- Embrio-list - ecn.purdue.edu

End of Week Reminders: Register for the LSFM Workshop, Next All-Hands Oct. 20th on using Neural Networks
by Brent Thomas Ladd 10 Oct '25

10 Oct '25

Dear EMBRIO Members: A few reminders below. Those traveling for conference and/or Fall Break (Purdue's is next Monday - Tuesday) have safe and enjoyable travels. Light-Sheet Fluorescence Microscopy Workshop: Advanced 3D Imaging for Biological Research Led by Purdue Bindley Bioscience Center (with Dr. Weiwei Zhang), together with Bruker and EMBRIO Institute. This is an excellent opportunity for EMBRIO members to learn and gain skills in this imaging modality. The workshop will be held October 28-29, 2025, on the Purdue campus, with options for the first half of day one via Zoom. For EMBRIO members at our partner locations interested in attending this training, please contact Brent regarding travel (laddb(a)purdue.edu) For questions about the workshop please contact Weiwei (zhan2190(a)purdue.edu ) See the attached flyer and registration page for details. Registration is free: https://purdue.ca1.qualtrics.com/jfe/form/SV_1GrEoUEHdatNBFY<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> All-Hands Lab Meeting October 20th at 3pm ET Plan to join our All-Hands Lab Meeting Monday, October 20th at 3pm ET, featuring research incorporating neural networks with presentation led by Linlin Li (Umulis Lab) and collaborators. Zoom link: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Thank you to Razeen Shaikh for presenting during our previous session "MIDOE: Maximally-informed Design of Experiment to infer experimentally inaccessible transcription factors dynamics". If you missed or would like to access the associated video and materials (including a summary of the session and Q&A) this is available on our shared Box account under All-Hands Meeting Recordings > 2025, direct link: https://app.box.com/s/nmvz4sy940bvse6m4tdkl94i1eujf11m<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> For anyone new-ish to EMBRIO or wanting a refresher about the Institute's structure and outcomes we are striving for with research integration are encouraged to check out the materials in the Orientation folder on Box: https://app.box.com/s/om3brzae0z3o9s3c7x2fhxw6n2h1ipjt<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> 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 3pm Today: Maximally Informed Design of Experiments, LSFM Workshop Registration, and more
by Brent Thomas Ladd 06 Oct '25

06 Oct '25

[cid:992ce85c-f893-44db-9c7e-3d3e9a845761] Dear EMBRIO Members: All-Hands Lab Meeting this afternoon at 3pm ET Plan to join our All-Hands Lab Meeting this afternoon at 3pm ET, featuring 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". 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…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> 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.c…> Light-Sheet Fluorescence Microscopy Workshop: Advanced 3D Imaging for Biological Research Led by Purdue Bindley Bioscience Center (with Dr. Weiwei Zhang), together with Bruker and EMBRIO Institute. This is an excellent opportunity for EMBRIO members to learn and gain skills in this imaging modality. The workshop will be held October 28-29, 2025, on the Purdue campus, with options for the first half of day one via Zoom. For EMBRIO members at our partner locations interested in attending this training, please contact Brent regarding travel (laddb(a)purdue.edu) For questions about the workshop please contact Weiwei (zhan2190(a)purdue.edu ) See the attached flyer and registration page for details. Registration is free: https://purdue.ca1.qualtrics.com/jfe/form/SV_1GrEoUEHdatNBFY<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> 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.wikipe…> Best, Qing qingdeng(a)purdue.edu https://www.denglab.us<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dengl…> 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/ed…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> 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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Monday All-Hands led by the Reeves Lab; New Collaborative EMBRIO Publication
by Brent Thomas Ladd 03 Oct '25

03 Oct '25

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…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> 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.c…> 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%2…> 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.g…> 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.wikipe…> Best, Qing qingdeng(a)purdue.edu https://www.denglab.us<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dengl…> 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 30 Sep '25

30 Sep '25

[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…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> 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.c…> 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.wikipe…> Best, Qing qingdeng(a)purdue.edu https://www.denglab.us<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dengl…> 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/ed…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> 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(a)purdue.edu

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Today: All-Hands Lab Meeting 3pm: “Role of mechanosensitive ion channels in epithelial wound closure”.
by Brent Thomas Ladd 22 Sep '25

