[Embrio-list] Emergence Newsletter: Issue 43 - July 23, 2025

Wed Jul 23 15:27:51 EDT 2025

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

Issue 43: July 23, 2025

DIRECTORS' NOTE

Dear EMBRIO Members:

Summer is always a time of energy and progress at EMBRIO—and this year is no exception. July has brought new milestones in outreach, scholarship, and community.

Earlier this month, EMBRIO investigators led a standing-room-only workshop on computational modeling at the International Zebrafish Conference (IZFS), and several of our researchers gave invited talks at the Society for Mathematical Biology meeting. We’re also proud to feature our summer undergraduate researchers, new publications, upcoming training events, and some exciting promotions and honors across the institute.

Don’t miss the call for submissions to our annual Scientific Figure and Video Awards—now extended through August 15. And if you haven’t scheduled your one-on-one evaluation interview with Soumi Mukherjee, please do so soon.

We encourage all EMBRIO members to check out the latest materials from our Summer School and Annual Retreat (links inside), and follow us on LinkedIn to help spread the word about our collaborative, interdisciplinary mission.

We hope the rest of your summer is both productive and rejuvenating.

Sincerely, Your EMBRIO Leadership Team

[https://mailimages.purdue.edu/purdue-oevprp-rche/EMBRIO_Group_1.jpg]

CONFERENCE TALKS AND WORKSHOPS

EMBRIO Leads Workshop on Computational Modeling and Quantitative Biology at IZFS 2025

On July 10, EMBRIO investigators led an engaging and well-attended workshop at the 19th International Zebrafish Conference (IZFS) in Madison, WI. With over 80 participants, the session titled “Integration of Computational Modeling and Quantitative Biology” explored the powerful intersection of experimental biology and computational approaches in zebrafish research.

The workshop began with a biology-focused overview of how computational modeling enhances our understanding of embryonic development in zebrafish, providing foundational insights into modeling strategies. Speakers then presented advanced workflows for multi-scale modeling from single-cell dynamics to complex tissue-level processes, followed by examples of how machine learning and AI techniques are accelerating image analysis, data quantification, and model optimization.

Throughout the session, attendees explored interdisciplinary case studies highlighting the collaboration between biologists and engineers. These included models of BMP patterning in early dorsal-ventral body-axis formation, mechanistic models of epiboly and notochord mechanics, and calcium signaling models in larval fin wound healing.

The workshop served as a forum for sharing innovative tools and approaches that bridge experimental and computational disciplines. Participants left with new perspectives and techniques to apply in their research, further advancing the zebrafish community’s capabilities in systems-level biology.

For more information on the IZFS program, visit: https://www.izfs.org/education/19izfc/program<https://maillinks.purdue.edu/t/47980411/1651405863/106333579/0/1006595/?x=f6b9394b>

[Names (L to R) per the photo: Nissa Larson - Purdue University; Priyom Adhyapok - Duke University; Linlin Li - Purdue University; Bakary Samasa - University of Pennsylvania Perelman School of Medicine; Chang Ding - Purdue University; Nilay Kumar - Purdue University; Sharon Minsuk – Indiana University; Qing Deng (moderator) - Purdue University; (not pictured, but presenter or organizer: Shelly Tan - Purdue University; Michel Bagnat - Duke University; Mary Mullins -  University of Pennsylvania Perelman School of Medicine)]Names (L to R):

Nissa Larson - Purdue University; Priyom Adhyapok - Duke University; Linlin Li - Purdue University; Bakary Samasa - University of Pennsylvania Perelman School of Medicine; Chang Ding - Purdue University; Nilay Kumar - Purdue University; Sharon Minsuk – Indiana University; Qing Deng (moderator) - Purdue University; (not pictured, but presenter or organizer: Shelly Tan - Purdue University; Michel Bagnat - Duke University; Mary Mullins - University of Pennsylvania Perelman School of Medicine)

