Emergence: A newsletter of discovery, education, and outreach from the EMBRIO Institute

 

Issue 40: March 27, 2025

 

DIRECTORS’ NOTE 

Plan to join us for the Institute’s next all-hands seminar Monday, April 7th, 3PM EDT with the Staiger lab and Iyer-Pascuzzi lab leading the presentation for Thrust 2A. If you missed any previous seminars, you can find the recording on our shared Box drive in the All-Hands Meetings Recordings folder. The upcoming Thrust level seminar schedule is below.

 

Investigators: emails went out March 14th with requests for progress reports (due April 14th) and information about Y5 budgeting. We’ve just received today a revised annual reporting template from NSF that will slightly alter how you report some activity. Brent will be in touch directly with details.

 

Please hold on your calendars (calendar invites were sent in February) the week of June 9-13 for the annual EMBRIO Summer School (Mon-Wed) and Annual Meeting (Thurs-Fri). A forthcoming poll will solicit input from all members regarding formats and topics. This year we are announcing both Best Paper and Best Scientific Figure Competitions – please see the attached announcements – deadline for Best Paper submission is April 9th, and Best Scientific Figure is June 1st.

 

EMBRIO is participating in the Q-Bio Symposium: “Harnessing Complexity, Revealing Simplicity” happening on Friday, April 11th at University of Notre Dame. RSVP by tomorrow Friday, March 28th. The symposium, planned and hosted by the quantitative biology student committee – including the Zartman Lab at the University of Notre Dame, will feature EMBRIO speakers. Trainees and collaborators there is still time to submit a poster. More details about the event can be found below.

You can always check out the latest on EMBRIO research being released in pre-print and peer-reviewed publication on our Institute Google Scholar page. A new preprint on Digital Cousins is out from the Umulis lab:
Li, L., Mdluli, T., Buzzard, G., and Umulis, D. Digital Cousins: Simultaneous optimization of one model for BMP signaling in distant relatives reveals essential core. March 1, 2025. https://www.biorxiv.org/content/10.1101/2025.02.25.640248v1

 

Congrats to co-first authors Mayesha Mim and Nilay Kumar, along with EMBRIO co-authors from the Zartman lab, for being awarded the Outstanding CBE Department Paper of 2024 at Notre Dame for work on Piezo in Cell Reports:

 

Mim M.S., Kumar, N., Levis,M..,  Unger, M.F., Miranda,G., Gazzo, D., Robinett,T., and  Zartman, J.J. (2024) Piezo regulates epithelial topology and promotes precision in organ size control, Cell Reports, 43, Issue 7,114398, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2024.114398

 

 

Other opportunities and workshops coming up include the free virtual Sloan Mentorship Community of Practice Workshop: Rubrics for Holistic Competitive Decisions, April 22nd, with leadership from EMBRIO Investigator Stephanie Gardner. Please see the attached flyer for details and QR code for the zoom link, but consider registering in advance for this meeting: https://purdue-edu.zoom.us/meeting/register/UvqM_3QWTdacKoLsbGk0Sg   After registering, you will receive a confirmation email containing information about joining the meeting.

 

The American Society for Cell Biology has opportunity for organizing a workshop session. Those interested please contact Brent (laddb@purdue.edu) or Jeremy Zartman (jzartman@nd.edu) The deadline for workshop proposals is April 8th https://www.ascb.org/cellbio2025/sessionproposals/

 

An additional reminder:  The postdoctoral fellowship opportunity at Notre Dame for those who have successfully completed all requirements for a doctoral degree between June 2023 and September 2025  (deadline is April 6th): Jeremy Zartman is interested in supporting anyone for this fellowship if they are interested and eligible to work in his Multicellular Systems Engineering lab. Please contact Dr. Zartman to discuss. Details on the University of Notre Dame Provost's Postdoctoral Fellowship in Engineering (deadline is April 6th):  https://engineering.nd.edu/provosts-postdoctoral-fellowships-in-engineering-program/

 

David, Jeremy, Chris, Anjali, Janice, Alejandra, Elsje, and Brent

 

 

QUICK LINKS 

 

All-Hands Meetings Recordings

 

Q-Bio Symposium RSVP

 

Materials from Summer School & Annual Retreat

 

Institute Skills and Strengths Sharing Platform

 

Orientation to EMBRIO

Sign the Data Sharing Policy Agreement

 

EMBRIO Personnel List

 

Hot Off the Press: New & Recent EMBRIO Journal Papers and Preprints

Let us know about new papers you want to highlight for the EMBRIO community!

Check out our Google Scholar Page

See a more complete list of Scholarly Products produced under support of EMBRIO Institute

 

Li, L., Mdluli, T., Buzzard, G., and Umulis, D. Digital Cousins: Simultaneous optimization of one model for BMP signaling in distant relatives reveals essential core. March 1, 2025. https://www.biorxiv.org/content/10.1101/2025.02.25.640248v1

 

REMINDER: EMBRIO Acknowledgement for Scholarly Papers and Posters.

For EMBRIO related research publications, NSF requires acknowledgement of EMBRIO NSF funding for our Institute to claim the work in our reporting back to NSF. Please include the following acknowledgement in your journal and conference papers and posters: “This work is based upon efforts supported by EMBRIO Institute, contract #2120200, a National Science Foundation (NSF) Biology Integration Institute.”

 

UPCOMING DEADLINES, IMPORTANT DATES, OPPORTUNITIES & INFO 

 

EMBRIO All-hands Meeting Schedule, Monday’s 3-4pm ET.
Zoom Link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC.1&from=addon

Previous All Hands Recordings

Trainees and collaborators encouraged to co-present during the Thrust seminars this semester.