22 Sep '25

Dear EMBRIO Members, Join us this afternoon for the All-Hands Lab Meeting 3pm ET, featuring integrative research building from the Piezo research by the Zartman lab now extended into investigating the role of Piezo during wound closure across different model systems. The collaboration involves multiple EMBRIO labs including Zartman lab, Umulis Lab, Pienaar lab, and the Deng lab. Jeremy Zartman will introduce the topic and Nilay Kumar will be the lead presenter laying out the “Role of mechanosensitive ion channels in epithelial wound closure”. There will be plenty of time for group discussion and engagement. Zoom link: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Cheers, 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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All-Hands Lab Meeting Monday, Denise Montrell visit, Labs- data management check in
by Brent Thomas Ladd 19 Sep '25

19 Sep '25

[cid:7d238b82-85bc-4009-afff-34abf436a1d6] Dear EMBRIOphytes, All-Hands Lab Meeting Monday, September 22, 3pm ET Our upcoming All-Hands Lab Meeting on Monday, September 22, 3pm ET, will feature integrative research building from the Piezo research by the Zartman lab now extended into investigating the role of Piezo during wound closure across different model systems. The collaboration involves multiple EMBRIO labs including Zartman lab, Umulis Lab, Pienaar lab, and the Deng lab. Jeremy Zartman will introduce the topic and Nilay Kumar will be the lead presenter laying out the “Role of mechanosensitive ion channels in epithelial wound closure”. There will be plenty of time for group discussion and engagement. Zoom link: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> To access the introductory sessions on Biological Modeling Workflow from our last 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.c…> Opportunity to meet with Dr. Montell October 6 - 7 at Purdue (note from Qing Deng) 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. She would 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.wikipe…> Best, Qing qingdeng(a)purdue.edu https://www.denglab.us<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dengl…> EMBRIO Labs: Get Your Experimental Data Associated with EMBRIO Publications Ready and Connected with our Data Management System We have an obligation to make our published data accessible to the broader scientific community. With the fall semester starting up again, now is a great opportunity to begin using OMERO to store your experimental data taken at the microscope. You can store your data with detailed experimental text to keep your images organized with context. This will benefit your science because: * Identifying experiments no longer requires searching image filenames written in your notebook * Original data is stored in a viewable format in a central location * Data can be reviewed by everyone in the lab without downloading a local copy and opening in ImageJ * Comments, tags, and keywords can be annotated at any time that stays with the image(s) * Support for Fiji (ImageJ) is built-in – you can use a plugin to work with the image data directly in OMERO * Image data can be published as a persistent link in PURR for your publications Thanks to the labs who are already adopting OMERO into their workflow. We encourage everyone in EMBRIO who performs microscopy experiments to take advantage of this new tool. We hope it will improve your workflow and make the management of your microscopy data easier. For more information and help getting started, please contact Scott Bolton at boltons(a)purdue.edu<mailto:boltons@purdue.edu>. EMBRIO Manuscripts Newly Accepted for Publication A brief announcement that EMBRIO collaborations have led to two recent research manuscripts being accepted for publication, with Postdoctoral Scholar Maria Unger as lead author with the Zartman lab (with Umulis lab and Pienaar lab) in Cell Communication and Signaling, and a paper in Biophysics Journal with lead author Chang Ding, Graduate Student with the Deng lab (with Umulis lab, Chan lab, Staiger lab, and Buganza-Tepole lab). We'll have highlights of these papers once the journals have made them available. Thanks! Brent ps. I will be out of office all next week back Monday 9/29 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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Best Sci. Fig Awards, New Paper from Gardner Lab, Denise Montrell visit, and more
by Brent Thomas Ladd 10 Sep '25

