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EMBRIO Seminar T2A Today 3pm Staiger + Iyer-Pascuzzi labs, Best Paper Award Submission Due April 9th
by Ladd, Brent Thomas 07 Apr '25

07 Apr '25

Dear EMBRIOphytes, Thrust 2A Seminar, Today, 3-4PM EDT Plan to join us for the Institute’s next all-hands seminar 3PM EDT today with the Staiger lab and Iyer-Pascuzzi lab leading the presentation for Thrust 2A. Zoom Link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. If you've missed any previous seminars, recordings are available on our shared Box drive in the All-Hands Meetings Recordings folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. EMBRIO Best Paper Award Submissions - Due April 9th Submission online.<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Grads, Postdocs, and Staff Research Scientists: If you've published EMBRIO research as a first author or first co-author, you are invited and encouraged to submit your paper in the EMBRIO Best Paper Award competition. The deadline is this Wednesday, April 9th. Submission online.<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> There will be a division for Grads and a division for postdocs and staff research scientists. Details attached, along with the Best Scientific Figure competition (deadline June 1). Sloan Mentorship Community of Practice Workshop: Rubrics for Holistic Competitive Decisions, April 22nd, with leadership from EMBRIO Investigator Stephanie Gardner. Please see the attached flyer for details and QR code for the zoom link, but consider registering in advance for this meeting: https://purdue-edu.zoom.us/meeting/register/UvqM_3QWTdacKoLsbGk0Sg<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> After registering, you will receive a confirmation email containing information about joining the meeting. EMBRIO is participating in the Q-Bio Symposium: “Harnessing Complexity, Revealing Simplicity” happening this Friday, April 11th at University of Notre Dame. The symposium, planned and hosted by the quantitative biology student committee – including the Zartman Lab at the University of Notre Dame, will feature EMBRIO speakers and posters. Q-Bio Symposium RSVP and Schedule<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> 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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EMBRIO Reminders - T2A Seminar Monday, Best Paper Submissions, Mentorship CoP wkshp, Q-Bio Symposium
by Ladd, Brent Thomas 04 Apr '25

04 Apr '25

Dear EMBRIOphytes, Thrust 2A Seminar, Monday April 7th , 2-3PM EDT Plan to join us for the Institute’s next all-hands seminar Monday, April 7th, 3PM EDT with the Staiger lab and Iyer-Pascuzzi lab leading the presentation for Thrust 2A. Zoom Link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. If you missed any previous seminars, recordings are available on our shared Box drive in the All-Hands Meetings Recordings folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. EMBRIO Best Paper Award Submissions - Due April 9th Grads, Postdocs, and Staff Research Scientists: If you've published EMBRIO research as a first author or first co-author, you are invited and encouraged to submit your paper in the Best EMBRIO Paper Award competition. The deadline is next Wednesday, April 9th. Submission online<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…>. Details attached, along with the Best Scientific Figure competition (deadline June 1). Sloan Mentorship Community of Practice Workshop: Rubrics for Holistic Competitive Decisions, April 22nd, with leadership from EMBRIO Investigator Stephanie Gardner. Please see the attached flyer for details and QR code for the zoom link, but consider registering in advance for this meeting: https://purdue-edu.zoom.us/meeting/register/UvqM_3QWTdacKoLsbGk0Sg<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> After registering, you will receive a confirmation email containing information about joining the meeting. EMBRIO is participating in the Q-Bio Symposium: “Harnessing Complexity, Revealing Simplicity” happening on Friday, April 11th at University of Notre Dame. The symposium, planned and hosted by the quantitative biology student committee – including the Zartman Lab at the University of Notre Dame, will feature EMBRIO speakers and posters. Q-Bio Symposium RSVP and Schedule<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> 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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Announcements + Reminders
by Ladd, Brent Thomas 31 Mar '25

31 Mar '25

Dear EMBRIO Community, Plan to join us for the Institute’s next all-hands seminar Monday, April 7th, 3PM EDT with the Staiger lab and Iyer-Pascuzzi lab leading the presentation for Thrust 2A. If you missed any previous seminars, you could find the recording on our shared Box drive in the All-Hands Meetings Recordings folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. EMBRIO Best Paper and Best Scientific Figure Competitions – please see the attached announcements – deadline for Best Paper submission is April 9th, and Best Scientific Figure is June 1st. Upcoming Events: April 11, 2025. Q-Bio Symposium, University of Notre Dame. For additional details, visit qbio.nd.edu<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fqbio.nd.ed…> for event details<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> or feel free to reach out to sraha(a)nd.edu or dgazzo(a)nd.edu with any questions. Looking forward to a day of exciting discussions and collaboration! April 22, 2025. Sloan Mentorship Community of Practice Virtual Workshop: Rubrics for Holistic Competitive Decisions, with leadership from EMBRIO Investigator Stephanie Gardner. Please see the attached flyer for details and QR code for the zoom link, but consider registering in advance for this meeting: https://purdue-edu.zoom.us/meeting/register/UvqM_3QWTdacKoLsbGk0Sg<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> After registering, you will receive a confirmation email containing information about joining the meeting. June 9-13, 2025. EMBRIO Summer School and Annual Meeting, Purdue University. Additional Details forthcoming. See the attached for Best Paper and Best Scientific Figure Competitions. July 9-13, 2025. International Zebrafish Conference<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.izfs.…>. Madison, WI, USA. October 8-11, 2025. BMES 2025, San Diego, CA. https://www.bmes.org/2025/annualmeeting<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bmes.…> December 6-10, 2025. Cell Bio 25, ASCB, Philadelphia, PA. https://www.ascb.org/cellbio2025/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ascb.…> 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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Emergence Newsletter Issue 40 - announcements and attachments
by Ladd, Brent Thomas 27 Mar '25