 

 

 

 

April 11, 2025. Q-Bio Symposium, University of Notre Dame. (details below)

April 22, 2025. Sloan Mentorship Community of Practice Virtual Workshop: Rubrics for Holistic Competitive Decisions, with leadership from EMBRIO Investigator Stephanie Gardner. Please see the attached flyer for details and QR code for the zoom link, but consider registering in advance for this meeting: https://purdue-edu.zoom.us/meeting/register/UvqM_3QWTdacKoLsbGk0Sg   After registering, you will receive a confirmation email containing information about joining the meeting.

 

May 12-16, 2025 Cytoskeleton Modeling Workshop, NC State (Details below)

June 9-13, 2025. EMBRIO Summer School and Annual Meeting, Purdue University. Additional Details forthcoming. See the attached for Best Paper and Best Scientific Figure Competitions.

July 9-13, 2025. International Zebrafish Conference. Madison, WI, USA.

 

Quantitative Biology Symposium

Joint Event: Q-Bio@ND + EMBRIO

Location: University of Notre Dame Campus (Hesburg Library and Jordan Hall of Science)
Date: Friday, April 11th. RSVP by this Friday, March 28th. 

Schedule     RSVP

 

On behalf of the Q-Bio@ND community, we are excited to invite you to the upcoming Quantitative Biology Symposium, a joint event with EMBRIO, taking place on Friday, April 11, 2025, on Notre Dame's Campus in the Carey Auditorium & the Jordan Hall of Science, from 8:30 AM to 7:00 PM.

This full-day symposium offers a valuable opportunity to connect ND and EMBRIO researchers, exchange insights, and foster collaborations in quantitative and computational biology. The event will feature engaging research discussions, networking opportunities, and complimentary meals throughout the day. If you are interested in any of the following research themes, please join us: Mathematical and Theoretical Biology, Computational Biology and Bioinformatics, Biostatistics, Population Biology and Epidemiology, Systems and Synthetic Biology

 

Event Highlights:

We’d love to have you join us! If you’re interested, please RSVP here

For additional details, visit qbio.nd.edu for event details or feel free to reach out to sraha@nd.edu or dgazzo@nd.edu with any questions.

Looking forward to a day of exciting discussions and collaboration!

Cheers,

David

 

Additional Gatherings
On the evening of Thursday, April 10, we are tentatively planning to host an informal dinner gathering for EMBRIO investigators and key personnel, with further details to be shared closer to the event. For trainees arriving the night before, we will also hold an informal gathering option as well!

 

 

Full Links

RSVP: https://docs.google.com/forms/d/e/1FAIpQLSd22Fw8gUkR3MUWZeWxfAQlIGTHoVxQZoA5a1zF9droemvQSg/viewform?usp=header

Event Details: https://qbio.nd.edu/events/2025/04/11/q-bio-nd-embrio-joint-symposium/

Cytoskeleton Modeling Workshop, NC State

From: Julio Monti Belmonte <jbelmon2@ncsu.edu>
Date: Thu, Feb 6, 2025, 4:38 PM
Subject: Cytoskeleton Modelling Workshop May 12-16 at NC State
To: <cytosimworkshop@ncsu.edu>

 

Dear Colleagues,

We are pleased to announce the first in-person Cytoskeleton Modeling Workshop in the United States, utilizing the CytoSim software. This workshop will be held at NC State, Raleigh, NC, from May 12-16, 2025.

Over the course of five days, the workshop will feature a combination of lectures, guest talks, and hands-on hackathon sessions. This workshop is open to individuals from a wide range of backgrounds, including Physics, Biology, Chemistry, and related fields, as well as participants at all career stages (undergraduate students to faculty). No prior programming experience is required.

Key Learning Outcomes:
 - How to download, install, and run CytoSim simulations on your own machine
 - An overview of the biophysical properties and dynamics of various cytoskeletal systems and their components
 - An introduction to all the features and functionalities available in CytoSim
 - Techniques and scripts for extracting and analyzing simulation data
 - Methods for performing parameter scans and running simulations on computer clusters

In the final days of the workshop, we will host hackathon sessions, where participants can apply the knowledge gained throughout the workshop to work on projects of their choosing, either independently or in groups, with the support of our instructors: François Nédélec, Daniel Cortes and Julio Belmonte.

Additional Information:
 - There are no registration fees for this workshop; however, participants are responsible for their own travel and lodging expenses. Discounted accommodation rates are available at a nearby university dormitory.
- Lunch and coffee will be provided throughout the workshop.

For more details and to register, please visit the workshop website:
https://cytosimworkshop.wordpress.ncsu.edu

Registration Deadline: March 30, 2025
Given limited space, applicants will be notified by early April regarding their acceptance to the workshop.

We encourage you to share this announcement with any colleagues who may be interested in attending.

We look forward to welcoming you to Raleigh in May!

Best regards,
Julio M. Belmonte
Assistant Professor
Department of Physics
NC State University

 

 

 

Awards

Congrats to co-first authors Mayesha Mim and Nilay Kumar, along with EMBRIO co-authors from the Zartman lab, for being awarded the Outstanding CBE Department Paper of 2024 at Notre Dame for work on Piezo in Cell Reports:

 

Mim M.S., Kumar, N., Levis,M..,  Unger, M.F., Miranda,G., Gazzo, D., Robinett,T., and  Zartman, J.J. (2024) Piezo regulates epithelial topology and promotes precision in organ size control, Cell Reports, 43, Issue 7,114398, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2024.114398

 

 

New Lab Members?

Did you recently have new students or staff members join your EMBRIO projects? We want to add them to the listserv, Box account, demographics survey, and Personnel List for ensuring their inclusion in communications and participation. If they are not already on our Personnel spreadsheet , or they have graduated, let Brent know their names and email contacts (laddb@purdue.edu )