- Embrio-list - ecn.purdue.edu

Vote on 2025 EMBRIO Best Scientific Figure or Video
by Brent Thomas Ladd 27 Aug '25

27 Aug '25

Dear EMBRIOphytes, 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 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

1 0

Y5 Funding Increment, Today’s All-Hands Lab, Data Management, Best Sci. Figure Voting
by Brent Thomas Ladd 25 Aug '25

25 Aug '25

[cid:2d98bcc4-626c-44e6-be1f-7268be523391] Dear EMBRIOnic People, Best wishes to all for a great start to the Fall semester! Announcements below include: * Y5 funding announcement from EMBRIO’s Co-Director and PI, David Umulis * All-Hands Lab Meeting this afternoon "The Biological Modeling Workflow: A Brief Introduction" * Get your EMBRIO published experimental data ready and uploaded to our central repository * Voting on EMBRIO Best Scientific Figure 2025. Y5 Funding Increment The Institute has officially received our Y5 increment from NSF to complete ongoing projects in our final year. The increment includes a budget reduction, however with the recent decision by the NSF to end the BII program and cancellation of submitted grants (including our submission), we are very happy to have resources to complete the work we set out to do in our first grant period. We are excited about our potential to make significant progress, and we will intentionally maximize this final year of BII funding by emphasizing and supporting: 1) activity with the most promise of producing impactful outcomes by the end of next summer, and 2) the need to identify and position small teams and the Institute for new sources of funding. Please know that there is an expectation from NSF to wind down our BII project. Therefore, no new positions or hiring will be allowed on EMBRIO projects. David as PI and Jeremy as Co-Director, with the input of the Leadership Team, are reviewing the original Y5 funding requests and plans. Be assured that we'll be in communication with each investigator as soon as possible regarding clarifications and Y5 activity and allocations. David Umulis, EMBRIO Co-Director and PI EMBRIO All-Hands "Lab Meeting" Monday, August 25th 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…> We are looking forward to kicking off the fall semester with a session and open discussion on biological modeling workflow led by Hayden Fennell, Postdoc Fellow at IU in Biocomplexity Institute of the Glazier lab. Title: The Biological Modeling Workflow: A Brief Introduction 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. Examples will be given to illustrate the workflow in practice, and a template will be provided for participants to brainstorm how to apply the workflow to their own biological problems of interest. The second half of the lab meeting will offer continued Q&A on the main topic, along with breakout rooms for specific topics or smaller group chats. Let me (laddb(a)purdue.edu) know if you have a specific topic/break out room you would like to have available. 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>. Voting for EMBRIO Best Scientific Figure 2025 Thanks to all who have submitted figures or videos for our 2025 competition. As we continue to recognize and celebrate members’ research outcomes and integrative progress of the Institute, please look for a separate forthcoming message about viewing and voting on submissions in two divisions: Graduate Student, and Postdoctoral/Research Scientist. 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

1 0

End of Week Reminders
by Brent Thomas Ladd 22 Aug '25

22 Aug '25

[cid:a70f400f-d432-4863-978e-2b024809b79b] Dear EMBRIOnic People, * All-Hands Lab Meeting on Monday: "The Biological Modeling Workflow: A Brief Introduction" * EMBRIO Labs: Get Your Experimental Data Associated with EMBRIO Publications Ready and Connected with EMBRIO's Data Management System EMBRIO All-Hands "Lab Meeting" August 25th 3-4pm EDT Zoom link: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> We are looking forward to kicking off the fall semester with a session and open discussion on biological modeling workflow led by Hayden Fennell, Postdoc Fellow at IU in Biocomplexity Institute of the Glazier lab. Title: The Biological Modeling Workflow: A Brief Introduction 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. Examples will be given to illustrate the workflow in practice, and a template will be provided for participants to brainstorm how to apply the workflow to their own biological problems of interest. The second half of the lab meeting will offer continued Q&A on the main topic, along with breakout rooms for specific topics or smaller group chats. Let me know if you have a specific topic/break out room you would like to have available. 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

1 0

End of the week announcements: EMBRIO Data Management; Best Sci. Fig or Video submissions due Monday
by Brent Thomas Ladd 15 Aug '25