27 Mar '25

[cid:3e5e0ac8-67f7-424b-abe5-0223a3c99ef5] Emergence: A newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 40: March 27, 2025 DIRECTORS’ NOTE Plan to join us for the Institute’s next all-hands seminar Monday, April 7th, 3PM EDT with the Staiger lab and Iyer-Pascuzzi lab leading the presentation for Thrust 2A. If you missed any previous seminars, you can find the recording on our shared Box drive in the All-Hands Meetings Recordings folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. The upcoming Thrust level seminar schedule is below. Investigators: emails went out March 14th with requests for progress reports (due April 14th) and information about Y5 budgeting. We’ve just received today a revised annual reporting template from NSF that will slightly alter how you report some activity. Brent will be in touch directly with details. Please hold on your calendars (calendar invites were sent in February) the week of June 9-13 for the annual EMBRIO Summer School (Mon-Wed) and Annual Meeting (Thurs-Fri). A forthcoming poll will solicit input from all members regarding formats and topics. This year we are announcing both Best Paper and Best Scientific Figure Competitions – please see the attached announcements – deadline for Best Paper submission is April 9th, and Best Scientific Figure is June 1st. EMBRIO is participating in the Q-Bio Symposium: “Harnessing Complexity, Revealing Simplicity” happening on Friday, April 11th at University of Notre Dame. RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> by tomorrow Friday, March 28th. The symposium, planned and hosted by the quantitative biology student committee – including the Zartman Lab at the University of Notre Dame, will feature EMBRIO speakers. Trainees and collaborators there is still time to submit a poster. More details about the event can be found below. You can always check out the latest on EMBRIO research being released in pre-print and peer-reviewed publication on our Institute Google Scholar page<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.g…>. A new preprint on Digital Cousins is out from the Umulis lab: Li, L., Mdluli, T., Buzzard, G., and Umulis, D. Digital Cousins: Simultaneous optimization of one model for BMP signaling in distant relatives reveals essential core. March 1, 2025. https://www.biorxiv.org/content/10.1101/2025.02.25.640248v1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biorx…> Congrats to co-first authors Mayesha Mim and Nilay Kumar, along with EMBRIO co-authors from the Zartman lab, for being awarded the Outstanding CBE Department Paper of 2024 at Notre Dame for work on Piezo in Cell Reports: Mim M.S., Kumar, N., Levis,M.., Unger, M.F., Miranda,G., Gazzo, D., Robinett,T., and Zartman, J.J. (2024) Piezo regulates epithelial topology and promotes precision in organ size control, Cell Reports, 43, Issue 7,114398, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2024.114398<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> Other opportunities and workshops coming up include the free virtual Sloan Mentorship Community of Practice Workshop: Rubrics for Holistic Competitive Decisions, April 22nd, with leadership from EMBRIO Investigator Stephanie Gardner. Please see the attached flyer for details and QR code for the zoom link, but consider registering in advance for this meeting: https://purdue-edu.zoom.us/meeting/register/UvqM_3QWTdacKoLsbGk0Sg After registering, you will receive a confirmation email containing information about joining the meeting. The American Society for Cell Biology has opportunity for organizing a workshop session. Those interested please contact Brent (laddb(a)purdue.edu<mailto:laddb@purdue.edu>) or Jeremy Zartman (jzartman(a)nd.edu<mailto:jzartman@nd.edu>) The deadline for workshop proposals is April 8th https://www.ascb.org/cellbio2025/sessionproposals/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ascb.…> An additional reminder: The postdoctoral fellowship opportunity at Notre Dame for those who have successfully completed all requirements for a doctoral degree between June 2023 and September 2025 (deadline is April 6th): Jeremy Zartman is interested in supporting anyone for this fellowship if they are interested and eligible to work in his Multicellular Systems Engineering lab<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.nd.…>. Please contact Dr. Zartman to discuss. Details on the University of Notre Dame Provost's Postdoctoral Fellowship in Engineering (deadline is April 6th): https://engineering.nd.edu/provosts-postdoctoral-fellowships-in-engineering…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fengineeri…> David, Jeremy, Chris, Anjali, Janice, Alejandra, Elsje, and Brent QUICK LINKS All-Hands Meetings Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Q-Bio Symposium RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> Materials from Summer School & Annual Retreat<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Institute Skills and Strengths Sharing Platform<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Sign the Data Sharing Policy Agreement<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> EMBRIO Personnel List<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Hot Off the Press: New & Recent EMBRIO Journal Papers and Preprints Let us know about new papers you want to highlight for the EMBRIO community! Check out our Google Scholar Page<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.g…> See a more complete list of Scholarly Products produced under support of EMBRIO Institute<https://www.purdue.edu/research/embrio/research/scholarly-products.php> Li, L., Mdluli, T., Buzzard, G., and Umulis, D. Digital Cousins: Simultaneous optimization of one model for BMP signaling in distant relatives reveals essential core. March 1, 2025. https://www.biorxiv.org/content/10.1101/2025.02.25.640248v1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biorx…> REMINDER: EMBRIO Acknowledgement for Scholarly Papers and Posters. For EMBRIO related research publications, NSF requires acknowledgement of EMBRIO NSF funding for our Institute to claim the work in our reporting back to NSF. Please include the following acknowledgement in your journal and conference papers and posters: “This work is based upon efforts supported by EMBRIO Institute, contract #2120200, a National Science Foundation (NSF) Biology Integration Institute.” UPCOMING DEADLINES, IMPORTANT DATES, OPPORTUNITIES & INFO EMBRIO All-hands Meeting Schedule, Monday’s 3-4pm ET. Zoom Link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Previous All Hands Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Trainees and collaborators encouraged to co-present during the Thrust seminars this semester. Month Day Spring Semester 2025 Jan 13 Denise Driscoll, Purdue (ABIDES Invited Scholar) Jan 27 Scott Howard, Notre Dame Feb 10 Krishna Jayant Lab; Thrust 1A Feb 24 Janice Evans Lab; Thrust 1B Mar 10 Qing Deng Lab; Thrust 3B Mar 24 Jeremiah Zartman Lab; Thrust 2B Apr 7 Chris Staiger and Anjali Iyer-Pascuzzi Labs; Thrust 2A Apr 21 Mary Mullins Lab; Thrust 3A May 5 Stephanie Gardner Lab; Thrust 4 May 19 Ale Magana Lab; Thrust 4 April 11, 2025. Q-Bio Symposium, University of Notre Dame. (details below) April 22, 2025. Sloan Mentorship Community of Practice Virtual Workshop: Rubrics for Holistic Competitive Decisions, with leadership from EMBRIO Investigator Stephanie Gardner. Please see the attached flyer for details and QR code for the zoom link, but consider registering in advance for this meeting: https://purdue-edu.zoom.us/meeting/register/UvqM_3QWTdacKoLsbGk0Sg After registering, you will receive a confirmation email containing information about joining the meeting. May 12-16, 2025 Cytoskeleton Modeling Workshop, NC State (Details below) June 9-13, 2025. EMBRIO Summer School and Annual Meeting, Purdue University. Additional Details forthcoming. See the attached for Best Paper and Best Scientific Figure Competitions. July 9-13, 2025. International Zebrafish Conference<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.izfs.