[Embrio-list] Monday All-Hands led by the Reeves Lab; New Collaborative EMBRIO Publication

Fri Oct 3 11:51:18 EDT 2025

Dear EMBRIOphytes,

All-Hands Lab Meeting Monday, October 6, 3pm ET
Plan to join in the All-Hands Lab Meeting on Monday,  October 6, 3pm ET, will feature integrative research led by Razeen Shaikh and Greg Reeves (Reeves Lab, Texas A&M) presenting "MIDOE: Maximally-informed Design of Experiment to infer experimentally inaccessible transcription factors dynamics". The collaboration involves multiple EMBRIO labs including Zartman lab and Umulis Lab.
Abstract:
The TGF-β/Smad signaling pathway regulates growth, development, and homeostasis of tissues across the animal kingdom. The pathway is activated when transforming growth factor -β (TGF-β) binds to its cognate transmembrane receptors to activate Smad2 by phosphorylation. The activated phosphor-Smad2 (PSmad2) undergoes a series of biochemical interactions with transcriptional activator Smad4 to form several oligomers, including the transcription factor (PSmad2)2/Smad4, which regulates target gene expression. Quantitative live cell imaging and mathematical modeling have been used to estimate the dynamics of (PSmad2)2/Smad4. However, due to the emergent nature of Smad2-Smad4 interactions, deconvolving the dynamics of the (PSmad2)2/Smad4 is challenging. We show that the Smad model is sloppy, has large parameter uncertainties (Ο∼1015), and the eigenvalues of the Fisher Information Matrix span over several decades. As such, well-fit parameter sets generate highly under-constrained predictions. To overcome this, we employ Profile Log-Likelihood to guide maximally informed design of experiments (MIDOE) and infer the dynamics of (PSmad2)2/Smad4. We generate these experiments computationally and validate that MIDOE can optimally constrain model predictions. We demonstrate that such careful analysis would not only improve the predictive power of models in systems biology but also reduce the time and expense of performing non-optimal experiments.

Zoom link: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3.1&from=addon<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-edu.zoom.us%2Fj%2F92061591849%3Fpwd%3DwclgpzLpzWKsZ9M2XYwM7Kbumaabr3.1%26from%3Daddon&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C0800fbd5bf1b44b8c54108de0294b168%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638951034802231756%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=rlu4BRa4nEoYP4PpvGSlG%2BhqgrNDRhxQVC4qP47%2FUXU%3D&reserved=0>

To access the introductory sessions on Biological Modeling Workflow from our first two all-hands lab meetings, see the slides and materials from Hayden Fennel and the Glazier lab via our shared box account under "All-Hands Meeting Recordings > 2025 ": https://app.box.com/s/vmoaq3w216ye0c78vxhyzmhh0j4vr8mx<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.com%2Fs%2Fvmoaq3w216ye0c78vxhyzmhh0j4vr8mx&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C0800fbd5bf1b44b8c54108de0294b168%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638951034802247306%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=0GC5TVX%2B4oVFtzzxdrtYep27RxAgNMr2TijsJKLIWys%3D&reserved=0>

New Publication on ROS and Wound Healing
The latest work led by the Deng lab collaborating with the Umulis, Chan, and Buganza labs has just been published in Biophysical Journal

“Reactive Oxygen Species Counteract Zebrafish Wound Contraction and Promote Wound Healing”
by C. Ding, L. Li, Y. Wang, H.A.A. Nguyen, D.D. Chan, D.M. Umulis, A.T. Buganza, and Q. Deng

📄 Read the full article here: https://doi.org/10.1016/j.bpj.2025.09.027<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.bpj.2025.09.027&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C0800fbd5bf1b44b8c54108de0294b168%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638951034802259793%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=1O%2Bu7shvbSMVltiKK9T82BW5eUPgd8t1j3LmTHqTysE%3D&reserved=0>

The experimental research integrating in silico linear elasticity simulation and atomic force microscopy (AFM) has uncovered a fascinating role of reactive oxygen species (ROS) in wound healing. Contrary to the traditional view of ROS in wound healing, the findings show that ROS can counteract wound contraction and actively promote tissue repair in zebrafish models.

Why it matters:
• Provides new insights into the mechanobiology of wound healing
• Highlights potential therapeutic strategies for improving tissue regeneration
• Bridges fundamental biology with translational applications

Thank you to the collaborators and team, and to our funder at NSF (Award: 2120200) for supporting this important research.

You can check out all of the Institute's publications and pre-prints available on our Google Scholar Page<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.google.com%2Fcitations%3Fhl%3Den%26user%3D-gQWba8AAAAJ%26sortby%3Dpubdate%26authuser%3D1%26scilu%3D%26scisig%3DACUpqDcAAAAAaN_nHGtV9FNuy0_b7TkdT4HQAaM%26gmla%3DAH8HC4wjBgP0xT8HhehUfr5ejtaUaTiz9p80fG5UQQQ_gVNlObQvIigvAeFOyjbBIdM9gfFfkSPnaHsUEzSXg0YHJQuSrOUAmuNWtYg%26sciund%3D10408753515222267636&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C0800fbd5bf1b44b8c54108de0294b168%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638951034802268738%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=YdRCPIajVqtZFJbQ%2Bw4AMcudYhoysIAzrn0psvF%2F8JQ%3D&reserved=0>

The 150th Karling Lecture at Purdue University's Department of Biological Sciences will be given by Dr. Denise Montell on October 7, 2025
Dear EMBRIO Investigators,

I am hosting Dr. Denise Montell, a world-renowned cell biologist, in the fall. She will deliver our department's Karling Lecture on Oct 7, 12:30-1:30 pm in DLR 131.
I have attached her Wikipedia page FYI:  https://en.wikipedia.org/wiki/Denise_Montell<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FDenise_Montell&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C0800fbd5bf1b44b8c54108de0294b168%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638951034802278603%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ZmiJWAvmJ4UFhvZOtbKUPjNCHRyMea9ArNGCjyDtNLc%3D&reserved=0>

Best,
Qing
qingdeng at purdue.edu
https://www.denglab.us<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.denglab.us%2F&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C0800fbd5bf1b44b8c54108de0294b168%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638951034802287832%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=t3pSZtej2rTsN7DBXb8ao3ZeEm29bEtLvhhNNZWsxyY%3D&reserved=0>

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 at purdue.edu

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