15 Aug '25

[cid:cfc5b204-9b27-4352-9da5-fcae54dfc069] Dear EMBRIO Community, A couple of end -of - week announcements: * EMBRIO Labs: Get Your Experimental Data associated with EMBRIO Publications Ready and Connected with EMBRIO's Data Management System * EMBRIO Trainees and Staff: Submissions due Monday for the 2025 EMBRIO Best Scientific Figure or Video Award 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>. Reminder: Get Your Submission in for the 2025 EMBRIO Best Scientific Figure or Video Award! As announced during the annual retreat, this is a reminder and encouragement for all EMBRIO Graduate Students, Postdocs, and Staff Research Scientists to share your best work with our community! As they say, a picture can be worth a thousand words. This is certainly true when creating visually clear and elegant representations to demonstrate your research findings for the community of scientists who will learn about and digest your findings. We will have two divisions: graduate students (division I), postdocs and research scientists (division II). Submissions can also include collaborative efforts where multiple people have derived the figure or video. The deadline is August 18th. Submission link https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://maillinks.purdue.edu/t/47980411/1651405863/106333584/0/1006595/?x=3…> Eligible figures can be at the stage of submitted, accepted, published journal or peer-reviewed conference, as well as in pre-prints or at a pre-publication stage but must be “complete” figures ready for publication. Videos can be live cell timelapse, or model simulation, or similar. A single figure or a single video nomination and submission may be made by the graduate student, postdoc or research scientist, or can be made by faculty advisers on their behalf. Nominations with submission are due by August 18th, no exceptions. Rules and criteria for evaluation are below. Rules: * Submissions must be a single PowerPoint slide with the figure or video embedded that includes on the slide in this order: title of figure or video, context or annotation or data that explains the purpose of the figure or video, lead author name, faculty advisor’s name, any other authors or contributors, and if available, citation for where the figure or video has been published, submitted, in a preprint, presented at a conference. * To be considered, complete submissions must be in by Monday, August 18th. Submission form: https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> * All submissions will be made available on an EMBRIO-only website page for members to view prior to voting. * A winning figure or video can’t be re-submitted in future year competitions. Evaluation criteria: Each figure or video will be evaluated by the criteria below and ranked by members of EMBRIO who wish to participate in voting: * Impact and innovation * Originality and novelty * Degree to which the figure or video conveys or explains the data, mechanism, process or method * Degree of Integration with other EMBRIO authors and labs Awards: Community-wide and public recognition! The award will be non-monetary – we are restricted on use of our NSF funding in this regard. We’ll promote the top vote getters (and figure or video if already published or as appropriate) through our social media, website, and news channels, highlighting the winners’ research, mentor labs and collaborations with EMBRIO labs that led to the figure or video being produced. 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

1 0

Mid-Week Reminders: Scientific Figure/Video Submissions, All-Hands Biweekly starts Aug. 25th
by Brent Thomas Ladd 13 Aug '25