…>. Madison, WI, USA. Quantitative Biology Symposium Joint Event: Q-Bio@ND + EMBRIO Location: University of Notre Dame Campus (Hesburg Library and Jordan Hall of Science) Date: Friday, April 11th. RSVP by this Friday, March 28th. Schedule<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> On behalf of the Q-Bio@ND community, we are excited to invite you to the upcoming Quantitative Biology Symposium, a joint event with EMBRIO, taking place on Friday, April 11, 2025, on Notre Dame's Campus in the Carey Auditorium & the Jordan Hall of Science, from 8:30 AM to 7:00 PM. This full-day symposium offers a valuable opportunity to connect ND and EMBRIO researchers, exchange insights, and foster collaborations in quantitative and computational biology. The event will feature engaging research discussions, networking opportunities, and complimentary meals throughout the day. If you are interested in any of the following research themes, please join us: Mathematical and Theoretical Biology, Computational Biology and Bioinformatics, Biostatistics, Population Biology and Epidemiology, Systems and Synthetic Biology Event Highlights: * Opening remarks by Dean Santiago Schnell<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fschnell-l…> * Research talks by ND and EMBRIO/Purdue faculty * Trainee short talks featuring research from graduate students, postdocs, and research scientists * Poster presentation session (open to all research topics—postdocs, graduate, and undergraduate students encouraged to participate!) * Informal networking sessions to build connections within and across research communities We’d love to have you join us! If you’re interested, please RSVP here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> For additional details, visit qbio.nd.edu<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fqbio.nd.ed…> for event details<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> or feel free to reach out to sraha(a)nd.edu or dgazzo(a)nd.edu with any questions. Looking forward to a day of exciting discussions and collaboration! Cheers, David Additional Gatherings On the evening of Thursday, April 10, we are tentatively planning to host an informal dinner gathering for EMBRIO investigators and key personnel, with further details to be shared closer to the event. For trainees arriving the night before, we will also hold an informal gathering option as well! Full Links RSVP: https://docs.google.com/forms/d/e/1FAIpQLSd22Fw8gUkR3MUWZeWxfAQlIGTHoVxQZoA…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> Event Details: https://qbio.nd.edu/events/2025/04/11/q-bio-nd-embrio-joint-symposium/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> Cytoskeleton Modeling Workshop, NC State From: Julio Monti Belmonte <jbelmon2(a)ncsu.edu<mailto:jbelmon2@ncsu.edu>> Date: Thu, Feb 6, 2025, 4:38 PM Subject: Cytoskeleton Modelling Workshop May 12-16 at NC State To: <cytosimworkshop(a)ncsu.edu<mailto:cytosimworkshop@ncsu.edu>> Dear Colleagues, We are pleased to announce the first in-person Cytoskeleton Modeling Workshop in the United States, utilizing the CytoSim<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcytosim.or…> software<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcytosim.or…>. This workshop will be held at NC State, Raleigh, NC<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…>, from May 12-16, 2025. Over the course of five days, the workshop will feature a combination of lectures<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…>, guest talks<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…>, and hands-on hackathon sessions. This workshop is open to individuals from a wide range of backgrounds, including Physics, Biology, Chemistry, and related fields, as well as participants at all career stages (undergraduate students to faculty). No prior programming experience is required. Key Learning Outcomes: - How to download, install, and run CytoSim simulations on your own machine - An overview of the biophysical properties and dynamics of various cytoskeletal systems and their components - An introduction to all the features and functionalities available in CytoSim - Techniques and scripts for extracting and analyzing simulation data - Methods for performing parameter scans and running simulations on computer clusters In the final days of the workshop, we will host hackathon sessions, where participants can apply the knowledge gained throughout the workshop to work on projects of their choosing, either independently or in groups, with the support of our instructors: François Nédélec<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.slcu.…>, Daniel Cortes<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcorteslab…> and Julio Belmonte<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbelmonte.…>. Additional Information: - There are no registration<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…> fees for this workshop; however, participants are responsible for their own travel and lodging expenses. Discounted accommodation rates are available at a nearby university dormitory<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…>. - Lunch and coffee will be provided throughout the workshop. For more details and to register, please visit the workshop website: https://cytosimworkshop.wordpress.ncsu.edu<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…> Registration Deadline: March 30, 2025 Given limited space, applicants will be notified by early April regarding their acceptance to the workshop. We encourage you to share this announcement with any colleagues who may be interested in attending. We look forward to welcoming you to Raleigh in May! Best regards, Julio M. Belmonte Assistant Professor Department of Physics NC State University Awards Congrats to co-first authors Mayesha Mim and Nilay Kumar, along with EMBRIO co-authors from the Zartman lab, for being awarded the Outstanding CBE Department Paper of 2024 at Notre Dame for work on Piezo in Cell Reports: Mim M.S., Kumar, N., Levis,M.., Unger, M.F., Miranda,G., Gazzo, D., Robinett,T., and Zartman, J.J. (2024) Piezo regulates epithelial topology and promotes precision in organ size control, Cell Reports, 43, Issue 7,114398, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2024.114398<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> New Lab Members? 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://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> , or they have graduated, let Brent know their names and email contacts (laddb(a)purdue.edu<mailto:laddb@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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Seminar by the Zartman Lab T2B Today 3pm + Q-Bio Symposium + Reminders
by Ladd, Brent Thomas 24 Mar '25

