July 2025 - Embrio-list - ecn.purdue.edu

Emergence Newsletter: Issue 43 - July 23, 2025
by Brent Thomas Ladd 23 Jul '25

23 Jul '25

[header] 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=f…> [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=a…> * 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=8…> * 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=b…> 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.jp…] [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=5…> 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=7…> [https://mailimages.purdue.edu/purdue-oevprp-rche/Root_hair_elongation_pub_S…] 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=1…> 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=a…> Please click this link<https://maillinks.purdue.edu/t/47980411/1651405863/106335091/0/1006595/?x=6…> 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=3…> 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(a)gmail.com<mailto:compucell3d.iu@gmail.com> or visit www.compucell3d.org/Workshop25<https://maillinks.purdue.edu/t/47980411/1651405863/106333582/0/1006595/?x=3…>. Register at: www.tinyurl.com/CC3D2025<https://maillinks.purdue.edu/t/47980411/1651405863/106333583/0/1006595/?x=2…>. 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=88…> 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=8…> Institute Skills and Strengths Sharing Platform<https://maillinks.purdue.edu/t/47980411/1651405863/106326938/0/1006595/?x=5…> Orientation to EMBRIO<https://maillinks.purdue.edu/t/47980411/1651405863/106326941/0/1006595/?x=b…> Sign the Data Sharing Policy Agreement<https://maillinks.purdue.edu/t/47980411/1651405863/106326942/0/1006595/?x=c…> EMBRIO Personnel List<https://maillinks.purdue.edu/t/47980411/1651405863/106326943/0/1006595/?x=6…> Materials from Summer School & Annual Retreat<https://maillinks.purdue.edu/t/47980411/1651405863/106326936/1/1006595/?x=f…> Annual Retreat Photos<https://maillinks.purdue.edu/t/47980411/1651405863/106326939/0/1006595/?x=b…> Summer School Photos<https://maillinks.purdue.edu/t/47980411/1651405863/106326940/0/1006595/?x=8…> Follow us on LinkedIN<https://maillinks.purdue.edu/t/47980411/1651405863/106326944/0/1006595/?x=c…> 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=0…> 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=b…>) 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=9…>, or they have graduated, let Brent know their names and email contacts (laddb(a)purdue.edu<mailto:laddb@purdue.edu> ) Follow us on: [https://mailimages.purdue.edu/share/linkedin-solid-circle.png]<https://maillinks.purdue.edu/t/47980411/1651405863/106335358/2/1006595/?e4e…> EMBRIO Website<https://maillinks.purdue.edu/t/47980411/1651405863/89297759/0/1006595/?x=c3…> Thanks to Jen Goad for assembling our newsletter this month!

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EMBRIO mandatory virtual Interviews with Soumi - please schedule yours asap
by Brent Thomas Ladd 15 Jul '25