Society for Mathematical Biology Annual Meeting

Both Sharon Minsuk (Postdoc Fellow, Glazier Lab, IU) and Taeyoon Kim (Asst. Prof., Kim Lab, Purdue) gave invited talks this month at the Society for Mathematical Biology Annual Meeting: https://2025.smb.org/<https://maillinks.purdue.edu/t/47980411/1651405863/106326933/0/1006595/?x=a3ed03a5>

  *   Sharon’s talk was entitled "The Role of Embryo, Tissue, and Cell Shape in Morphogenesis: Modeling the Cellular Dynamics of Tissue Deformation,” given during the invited symposium of "Modeling the Role of Geometry and Topology in Shaping Cell Behavior, Function, and Tissue Patterns”. Abstract: https://2025.smb.org/MS05/MS-CDEV-06-Part-1.html<https://maillinks.purdue.edu/t/47980411/1651405863/106326934/0/1006595/?x=8820fa6d>
  *   Taeyoon’s talk entitled "Reconstituting the Mechanical and Dynamic Behaviors of the Actin Cytoskeleton" was given during the invited mini-symposium of Agent-based modelling of cell cytoskeletal phenomena. Abstract: https://2025.smb.org/CDEV/MS-CDEV-08.html<https://maillinks.purdue.edu/t/47980411/1651405863/106326935/0/1006595/?x=b1f2dd6b>

Society for the Advancement of Biology Education Research Annual Meeting

The Gardner Lab has been conducting community of practice, interdisciplinary identity, and evaluation research with EMBRIO as part of our Thrust 4 efforts. This month Co-PI, Stephanie Gardner, with graduate students Soumi Mukherjee and Emily Georgopoulos, presented research at SABRE (Society for the Advancement of Biology Education Research).

Interdisciplinary (ID) STEM research allows researchers to cross-disciplinary boundaries and generate new knowledge. Emily’s poster discusses the ways BII graduate student trainees develop interdisciplinary research identities, and Soumi’s discusses the ways BII members develop as ID professionals. These will provide insights as we continue to evaluate the growth and development of EMBRIO, thereby enhancing institutional goals and outcomes. With the rise of ID research and centers, these studies provide insights into bolstering ID education, supporting students in crossing disciplinary and contextual boundaries, and preparing the next generation of ID scientists.

Mukherjee, S, Georgopoulos E, and Gardner SM. 2025, Mapping Success: A Member-Driven Competency-Based Approach to Interdisciplinary Professional Growth within a Biology Integration Institute. SABRE Annual Meeting, July 10-13, 2025.

Georgopoulos E, and Gardner SM. 2025. Exploring Interdisciplinary STEM Identity Development of Graduate Students in Interdisciplinary Biology Integration Institutes. SABRE Annual Meeting, July 10-13, 2025.

Related to this work, EMBRIO members who haven't conducted or scheduled their follow-up interviews with Soumi please see below under Belonging in Team Science @EMBRIO.

[https://mailimages.purdue.edu/purdue-oevprp-rche/Georgopoulus-SABRE-2025.jpeg]

[https://mailimages.purdue.edu/purdue-oevprp-rche/Mukherjee_SABRE_2025.jpeg]

NEW PUBLICATIONS

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

See a more complete list of Scholarly Products produced under support of EMBRIO Institute<https://maillinks.purdue.edu/t/47980411/1651405863/106327243/0/1006595/?x=5260aade>

Weiwei Zhang and Chris Staiger are co-authors on a new publication in the New Phytologist with findings that propose MLO’s act downstream of FER to mediate Ca++ influx and promote ROS production to regulate root hair tip growth:

Ogawa, S.T., W. ZhangP, C.J. Staiger, and S.A. Kessler. 2025. MLO-mediated Ca2+ influx regulates root hair tip growth in Arabidopsis. New Phytol, July 13, 2025. https://doi.org/10.1111/nph.70378<https://maillinks.purdue.edu/t/47980411/1651405863/106327244/0/1006595/?x=799b1cb6>