24 Mar '25

Dear EMBRIOphytes, Today's seminar from 3-4 pm EDT will feature the Zartman Lab with the Thrust 2B project. Zoom link for the spring semester seminars: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Related news to Thrust 2B includes a University of Notre Dame Provost's Postdoctoral Fellowship in Engineering (deadline April 6th - see details below), and congrats to co-first authors Mayesha Mim and Nilay Kumar, along with EMBRIO co-authors from the Zartman lab, for being awarded the Outstanding CBE Department Paper of 2024 at Notre Dame for work on Piezo in Cell Reports: Mim M.S., Kumar, N., Levis,M.., Unger, M.F., Miranda,G., Gazzo, D., Robinett,T., and Zartman, J.J. (2024) Piezo regulates epithelial topology and promotes precision in organ size control, Cell Reports, 43, Issue 7,114398, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2024.114398<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> BTW, EMBRIO graduate students, postdocs, and staff research scientists: stay tuned for an announcement on submitting your best work for EMBRIO's Best Paper Award, as well as Best Scientific Figure Award. ==> A reminder that EMBRIO is partnering with the Q-Bio@ND community for a joint symposium taking place in-person April 11th. Symposium details and RSVP from David Gazzo and the Q-Bio@ND group are below. Please RSVP by March 28th . Reach out to sraha(a)nd.edu or dgazzo(a)nd.edu with any questions. Depending on interest, we will look to organize carpools from Purdue for transportation to and from South Bend. If you are interested in any of the following research themes, please join us: Mathematical and Theoretical Biology, Computational Biology and Bioinformatics, Biostatistics, Population Biology and Epidemiology, Systems and Synthetic Biology Trainees: An opportunity to spotlight your research at The Chicago Cytoskeleton Society April 25th meeting through their lightning talk contest (submissions due today March 24). Please see details and instructions below in the announcement from Holly Goodson. See you all this afternoon for the seminar! 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 A postdoctoral fellowship opportunity at Notre Dame For those who have successfully completed all requirements for a doctoral degree between June 2023 and September 2025 (deadline is April 6th): Jeremy Zartman is interested in supporting anyone for this fellowship if they are interested and eligible to work in his Multicellular Systems Engineering lab<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.nd.…>. Please contact Dr. Zartman to discuss. Details on the University of Notre Dame Provost's Postdoctoral Fellowship in Engineering (deadline is April 6th): https://engineering.nd.edu/provosts-postdoctoral-fellowships-in-engineering…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fengineeri…> Quantitative Biology Symposium Joint Event: Q-Bio@ND + EMBRIO Location: University of Notre Dame Campus (Hesburg Library and Jordan Hall of Science) Date: Friday, April 11th. RSVP by this Friday, March 28th. Schedule<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> On behalf of the Q-Bio@ND community, we are excited to invite you to the upcoming Quantitative Biology Symposium, a joint event with EMBRIO, taking place on Friday, April 11, 2025, on Notre Dame's Campus in the Carey Auditorium & the Jordan Hall of Science, from 8:30 AM to 7:00 PM. This full-day symposium offers a valuable opportunity to connect ND and EMBRIO researchers, exchange insights, and foster collaborations in quantitative and computational biology. The event will feature engaging research discussions, networking opportunities, and complimentary meals throughout the day. If you are interested in any of the following research themes, please join us: Mathematical and Theoretical Biology, Computational Biology and Bioinformatics, Biostatistics, Population Biology and Epidemiology, Systems and Synthetic Biology Event Highlights: * Opening remarks by Dean Santiago Schnell<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fschnell-l…> * Research talks by ND and EMBRIO/Purdue faculty * Trainee short talks featuring research from graduate students, postdocs, and research scientists * Poster presentation session (open to all research topics—postdocs, graduate, and undergraduate students encouraged to participate!) * Informal networking sessions to build connections within and across research communities We’d love to have you join us! If you’re interested, please RSVP here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> For additional details, visit qbio.nd.edu<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fqbio.nd.ed…> for event details<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> or feel free to reach out to sraha(a)nd.edu or dgazzo(a)nd.edu with any questions. Looking forward to a day of exciting discussions and collaboration! Cheers, David Additional Gatherings On the evening of Thursday, April 10, we are tentatively planning to host an informal dinner gathering for EMBRIO investigators and key personnel, with further details to be shared closer to the event. For trainees arriving the night before, we will also hold an informal gathering option as well! [image.png] Full Links RSVP: https://docs.google.com/forms/d/e/1FAIpQLSd22Fw8gUkR3MUWZeWxfAQlIGTHoVxQZoA…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> Event Details: https://qbio.nd.edu/events/2025/04/11/q-bio-nd-embrio-joint-symposium/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> Chicago Cytoskeleton Society Lightning Talk Contest - Deadline Today -------- Forwarded Message -------- Subject: Chicago Cytoskeleton Lighting talk contest! Date: Sun, 9 Mar 2025 17:37:14 -0400 From: Holly Goodson <holly.v.goodson.1(a)nd.edu><mailto:holly.v.goodson.1@nd.edu> To: Vladimir I Gelfand <vgelfand(a)northwestern.edu><mailto:vgelfand@northwestern.edu> CC: Vanessa González <vanessa.g(a)northwestern.edu><mailto:vanessa.g@northwestern.edu> Hi Everyone, It is time for the lightning talk contest to determine who are the four trainees who will speak at the second (and last!) CC meeting of the year Friday April 25. The winners will speak before the joint plenary lecture to be given by the collaborating team of Sue Biggins (Fred Hutchison) and Chip Asbury (U. Washington). After the talks, we will have the yearly CC poster session. Meeting Time and Place: April 25, 3:00-7:30pm, Baldwin Auditorium, See the attached venue and parking PDF for more details. More info will come soon about the meeting itself. Lighting Talk and poster session deadlines: • So that we can announce the winners one month before the CC meeting, the deadline for submitting your lighting talk is two weeks from tomorrow, Monday March 24. • If you want to present a poster only, the deadline for abstract submission is Monday April 11. Details on how to submit recordings and poster abstracts are provided below. • Parking: please submit parking voucher requests (link below) by April 18. We are looking forward to hearing about your work in April! -Holly Goodson and the Chicago Cytoskeleton Steering Committee p.s. Please distribute this to your lab members, friends, and colleagues! ********* Lighting talk and poster session information Did you or someone in your lab present a lightning talk or poster at ASCB, Biophysics, or another conference? Give that presentation a new life through Chicago Cytoskeleton! Or perhaps you want to put together a new presentation? CC is a great place to try it out! Key points about the lightning talk contest and poster session: • If you want to compete for an April 25 speaker slot: please submit (details below) a pre-recorded 3-5 minute lightning talk that will be viewed and judged by the Steering Committee. > The Deadline for submitting your recording is Monday March 24. • If you just want to present a poster without competing: please simply submit an abstract by Monday April 11. ****** LIGHTNING TALK AND POSTER ABSTRACT SUBMISSION INFO******** If you want to participate in the lightning talk competition: 1) Please ASAP send an email to me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) with the subject line "CC lightning talk competition." I'll then email you a non-public Google Drive link into which you can submit your e-poster talk as well your abstract and (recommended but not required) a PDF of the associated poster. The only people with access to this link will be the poster submitters and the Steering Committee. 2) Please create in this Google Drive a folder with you name, and put in this folder: i) your pre-recorded lightning talk (3-5 minutes) ii) the abstract for the associated poster (we will put this along with the other abstracts in the ebooklet for the March 15 meeting) iii) a PDF of your poster (helpful but not required for following along with your talk; if you prefer, you can submit slides instead of a poster). >> Please upload all this information by the deadline of Monday March 24. If you simply want to present a poster April 25: By Friday April 11, please send an email to me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) with the subject line "CC poster abstract", and attach your abstract in .docx format > Please be sure to include the title (!), authors, and affiliations in your file. > Please be sure to use .docx and not PDF. Other notes: • For your recording, please use Zoom or a similar method, presenting your poster via presenter mode. Alternatively, you could prepare and present separate slides. Either works. • Please keep the talk and poster to reasonable sizes - less than 25MB if possible. • Please let me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) know if you have any questions or concerns! ++++++++++ Parking Voucher Request form: https://forms.feinberg.northwestern.edu/view.php?id=3523972<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforms.fei…> ++++++++++ Regarding lodging, both the Ivy Hotel and Club Quarters have offered Northwestern’s reduced rates for guests attending the conference in April. Instructions for securing lodging using the discounted rate is below. Ivy Hotel (2-3 minutes from campus): 233 E Ontario St, Chicago, IL 60611 Phone: (312) 643-3400 Click below to secure reduced room rate [Note from Holly: this link didn't work for me - I will have to get a new link and send it in a future email] https://bookings.travelclick.com/114842?&RatePlanId=5932744#/guestsandrooms<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens…> Club Quarters Hotel Wacker at Michigan (20-minute walk to campus, along the river): 75 East Wacker Drive, Chicago, IL 60601 Phone: (312) 357-6400 Click below to secure reduced room rate https://clubquartershotels.com/northwestern-university<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fclubquart…>

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EMBRIO Seminar 3PM ET Today, Q-Bio Symposium April 11th, Trainee spotlight talk opp at Chicago Cytoskeleton
by Ladd, Brent Thomas 10 Mar '25

