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

 

Issue 39: February 20, 2025

 

DIRECTORS’ NOTE 

Plan to join us for the Institute’s all-hands seminar this coming Monday, February 24th, 3PM ET with Janice Evan’s lab leading the presentation for Thrust 1B. 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.

 

Please hold on your calendars (calendar invites were sent today) the week of June 9-13 for the annual EMBRIO Summer School (Mon-Wed) and Annual Meeting (Thurs-Fri). Due to several research conferences and schedule conflicts for June and July, this is the best week available. Stay tuned for more details.

 

An exciting event that EMBRIO is participating in will be the Q-Bio Symposium slated for Friday, April 11th planned and hosted by the quantitative biology student committee at the University of Notre Dame, in South Bend, Indiana, including trainees in the Zartman lab. EMBRIO researchers are being invited to present research talks, and a poster session will be held. EMBRIO trainees and collaborators are encouraged to submit and present a poster. Additional details on speakers, posters, registration will be forthcoming.

 

As a result of changes to the NSF BII program in 2024, EMBRIO placed considerable focus the last six months on unifying our collective progress and expertise into an innovative vision for the future of the Institute. The near-term outcome of this effort resulted in successfully submitting a new funding proposal to NSF this week. Although uncertainties abound at the federal level, we will stay in communication with NSF as the review process unfolds. A huge thank you to Jeremy Zartman for his tireless commitment leading the writing effort. As Institute Co-Director with David Umulis, along with the core writers and all who provided input, reviews and feedback, we were able to shape our collective expertise into an innovative vision for the future of the Institute. This would not have been possible without you, the EMBRIO community of investigators, researchers, and trainees, who have collaborated and learned from one another to build a solid foundation of research and knowledge in these first 3.5 years.

 

Continuing with those thoughts, congrats to all who have submitted journal manuscripts for review and/or as preprints and have published EMBRIO research this winter (~ the last 4+ months). Check out the latest EMBRIO research findings from these Institute labs in the “Hot of the Press Publications & Preprints” section below: Glazier, Iyer-Pascuzzi, Jayant, Kim, Kinzer-Ursem, Mullins, Pienaar, Staiger, Umulis, and Zartman. Please let Brent know (laddb@purdue.edu)  if we’ve missed a recent publication, preprint, or submission. Trainees and Research Staff: stay tuned for details on an EMBRIO Best Manuscript Competition.

 

Congratulations to Dr. Shulan Xiao on successfully defending her Ph.D. dissertation earlier this month! Shulan’s research in the Jayant lab, along with collaborating in Thrust 1, led to her work being published in Cell Reports. You can check out that paper here: https://doi.org/10.1016/j.celrep.2024.114413

 

A last reminder to EMBRIO investigators at Purdue if you haven’t yet posted your summer intern research projects in SURF, please do so. EMBRIO will cover the faculty portion of the stipend and housing agreement. The SURF program provides an 11-week on campus research experience. Get your project posted now for consideration (details and links below).

 

EMBRIO members check out these conferences in 2025: Multicellular Engineered Living Systems (M-CELS) Symposium 2025. Organizers invite you to participate in the “M-CELS: Advances in Basic Research and Translational Opportunities” symposium, which will be held on March 26-28, 2025, at the OMNI Hilton Head Resort in South Carolina, USA.

 July 9-13, 2025 the International Zebrafish Conference will be held in Madison, WI, with potential for an EMBRIO Workshop to be hosted there – stay tuned!

 

 

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

 

 

QUICK LINKS 

 

All-Hands Meetings Recordings

 

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

 

Ding, Shihang, Pei-En Chou, Shinji Deguchi, and Taeyoon Kim. 2025. “Impacts of Structural Properties of Myosin II Filaments on Force Generation,” eLife, February 7, 2025 reviewed preprint. https://doi.org/10.7554/elife.105236.1 .

Gazzo, D., T.L. Kinzer-Ursem, and J.J. Zartman. 2024. “Proteins clump: Mechanics and transport during neurodegeneration.” Biophysical Journal, 123,1-3. https://doi.org/10.1016/j.bpj.2024.06.004 .

Gazzo, David V., and Jeremiah J. Zartman. 2025. “Calcium Imaging in Drosophila.” In Calcium Signaling: Methods and Protocols, edited by Caroline M. Gorvin, 257–71. New York, NY: Springer US. https://doi.org/10.1007/978-1-0716-4164-4_19.

