Progress 09/01/23 to 08/31/24
Outputs
Target Audience:This project aimed to provide genomics and bioinformatics training to students in agricultural and biological sciences. The target audience was graduate and undergraduate students at the University of Puerto Rico and other professionals in agricultural sciences on the island of Puerto Rico. During this reporting period, we conducted the first pilot workshop, which was attended by a total of 27 students. Of these, 4 % were undergraduates, 22 % were master's students, 56% were PhD students, and 7% were postdoctoral fellows. In addition, the workshop was also attended by faculty members (4%) and professionals who work for the USDA-ARS Tropical Agriculture Research Station in Puerto Rico (7%). In addition, 4% percent of the attendees were affiliated with the University of Puerto Rico, Ponce, a primarily undergraduate institution. All students enrolled in the workshop were from underrepresented minorities: 96.3% Hispanic and 3.7% African descent. Changes/Problems:The workshop was implemented as planned and proceeded smoothly with no problems that could not be readily addressed at the time of their occurrence. One of the problems we encountered was the ability of some students to have viable internet connections at all times. This shortcoming was resolved by connecting students via working groups, providing instructional information on the website, and facilitating communication between students and instructors via email. On the other hand, there were some delays that impacted the rate of expenditure for year 1. Even though the grant was activated in September 2024, the official project start date was November 1, 2024, as originally specified in the proposal submitted. This caused a slight decrease in the expenditure for year 1. Due to an administrative delay, the contract for Dr. Zimin (bioinformatics consultant) was not finalized until the end of year 1. Thus, his role inone-on-one training with studentshas shifted from years 1 and 2 to years 2 and 3 of the project. Due to ongoing renovations in the computing framework at the UPR High-Performance Computing facility, the purchasing of computing nodes to enhance the HPCf cluster was postponed to year 2. The HPCf administrators recommended that we wait until this upgrade is complete before purchasing new computing nodes. It is important to note that these expenditure delays did not affect the project schedule or goals. All expenditure delays will be remedied in years two and three of the project. What opportunities for training and professional development has the project provided?For students, this workshop served as a means to acquire a new skill set that facilitated the completion of their research projects and, therefore, facilitated the attainment of their higher educational degree. For professionals (post-docs, research faculty, and USDA investigators), the workshop provided new analysis skills that have broadened their research fields. In addition, experts in genomics sequencing, bioinformatics, and big data management were invited to present and interact with participants, providing new knowledge and networking opportunities. We organized three seminars/workshops with invited speakers open to the university community. This seminar included talks by: Sara Goodwin, PhD.Research Assistant Professor and Genomics Core Head at Cold Spring Harbor Laboratory: "Third Generation Sequencing Technologies" Jianguo (Jeff) Xia, PhD.Associate Professor and the Canada Research Chair in Bioinformatics and Big Data Analytics from McGill University, Macdonald Campus. "Networkanalyst a platform for comprehensive gene expression profiling via network visual analytics" Peter Cooper, PhD.Staff Scientist at the National Library of Medicine, National Institute of Health: "Exploring NCBI Gene Expression and Other Biomolecular Resources" How have the results been disseminated to communities of interest?All workshop material (videos, assignments, reading material, and student presentations) has been posted on the official course website, which is freely accessibleand available to everyone. What do you plan to do during the next reporting period to accomplish the goals? Provide hands-on training on bioinformatic pipelines for genomic analyses: Evaluate participants learning outcomes during the first round of the workshop using the pre- and post-course student surveys obtained as part of the workshop. Curate the videos created during the first reporting period to streamline and annotate content to facilitate future navigation. Develop the second workshop focused on genome assembly and annotation. One-on-one training with students: We will continue to provide one-on-one training to students enrolled in the next reporting period, focusing on a new bioinformatic topic: Genome assembly and annotation. Fostering collaborative interactions: We will continue to promote collaborations between students and faculty as in the previous reporting period. We will also organize another series of speakers to complement the workshop topic. Facilitate genomic research: For the next reporting period, we expect to train a new cohort of students and continue to enhance their research projects by developing new genomic and bioinformatic skills.