10 Mar '25

Dear EMBRIOphytes, Today's seminar will feature a collaboration colleague from the Thrust 3B project between the Deng and Umulis Labs with Jesse Chi Zhang, Ph.D., presenting "Chemically Selective Imaging and Control of Biomolecular Functions in Live Cells" March 10th 3pm EST. Please see the attached pdf flyer for zoom link, abstract and bio. EMBRIO is excited to be partnering with the Q-Bio@ND community for a joint symposium taking place in-person April 11th. Symposium details and RSVP from David Gazzo and the Q-Bio@ND group are below. Please RSVP by March 21st . Reach out to sraha(a)nd.edu or dgazzo(a)nd.edu with any questions. We will look to organize carpools from Purdue for transportation to and from South Bend. Trainees: An opportunity to spotlight your research at The Chicago Cytoskeleton Society April 25th meeting through their lightning talk contest (submissions due March 24). Please see details and instructions below in the announcement from Holly Goodson. See you all this afternoon for the seminar! 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 Quantitative Biology Symposium Joint Event: Q-Bio@ND + EMBRIO Location: University of Notre Dame Campus (Hesburg Library and Jordan Hall of Science) Date: Friday, April 11th Schedule<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> On behalf of the Q-Bio@ND community, we are excited to invite you to the upcoming Quantitative Biology Symposium, a joint event with EMBRIO, taking place on Friday, April 11, 2025, on Notre Dame's Campus in the Carey Auditorium & the Jordan Hall of Science, from 8:30 AM to 7:00 PM. This full-day symposium offers a valuable opportunity to connect ND and EMBRIO researchers, exchange insights, and foster collaborations in quantitative and computational biology. The event will feature engaging research discussions, networking opportunities, and complimentary meals throughout the day. Event Highlights: * Opening remarks by Dean Santiago Schnell<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fschnell-l…> * Research talks by ND and EMBRIO/Purdue faculty * Trainee short talks featuring research from graduate students, postdocs, and research scientists * Poster presentation session (open to all research topics—postdocs, graduate, and undergraduate students encouraged to participate!) * Informal networking sessions to build connections within and across research communities We’d love to have you join us! If you’re interested, please RSVP here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> For additional details, visit qbio.nd.edu<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fqbio.nd.ed…> for event details<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> or feel free to reach out to sraha(a)nd.edu or dgazzo(a)nd.edu with any questions. Looking forward to a day of exciting discussions and collaboration! Cheers, David Additional Gatherings On the evening of Thursday, April 10, we are tentatively planning to host an informal dinner gathering for EMBRIO investigators and key personnel, with further details to be shared closer to the event. For trainees arriving the night before, we will also hold an informal gathering option as well! [image.png] Full Links RSVP: https://docs.google.com/forms/d/e/1FAIpQLSd22Fw8gUkR3MUWZeWxfAQlIGTHoVxQZoA…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> Event Details: https://qbio.nd.edu/events/2025/04/11/q-bio-nd-embrio-joint-symposium/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> Chicago Cytoskeleton Society Lightning Talk Contest -------- Forwarded Message -------- Subject: Chicago Cytoskeleton Lighting talk contest! Date: Sun, 9 Mar 2025 17:37:14 -0400 From: Holly Goodson <holly.v.goodson.1(a)nd.edu><mailto:holly.v.goodson.1@nd.edu> To: Vladimir I Gelfand <vgelfand(a)northwestern.edu><mailto:vgelfand@northwestern.edu> CC: Vanessa González <vanessa.g(a)northwestern.edu><mailto:vanessa.g@northwestern.edu> Hi Everyone, It is time for the lightning talk contest to determine who are the four trainees who will speak at the second (and last!) CC meeting of the year Friday April 25. The winners will speak before the joint plenary lecture to be given by the collaborating team of Sue Biggins (Fred Hutchison) and Chip Asbury (U. Washington). After the talks, we will have the yearly CC poster session. Meeting Time and Place: April 25, 3:00-7:30pm, Baldwin Auditorium, See the attached venue and parking PDF for more details. More info will come soon about the meeting itself. Lighting Talk and poster session deadlines: • So that we can announce the winners one month before the CC meeting, the deadline for submitting your lighting talk is two weeks from tomorrow, Monday March 24. • If you want to present a poster only, the deadline for abstract submission is Monday April 11. Details on how to submit recordings and poster abstracts are provided below. • Parking: please submit parking voucher requests (link below) by April 18. We are looking forward to hearing about your work in April! -Holly Goodson and the Chicago Cytoskeleton Steering Committee p.s. Please distribute this to your lab members, friends, and colleagues! ********* Lighting talk and poster session information Did you or someone in your lab present a lightning talk or poster at ASCB, Biophysics, or another conference? Give that presentation a new life through Chicago Cytoskeleton! Or perhaps you want to put together a new presentation? CC is a great place to try it out! Key points about the lightning talk contest and poster session: • If you want to compete for an April 25 speaker slot: please submit (details below) a pre-recorded 3-5 minute lightning talk that will be viewed and judged by the Steering Committee. > The Deadline for submitting your recording is Monday March 24. • If you just want to present a poster without competing: please simply submit an abstract by Monday April 11. ****** LIGHTNING TALK AND POSTER ABSTRACT SUBMISSION INFO******** If you want to participate in the lightning talk competition: 1) Please ASAP send an email to me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) with the subject line "CC lightning talk competition." I'll then email you a non-public Google Drive link into which you can submit your e-poster talk as well your abstract and (recommended but not required) a PDF of the associated poster. The only people with access to this link will be the poster submitters and the Steering Committee. 2) Please create in this Google Drive a folder with you name, and put in this folder: i) your pre-recorded lightning talk (3-5 minutes) ii) the abstract for the associated poster (we will put this along with the other abstracts in the ebooklet for the March 15 meeting) iii) a PDF of your poster (helpful but not required for following along with your talk; if you prefer, you can submit slides instead of a poster). >> Please upload all this information by the deadline of Monday March 24. If you simply want to present a poster April 25: By Friday April 11, please send an email to me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) with the subject line "CC poster abstract", and attach your abstract in .docx format > Please be sure to include the title (!), authors, and affiliations in your file. > Please be sure to use .docx and not PDF. Other notes: • For your recording, please use Zoom or a similar method, presenting your poster via presenter mode. Alternatively, you could prepare and present separate slides. Either works. • Please keep the talk and poster to reasonable sizes - less than 25MB if possible. • Please let me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) know if you have any questions or concerns! ++++++++++ Parking Voucher Request form: https://forms.feinberg.northwestern.edu/view.php?id=3523972<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforms.fei…> ++++++++++ Regarding lodging, both the Ivy Hotel and Club Quarters have offered Northwestern’s reduced rates for guests attending the conference in April. Instructions for securing lodging using the discounted rate is below. Ivy Hotel (2-3 minutes from campus): 233 E Ontario St, Chicago, IL 60611 Phone: (312) 643-3400 Click below to secure reduced room rate [Note from Holly: this link didn't work for me - I will have to get a new link and send it in a future email] https://bookings.travelclick.com/114842?&RatePlanId=5932744#/guestsandrooms<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens…> Club Quarters Hotel Wacker at Michigan (20-minute walk to campus, along the river): 75 East Wacker Drive, Chicago, IL 60601 Phone: (312) 357-6400 Click below to secure reduced room rate https://clubquartershotels.com/northwestern-university<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fclubquart…>

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EMBRIO Seminar March 10th and Q-Bio Symposium April 11th Details
by Ladd, Brent Thomas 03 Mar '25