 

Hiles, Rachel, Abigail Rogers, Namrata Jaiswal, Weiwei Zhang, Jules Butchacas, Marcus V. Merfa, Taylor Klass, et al. 2024. “A Ralstonia Solanacearum Type III Effector Alters the Actin and Microtubule Cytoskeleton to Promote Bacterial Virulence in Plants.” PLOS Pathogens 20 (12): e1012814. https://doi.org/10.1371/journal.ppat.1012814 .

Khan, Hammad F., Sayan Dutta, Alicia N. Scott, Shulan Xiao, Saumitra Yadav, Xiaoling Chen, Uma K. Aryal, Tamara L. Kinzer-Ursem, Jean-Christophe Rochet, and Krishna Jayant. 2024. “Site-Specific Seeding of Lewy Pathology Induces Distinct Pre-Motor Cellular and Dendritic Vulnerabilities in the Cortex.” Nature Communications 15 (1): 10775. https://doi.org/10.1038/s41467-024-54945-0 .

Kim, June Hyung, and Taeyoon Kim. 2024. “The Mechanism of Dynamic Steady States in Lamellipodia.” bioRxiv, January, 2024.11.18.62420. https://doi.org/10.1101/2024.11.18.624201 .

Matin, Meisam Habibi, Shulan Xiao, and Krishna Jayant. 2024. “Mild Focal Cooling Selectively Impacts Computations in Dendritic Trees.” bioRxiv, January, 2024.11.02.621672. https://doi.org/10.1101/2024.11.02.621672 .

 

Minsuk, Sharon B., T. J. Sego, David M. Umulis, Mary C. Mullins, and James A. Glazier. 2025. “Modeling Epithelial Morphogenesis and Cell Rearrangement during Zebrafish Epiboly: Tissue Deformation, Cell-Cell Coupling, and the Mechanical Response to Stress.” bioRxiv, January, 2025.02.12.637977. https://doi.org/10.1101/2025.02.12.637977 .

 

Ogawa, S.T., W. ZhangP, C.J. Staiger, and S.A. Kessler.* 202X. MLO-mediated Ca2+ influx regulates root hair tip growth in Arabidopsis. New Phytol. Submitted 01-28-25.

 

Rabbi, Md Foysal, Gijsje H. Koenderink, Yuval Mulla, and Taeyoon Kim. 2025. “Fine-Tuning of Material Properties via Catch Bonds.” bioRxiv, January, 2025.01.09.632258. https://doi.org/10.1101/2025.01.09.632258 .

 

Slater, Brandon, Alfredo Sciortino, Andreas R. Bausch, and Taeyoon Kim. 2024. “Cluster Formation and Phase Separation Driven by Mobile Myosin Motors in the Motility Assay.” bioRxiv, January, 2024.11.30.626189. https://doi.org/10.1101/2024.11.30.626189 .

 

Xu, Liyuan, Weiwei Zhang, Lei Huang, Chunhua Zhang, and Christopher J. Staiger. 2025. “Actomyosin and the Arp2/3 Complex Are Involved in the Internalization of Cellulose Synthase Complexes.” bioRxiv, January, 2025.01.19.633783. https://doi.org/10.1101/2025.01.19.633783 .

 

Zhang, Weiwei, Nilay Kumar, Jessica R. Helwig, Alexis Hoerter, Anjali S. Iyer-Pascuzzi, David M. Umulis, Elsje Pienaar, and Christopher J. Staiger. 2025. “Local Traveling Waves of Cytosolic Calcium Elicited by Defense Signals or Wounding Are Propagated by Distinct Mechanisms.” bioRxiv, January, 2025.01.23.634554. https://doi.org/10.1101/2025.01.23.634554 .

 

 

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.”

 

 

EMBRIO Partnership with SURF (Summer Undergraduate Research Fellowship)

Purdue EMBRIO faculty, it is time to post your summer research projects to recruit undergraduate researchers to your lab!

 

 

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.

 

 

 

March 26-28, 2025. Multicellular Engineered Living Systems (M-CELS) Symposium 2025. Organizers invite you to participate in the “M-CELS: Advances in Basic Research and Translational Opportunities” symposium, which will be held on March 26-28, 2025, at the OMNI Hilton Head Resort in South Carolina, USA. 

April 11, 2025. Q-Bio Symposium, University of Notre Dame. Registration, Speakers, Poster Session Details forthcoming.

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.

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

 

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

Let us know about your grants and other awards!

 

 

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 )