August 2025 - Embrio-list - ecn.purdue.edu

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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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

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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

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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

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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

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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

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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

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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

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