03 Mar '25

[cid:bc905962-40c3-4f6c-86f5-91e5b598700d] Dear EMBRIOphytes, Next Monday's seminar will feature a collaboration colleague from the Thrust 3B project between the Deng and Umulis Labs with Jesse Chi Zhang, Ph.D., who will present "Chemically Selective Imaging and Control of Biomolecular Functions in Live Cells" March 10th 3pm EST. Please see the attached pdf flyer for zoom link, abstract and bio. EMBRIO is excited to be partnering with the Q-Bio@ND community for a joint symposium taking place in-person April 11th. Symposium details and RSVP from David Gazzo and the Q-Bio@ND group are below. Please RSVP by March 21st . Reach out to sraha(a)nd.edu or dgazzo(a)nd.edu with any questions. We will look to organize carpools from Purdue for transportation to and from South Bend. Quantitative Biology Symposium Joint Event: Q-Bio@ND + EMBRIO Location: University of Notre Dame Campus (Hesburg Library and Jordan Hall of Science) Date: Friday, April 11th Schedule<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> On behalf of the Q-Bio@ND community, we are excited to invite you to the upcoming Quantitative Biology Symposium, a joint event with EMBRIO, taking place on Friday, April 11, 2025, on Notre Dame's Campus in the Carey Auditorium & the Jordan Hall of Science, from 8:30 AM to 7:00 PM. This full-day symposium offers a valuable opportunity to connect ND and EMBRIO researchers, exchange insights, and foster collaborations in quantitative and computational biology. The event will feature engaging research discussions, networking opportunities, and complimentary meals throughout the day. Event Highlights: * Opening remarks by Dean Santiago Schnell<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fschnell-l…> * Research talks by ND and EMBRIO/Purdue faculty * Trainee short talks featuring research from graduate students, postdocs, and research scientists * Poster presentation session (open to all research topics—postdocs, graduate, and undergraduate students encouraged to participate!) * Informal networking sessions to build connections within and across research communities We’d love to have you join us! If you’re interested, please RSVP here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> For additional details, visit qbio.nd.edu<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fqbio.nd.ed…> for event details<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> or feel free to reach out to sraha(a)nd.edu or dgazzo(a)nd.edu with any questions. Looking forward to a day of exciting discussions and collaboration! Cheers, David Additional Gatherings On the evening of Thursday, April 10, we are tentatively planning to host an informal dinner gathering for EMBRIO investigators and key personnel, with further details to be shared closer to the event. For trainees arriving the night before, we will also hold an informal gathering option as well! [image.png] Full Links RSVP: https://docs.google.com/forms/d/e/1FAIpQLSd22Fw8gUkR3MUWZeWxfAQlIGTHoVxQZoA…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> Event Details: https://qbio.nd.edu/events/2025/04/11/q-bio-nd-embrio-joint-symposium/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqbio.nd.e…> 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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Invitation to the Quantitative Biology Symposium – Joint Event with EMBRIO
by David Gazzo 28 Feb '25

28 Feb '25

Dear EMBRIO Members, On behalf of the *Q-Bio@ND* community, we are excited to invite you to the upcoming *Quantitative Biology Symposium*, a joint event with *EMBRIO*, taking place on *Friday, April 11, 2025*, on *Notre Dame's Campus* in the Carey Auditorium & the Jordan Hall of Science, from *8:30 AM to 7:00 PM*. This full-day symposium offers a valuable opportunity to connect *ND* and *EMBRIO researchers*, exchange insights, and foster collaborations in *quantitative and computational biology*. The event will feature engaging research discussions, networking opportunities, and complimentary meals throughout the day. *Event Highlights:* - *Opening remarks* by *Dean Santiago Schnell <https://schnell-lab.nd.edu/>* - *Research talks* by *ND and EMBRIO/Purdue faculty* - *Trainee short talks* featuring research from graduate students, postdocs, and research scientists - *Poster presentation session* (open to all research topics—postdocs, graduate, and undergraduate students encouraged to participate!) - *Informal networking sessions* to build connections within and across research communities We’d love to have you join us! If you’re interested, please *RSVP here <https://docs.google.com/forms/d/e/1FAIpQLSd22Fw8gUkR3MUWZeWxfAQlIGTHoVxQZoA…>* For additional details, visit *qbio.nd.edu <http://qbio.nd.edu> for event details <https://qbio.nd.edu/events/2025/04/11/q-bio-nd-embrio-joint-symposium/>* or feel free to reach out to *sraha(a)nd.edu* or *dgazzo(a)nd.edu* with any questions. Looking forward to a day of exciting discussions and collaboration! Cheers, David *Additional Gatherings* On the evening of *Thursday, April 10*, we are tentatively planning to host an *informal dinner gathering* for *EMBRIO investigators and key personnel*, with further details to be shared closer to the event. For trainees arriving the night before, we will also hold an informal gathering option as well! [image: image.png] Full Links RSVP: https://docs.google.com/forms/d/e/1FAIpQLSd22Fw8gUkR3MUWZeWxfAQlIGTHoVxQZoA… Event Details: https://qbio.nd.edu/events/2025/04/11/q-bio-nd-embrio-joint-symposium/ -- David Gazzo University of Notre Dame Graduate Student Researcher | Zartman Lab <http://sites.nd.edu/zartmanlab/> Bioengineering Graduate Program <https://bioengineering.nd.edu/> Aerospace and Mechanical Engineering <https://ame.nd.edu/> Chemical and Biomolecular Engineering <https://cbe.nd.edu/>

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EMBRIO All-Hands Seminar Today 3pm Evans and Kim Labs Present Thrust 1B Updates
by Ladd, Brent Thomas 24 Feb '25

24 Feb '25

Dear EMBRIOphytes, Plan to join us for the Institute’s all-hands seminar this afternoon at 3PM ET with Thrust 1B collaborative project presented by Janice Evan’s lab (Zachery Tawfiq Kyner) and Taeyoon Kim's lab (Jeffery Coulter) . The zoom link for all seminars this spring semester: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> If you missed any previous seminars, you may find the recordings on our shared Box drive in the All-Hands Meetings Recordings folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. The upcoming Thrust level seminar schedule is below. See you all this afternoon! Brent UPCOMING DEADLINES, IMPORTANT DATES, OPPORTUNITIES & INFO EMBRIO All-hands Meeting Schedule, Monday’s 3-4pm ET. Zoom Link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Previous All Hands Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Trainees and collaborators encouraged to co-present during the Thrust seminars this semester. Month Day Spring Semester 2025 Jan 13 Denise Driscoll, Purdue (ABIDES Invited Scholar) Jan 27 Scott Howard, Notre Dame Feb 10 Krishna Jayant Lab; Thrust 1A Feb 24 Janice Evans + Taeyoon Kim Labs; Thrust 1B Mar 10 Chris Staiger and Anjali Iyer-Pascuzzi Labs; Thrust 2A Mar 24 Jeremiah Zartman Lab; Thrust 2B Apr 7 Qing Deng Lab; Thrust 3B Apr 21 Mary Mullins Lab; Thrust 3A May 5 Stephanie Gardner Lab; Thrust 4 May 19 Ale Magana Lab; Thrust 4 March 26-28, 2025. Multicellular Engineered Living Systems (M-CELS) Symposium 2025. Organizers invite you to participate in the “M-CELS: Advances in Basic Research and Translational Opportunities<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens…>” symposium, which will be held on March 26-28, 2025, at the OMNI Hilton Head Resort in South Carolina, USA. April 11, 2025. Q-Bio Symposium, University of Notre Dame. Registration, Speakers, Poster Session Details forthcoming. May 12-16, 2025 Cytoskeleton Modeling Workshop, NC State. For more details and to register, please visit the workshop website: https://cytosimworkshop.wordpress.ncsu.edu<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…> Registration Deadline: March 30, 2025 June 9-13, 2025. EMBRIO Summer School and Annual Meeting, Purdue University. Additional Details forthcoming. July 9-13, 2025. International Zebrafish Conference<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.izfs.…>. Madison, WI, USA. 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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Emergence Newsletter Issue 39: Events, Dates, New Publications and more...
by Ladd, Brent Thomas 20 Feb '25