10 Sep '25

[cid:4f79b956-47a5-4a88-a40e-00e69fb99f2b] Dear EMBRIOphytes, Results of the annual Best Scientific Figure competition are in. Congratulations to Boyu Jiang and Maria Unger for receiving top votes, and a big thank you to all who developed and submitted figures and videos for consideration. We have many talented researchers in EMBRIO who craft amazing images and simulations, elegantly visualizing the story of the data and cellular mechanisms. Kudos to everyone for participating and for voting. Our next All-Hands Lab Meeting will be September 22, 3pm ET (more details to be shared). For those that want to access the introductory sessions on Biological Modeling Workflow from our last two all-hands lab meetings, see the slides and materials 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.c…> Thank you to Hayden Fennell for leading those two sessions. If you would like to get input and help in thinking through your biological problem of interest before Sept. 8th, please reach out to Hayden Fennell (haydenfennell(a)gmail.com) and James Glazier (jaglazier(a)gmail.com) A new peer-reviewed publication by members of the Gardner lab is available that focuses on EMBRIO Institute by lead author and Ph.D. Candidate, Soumi Mukherjee titled: "Building and Sustaining a Community of Practice: Repair Mechanisms in a Biology Integration Institute." See more about the paper below. There are details below from Qing Deng about an opportunity to meet with renowned cell biologist, Dr. Denise Montell, in October when she speaks at Purdue, as well as earlier reminders and announcements on the new CalciumInsights tool and making sure your experimental and computational data published as part of EMBRIO projects is properly uploaded and shared to EMBRIO repositories. EMBRIO 2025 Best Scientific Figure Awards Division I: Graduate Students Top vote: Boyu Jiang (Graduate Student member with affiliate Baloni Lab at Purdue) Faculty advisor: Priyanka Baloni Other authors: Anke Tukker, Hyunjin Kim, Shuang Wang, Juexin Wang, Aaron Bowman Division II: Postdocs and Research Staff Top vote: Maria Unger (Postdoc Scholar member in the Zartman Lab at Notre Dame) Adviser: Jeremiah J. Zartman, University of Notre Dame Co-authors: Vijay Velagala, Dharsan K. Soundarrajan, David Gazzo, Nilay Kumar, Marycruz Flores Flores, Jinwen Liu, Jun Li, Jeremiah J. Zartman Collaboration: Nilay Kumar, Purdue University Division I Winner: Boyu Jiang [A diagram of a model of neurons AI-generated content may be incorrect.] ================================================= Division II Winner: Maria Unger [A screenshot of a computer screen AI-generated content may be incorrect.] New Paper on EMBRIO as a Community of Practice Published by American Educational Research Association. “Building and Sustaining a Community of Practice: Repair Mechanisms in a Biology Integration Institute." Authors: Soumi Mukherjee, Purdue University; Emily Georgopoulos, Purdue University; Stephanie M. Gardner, Purdue University The paper documents the evolution of EMBRIO as a Biology Integration Institute through the lens of Community of Practice (CoP) change theory, highlighting its meaningful activities and evaluation feedback loops, which led to the implementation of several repair mechanisms to support members in becoming experts within the community. The study provides insights that could enable other Institutes to implement intentional structures, activities, and evaluation strategies to develop a CoP, fostering meaningful interactions and enhancing collaborative efforts. 📖 Access the full paper: https://doi.org/10.3102/2195576<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> Opportunity to meet with Dr. Montell October 6 - 7 at Purdue (note from Qing Deng) 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. She would 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.wikipe…> Best, Qing qingdeng(a)purdue.edu https://www.denglab.us<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dengl…> EMBRIO Labs: Get Your Experimental Data Associated with EMBRIO Publications Ready and Connected with our Data Management System We have an obligation to make our published data accessible to the broader scientific community. With the fall semester starting up again, now is a great opportunity to begin using OMERO to store your experimental data taken at the microscope. You can store your data with detailed experimental text to keep your images organized with context. This will benefit your science because: * Identifying experiments no longer requires searching image filenames written in your notebook * Original data is stored in a viewable format in a central location * Data can be reviewed by everyone in the lab without downloading a local copy and opening in ImageJ * Comments, tags, and keywords can be annotated at any time that stays with the image(s) * Support for Fiji (ImageJ) is built-in – you can use a plugin to work with the image data directly in OMERO * Image data can be published as a persistent link in PURR for your publications Thanks to the labs who are already adopting OMERO into their workflow. We encourage everyone in EMBRIO who performs microscopy experiments to take advantage of this new tool. We hope it will improve your workflow and make the management of your microscopy data easier. For more information and help getting started, please contact Scott Bolton at boltons(a)purdue.edu<mailto:boltons@purdue.edu>. Check Out CalciumInsights Application [image] EMBRIO members at University of Puerto Rico at Mayagüez, in collaboration with labs in the Institute, developed CalciumInsights, an interactive application built in R that is designed to analyze tissue-agnostic calcium traces. The tool is now available on the Institute's central GitHub (of which we'll be forking more projects and materials soon): https://github.com/orgs/EMBRIOInstitute/repositories<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.co…> For details, please contact Deiver Suarez (deiver.suarez(a)upr.edu ), Mauricio Cabrerra (mauricio.cabrera1(a)upr.edu ) and Clara Isaza (clara.isaza(a)upr.edu ). 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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Today: All-Hands Lab Meeting Session II of The Biological Modeling Workflow: A Brief Introduction
by Brent Thomas Ladd 08 Sep '25

