November 2025 - Embrio-list

EMBRIO Progress and Continued Funding Efforts
by Brent Thomas Ladd 24 Nov '25

24 Nov '25

[cid:4781ccbc-78b0-42d7-a0b2-446e84fcb0ce] Dear EMBRIO Membership, As an Institute, our collectively achieved progress toward delineating mechanisms of cellular defense and wound repair—properties vital to animal, plant, and human health and biotechnology advancements—is a testament to the power of integrating our expertise. Leveraging this momentum, we are actively assembling teams now to develop new proposals and support co-collaborator proposal writing. Please contact us as soon as possible if you are interested in participating (laddb(a)purdue.edu<mailto:laddb@purdue.edu>, Cc: dumulis(a)purdue.edu<mailto:dumulis@purdue.edu> , jzartman(a)nd.edu<mailto:jzartman@nd.edu> ). We are starting with an NIH RM1 for Multidisciplinary Teams<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgrants.ni…>. For active and potential funding opportunities that align with EMBRIO 2.0 ideas, visit our proposals spreadsheet<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>. Your willingness to learn, share, and tackle the challenging work of integrating ML/AI, simulation, and life-science research, along with educational research and research into the evolution of interdisciplinary identity and teams, have together made EMBRIO a paradigm for integrative discovery. This integrative effort, since late 2021 involving over a hundred investigators, staff, and trainees, has yielded impactful products and fundamental discoveries (a Summary of Outcomes<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> PDF is available on our shared Box account). Perhaps the most important legacy is our trainees. The advancement of sixty-five graduate students and postdocs and sixty undergraduate researchers, at the intersection of predictive computational simulations and biology is directly supporting a growing community of practice, and the long-term growth of the U.S. Bioeconomy. Keep up the transformative research and education to make this fifth year as a Biology Integration Institute our best one yet! 🦃 Enjoy the Thanksgiving Holiday. Your EMBRIO Leadership Team, Leadership Role David Umulis Institute Co-Director Jeremiah Zartman Institute Co-Director Chris Staiger Associate Director Anjali Iyer-Pascuzzi Team Science Lead Alejandra Magana Educational Science Lead Elsje Pienaar Core Modeling Lead Janice Evans Community Advocate Lead Brent Ladd Managing Director

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EMBRIO Weekly Update: Presentation recordings + New Publication in J. Cell Biol.
by Brent Thomas Ladd 20 Nov '25

20 Nov '25

[cid:916c62ac-7c52-4a7f-bf7a-f2e97a6434ee] Dear EMBRIO Members, All-Hands Labs Thanks again to recent presenters this past Monday, Alex Nguyen (Ph.D. Student in the Chan Lab) with Chrissy Boody (Ph.D. Student in the Evans Lab), and Chang Ding (Ph.D. Student in the Deng Lab) presenting their collaborative research: "Measuring cell and tissue-level stiffnesses with atomic force microscopy" in oocytes and zebrafish. On November 3rd we featured the Kim lab with Ph.D. student Jeffery Coulter presenting his collaborations with the Evans Lab and Kinzer-Ursem Lab on "Hybrid models of the mouse egg and dendritic spine", and presented June Kim's work and future directions Modeling the plant cortical cytoskeleton with the Staiger and Iyer-Pascuzzi Labs . You can locate recordings, chat files, and summaries of these talks, and all of the Institute's previous regular seminar sessions going back to 2021 on our shared Box drive under EMBRIO Institute > All-Hands Meeting Recordings: https://app.box.com/s/48uqgrgoy5ygp1tsj2l3lafoy8ubgkop<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> (please note these are for use w/in EMBRIO, and not to be distributed w/o permission). ________________________________ New Publications Exciting New Research on Immune Cell Navigation! Led by the Qing Deng Lab, four EMBRIO Institute labs (Deng, Staiger, Jayant, Zhang) have collaborated on research just published online in Journal of Cell Biology. Results point to a critical role for inwardly rectifying potassium channels (Kir) in guiding neutrophils during chemotaxis. Wang, T., D.H. Kim, C. Ding, D. Wang, W. Zhang, M. Silic, X. Cheng, K. Shao, T.H. Ku, C. Zheng, J. Xie, C., Xiao, S., Jayant, K., Yuan, A. Chubykin, C.J. Staiger, G.J. Zhang, and Q. Deng. (2026). Inwardly rectifying potassium channels regulate direction sensing during neutrophil chemotaxis. J. Cell Biol., 225(1): pgs. https://doi.org/10.1083/jcb.202503037<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> 🔍 Key Findings: * Kir7.1 helps maintain resting membrane potential and enables directional sensing in neutrophils. * Disrupting Kir channels impairs the ability of immune cells to orient toward chemo-attractants. * Using voltage indicators and optogenetics, show that membrane potential oscillations are integral to pseudopod selection and migration. 💡 This work introduces membrane potential as a key player in the feedforward mechanisms that steer immune cells through complex tissue environments—linking electrical signaling with GPCR pathways and cytoskeletal dynamics. 📄 Read the full article here: Inwardly rectifying potassium channels promote directional sensing during neutrophil chemotaxis<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Frupress.o…> [cid:41a99081-9b40-4606-8de9-0dbcf0b0fb97] Find our list of published papers and pre-prints on the EMBRIO Institute Google Scholar page<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.g…>, as well as a full list of scholarly products<https://www.purdue.edu/research/embrio/research/scholarly-products.php> <https://www.purdue.edu/research/embrio/research/scholarly-products.php> at our website. 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