[https://mailimages.purdue.edu/purdue-oevprp-rche/Root_hair_elongation_pub_Staiger.jpg]

MLO15 contributes to Arabidopsis root hair elongation

Check out EMBRIO’s publications and pre-prints on our Google Scholar Page<https://maillinks.purdue.edu/t/47980411/1651405863/106327245/0/1006595/?x=128a9ce2>

BELONGING IN TEAM SCIENCE @ EMBRIO

EMBRIO mandatory virtual Interviews with Soumi - please schedule yours asap

If you have not yet done so, please sign up for a follow-up virtual interview with Soumi Mukherjee to help capture your experience with collaborating and integrating in the EMBRIO research community. There are available times now through most of August. See the link and details from Soumi below.

Schedule link for signing up now https://www.when2meet.com/?30848105-sqcQL<https://maillinks.purdue.edu/t/47980411/1651405863/106335090/0/1006595/?x=a8b8c360>

Please click this link<https://maillinks.purdue.edu/t/47980411/1651405863/106335091/0/1006595/?x=6e78d3ea> regarding participation in a one-on-one interview to capture your experience in the Institute. This is a crucial part of our mandatory evaluation process in reporting to NSF. Link to sign up is at the bottom of the message.

UPCOMING OPPORTUNITIES & WORKSHOPS

EMBRIO Best Scientific Figure and Video Award Submission

Call for EMBRIO’s Best Scientific Figure and Video Award Submission from Graduate Students, Postdocs, and Staff Research Scientists – these have been extended, with the deadline of August 15th.
Extended Deadline for 2025 Best Scientific Figure or Live Video Awards: Submission link https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://maillinks.purdue.edu/t/47980411/1651405863/106333584/0/1006595/?x=36b7e396>

2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon

Our partners at I.U. in the Glazier Lab and Biocomplexity Institute have announced the 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon at Indiana University, Bloomington, July 28th to August 10th, 2025. Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu at gmail.com<mailto:compucell3d.iu at gmail.com> or visit www.compucell3d.org/Workshop25<https://maillinks.purdue.edu/t/47980411/1651405863/106333582/0/1006595/?x=3e1cab22>.

Register at: www.tinyurl.com/CC3D2025<https://maillinks.purdue.edu/t/47980411/1651405863/106333583/0/1006595/?x=2639357f>.

EMBRIO SUMMER INTERNS AT PURDUE

EMBRIO projects have included ten undergraduates this summer at Purdue working on research in multiple labs. Our summer interns will be presenting their work during the Purdue Summer Undergraduate Research Symposium, July 30 on campus: https://www.purdue.edu/undergrad-research/conferences/summer/index.php<https://maillinks.purdue.edu/t/47980411/1651405863/97057485/0/1006595/?x=88c75106>

EMBRIO Summer Research Intern: SURF Purdue

Project Title

EMBRIO Faculty Mentor

Graduate Or Postdoc Mentor

Siefken, Kenneth David

Computational modeling to assess spatial calcium signaling patterns and mechanisms in plant defense.

Pienaar, Elsje

Kuman, Nilay

Akkinapally, Kashyap

Generate tissue-specific transgenic zebrafish lines for cellular voltage and calcium signaling.

Zhang, GuangJun

Dong, Ziyu

Zhou, Alice Yahui

Generate tissue-specific transgenic zebrafish lines for cellular voltage and calcium signaling.

Zhang, GuangJun

Dong, Ziyu

Mallepalli, Aditya

Light-Sheet Imaging and Imaging Processing of Protein and Ca Signaling in Developing Tissues

Umulis, David

Li, Linlin

Rivera, Rachel Marie

Light-Sheet Imaging and Imaging Processing of Protein and Ca Signaling in Developing Tissues

Umulis, David

Li, Linlin

Lam, Ian Kwan Yin

Light-Sheet Imaging and Imaging Processing of Protein and Ca Signaling in Developing Tissues