15 Jul '25

Dear EMBRIO Community, 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. Thank you, Brent Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering, Purdue University Office: Hall for Discovery Learning and Research, Ste. 203 207 S. Martin Jischke Drive West Lafayette, IN 47907 laddb(a)purdue.edu ================== Schedule link for signing up now https://www.when2meet.com/?30848105-sqcQL<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.when2…> Please see the message below 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. “My name is Soumi Mukherjee, a graduate student in the Department of Biological Sciences at Purdue University. Along with my advisor, Dr. Stephanie Gardner, and lab mate, Emily Georgopoulos, I have been leading an institute-wide evaluation study as part of the EMBRIO Thrust 4 initiative. Our initial round of interviews and surveys has been instrumental in capturing your experiences as a member of EMBRIO. This work has informed formative evaluation reports submitted to the NSF and contributed to shaping the institute's competency framework. We are now entering the final phase of our evaluation study and would greatly value your participation in a follow-up interview. This round aims to capture how your collaborations have evolved over time and how these experiences have supported EMBRIO’s interdisciplinary and integrative mission. Your insights will also help us refine the institutional evaluation survey and better understand how EMBRIO’s structural changes have influenced both individual research trajectories and broader institute goals. The findings from this phase will be critical in guiding the evaluation design of EMBRIO 2.0 and ensuring our evaluation efforts continue to support a collaborative and innovative research environment. We truly appreciate your time and contribution to this important work. If you are a member of the EMBRIO institute currently doing a research project, we would like to invite you for participating in this study. Participation in the evaluation process is MANDATORY for all the members of the institute. As a part of the evaluation process, you will take part in an online session (via Zoom), which includes an interview and a brief survey, and the entire process should be completed in an hour. Interviews session would not exceed an hour and would be completed in a day. Everything will be similar to the interviews we did last time. Please fill in all the times on the table you may be available for our interviews using the link below with either your name or email address. Make sure your time merges with Soumi’s availability). Fill this for 1 hour and 15 mins. We may not require the entire duration for the interview, but this would ensure us to have the maximum possible time so that you do not feel rushed. https://www.when2meet.com/?30848105-sqcQL<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.when2…> This information is requested so that we may contact you to set up an online session, but we will use a randomly generated 4-digit code in place of your name to identify all your information for the data collection and analysis. Your participation will not affect any aspect of your association with the EMBRIO institute. If you have any doubts regarding the evaluation process, please reach out to me at mukher42(a)purdue.edu<mailto:mukher42@purdue.edu>.” With Regards, Soumi Mukherjee PhD Candidate | Gardner Research Group Dept of Biology

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REMINDER: Pls Schedule your EMBRIO Interview with Soumi - thanks to all who have done so!
by Brent Thomas Ladd 01 Jul '25

01 Jul '25

Dear EMBRIO Community, 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. Thank you, Brent Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering, Purdue University Office: Hall for Discovery Learning and Research, Ste. 203 207 S. Martin Jischke Drive West Lafayette, IN 47907 laddb(a)purdue.edu ================== Schedule link for signing up now https://www.when2meet.com/?30848105-sqcQL<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.when2…> Please see the message below 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. “My name is Soumi Mukherjee, a graduate student in the Department of Biological Sciences at Purdue University. Along with my advisor, Dr. Stephanie Gardner, and lab mate, Emily Georgopoulos, I have been leading an institute-wide evaluation study as part of the EMBRIO Thrust 4 initiative. Our initial round of interviews and surveys has been instrumental in capturing your experiences as a member of EMBRIO. This work has informed formative evaluation reports submitted to the NSF and contributed to shaping the institute's competency framework. We are now entering the final phase of our evaluation study and would greatly value your participation in a follow-up interview. This round aims to capture how your collaborations have evolved over time and how these experiences have supported EMBRIO’s interdisciplinary and integrative mission. Your insights will also help us refine the institutional evaluation survey and better understand how EMBRIO’s structural changes have influenced both individual research trajectories and broader institute goals. The findings from this phase will be critical in guiding the evaluation design of EMBRIO 2.0 and ensuring our evaluation efforts continue to support a collaborative and innovative research environment. We truly appreciate your time and contribution to this important work. If you are a member of the EMBRIO institute currently doing a research project, we would like to invite you for participating in this study. Participation in the evaluation process is MANDATORY for all the members of the institute. As a part of the evaluation process, you will take part in an online session (via Zoom), which includes an interview and a brief survey, and the entire process should be completed in an hour. Interviews session would not exceed an hour and would be completed in a day. Everything will be similar to the interviews we did last time. Please fill in all the times on the table you may be available for our interviews using the link below with either your name or email address. Make sure your time merges with Soumi’s availability). Fill this for 1 hour and 15 mins. We may not require the entire duration for the interview, but this would ensure us to have the maximum possible time so that you do not feel rushed. https://www.when2meet.com/?30848105-sqcQL<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.when2…> This information is requested so that we may contact you to set up an online session, but we will use a randomly generated 4-digit code in place of your name to identify all your information for the data collection and analysis. Your participation will not affect any aspect of your association with the EMBRIO institute. If you have any doubts regarding the evaluation process, please reach out to me at mukher42(a)purdue.edu<mailto:mukher42@purdue.edu>.” With Regards, Soumi Mukherjee PhD Candidate | Gardner Research Group Dept of Biology

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