20 Feb '25

[cid:47818416-c9cb-49e7-ad46-697a255f398b] Emergence: A newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 39: February 20, 2025 DIRECTORS’ NOTE Plan to join us for the Institute’s all-hands seminar this coming Monday, February 24th, 3PM ET with Janice Evan’s lab leading the presentation for Thrust 1B. If you missed any previous seminars you can find the recording on our shared Box drive in the All-Hands Meetings Recordings folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. The upcoming Thrust level seminar schedule is below. Please hold on your calendars (calendar invites were sent today) the week of June 9-13 for the annual EMBRIO Summer School (Mon-Wed) and Annual Meeting (Thurs-Fri). Due to several research conferences and schedule conflicts for June and July, this is the best week available. Stay tuned for more details. An exciting event that EMBRIO is participating in will be the Q-Bio Symposium slated for Friday, April 11th planned and hosted by the quantitative biology student committee at the University of Notre Dame, in South Bend, Indiana, including trainees in the Zartman lab. EMBRIO researchers are being invited to present research talks, and a poster session will be held. EMBRIO trainees and collaborators are encouraged to submit and present a poster. Additional details on speakers, posters, registration will be forthcoming. As a result of changes to the NSF BII program in 2024, EMBRIO placed considerable focus the last six months on unifying our collective progress and expertise into an innovative vision for the future of the Institute. The near-term outcome of this effort resulted in successfully submitting a new funding proposal to NSF this week. Although uncertainties abound at the federal level, we will stay in communication with NSF as the review process unfolds. A huge thank you to Jeremy Zartman for his tireless commitment leading the writing effort. As Institute Co-Director with David Umulis, along with the core writers and all who provided input, reviews and feedback, we were able to shape our collective expertise into an innovative vision for the future of the Institute. This would not have been possible without you, the EMBRIO community of investigators, researchers, and trainees, who have collaborated and learned from one another to build a solid foundation of research and knowledge in these first 3.5 years. Continuing with those thoughts, congrats to all who have submitted journal manuscripts for review and/or as preprints and have published EMBRIO research this winter (~ the last 4+ months). Check out the latest EMBRIO research findings from these Institute labs in the “Hot of the Press Publications & Preprints” section below: Glazier, Iyer-Pascuzzi, Jayant, Kim, Kinzer-Ursem, Mullins, Pienaar, Staiger, Umulis, and Zartman. Please let Brent know (laddb(a)purdue.edu<mailto:laddb@purdue.edu>) if we’ve missed a recent publication, preprint, or submission. Trainees and Research Staff: stay tuned for details on an EMBRIO Best Manuscript Competition. Congratulations to Dr. Shulan Xiao on successfully defending her Ph.D. dissertation earlier this month! Shulan’s research in the Jayant lab, along with collaborating in Thrust 1, led to her work being published in Cell Reports. You can check out that paper here: https://doi.org/10.1016/j.celrep.2024.114413<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> A last reminder to EMBRIO investigators at Purdue if you haven’t yet posted your summer intern research projects in SURF, please do so. EMBRIO will cover the faculty portion of the stipend and housing agreement. The SURF program provides an 11-week on campus research experience. Get your project posted now for consideration (details and links below). EMBRIO members check out these conferences in 2025: Multicellular Engineered Living Systems (M-CELS) Symposium 2025. Organizers invite you to participate in the “M-CELS: Advances in Basic Research and Translational Opportunities<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens…>” symposium, which will be held on March 26-28, 2025, at the OMNI Hilton Head Resort in South Carolina, USA. July 9-13, 2025 the International Zebrafish Conference<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.izfs.…> will be held in Madison, WI, with potential for an EMBRIO Workshop to be hosted there – stay tuned! David, Jeremy, Chris, Anjali, Janice, Alejandra, Elsje, and Brent QUICK LINKS All-Hands Meetings Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Materials from Summer School & Annual Retreat<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Institute Skills and Strengths Sharing Platform<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Sign the Data Sharing Policy Agreement<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> EMBRIO Personnel List<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Hot Off the Press: New & Recent EMBRIO Journal Papers and Preprints Let us know about new papers you want to highlight for the EMBRIO community! Check out our Google Scholar Page<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.g…> See a more complete list of Scholarly Products produced under support of EMBRIO Institute<https://www.purdue.edu/research/embrio/research/scholarly-products.php> Ding, Shihang, Pei-En Chou, Shinji Deguchi, and Taeyoon Kim. 2025. “Impacts of Structural Properties of Myosin II Filaments on Force Generation,” eLife, February 7, 2025 reviewed preprint. https://doi.org/10.7554/elife.105236.1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> . Gazzo, D., T.L. Kinzer-Ursem, and J.J. Zartman. 2024. “Proteins clump: Mechanics and transport during neurodegeneration.” Biophysical Journal, 123,1-3. https://doi.org/10.1016/j.bpj.2024.06.004<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> . Gazzo, David V., and Jeremiah J. Zartman. 2025. “Calcium Imaging in Drosophila.” In Calcium Signaling: Methods and Protocols, edited by Caroline M. Gorvin, 257–71. New York, NY: Springer US. https://doi.org/10.1007/978-1-0716-4164-4_19. Hiles, Rachel, Abigail Rogers, Namrata Jaiswal, Weiwei Zhang, Jules Butchacas, Marcus V. Merfa, Taylor Klass, et al. 2024. “A Ralstonia Solanacearum Type III Effector Alters the Actin and Microtubule Cytoskeleton to Promote Bacterial Virulence in Plants.” PLOS Pathogens 20 (12): e1012814. https://doi.org/10.1371/journal.ppat.1012814<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> . Khan, Hammad F., Sayan Dutta, Alicia N. Scott, Shulan Xiao, Saumitra Yadav, Xiaoling Chen, Uma K. Aryal, Tamara L. Kinzer-Ursem, Jean-Christophe Rochet, and Krishna Jayant. 2024. “Site-Specific Seeding of Lewy Pathology Induces Distinct Pre-Motor Cellular and Dendritic Vulnerabilities in the Cortex.” Nature Communications 15 (1): 10775. https://doi.org/10.1038/s41467-024-54945-0<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> . Kim, June Hyung, and Taeyoon Kim. 2024. “The Mechanism of Dynamic Steady States in Lamellipodia.” bioRxiv, January, 2024.11.18.62420. https://doi.org/10.1101/2024.11.18.624201<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> . Matin, Meisam Habibi, Shulan Xiao, and Krishna Jayant. 2024. “Mild Focal Cooling Selectively Impacts Computations in Dendritic Trees.” bioRxiv, January, 2024.11.02.621672. https://doi.org/10.1101/2024.11.02.621672<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> . Minsuk, Sharon B., T. J. Sego, David M. Umulis, Mary C. Mullins, and James A. Glazier. 2025. “Modeling Epithelial Morphogenesis and Cell Rearrangement during Zebrafish Epiboly: Tissue Deformation, Cell-Cell Coupling, and the Mechanical Response to Stress.” bioRxiv, January, 2025.02.12.637977. https://doi.org/10.1101/2025.02.12.637977<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> . Ogawa, S.T., W. ZhangP, C.J. Staiger, and S.A. Kessler.