08 Sep '25

Dear EMBRIOnic People, Don't miss our "All-Hands "Lab Meeting" this afternoon at 3pm ET Session II of The Biological Modeling Workflow: A Brief Introduction Monday, September 8th 3-4pm EDT Zoom link for the semester: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Hayden Fennell, Postdoc Fellow at IU in Biocomplexity Institute of the Glazier lab, will continue with session II of The Biological Modeling Workflow: A Brief Introduction. All who are interested are encouraged to check out the modeling template and other resources from Session I on our Box account<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> (EMBRIO Institute > All-Hands Meetings Recordings > 2025). If you would like to get input and help in thinking through your biological problem of interest, please reach out to Hayden (haydenfennell(a)gmail.com) and James Glazier (jaglazier(a)gmail.com) Description: Computational modeling is becoming more and more ubiquitous in essentially all fields of scientific study. Biology is no exception, although the usefulness of computation in biology can sometimes be less obvious, given the methodological "distance" from practices in wet-lab experimentation. This seminar will discuss the benefits and challenges of computational modeling in biology, as well as provide a computational modeling workflow that can be applied to a wide variety of biological problems. Session II will focus on examples to illustrate the workflow in practice, and a template has been provided for participants to brainstorm how to apply the workflow to their own biological problems of interest. View the materials on Box<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. The second part of the lab meeting will offer continued Q&A on the main topic, with potential breakout rooms for small groups wanting to get started on their own modeling template. If you would like to get input and help in thinking through your biological problem of interest before Sept. 8th, please reach out to Hayden Fennell (haydenfennell(a)gmail.com) and James Glazier (jaglazier(a)gmail.com) 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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Reminders: Vote for Best Sci. Fig., All-Hands Lab next Monday, CalciumInsights on GitHub, Data Management
by Brent Thomas Ladd 05 Sep '25

