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Regional Node Meeting

Members took a group selfie while working in the lab

NY/NJ Regional Node Meeting – June 3, 2022

NEW YORK, NY, June 3, 2022.

The New York and New Jersey Regional Node had a one-day, professional development event hosted by Dr. Shubha Govind at City College New York.

Dr. Johnny Ramroop and undergraduate Jennifer Chou trained GEP members on working with parasitoid wasps. Following an introductory lecture, GEP members dissected Drosophila larvae infected with wasp eggs and larvae.

Node members using lab equipment to dissect infected fly larvae

Confocal microscopy images of Drosophila hemocytes stained with nuclear and cytoplasmic markers

 

 

Drosophila hemocytes were collected, stained with nuclear and cytoplasmic markers, and observed using confocal microscopy.

Members sitting around conference table while eating lunch

 

Following lunch, members discussed curriculum successes and frustrations from the past year. Possible node initiatives such as Node-based student teaching assistants and virtual professor office hours, when teaching annotation in the same semester, were proposed and 2022-2023 Node events were planned.

Since the Node event fell on a day when Alumni Workshop 2022 events were planned, we were able to join the virtual event together as a watch party. 

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

Probably would have been better to use a conference room or a classroom for the hybrid sessions, difficulty getting multiple computers online, plugged in (if we had used rooms typically used for this function, would not have had to try to plan for extra extension cords, etc.)

What lessons were learned from challenges in the planning or execution of the event that might be helpful to others? 

Personal emails to new members to encourage them to come, rather than group email blast.



Carolinas Regional Node Meeting April 22, 2022

Carolinas Regional Node Meeting – April 22, 2022

The Carolinas Regional Node Meeting was held virtually on Friday, April 22, 2022, 9:00am-12:15pm (ET). The meeting kicked off with brief welcome remarks by Jeff French, a Node member from North Greenville University, SC, who also introduced our keynote speaker. Nate Mortimer from Illinois State University, who leads the Parasitoid Wasps Project in the GEP, gave an inspiring talk on “Invasion of the Body Snatchers: Parasitoid Wasps of Drosophila.” We had a break between 9:50-10am to allow for preparation for students’ presentations. Right before diving on these, Marisol Santisteban from UNC at Pembroke, current Carolinas Node leader, gave a brief introduction to the GEP and acquainted attendees with the organization: membership, different modes of participation, and the projects that are currently pursued. 

Engaging presentations by five students from South Wesleyan University (Michelle Eller, advisor) and Appalachian State University (Clare Scott Chialvo, advisor) took us into the intricacies of their projects in the Insulin Signaling Pathways Project and in an emerging new project on detoxification genes, and the challenges of manual annotation of species closely related to D. melanogaster, such as D. immigrants. After a break from 11-11:15, the last hour of the day was a professional development event geared towards students. The “Careers in Genomics” panel hosted 5 experts from different Genomics fields, with different levels of education (not all PhDs), and not all from academia. All panelists were female and from diverse backgrounds. Four of the five panelists also work in North Carolina which shows our Carolinas students that there is a future for them in this field that’s also close to home. Sabrina Powell, Education Program Director of the Precision Medicine in Health Care in the Department of Genetics at UNC Chapel Hill School of Medicine generously helped assemble this extraordinary array of experts and prepared a fictional but realistic scenario about a 3-year-old boy diagnosed with autism, who is referred to the UNC Genetics Clinic for further testing. The testing reveals two specific variants in Mateo’s exome, one which is known to cause a specific subtype of autism and another which is associated with a high risk of adult-onset dementia. There was a role for professionals at each of our panelists’ positions:

  • Kate Foreman, CGC, Genetic Counselor (University of North Carolina at Chapel Hill);
  • Meghan Halley, PhD, MPH, Senior Research Scholar (Center for Biomedical Ethics, Stanford University);
  • Julie Horvath, PhD, Head of Genomics & Microbiology Research Lab (NC Museum of Natural Sciences) and Research Associate Professor, Biological and Biomedical Sciences (NC Central University);
  • Halina Krzystek, Bioinformaticist, Bioinformatics Data Services, Q-Squared Solutions; and
  • Janae Simons, Bioinformatics Software Developer (Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill).


The meeting was attended by 34  people, of which 8 were undergraduate students, and three Community College instructors, two if which had expressed interest in knowing more about GEP and had been invited to New Member Trainings.

Zoom Meeting Room screenshot of participants

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

Using the opportunity that came with the “online” format we were able to host an outstanding keynote speaker (our very own Nate Mortimer from Illinois State University) and panel of experts in different fields of genomics for our “Careers in Genomics” panel; many were in North Carolina, but we had a person from Stanford. It would not have been possible to assemble this array of experts if it had been an in-person event. I would recommend some “professional development” event for students, like the “Careers in Genomics” panel that we had. We hosted individuals in different fields, with different education degrees (not all PhDs), and not all from academia. I believe the students really found this session interesting and useful. Making a program and emailing it to all participants was a plus and we also emailed certificates to the student presenters which is a nice touch of appreciation.

