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Regional Node Meeting

GEP Regional Node Meeting Virtual

NY/NJ Regional Node Meeting – April 25, 2023

The New York & New Jersey Regional Node held its Spring 2023 professional development meeting virtually with six GEP members and three undergraduate students in attendance. The meeting began with brief introductions followed by three undergraduate student presentations. Alexis Lemberikman (Baruch College) gave a presentation on her work on the Pathways Project (under the mentorship of Dr. Krista Dobi) and two students from Hofstra University (Angad Dev and Margaret Peck) gave presentations on their projects on the Parasitoid Wasps Project (under the mentorship of Dr. Brittany Miller).

Afterwards, students went to a breakout room to meet with each other while the faculty presented short implementation talks. Dr. Brittany Miller gave a short presentation on her experiences implementing the Parasitoid Wasps Project in her bioinformatics class and Dr. Rebecca Spokony talked about how she has used the Understanding Eukaryotic Genes Modules in her developmental biology class. The meeting ended with a discussion of possible Regional Node Events for next academic year. This one and a half hour meeting was an excellent opportunity for members to learn from each other and support the accomplishments of our amazing students.  

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

A survey was sent to the Node well in advance of the event to find out which general dates and times worked for them as well as ask if there were any faculty who wanted to give a short talk or had students who might be interested. This enabled the event organizer to focus on a date and time that worked best for the speakers and members of the Node.

What would your Node do differently based on your experiences?

Organizers discussed offering talks that were not about projects that have already been implemented, but instead about projects that the faculty plan to implement so the rest of the group could give feedback prior to the implementation. This is the plan for next time!

tamarisk beetle - about 3/8 inch (9 mm) long, They are mostly yellowish brown or green with brown to dark green longitudinal stripes on the wing covers.

Rocky Mountain Regional Node Meeting – November 12, 2022

The Rocky Mountain Regional Node met virtually, to accommodate its distant members, on November 12, 2022. Dr. Amanda Stahlke gave a riveting talk about the tamarisk beetle species that have been introduced to the western United States as a biocontrol measure against the invasive tamarisk plant, which is threatening our dwindling water supply. She is investigating the genetic underpinning of the success different species have had in different geographical locations. Her research includes the annotation of genes from the species’ recently completed genomes that might be related to the species’ success.

Dr. Stahlke is moving forward with plans to use GEP tools to implement such annotation into a course she is co-teaching with Node member Dr. Zeynep Ozsoy. They are interested in developing this research project as a regular GEP science project that can be implemented by other GEP members in the future. The Node members were very supportive of this idea and discussed ways that we might be able to help them move forward.

GEP member Dr. Shan Hays presented his implementation of TSS annotation and members discussed ways they could add TSS annotation to their courses as well.

Finally, the Node name you now see was adopted and the newly inaugurated “Rocky Mountain Regional Node” discussed plans to meet virtually again in the spring. Overall, it was a great opportunity for the group to connect and talk about science and GEP!

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

The event was pre-planned and the Node, as a group, decided to focus on the major outcomes that were expected from it.

What would your Node do differently based on your experiences?

Event organizers needed to stay on top of communications, especially since it was nearing the end of the semester and everyone was busy.

GEP Regional Node Meeting Virtual

Midwest North Regional Node Meeting – January 26, 2023

The Midwest North Regional Node, which covers Michigan, Ohio, Illinois, Indiana, and Wisconsin, held a Regional Node Meeting virtually on January 26, 2023. The meeting was organized by the Node Leader,  Dr. Jackie Wittke-Thompson (University of St. Francis). The 28 attendees were from 21 institutions and included 19 GEP faculty, 6 prospective GEP faculty, and 3 undergraduates. The purpose of the meeting was to introduce GEP to community college faculty in the Midwest North region and to give an opportunity for undergraduate students to share their recent annotation projects. Sessions at the Regional Node Meeting included a presentation by Dr. Paula Croonquist (Anoka-Ramsey Community College) on the impact of using CUREs at community colleges and the support from GEP for implementing genomics CUREs, a discussion with Dr. Natalie Minkovsky (Community College of Baltimore County) on the trials and successes of implementing GEP CUREs at a community college, and three undergraduate research presentations by Jacob Jones and Kwame Asamoah from Taylor University, and Julia Kaniuk from Loyola University Chicago. This successful event is meant to be the precursor to a Regional Node Training for the Midwest North Node during Summer/Fall 2023. 

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

Event organizers sent personal invitations to colleagues at community colleges. The event was also held using the Zoom platform, which includes various accessibility features, such as recordings, auto-generated captions, and text formatting.

What would your Node do differently based on your experiences?

Organizers started planning the event in mid-December. Between the Holidays and everyone being busy during the start of the Spring Semester, there wasn’t much time to send out invitations and recruit students for presentations. Future events need to be planned earlier in advance and invitations need to be sent out with enough time for faculty and students to register.