05 Sep '25

[cid:da855d1d-c6a7-472b-a037-2aa5490c490a] Dear EMBRIO Community, * Open voting ends tomorrow night (Thursday) for choosing the EMBRIO Best Scientific Figure 2025. (view the webpage<https://www.purdue.edu/research/embrio/research/sci-fig-comp.php>) * All-Hands Lab Meeting Monday, September 8th, "Session II: The Biological Modeling Workflow" (Materials for Session I and II<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>) * CalciumInsights application, led by our members at University of Puerto Rico at Mayagüez, is now available on the Institute's central GitHub (of which we'll be forking more projects, publications, and materials soon): https://github.com/orgs/EMBRIOInstitute/repositories<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.co…> * Reminder to have your EMBRIO published experimental data uploaded to our central repository (contact Scott Bolton: boltons(a)purdue.edu<mailto:boltons@purdue.edu>) * For those new(ish) to EMBRIO who would like more details of what our Institute is about, check out our orientation materials on our shared Box Account: https://app.box.com/s/om3brzae0z3o9s3c7x2fhxw6n2h1ipjt<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Vote for your selections in the 2025 EMBRIO Best Scientific Figure or Video (view the webpage<https://www.purdue.edu/research/embrio/research/sci-fig-comp.php>) It's time to vote on the best scientific figure or video from member submissions. The webpage link above contains the instructions and PowerPoint file of the submissions. Thanks to the graduate students, postdocs, and research scientists who have developed these figures and videos and submitted them for consideration. Voting will be open through next Thursday, September 4th.  Division Name ID Slide# Thrust Type II Nilay Kumar/Linlin Li/Chang Ding/David Gazzo/Naomi Ross/Maria Unger PD1 2 CORE + 2 + 3 Figure II Sharon Minsuk PD2 3 CORE + 3 Video II Maria Unger PD3 4 2 Figure I Bakary Samasa G1 5 3 Video I David Gazzo G2 6 2 Figure I Agnes Doszpoly G3 7 1 Figure I Boyu Jiang G4 8 CORE Figure EMBRIO All-Hands "Lab Meeting" Session II of The Biological Modeling Workflow: A Brief Introduction Monday, September 8th 3-4pm EDT Zoom link for the semester: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Hayden Fennell, Postdoc Fellow at IU in Biocomplexity Institute of the Glazier lab, will continue with session II of The Biological Modeling Workflow: A Brief Introduction. All who are interested are encouraged to check out the modeling template and other resources from Session I on our Box account<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> (EMBRIO Institute > All-Hands Meetings Recordings > 2025). If you would like to get input and help in thinking through your biological problem of interest, please reach out to Hayden (haydenfennell(a)gmail.com) and James Glazier (jaglazier(a)gmail.com) Description: Computational modeling is becoming more and more ubiquitous in essentially all fields of scientific study. Biology is no exception, although the usefulness of computation in biology can sometimes be less obvious, given the methodological "distance" from practices in wet-lab experimentation. This seminar will discuss the benefits and challenges of computational modeling in biology, as well as provide a computational modeling workflow that can be applied to a wide variety of biological problems. Session II will focus on examples to illustrate the workflow in practice, and a template has been provided for participants to brainstorm how to apply the workflow to their own biological problems of interest. View the materials on Box<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. The second part of the lab meeting will offer continued Q&A on the main topic, with potential breakout rooms for small groups wanting to get started on their own modeling template. If you would like to get input and help in thinking through your biological problem of interest before Sept. 8th, please reach out to Hayden Fennell (haydenfennell(a)gmail.com) and James Glazier (jaglazier(a)gmail.com) Check Out CalciumInsights Application [image] EMBRIO members at University of Puerto Rico at Mayagüez, in collaboration with labs in the Institute, developed CalciumInsights, an interactive application built in R that is designed to analyze tissue-agnostic calcium traces. The tool is now available on the Institute's central GitHub (of which we'll be forking more projects and materials soon): https://github.com/orgs/EMBRIOInstitute/repositories<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.co…> For details, please contact Deiver Suarez (deiver.suarez(a)upr.edu ), Mauricio Cabrerra (mauricio.cabrera1(a)upr.edu ) and Clara Isaza (clara.isaza(a)upr.edu ). EMBRIO Labs: Get Your Experimental Data Associated with EMBRIO Publications Ready and Connected with our Data Management System We have an obligation to make our published data accessible to the broader scientific community. With the fall semester starting up again, now is a great opportunity to begin using OMERO to store your experimental data taken at the microscope. You can store your data with detailed experimental text to keep your images organized with context. This will benefit your science because: * Identifying experiments no longer requires searching image filenames written in your notebook * Original data is stored in a viewable format in a central location * Data can be reviewed by everyone in the lab without downloading a local copy and opening in ImageJ * Comments, tags, and keywords can be annotated at any time that stays with the image(s) * Support for Fiji (ImageJ) is built-in – you can use a plugin to work with the image data directly in OMERO * Image data can be published as a persistent link in PURR for your publications Thanks to the labs who are already adopting OMERO into their workflow. We encourage everyone in EMBRIO who performs microscopy experiments to take advantage of this new tool. We hope it will improve your workflow and make the management of your microscopy data easier. For more information and help getting started, please contact Scott Bolton at boltons(a)purdue.edu<mailto:boltons@purdue.edu>. 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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End of Week Reminders
by Brent Thomas Ladd 29 Aug '25