Umulis, David

Li, Linlin

Stephens, Morgan

Piezo in zebrafish wound closure

Deng, Qing

Ding, Chang

Rocha Ripari, Mateus

How does a bacterial virulence protein manipulate the plant cytoskeleton

Iyer-Pascuzzi, Anjali

Rogers, Abigail Keelin

Muthamsetty, Srikushal

Computational Investigation of the Actin Cytoskeleton in Plant Cells

Kim, Taeyoon

Coulter, Jeffery

Avila Martinez, Paula Daniela

Imaging CaMKII/actin/Tiam1 in eggs (T1 with Evans lab)

Kinzer-Ursem, Tami

Doszpoly, Agnes and McCarthy, Allyson

QUICK LINKS

All-Hands Meetings Recordings<https://maillinks.purdue.edu/t/47980411/1651405863/106326936/0/1006595/?x=86fd025b>

Institute Skills and Strengths Sharing Platform<https://maillinks.purdue.edu/t/47980411/1651405863/106326938/0/1006595/?x=5f3bafef>

Orientation to EMBRIO<https://maillinks.purdue.edu/t/47980411/1651405863/106326941/0/1006595/?x=be7e9ddc>

Sign the Data Sharing Policy Agreement<https://maillinks.purdue.edu/t/47980411/1651405863/106326942/0/1006595/?x=c4a260b6>

EMBRIO Personnel List<https://maillinks.purdue.edu/t/47980411/1651405863/106326943/0/1006595/?x=6d393fa7>

Materials from Summer School & Annual Retreat<https://maillinks.purdue.edu/t/47980411/1651405863/106326936/1/1006595/?x=f4c9da98>

Annual Retreat Photos<https://maillinks.purdue.edu/t/47980411/1651405863/106326939/0/1006595/?x=b21065d2>

Summer School Photos<https://maillinks.purdue.edu/t/47980411/1651405863/106326940/0/1006595/?x=8a5fb6e4>

Follow us on LinkedIN<https://maillinks.purdue.edu/t/47980411/1651405863/106326944/0/1006595/?x=cc778b3c>

AWARDS & PROMOTIONS

Congrats to Clara Isaza for being promoted to Associate Professor at University of Puerto Rico at Mayagüez!

Congrats to Shulan Xiao in the Jayant Lab for completing her Doctorate this summer! Xiao, Shulan (2025). Dendritic mechanisms underlying multiplexing and feature selectivity in cortical layer 5 pyramidal neurons. Purdue University Graduate School. Thesis. https://doi.org/10.25394/PGS.28876730.v1<https://maillinks.purdue.edu/t/47980411/1651405863/106333580/0/1006595/?x=0a38a5c4>

Brent Ladd received the Bravo+ Award at Purdue. Bravo+ is awarded for accomplishments above and beyond expectations (LinkedIn post from Weldon School of Biomedical Engineering<https://maillinks.purdue.edu/t/47980411/1651405863/106335092/0/1006595/?x=b84f3c38>)

Let us know about your awards and promotions!

NEW LAB MEMBER?

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<https://maillinks.purdue.edu/t/47980411/1651405863/106326943/1/1006595/?x=919b51e8>, or they have graduated, let Brent know their names and email contacts (laddb at purdue.edu<mailto:laddb at purdue.edu> )

Follow us on:

[https://mailimages.purdue.edu/share/linkedin-solid-circle.png]<https://maillinks.purdue.edu/t/47980411/1651405863/106335358/2/1006595/?e4eaa8c3=MTAwNjU5NQ&8823dc38=MzZjNzY1M2MtNDQ5OS00YTBiLTgyYmYtNmI0Nzg3MjU3NDJk&2fc32d01=ZjFlZDlkMzctYjBiMi00NTM3LTg5MzEtZDQyM2JmMDI0MDdk&18fc3884=NDc5ODA0MTE&x=885dabef>

EMBRIO Website<https://maillinks.purdue.edu/t/47980411/1651405863/89297759/0/1006595/?x=c3810b6d>

Thanks to Jen Goad for assembling our newsletter this month!
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