Twelve undergraduate students shared their recent research annotating genes as part of the Pathways Project at the third semi-annual virtual Southeast Regional Node Meeting and research symposium on April 22, 2022. The event began with an engaging talk by Dr. Rebecca Varney, Postdoc at the University of California—Santa Barbara, on how gene annotation efforts can be especially helpful when working with non-model organisms.
Dr. Stephen Klusza, a GEP Member since 2020, was recently featured in Genes to Genomes, a blog from the Genetics Society of America.
The GEP Southeast Regional Node held a virtual meeting on November 12, 2021, with 43 students and faculty in attendance, representing colleges and universities from Alabama, Florida, Georgia, and Tennessee. Keynote speaker Dr. Sarthok Rahman, a postdoctoral researcher at The University of Alabama, discussed how bumblebees got their colors. His address described scales of life ranging from molecular to ecological, including aspects of epigenetics, gene mapping, signal transduction, developmental biology, convergent evolution, Müllerian mimicry, biogeography, and more. Dr. Sarthok’s presentation exemplified how high-quality genome annotations are useful for comparative genomics.
After the keynote address and ensuing discussion, the 30 undergraduates were divided into two breakout rooms, where they presented their research as five-minute talks. Students shared their challenges, progress, and results in reconciling, annotating coding sequences, and annotating promoter regions.
Students reported that the annotation projects have been a valuable introduction to the world of bioinformatics and participating in our Course-based Undergraduate Research Experience has helped them to make order and sense from overwhelming amounts of data. Faculty reported that it was interesting to hear a broad diversity of student talks.
The two-hour event continued a series of community-building Southeast Regional Node events. We look forward to seeing faculty and hearing from more students at the next meeting!
Collectively, the Summer Fellows reconciled 102 gene models. Approximately 10% of the submitted gene models were in congruence with the final gene models. The most common annotation error in the submitted gene models was improperly assigning synteny (62%). The image above illustrates the preliminary reconciliation statistics for the types of annotation errors for the Pathways Project in Summer 2021.
Reconcilers primarily focused on a single gene each, so that they could perform deeper analysis on the evolution of that gene within our selected clade. Presentations summarizing each of their work are publicly available on Box.
The Summer Fellows also generated microPublication documents. Multiple models of four genes (Tor, Ilp3, raptor, and Dsor1) will be sent to microPublication for review by the end of September 2021. Five of the reconcilers will continue to work with the Pathways Project team to reconcile gene models and send them for publication.
The University of Alabama’s 14th annual Undergraduate Research and Creative Activity Conference (URCA) was held on March 31, 2021.
Six GEP students (mentored by Dr. Laura Reed) presented at URCA 2021 one of which, Samantha Hoffman, won 1st place in her division.
Analyzing the evolutionary rate of wrd in connection to its position in the insulin signaling pathway
Abstract: The insulin signaling pathway is a metabolic pathway involved in glucose regulation and has been linked to cell growth, fat and protein metabolism, and disease. Insulin and its pathways can lead to Type II Diabetes, Cardiovascular Disease, and cancers in humans, which are some of the most common and fatal diseases in the United States. Since this pathway is well conserved across phyla, we are using Drosophila melanogaster to analyze the rate of evolution in the gene wrd, a negative regulator of the insulin receptor and TORC1 signaling pathways. The goal of this study is to use gene annotation to compare wrd across six different species of Drosophila and analyze the evolutionary differences and conservation patterns of this negative regulator.
The GEP’s Southeast Regional Node held its Spring 2021 Regional Node Meeting on Friday, April 23, with over 60 in attendance, including students and faculty from constituent states Alabama, Florida, Georgia, and Tennessee. The keynote speaker Whitley Kelley, MS, Certified Genetic Counselor at HudsonAlpha Institute for Biotechnology in Huntsville, AL, provided a fascinating overview of how genomics can be practically applied in careers in genetic counseling (see recording below). Faculty were inspired by the talk to include similar professional development training for students at their own institutions.
Following the keynote address, virtual breakout rooms offered a platform to undergraduate and graduate students to present 5-minute poster sessions on their GEP research projects. Again, faculty response was extremely positive; one professor commented, “Seeing the student presentations with the RNA-Seq provided even more weight to the benefits of the GEP Gene Annotation Curriculum in providing hands-on experiences with multiple data-sets and the feasibility of implementing this curriculum with other scientific questions.”
The two-hour online event served as a brief yet effective forum where students and faculty alike were empowered and motivated to continue active engagement in genomic research.
The Southeast Regional Node held its first New Member Training Welcome Workshop at The University of Alabama February 7-9, 2020. Please help us welcome these five outstanding trainees to the GEP community: Karen Rose and Dr. Marleshia Hall, Shelton State Community College; Dr. Kaleb Heinrich and Dr. Andy Chaudhuri, The University of Alabama; and Dr. Michael Sandel, University of West Alabama!