* 202X. MLO-mediated Ca2+ influx regulates root hair tip growth in Arabidopsis. New Phytol. Submitted 01-28-25. Rabbi, Md Foysal, Gijsje H. Koenderink, Yuval Mulla, and Taeyoon Kim. 2025. “Fine-Tuning of Material Properties via Catch Bonds.” bioRxiv, January, 2025.01.09.632258. https://doi.org/10.1101/2025.01.09.632258<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> . Slater, Brandon, Alfredo Sciortino, Andreas R. Bausch, and Taeyoon Kim. 2024. “Cluster Formation and Phase Separation Driven by Mobile Myosin Motors in the Motility Assay.” bioRxiv, January, 2024.11.30.626189. https://doi.org/10.1101/2024.11.30.626189<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> . Xu, Liyuan, Weiwei Zhang, Lei Huang, Chunhua Zhang, and Christopher J. Staiger. 2025. “Actomyosin and the Arp2/3 Complex Are Involved in the Internalization of Cellulose Synthase Complexes.” bioRxiv, January, 2025.01.19.633783. https://doi.org/10.1101/2025.01.19.633783<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> . Zhang, Weiwei, Nilay Kumar, Jessica R. Helwig, Alexis Hoerter, Anjali S. Iyer-Pascuzzi, David M. Umulis, Elsje Pienaar, and Christopher J. Staiger. 2025. “Local Traveling Waves of Cytosolic Calcium Elicited by Defense Signals or Wounding Are Propagated by Distinct Mechanisms.” bioRxiv, January, 2025.01.23.634554. https://doi.org/10.1101/2025.01.23.634554<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> . REMINDER: EMBRIO Acknowledgement for Scholarly Papers and Posters. For EMBRIO related research publications, NSF requires acknowledgement of EMBRIO NSF funding for our Institute to claim the work in our reporting back to NSF. Please include the following acknowledgement in your journal and conference papers and posters: “This work is based upon efforts supported by EMBRIO Institute, contract #2120200, a National Science Foundation (NSF) Biology Integration Institute.” EMBRIO Partnership with SURF (Summer Undergraduate Research Fellowship) Purdue EMBRIO faculty, it is time to post your summer research projects to recruit undergraduate researchers to your lab! Summer Undergraduate Research Fellowship (SURF)<https://maillinks.purdue.edu/t/46944966/1704294751/89814806/0/1007625/?x=5e…> PROJECT POSTINGS ARE OPEN! This 11-week, on-campus summer program provides a unique opportunity to mentor undergraduate students through hands-on research experiences. Students receive a $6,500 stipend, subsidized by the school/department and college affiliated with the project. Learn more about the program and submit your project today<https://maillinks.purdue.edu/t/46944966/1704294751/98563639/0/1007625/?x=f1…>! Priority Deadline: December 1, 2024. Submit now to maximize your project’s visibility! UPCOMING DEADLINES, IMPORTANT DATES, OPPORTUNITIES & INFO EMBRIO All-hands Meeting Schedule, Monday’s 3-4pm ET. Zoom Link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Previous All Hands Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Trainees and collaborators encouraged to co-present during the Thrust seminars this semester. Month Day Spring Semester 2025 Jan 13 Denise Driscoll, Purdue (ABIDES Invited Scholar) Jan 27 Scott Howard, Notre Dame Feb 10 Krishna Jayant Lab; Thrust 1A Feb 24 Janice Evans Lab; Thrust 1B Mar 10 Chris Staiger and Anjali Iyer-Pascuzzi Labs; Thrust 2A Mar 24 Jeremiah Zartman Lab; Thrust 2B Apr 7 Qing Deng Lab; Thrust 3B Apr 21 Mary Mullins Lab; Thrust 3A May 5 Stephanie Gardner Lab; Thrust 4 May 19 Ale Magana Lab; Thrust 4 March 26-28, 2025. Multicellular Engineered Living Systems (M-CELS) Symposium 2025. Organizers invite you to participate in the “M-CELS: Advances in Basic Research and Translational Opportunities<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens…>” symposium, which will be held on March 26-28, 2025, at the OMNI Hilton Head Resort in South Carolina, USA. April 11, 2025. Q-Bio Symposium, University of Notre Dame. Registration, Speakers, Poster Session Details forthcoming. May 12-16, 2025 Cytoskeleton Modeling Workshop, NC State (Details below) June 9-13, 2025. EMBRIO Summer School and Annual Meeting, Purdue University. Additional Details forthcoming. July 9-13, 2025. International Zebrafish Conference<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.izfs.…>. Madison, WI, USA. Cytoskeleton Modeling Workshop, NC State From: Julio Monti Belmonte <jbelmon2(a)ncsu.edu<mailto:jbelmon2@ncsu.edu>> Date: Thu, Feb 6, 2025, 4:38 PM Subject: Cytoskeleton Modelling Workshop May 12-16 at NC State To: <cytosimworkshop(a)ncsu.edu<mailto:cytosimworkshop@ncsu.edu>> Dear Colleagues, We are pleased to announce the first in-person Cytoskeleton Modeling Workshop in the United States, utilizing the CytoSim<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcytosim.or…> software<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcytosim.or…>. This workshop will be held at NC State, Raleigh, NC<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…>, from May 12-16, 2025. Over the course of five days, the workshop will feature a combination of lectures<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…>, guest talks<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…>, and hands-on hackathon sessions. This workshop is open to individuals from a wide range of backgrounds, including Physics, Biology, Chemistry, and related fields, as well as participants at all career stages (undergraduate students to faculty). No prior programming experience is required. Key Learning Outcomes: - How to download, install, and run CytoSim simulations on your own machine - An overview of the biophysical properties and dynamics of various cytoskeletal systems and their components - An introduction to all the features and functionalities available in CytoSim - Techniques and scripts for extracting and analyzing simulation data - Methods for performing parameter scans and running simulations on computer clusters In the final days of the workshop, we will host hackathon sessions, where participants can apply the knowledge gained throughout the workshop to work on projects of their choosing, either independently or in groups, with the support of our instructors: François Nédélec<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.slcu.…>, Daniel Cortes<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcorteslab…> and Julio Belmonte<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbelmonte.…>. Additional Information: - There are no registration<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…> fees for this workshop; however, participants are responsible for their own travel and lodging expenses. Discounted accommodation rates are available at a nearby university dormitory<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…>. - Lunch and coffee will be provided throughout the workshop. For more details and to register, please visit the workshop website: https://cytosimworkshop.wordpress.ncsu.edu<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcytosimwo…> Registration Deadline: March 30, 2025 Given limited space, applicants will be notified by early April regarding their acceptance to the workshop. We encourage you to share this announcement with any colleagues who may be interested in attending. We look forward to welcoming you to Raleigh in May! Best regards, Julio M. Belmonte Assistant Professor Department of Physics NC State University Awards Let us know about your grants and other awards! New Lab Members? 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://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> , or they have graduated, let Brent know their names and email contacts (laddb(a)purdue.edu<mailto:laddb@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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