What lessons were learned from challenges in the planning or execution of the event that might be helpful to others?

It is hard to come up with the “perfect” date. We considered weekday vs. weekend, all day vs. half a day, mid semester vs. late in the semester. We finally settled on a Friday because they tend to be lighter days for students, and only half a day (morning). We did it towards the end of the semester, so students would have made enough progress in their projects to present. Considering that Node meetings will be in-person in the future, I would recommend a weekend, maybe start on Friday evening with posters and maybe the keynote speaker and then talks on Saturday morning and some professional development event. Some people may choose to attend only one day but they won’t be a full day. Or maybe make it a whole day event on Saturday. Keeping some form of hybrid might be useful, especially for the keynote speaker or panels, because that allows inviting speakers that are not geographically close to the Node. 
As far as the execution, it is still hard to keep everyone engaged and have them turn on their cameras and ask questions. So as much as possible, I would recommend holding the student presentations in-person and if online, encourage folks to have their cameras on, and incentivize asking question with some form of reward. We provided a short bio of the panelist in the program that was emailed to the registrants the night before. If possible, do that earlier, so people may think of some questions to ask ahead, and openly ask them to try to do so.


Some students reported not receiving a link for the meeting, but they registered only minutes before the start of the meeting. If you plan to leave the registration open till the very start of the meeting, make sure someone in the Node does a last sweep. Ask the GEP staff to give access to registration to someone in the Node.

Keep the GEP staff in the loop for everything planning, they are incredible resourceful, helpful and efficient!

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
New York & New Jersey Regional Node Meeting March 5, 2022

NY/NJ Regional Node Meeting – March 5, 2022

The New York and New Jersey (NY/NJ) Node held a virtual Regional Node Meeting (RNM) on March 5, 2022, in which seven GEP members were in attendance. Dr. Nate Mortimer provided an introductory seminar on the Parasitoid Wasps Project which was followed by a walkthrough of all the project materials. Members learned how to sign-up for an annotation project, how to find the Genome Browser, which Browser tracks were important for the annotation and what types of evidence the tracks contain. Most importantly, members learned how to annotate genes without a good gene model from a closely related species. Overall, attendees thought it was a great way to get excited to implement this new project and teaching genomics.

CalNeAr Regional Node Meeting January 12, 2022

CalNeAr Regional Node Meeting – January 12, 2022

The CalNear node, which covers California, Nevada, and Arizona, had a virtual node meeting on January 12, 2022. The meeting was organized by Claudia Uhde-Stone (Node Leader), Chelsey Mckenna (Node Co-Leader), and Alexa Sawa.

The 19 attendees included 16 faculty, 1 undergraduate and 2 graduate students from 11 institutions (California State University, East Bay, College of Southern Nevada, College of the Desert, Chabot College, San Jose State University, Washington University in St Louis, California State University Northridge, California State University Los Angeles, Vanguard University, Central Arizona College, California Northstate University).

Sessions at the Regional Node Meeting included:

  • Introduction to GEP (Alexa Sawa)
  • Graduate student talks presenting GEP CURE data
  • Undergraduate student talk on benefits of being involved in GEP, and becoming a teaching assistant
  • Q&A session
  • GEP implementation in courses (Claudia Uhde-Stone)

The event was geared to inform and raise interest; we hope that some participants may have been inspired to join our GEP community.
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!

Pacific Northwest Regional Node Meeting November 7, 2021

Pacific Northwest Regional Node Meeting – November 7, 2021

The Pacific Northwest (PNW) Regional Node, which currently includes members from Oregon, Washington, and Idaho, held a virtual Regional Node Meeting (RNM) on November 7th, 2021. The meeting was organized by Norma Velazquez-Ulloa (Node Leader), with feedback from all current Node members: Catherine Reinke, James Bedard, Jack Vincent, Holly Paquette, and Tealia Slagle. There were five current members, three prospective members, and eight undergraduate students in attendance, from six different institutions (Lewis & Clark College, Linfield University, The University of the Fraser Valley, The University of Washington-Tacoma, The College of Western Idaho, Boise State University, and Portland Community College).

Sessions at the Regional Node Meeting included:

  • Undergraduate talks presenting GEP gene annotations on the F-Element and Pathways Projects
  • Faculty implementation talks
  • Q&A time for attendees

This successful event was the second RNM for the PNW Regional Node.
Texas and Oklahoma Regional Node Meeting November 5, 2021

TX/OK Regional Node Meeting – November 5, 2021

The Oklahoma Universities in the Texas/Oklahoma Regional Node held a node meeting at the Oklahoma Academies of Science Technical Meeting in Ada, OK at East Central University. Fifteen GEP students presented their annotation projects either in poster or oral formats. GEP students and faculty from East Central University and Oklahoma Christian University ate lunch together and shared experiences.

Scientific Talk on Parasitoid Wasps

Dr. Nathan “Nate” Mortimer gave a scientific talk on the GEP’s Parasitoid Wasps Project he is the Project Leader for at the Texas/Oklahoma Regional Node Meeting on January 5, 2021.

Southeast Regional Node Meeting – April 23, 2021

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.