13 Aug '25

[cid:2f716172-3795-4dff-9683-ca22aefd9182] Dear EMBRIOphytes, A couple of reminders as we near the start of Fall semester: * EMBRIO All-Hands Lab Meetings begin August 25th 3-4pm EDT, running biweekly (Zoom Link for the semester<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>) * Get Your Submission in for the 2025 EMBRIO Best Scientific Figure or Video Award - deadline 8/15. Submission link https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://maillinks.purdue.edu/t/47980411/1651405863/106333584/0/1006595/?x=3…> All-Hands Lab Meetings begin August 25th 3-4pm EDT -Biweekly (Zoom Link for the semester<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>) A calendar invite with zoom link was emailed Aug. 1st to all active members establishing our biweekly All-Hands Lab Meeting. We start August 25th 3-4pm EDT with a primer on the basics of modeling biological phenomena, followed by open discussion. Why the name change? The idea (this may evolve) is to reframe our seminar sessions to: * Include a primer for the session's topic that explains key foundational concept(s) supporting the research presentation (10 min, by the PI), * Keep topic presentation to a single most exciting finding or result, method, or idea that also invites input and exchange with the community (20 min max, by trainee or staff), and * Allow/encourage a higher level of engagement with open forums and/or breakout rooms to foster deeper discussions (25 min following presentation). Think of this biweekly all-hands as a regular lab meeting where brief updates, questions and input from all lab members, with exchanges generating ideas, solutions, and support for short-term goals and progress toward the milestones and overall mission. The full schedule of presenting labs and speakers is forthcoming. Reminder: Get Your Submission in for the 2025 EMBRIO Best Scientific Figure or Video Award! As announced during the annual retreat, this is a reminder and encouragement for all EMBRIO Graduate Students, Postdocs, and Staff Research Scientists to share your best work with our community! As they say, a picture can be worth a thousand words. This is certainly true when creating visually clear and elegant representations to demonstrate your research findings for the community of scientists who will learn about and digest your findings. We will have two divisions: graduate students (division I), postdocs and research scientists (division II). Submissions can also include collaborative efforts where multiple people have derived the figure or video. The deadline is August 18th. Submission link https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://maillinks.purdue.edu/t/47980411/1651405863/106333584/0/1006595/?x=3…> Eligible figures can be at the stage of submitted, accepted, published journal or peer-reviewed conference, as well as in pre-prints or at a pre-publication stage but must be “complete” figures ready for publication. Videos can be live cell timelapse, or model simulation, or similar. A single figure or a single video nomination and submission may be made by the graduate student, postdoc or research scientist, or can be made by faculty advisers on their behalf. Nominations with submission are due by August 18th, no exceptions. Rules and criteria for evaluation are below. Rules: * Submissions must be a single PowerPoint slide with the figure or video embedded that includes on the slide in this order: title of figure or video, context or annotation or data that explains the purpose of the figure or video, lead author name, faculty advisor’s name, any other authors or contributors, and if available, citation for where the figure or video has been published, submitted, in a preprint, presented at a conference. * To be considered, complete submissions must be in by Monday, August 18th. Submission form: https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> * All submissions will be made available on an EMBRIO-only website page for members to view prior to voting. * A winning figure or video can’t be re-submitted in future year competitions. Evaluation criteria: Each figure or video will be evaluated by the criteria below and ranked by members of EMBRIO who wish to participate in voting: * Impact and innovation * Originality and novelty * Degree to which the figure or video conveys or explains the data, mechanism, process or method * Degree of Integration with other EMBRIO authors and labs Awards: Community-wide and public recognition! The award will be non-monetary – we are restricted on use of our NSF funding in this regard. We’ll promote the top vote getters (and figure or video if already published or as appropriate) through our social media, website, and news channels, highlighting the winners’ research, mentor labs and collaborations with EMBRIO labs that led to the figure or video being produced. 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

1 0

EMBRIO Best Scientific Figure and Video Award Submissions Due August 18th
by Brent Thomas Ladd 08 Aug '25

08 Aug '25

Get Your Submission in for the 2025 EMBRIO Best Scientific Figure and Video Award! As announced during the annual retreat, this is a reminder and encouragement for all EMBRIO Graduate Students, Postdocs, and Staff Research Scientists to share your best work with our community! As they say, a picture can be worth a thousand words. This is certainly true when creating visually clear and elegant representations to demonstrate your research findings for the community of scientists who will learn about and digest your findings. We will have two divisions: graduate students (division I), postdocs and research scientists (division II). Submissions can also include collaborative efforts where multiple people have derived the figure or video. The deadline is August 18th. Submission link https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://maillinks.purdue.edu/t/47980411/1651405863/106333584/0/1006595/?x=3…> Eligible figures can be at the stage of submitted, accepted, published journal or peer-reviewed conference, as well as in pre-prints or at a pre-publication stage but must be “complete” figures ready for publication. Videos can be live cell timelapse, or model simulation, or similar. A single figure or a single video nomination and submission may be made by the graduate student, postdoc or research scientist, or can be made by faculty advisers on their behalf. Nominations with submission are due by August 18th, no exceptions. Rules and criteria for evaluation are below. The top figure or video in each division will be determined by EMBRIO open community voting this semester. Rules: * Submissions must be a single PowerPoint slide with the figure or video embedded that includes on the slide in this order: title of figure or video, context or annotation or data that explains the purpose of the figure or video, lead author name, faculty advisor’s name, any other authors or contributors, and if available, citation for where the figure or video has been published, submitted, in a preprint, presented at a conference. * To be considered, complete submissions must be in by August 18th. Submission form: https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> * All submissions will be made available on an EMBRIO-only website page for members to view prior to voting. * A winning figure or video can’t be re-submitted in future year competitions. Evaluation criteria: Each figure or video will be evaluated by the criteria below and ranked by members of EMBRIO who wish to participate in voting: * Impact and innovation * Originality and novelty * Degree to which the figure or video conveys or explains the data, mechanism, process or method * Degree of Integration with other EMBRIO authors and labs Awards: Community-wide and public recognition! The award will be non-monetary – we are restricted on use of our NSF funding in this regard. We’ll promote the top vote getters (and figure or video if already published or as appropriate) through our social media, website, and news channels, highlighting the winners’ research, mentor labs and collaborations with EMBRIO labs that led to the figure or video being produced. 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

