Sue Lamont (Animal Breeding and Genetics at Iowa State University) Tuskeegee University - direct email to Dr. Olga Bolden-Tiller Advertisement at the National Animal Science Meetings (ASAS - Oklahoma City) Changes/Problems:One major barrier that we faced was the timing of the recruitment activities. Changing the PD delayed our efforts, and we lost some time while sorting that out. An additional problem was the lack of applicants that are U.S. Citizens. Once our advertisements came out, we received a lot of interest, but not from candidates that possessed the correct citizenship documentation. That was a problem that we certainly did not see coming. What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we plan to have two students funded through the grant. Students will begin their coursework and start identifying potential projects for their dissertation research. Students will also participate in weekly seminar series and potentially participate in relevant conferences.
Impacts
What was accomplished under these goals?
Throughout the summer and early fall semester of 2022, we received 43 applications for the two Ph.D. fellowship positions available. One stipulation of the grant is that students must be U.S. Citizens or possess a green card. Out of 43 applicants, only two fit that bill. Therefore, we conducted on-site interviews with the two qualifying applicants. Ms. Kathryn Heffernan visited from Colorado State University. Ms. Heffernan has an M.S. in Animal Breeding and Genetics and has experience in the field of focus. Mr. Tyler Weide (veteran) visited the group. Mr. Weide is a non-traditional student finishing his B.S. in Biology, His experiences in the plant science laboratory align with wet lab techniques that can be used as part of this project. The grant team determined that both of these candidates were acceptable, and both candidates were encouraged to submit a formal application to the Graduate College at Iowa State University. Both students have applied and, once approved, will plan to start their program in January 2023.
Publications
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