GEP Regional Node Meeting Virtual

MN/IA/Dakotas Regional Node Meeting – September 30, 2022

The Minnesota, Iowa, and Dakotas Regional Node held a virtual meeting on September 30, 2022. The meeting began with introductions, laughs, and updates. Dr. Andy Arsham was the highlighted speaker from Bemidji State University. He gave an engaging research seminar on his current work with the Zas-Znf gene family in the Drosophila lineage. The second part of the Node workshop was an open work time and space for questions around advanced gene annotations in the Pathway Project. Two awesome GEP Virtual TAs joined to answer questions while participants worked through the problematic gene Shaggy in Drosophila willistoni. There were many isoforms and the group wanted to know the best way to approach all of the isoforms. This was a great success, and everyone took something new from the knowledgeable TAs. Finally, Node members discussed and planned the student research event for the spring. Save the Date – April 21st, 2023 at Saint Catherine University! The plan is for this event to be an all-day in person event with student presentations, guest speakers, and lots of food. 

Update: The in-person RNM was held on April 21, 2023 and went incredibly well. There were a total of  80 participants (including admin, staff, and STEM faculty from St. Catherine University). 

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

The Node decided to focus on the Pathways Project. Some of the main objectives of the event was to perform hands-on GEP curriculum training for current GEP members. In particular, members wanted to work on and ask questions about a really difficult gene in the project. The Node Leader sent out information on the gene that would be discussed a day before the workshop. Participants ended up talking through the process and then going through questions.

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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.
Zoom meeting screenshot of 10 participants

New England Regional Node Meeting – January 4, 2023

Pictured Left to Right
Top: Rachel Sterne-Marr, Tom Giarla, Shallee Page, & Evan Merkhofer
Middle: Daron Barnard, Jess Crowley, Shanna Cawley, & Matthew Skerritt
Bottom: Amie Jo McClellan & Cheng-Chiang Wu
The New England Regional Node has active members in Massachusetts, Vermont, New Hampshire and Upstate Eastern New York. The Regional Node Meeting was organized by the Node leader, Dr. Rachel Sterne-Marr, with help from Dr. Daron Barnard, and was held virtually, on January 4, 2023. There were ten attendees in total.

The six historical regulars:
Veteran GEPer, Dr. Matthew Skerritt from SUNY Corning Community College, Corning, NY, and three newly-minted GEP members, Dr. Jessica Crowley and Dr. Shanna Cawley, (Quinsigamond Community College, Worcester, MA), and Cheng-Chiang Wu, (Framingham State University, Framingham, MA) joined as well. Quinsigamond CC and Framingham State are Minority-Serving Institutions. With three new GEP members, this meeting focused on facilitating first-time implementation of GEP materials and projects.

As such, there were talks in the following four areas:
  • GEP Implementation at the Freshmen level (Amie)
  • GEP Implementation in Sophomore level genetics course (Shanna, Matthew and Rachel)
  • GEP Implementation in Junior/Senior molecular biology, bioinformatics and genomics courses with and without wet lab components (Shallee, Tom, Evan)
  • GEP Implementation in independent research (Shallee, Tom, Evan)

Requested resources were then posted on our Node Trello Board. The group committed to having an In-Person Regional Node Meeting with student presentations in January 2024 and Evan graciously agreed to join the node leadership in Summer 2023. Finally, Rachel gave an update on her collaborative efforts with Dr. Nate Mortimer, entitled ‘Proteomic Analysis of the Drosophila Immune Response to Parasitoid Wasp Infection.’ 

What worked well for your event that might help others plan similar events?
The general timing had previously been agreed upon by the node members.

What would your node do differently based on your experiences?
Hold it in person with undergraduate presenters, which was the original goal.
Jacob Kagey projecting slide on Fly-CURE, Research Coordination Network (RCN) which shows a U.S. map with several institutions listed across the country

NY/NJ Regional Node Meeting – September 23, 2022

The New York and New Jersey Regional Node hosted an in-person workshop on how to develop a research based laboratory course on September 23, 2022 at Baruch College, a constituent college of the City University of New York (CUNY) system. Five GEP members and one prospective member attended the event. Dr. Jacob Kagey, GEP faculty member and guest speaker from the Midwest Regional Node, gave a seminar entitled “Moving lab into the classroom” that focused on how to move research into the classroom, publishing and disseminating that work, and assessing student outcomes. Dr. Jacob Kagey leads a Course-based Undergraduate Research Experience (CURE) based research project as part of the Science Education Alliance – Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) research sequence at the University of Detroit-Mercy. Following lunch, all participants informally presented their ideas for new CUREs and discussed logistics for implementation.
What worked well for your event that might help others plan similar events?

The speaker was great and well received. Discussion regarding planning future CUREs went well and there was a lot of participation. Baruch College provided their conference center room for free, since the majority of the attendees were Baruch College faculty.

What would your Regional Node do differently based on your experiences?

The plan always was to have the entire event in-person, and everyone had RSVP’d with the understanding that the event would be held in-person; however, several members got COVID prior to the event, thus resulting in lower attendance. Participation was also down because people who were supposed to come in person did not feel comfortable to come after a recent event where someone told us afterwards that they were COVID positive. In retrospect, a virtual option should’ve been made available and planned accordingly, given that we were in the middle of a pandemic. 

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.
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!