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NY/NJ

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!

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. 

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.



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.

F Element Project Reconciliation Statistics Fall 2020-Spring 2021 Gene model submission statistics: reconciled 848 gene models; approximately 75% of the submitted gene models were in congruence with the final gene models. Breakdown of annotation errors (n=232; note: some models have multiple annotation errors): The most common annotation error in the submitted gene models is the selection of incorrect splice site boundaries (24%) followed by start/stop codon error (18%), extra/missing exon (12%), missing pseudogene or retrogene (12%), gene model missing (9%), not the orthologous model (8%), mislabeled/missing isoform (6%), novel isoform (6%), and submission error (5%).

2021 F Element GEP Summer Research Fellows

During Summer 2021, five Summer Fellows from New Jersey City University (NJCU), Rutgers University, and Washington University in St. Louis (WUSTL) reconciled coding region annotation projects from the Drosophila ananassae F element, the D. ananassae D element, and the D. bipectinata F element. The five Summer Fellows (Ishtar Olaveja, Jackie Hester, Annabelle Laughlin, Martin Dalling, and Alice Herrmann) were mentored by Dr. Cindy J. Arrigo at NJCU with support from Wilson Leung at WUSTL.

Collectively, the Summer Fellows reconciled 848 gene models and completed 21 unique TSS annotations. Approximately 75% of the submitted gene models were in congruence with the final gene models. The most common annotation error in the submitted gene models is the selection of incorrect splice site boundaries (24%). The image above illustrates the preliminary reconciliation statistics for the F element projects in Summer 2021. We anticipate that the final reconciliation statistics will be available in October 2021.

As part of reconciliation of the coding region annotation projects, the Summer Fellows also identified several interesting features on the F and D elements. These interesting features include a novel isoform for the Zyx gene and a partial duplication of Arl4 on the D. ananassae F element, three novel paralogs of a male-specific gene in D. ananassae (derived from CG3795), and a retrotransposed pseudogene derived from yin on the D. bipectinata F element. The presentations which summarize their work this Summer are publicly available through Box.

Three of the Summer Fellows plan to continue their reconciliation work and the data analysis of the reconciled gene models this Fall. Some of the Summer Fellows also plan to present their work at local conferences and undergraduate research symposia at their local institutions.

The Summer Fellows were supported by a grant from the National Science Foundation (Award #: 2114661).