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GEP Regional Node Meeting Virtual

Southeast Regional Node Meeting – November 17, 2023

On November 17, 2023, the Southeast Regional Node faculty and students came together for the Fall 2023 Virtual Symposium to highlight excellent student research in gene annotations of F-element and Pathways Projects. In addition, we were very fortunate to have as a keynote speaker Jason Williams of the Cold Spring Harbor Laboratory DNA Learning Center, where he gave some valuable insight into how his career came about in terms of computational biology, bioinformatics, and skills-based instruction and pedagogy with high school and college students. Jason Williams is also the founder of Life Science Trainers, as per a Hudson Alpha article. 

Many thanks to everyone for spending their Friday with us to share their work and ideas, we are looking forward to future virtual symposium events for more excellence.

What worked well for your event that might help others plan similar events?

Zoom was used to facilitate the event. Two breakout rooms were set up and students were assigned to one or the other. The schedule was sent out a day or two ahead of time, so that the students knew which breakout room they would be presenting in. Each breakout room was locally recorded and is available to watch on Box (contact Sarah Crocker-Buta for access).

What would your Node do differently based on your experiences?

It remains difficult to limit student presentations and Q&A to 5 minutes because of unexpected computer issues. In the future, Node organizers might need to consider having a moderator receive all presentations and share it on a working laptop for each speaker, in order to mitigate the technical difficulties. One breakout room had finished their presentations approximately 15 minutes before the other, which resulted in the guest speaker waiting in the main room for a period of time before the breakout rooms were closed. It was definitely a learning experience. 

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Southeast Regional Node Meeting – September 2022

Pictured Left to Right Top: John Stanga, Kathleen Roberts, Stephen Klusza, Tammy Dennis, Srebrenka Robic, & Laurie Stevison Bottom: Kaleb Heinrich, Laura Reed, & Sara Cline
The Southeast Regional Node held their first in-person Regional Node Meeting at The University of Alabama in Tuscaloosa, AL on September 8th and 9th, 2022. The meeting was organized by Dr. Stephen Klusza with the invaluable help of the GEP’s Program Assistant Sarah Crocker-Buta, Dr. Laura Reed, and the Regional Node leadership of Dr. Norma Velazquez-Ulloa and Dr. Melinda Yang. The meeting was attended primarily by Southeast faculty and staff, from a mixture of Community Colleges, Minority-Serving Institutions, and R1/R2 universities. The overall goals of the meeting were to discuss implementation strategies and perform faculty training.
Projecting overview of synteny diagrams used for micropublications that include target gene and genomic neighborhood for both D. melanogaster and the target species
Dr. Laura Reed provided an update on the microPublication pipeline.
Dr. Laurie Stevison facilitated the initial modules for R programming to give faculty experience in using R and providing feedback for further module improvement.
In addition, the participants discussed multiple aspects of GEP implementation in their classes, as well as future events to build community with faculty and students, including Virtual Student Research Symposiums to be held toward the end of the Fall and Spring semesters and future in-person meetings in the Spring.
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Thumbs up from John Stanga
Overall, it was a wonderful and rejuvenating experience for everyone in attendance, including GEP members who were trained virtually, during the first couple years of the pandemic. We were able to accomplish a lot in the space of a 6-hour meeting and look forward to future interactions with other Southeast Regional Node faculty as the academic year progresses.
What worked well for your event that might help others plan similar events?
Working with the Regional Node Leadership and staff allowed the organizers to easily plan out all aspects of the meeting.
What would your node do differently based on your experiences?
It is recommended that in the event of changing leadership, more time is given to the new leader to learn the process of scheduling events before actually having to do so. Event organizers essentially had a month or so to set up this meeting which went well, but it was a lot of last-minute decisions and emails.
GEP Southeast Regional Node Meeting virtual via laptop computer

Southeast Regional Node Meeting – April 21, 2023

The GEP’s Southeast Regional Node held its Spring 2023 Regional Node Meeting virtually on Friday, April 21st, with 20 participants from Alabama and Georgia, representing the University of Alabama, Clayton State University, Columbus State University, and Agnes Scott College. The keynote speaker Dr. Avery Davis Bell, a postdoc in Dr. Annalise Paaby’s lab at Georgia Tech, gave a fascinating talk on how genetic variation in different wildtype strains of C. elegans nematodes display striking divergence in transcriptomic responses to RNAi-mediated knockdown of par-1, indicating that downstream effects of RNAi knockdowns in the N2 reference strain are not necessarily recapitulated in other wildtype strains. In addition, Dr. Bell gave a wonderful account of her journey in academia, going from wet-lab work to computational biology due to disability, and tips and tricks for undergraduates and graduate students to find the right mentors and labs that will support them. Following the keynote address, Dr. Laura Reed and Dr. Brian Schwartz moderated the breakout rooms for students to give 5-minute presentations on gene annotation of multiple genes in the insulin signaling pathway, with some really surprising results. Students from Dr. Reed’s lab, Dr. Schwartz’s lab, and Dr. Srebrenka Robic’s lab presented their GEP-related research. Overall, this 2-hour event was highly successful in fostering stronger connections within the Southeast Regional Node on behalf of the students and faculty, as well as interacting with such an inspirational talk from Dr. Bell on genomics in C. elegans.

What worked well for your event that might help others plan similar events?

Working closely with Regional Nodes’ leadership via check-in meetings.

What worked well for your event that might help others plan similar events?

The virtual event itself was fine. There were still some issues with low participation from GEP Southeast Node faculty overall that requires more introspection on how to increase engagement in a virtual forum.
Southeast Regional Node Meeting April 22, 2022

Southeast Regional Node Meeting April 22, 2022

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.

How to crack a chiton: new challenges for gene annotation in non-model organisms Rebecca M. Varney University of California Santa Barabara Postdoc Twitter @RebeccaMVarney website: rebeccavarney.com
Southeast Regional Node Meeting November 12, 2021

Southeast Regional Node Meeting – November 12, 2021

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!

Pie chart of the Annotation Errors for the Pathways Project Reconciliation Statistics during Summer 2021 Synteny 61.6% Splice site boundaries 4.8% Extra/missing exon(s) 2.1% Mislabeled/missing 6.8% Gene model missing 1.4% Off By 1 2.7% Submission error 19.9%

2021 Pathways GEP Summer Research Fellows

During Summer 2021, nine Summer Fellows from The University of Alabama and Oklahoma Christian University reconciled coding region annotation projects from the Pathways Project. The Summer Fellows—James O’Brien, Ryan Dufur, Aidan Long, Cole A. Kiser, Ashley Morgan, Alyssa Koehler, Annie Backlund, Jhilam Dasgupta, and Rachael Cowan—were mentored by Dr. Laura K. Reed with support from Chinmay P. Rele both of which are at The University of Alabama.

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.

GEP Student Wins 1st Place at Research Conference

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. 

click to enlarge

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.