[Embrio-list] EMBRIO Weekly Update

Tue Sep 30 17:32:16 EDT 2025

[cid:d871aefb-99be-4490-bd1b-ba42a89286d1]

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%7Cd03536244e59483e143c08de0068d3d5%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638948647383612495%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=EYoEZJ5uuew4QHaG5uueQAcEQMxAa0oCn4kuEVknv%2FA%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%7Cd03536244e59483e143c08de0068d3d5%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638948647383649609%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=8wHvIrTDxpu0Kwxwq7m6ShTvxrmTaSmFOw69c%2BKitMw%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. She may have some time to meet faculty and students on the 7th and possibly the 6th. Please let me know if you would like to meet her. Each meeting slot will likely be 25-30 minutes.

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%7Cd03536244e59483e143c08de0068d3d5%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638948647383666980%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=1w4cMKQTlpbR7A4vCbVDGqgowk40PY0d50XYsU%2BIJhg%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%7Cd03536244e59483e143c08de0068d3d5%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638948647383682330%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=XrrzFqqyTIEQ62N%2F2hsx5it3YvmRzM04B67y1ZnmbTg%3D&reserved=0>

Faculty and Research Staff: Leveraging EMBRIO in Future Proposals
The beginnings of coordinating proposal efforts that dovetail with EMBRIO and member collaboration - see the editable Google spreadsheet to view potential opportunities and add new. Currently working on a strategy to best position and support these efforts among the membership.
https://docs.google.com/spreadsheets/d/1MzX5ZAyn5LjiEX5uKUm1RNz8W8URxU62/edit?usp=sharing&ouid=107962836095749734864&rtpof=true&sd=true<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fspreadsheets%2Fd%2F1MzX5ZAyn5LjiEX5uKUm1RNz8W8URxU62%2Fedit%3Fusp%3Dsharing%26ouid%3D107962836095749734864%26rtpof%3Dtrue%26sd%3Dtrue&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7Cd03536244e59483e143c08de0068d3d5%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638948647383696965%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=%2B2EonjHbELJuLvaL0VPv%2F9Vo32%2Bk6VC3AVH%2FJnIx4es%3D&reserved=0>

Faculty and Research Staff: Y5 Allocations Status
Our Y5 budget is moving through final sponsored program checks and will be processed soon!

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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