29 Aug '25

[cid:b78f1152-35f9-46ad-8768-b75c6a058067] Dear EMBRIOnic People, Best wishes to all for an enjoyable and safe holiday weekend. A few reminders: * Voting is open through next Thursday for choosing the EMBRIO Best Scientific Figure 2025. (view the webpage<https://www.purdue.edu/research/embrio/research/sci-fig-comp.php>) * Next All-Hands Lab Meeting Monday, September 8th, "Session II: The Biological Modeling Workflow" (Materials for Session I and II<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>) * Get your EMBRIO published experimental data ready and uploaded to our central repository (contact Scott Bolton: boltons(a)purdue.edu<mailto:boltons@purdue.edu>) * EMBRIO Investigators: Look for a RFI survey - due 9/3 - in a separate email Vote for your selections in the 2025 EMBRIO Best Scientific Figure or Video (view the webpage<https://www.purdue.edu/research/embrio/research/sci-fig-comp.php>) It's time to vote on the best scientific figure or video from member submissions. The webpage link above contains the instructions and PowerPoint file of the submissions. Thanks to the graduate students, postdocs, and research scientists who have developed these figures and videos and submitted them for consideration. Voting will be open through next Thursday, September 4th.  Division Name ID Slide# Thrust Type II Nilay Kumar/Linlin Li/Chang Ding/David Gazzo/Naomi Ross/Maria Unger PD1 2 CORE + 2 + 3 Figure II Sharon Minsuk PD2 3 CORE + 3 Video II Maria Unger PD3 4 2 Figure I Bakary Samasa G1 5 3 Video I David Gazzo G2 6 2 Figure I Agnes Doszpoly G3 7 1 Figure I Boyu Jiang G4 8 CORE Figure EMBRIO All-Hands "Lab Meeting" Monday, September 8th 3-4pm EDT Zoom link for the semester: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Hayden Fennell, Postdoc Fellow at IU in Biocomplexity Institute of the Glazier lab, will continue with session II of The Biological Modeling Workflow: A Brief Introduction. All who are interested are encouraged to check out the modeling template and other resources from Session I on our Box account<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> (EMBRIO Institute > All-Hands Meetings Recordings > 2025). If you would like to get input and help in thinking through your biological problem of interest, please reach out to Hayden (haydenfennell(a)gmail.com) and James Glazier (jaglazier(a)gmail.com) Description: Computational modeling is becoming more and more ubiquitous in essentially all fields of scientific study. Biology is no exception, although the usefulness of computation in biology can sometimes be less obvious, given the methodological "distance" from practices in wet-lab experimentation. This seminar will discuss the benefits and challenges of computational modeling in biology, as well as provide a computational modeling workflow that can be applied to a wide variety of biological problems. Session II will focus on examples to illustrate the workflow in practice, and a template has been provided for participants to brainstorm how to apply the workflow to their own biological problems of interest. View the materials on Box<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. The second part of the lab meeting will offer continued Q&A on the main topic, with potential breakout rooms for small groups wanting to get started on their own modeling template. If you would like to get input and help in thinking through your biological problem of interest before Sept. 8th, please reach out to Hayden Fennell (haydenfennell(a)gmail.com) and James Glazier (jaglazier(a)gmail.com) EMBRIO Labs: Get Your Experimental Data Associated with EMBRIO Publications Ready and Connected with our Data Management System We have an obligation to make our published data accessible to the broader scientific community. With the fall semester starting up again, now is a great opportunity to begin using OMERO to store your experimental data taken at the microscope. You can store your data with detailed experimental text to keep your images organized with context. This will benefit your science because: * Identifying experiments no longer requires searching image filenames written in your notebook * Original data is stored in a viewable format in a central location * Data can be reviewed by everyone in the lab without downloading a local copy and opening in ImageJ * Comments, tags, and keywords can be annotated at any time that stays with the image(s) * Support for Fiji (ImageJ) is built-in – you can use a plugin to work with the image data directly in OMERO * Image data can be published as a persistent link in PURR for your publications Thanks to the labs who are already adopting OMERO into their workflow. We encourage everyone in EMBRIO who performs microscopy experiments to take advantage of this new tool. We hope it will improve your workflow and make the management of your microscopy data easier. For more information and help getting started, please contact Scott Bolton at boltons(a)purdue.edu<mailto:boltons@purdue.edu>. 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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