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All-Hands Lab Today 3pm Alexandria Nguyen (Chan Lab) "Measuring cell and tissue-level stiffnesses with atomic force microscopy"
by Brent Thomas Ladd 17 Nov '25

17 Nov '25

[cid:b7afd18c-656d-43fd-858f-5e96be6c6b28] Dear EMBRIO Members, Our All-Hands Lab session this afternoon starts at 3pm ET featuring Alexandria Nguyen (Ph.D. Student in the Chan Lab) presenting her talk titled "Measuring cell and tissue-level stiffnesses with atomic force microscopy" . The talk and discussion will feature work in collaboration with the Evans and Deng labs: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> See you all this afternoon, 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

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EMBRIO Weekly Update
by Brent Thomas Ladd 14 Nov '25

14 Nov '25

[cid:6ad0b25d-55e9-40b2-9ac2-9ce1398ea1e9] Dear EMBRIOphytes, ALL-HANDS LAB Our next All-Hands Lab session will be this coming Monday, Nov. 17th, 3pm with Alexandria Nguyen (Chan Lab) presenting her talk titled "Measuring cell and tissue-level stiffnesses with atomic force microscopy" and will feature work in collaboration with the Evans and Deng labs: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> NEW EMBRIO PUBLICATIONS A new paper in PLOS Computational Biology is available: "Surrogate modeling of Cellular-Potts Agent-Based Models as a segmentation task using the U-Net neural network architecture." Congrats to James Glazier and his collaborators on this new work that employs a U-Net convolutional neural network to accelerate simulations of Cellular Potts Models (CPMs): https://doi.org/10.1371/journal.pcbi.1013626<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> 🔬 Key Findings of the Paper: * The authors developed a deep learning surrogate model using a U-Net convolutional neural network to accelerate simulations of Cellular Potts Models (CPMs). * CPMs are widely used to simulate multicellular biological systems, such as vasculogenesis. * The surrogate model predicts future states of CPMs up to 562× faster than traditional simulations, while preserving key emergent behaviors like vessel sprouting, extension, and anastomosis. * This approach enables efficient modeling of complex biological processes over larger spatial and temporal scales. There are several EMBRIO collaborative research papers that will be published in the next month that we'll highlight here in future announcements. As papers are made available live by the jounrnals, they are added to our Google Scholar page<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.g…>. See you all next Monday afternoon! 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

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Reminder: Today All-Hands Lab 3pm EST
by Brent Thomas Ladd 03 Nov '25

03 Nov '25

[cid:24243977-3891-4b4e-97f1-6fce7123867c] Dear EMBRIO Members, Join us this afternoon 3-4pm EST featuring the Kim lab with Ph.D. student Jeffery Coulter presenting on collaborations with the Evans Lab and Kinzer-Ursem Lab in Thrust 1 with modeling Ca2+ and actin in dendritic spines and oocytes! Zoom link: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Coming up on Nov. 17th Alexandria Nguyen (Chan Lab) will present AFM and Imaging collaborations with Evans Lab, Zartman Lab, and Deng Lab. 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

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