Impacts
What was accomplished under these goals?
Hands-on training on bioinformatic pipelines for genomic analyses: During the reporting period, we created and implementeda workshop on genomics and bioinformatics, focused on transcriptomic analysis. The workshop consisted of 15 lectures of 3 hours each and was led by six instructors with different expertise. The workshop covered three instructional modules: (1) Experimental Design for Agricultural Genomics, (2) Introduction to Computational Platforms and Bioinformatic Tools, and (3) Hands-on Analysis of RNA-seq data sets.Each lecture consisted of a theoretical introduction followed by a hands-on learning experience, where students implemented the learned knowledge on real-life biological problems. All lectures and activities were recorded and made available to students for further on-demand distance learning. A total of 45 hours of instructional videos were created and posted, along with supporting scientific literature, to serve as additional instructional material. A course webpage was created to administer the course, share supporting material (scientific articles, class videos, and take-home assignments), and as a means of communication between students and instructors/speakers for one-on-one assistance. This website will host the open-source distance-learning platform that will be the main product outcome of this proposal. One-on-one training with students: During this period, 27 students enrolled in the course were engaged in individual research projects. Students received individual support from course instructors. Students also received advice regarding the experimental design of their ongoing and future projects. Students were also trained in approaches to reporting their research findings and preparing for future publications. Fostering collaborative interactions: During the workshop, students were divided into teams to encourage interactions and individual contributions toward solving problems addressed in class. The student teams were encouraged to meet outside the workshop time to further practice skills acquired during the workshop. Members of the teams could also directly contact the instructors for advice and feedback. Facilitate genomic research: The workshop thus far has impacted the research of 14 different research laboratories at the University of Puerto Rico, Rio Piedras (11 labs), and the USDA Agricultural Station in Puerto Rico (3 labs). The research projects include an extensive array of topics, including but not limited to: Bacterial diversity of Puerto Rican coffee leaves. Enhancing agricultural practices for coffee production Coffee bean pathogens and biological control Fungal diversity and its effects on coffee bean health Integrated management of cover crops, biochar, andBeauveria bassianafor soil and plant health in coffee production. Effects of urban shade on seagrass health. Effects of soil microbiome on banana cultivation. Characterization of insulin-like growth factors in sea cucumberHolothuria glaberrima. Cellular and Molecular Characterization of Muscle Regeneration inHolothuria glaberrima. Characterization of astroglia markers in sea cucumbersHolothuria glaberrima. Molecular basis of holothurian radial nerve cord regeneration. Epigenetics of alcohol neuroadaptation inDrosophila. Insecticide resistance in mosquitoes. Alcohol neuroadaptation in insects. Environmental neuroadaptation in insects. Conservation of highland coqui species in Carite and El Yunque . Patterning and coloring of butterfly wings. Genomic characterization of land snails. Role of Septin9 in inflammatory breast cancer. Microbiome dynamics in inflammatory breast cancer. Role of Basonuclin-1 in inflammatory breast cancer. Genetic diversity and systematics of three species of Ilex from the Greater Antilles. Integrated pest management strategies on mango inflorescence in Puerto Rico. Molecular mechanisms for understanding interactions between tropical plants and pathogens. Enhancing cacao (Theobroma cacao) rootstock resilience: A comprehensive germplasm evaluation for drought tolerance. How does the microbiome on the host and parasitoid change at different locations?
Publications
- Type:
Journal Articles
Status:
Submitted
Year Published:
2024
Citation:
Avalos A., Scannapieco A, Monmany-Garzia AA, Marcelino J, Donthu R, Giordano R, Giray T, Galindo-Cardona (2024). Scientific Note: Relative representation of Africanization in Apis mellifera from Argentina. Apidologie (submitted).
|