1 0

EMBRIO Monday announcement and new publications
by Brent Thomas Ladd 04 Aug '25

04 Aug '25

Dear EMBRIO Members, As we enter the month of August, with Fall semesters being planned: All-Hands Lab Biweekly Meeting beginning August 25th 3-4pm EDT (Zoom Link for the semester<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>) A calendar invite with zoom link was emailed last Friday to all active members establishing our biweekly All-Hands Lab Meeting beginning August 25th 3-4pm EDT. Why the name change? The idea (this may evolve) is to reframe our seminar sessions to: * Include a primer for the topic that explains key foundational concept(s) supporting the research presentation (10 min, by the PI), * Keep topic presentation to a single most exciting finding or result, method, or idea that also invites input and exchange with the community (20 min max, by trainee or staff), and * Allow/encourage a higher level of engagement with open forums and/or breakout rooms to foster deeper discussions (25 min following presentation). Think of this biweekly all-hands as a regular lab meeting where brief updates, questions and input from all lab members, with exchanges generating ideas, solutions, and support for short-term goals and progress toward the milestones and overall mission. The schedule of presenting labs and speakers is forthcoming! New Publications: EMBRIO collaborations have been very active in translating impactful research findings into peer-reviewed publications (36 - w/ nearly half having multiple EMBRIO lab authors), as well as preprints (24) and conference papers and posters shared with the wider scientific community: EMBRIO Institute Google Scholar Page<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.g…>. A new paper published Friday in Cytoskeleton by an interdisciplinary team from the labs of Kim, Staiger, and Iyer-Pascuzzi: Kim, J.H., W. Zhang, A.S. Iyer-Pascuzzi, C.J. Staiger, and T. Kim. (2025). Agent-based modeling of the homeostatic cortical array in plant epidermal cells recapitulates the stochastic dynamic behavior of actin filaments. Cytoskeleton, 2025, 0:1-20. https://doi.org/10.1002/cm.70014<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> Congrats to the team on developing an agent-based computational model that successfully simulates the stochastic dynamics of actin filaments in plant epidermal cells. This work bridges experimental observations with computational modeling, offering new insights into the mechanisms of cytoskeletal homeostasis and remodeling. Read the full paper here: https://onlinelibrary.wiley.com/doi/10.1002/cm.70014<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fonlinelib…> ==== Weiwei Zhang and Chris Staiger are also co-authors on a recent EMBRIO supported publication in the New Phytologist with findings that propose MILDEW RESISTANCE LOCUS-O (MLO) proteins act downstream of FERONIA (FER) to mediate Ca++ influx and promote Reactive Oxygen Species (ROS) production to regulate root hair tip growth: Ogawa, S.T., W. Zhang, C.J. Staiger, and S.A. Kessler. 2025. MLO-mediated Ca2+ influx regulates root hair tipgrowth in Arabidopsis. New Phytol, July 13, 2025. https://doi.org/10.1111/nph.70378<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> ==== A recent paper in PLOS Computational Biology by our affiliate Baloni lab at Purdue in the School of Health Sciences (read a feature about Priyanka Baloni in Cell Reports Medicine<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cell.…>) developed the first cell-type-specific genome-scale metabolic model of human colonocytes, providing a novel computational resource for systems-level analysis of intestinal metabolism that offers a platform to explore disease mechanisms and potential therapeutic targets in inflammatory bowel disease and other digestive disorders. Jiang, B., Quinn-Bohmann, N., Diener, C., Nathan, V.B., Han-Hallett, Y., Reddivari, L., Gibbons, S.M. and Baloni, P., 2024. Understanding disease-associated metabolic changes in human colon epithelial cells using iColonEpithelium metabolic reconstruction. PLOS Computational Biology 21.7 (2025): e1013253. https://doi.org/10.1371/journal.pcbi.1013253<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> ----------------------------------------------------------------------------------------- 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

1 0

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!

1 0

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

1 0

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

1 0