November 2023 - Embrio-list

EMERGENCE issue 27: Nov. 29, 2023
by Ladd, Brent Thomas 29 Nov '23

29 Nov '23

[cid:61f8178c-fbed-472b-9120-0650a04d4dea] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 27: November 29, 2023 DIRECTORS’ NOTE As we enter the home stretch of the semester, we hope everyone had an enjoyable Thanksgiving break. This coming Monday don’t miss our next EMBRIO seminar, December 4th, by Javier Muñoz (Brubaker/Green Lab) titled Systems modeling for Multiomics Analysis Integration in Inflammatory Bowel Disease (abstract in this issue). If you missed the all-hands session last time featuring Dr. Weiwei Zhang presenting a thrust 2 seminar titled Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response, you can access the video in our Box account under the “All-Hands Meetings Recordings” folder. Purdue labs looking/planning for undergraduate researchers now or next summer (and our partner institutions who have students who want to come to Purdue for a summer research experience), the SURF REU program portal is open for faculty to submit your projects, with an early deadline of this Friday, Dec. 1st. See the info from Kay Kobak, their new Assoc. Director in this issue. When submitted your project, please indicate it is attached to the EMBRIO Institute, and note that EMBRIO will cover the PI’s portion of the SURF program cost. Please hold January 22-23 for the annual NSF BII conference. This year’s conference will be a hybrid, with most attending via zoom, and a smaller team in person at NSF headquarters. View the draft agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. A reminder that if you are new to EMBRIO (or want a refresher), we recommend that you take a look at the resources on the shared Box account in the Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> sub-folder. We will dedicate an all-hands session in the spring to this topic. We want to hear about your news and announcements. Send them to Brent (laddb(a)purdue.edu) by December 8th for inclusion in the next issue of Emergence. David, Chris, Stephanie, Anjali, Janice, Jeremy, and Brent Notable Quote "The real problem has far less to do with what is really out there than it does with our resistance to finding out what is really out there." ~ Barbara Brown Taylor, Learning to Walk in the Dark. QUICK LINKS BII Conference Agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> SURF Post a Research Project Portal<https://engineering.purdue.edu/Engr/Research/EURO/SURF/Research/Y2024/add_r…> All-Hands Meetings Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> ABIDES Culture and Mentoring resources<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Undergraduate Researchers Opportunities for EMBRIO Labs and Students Note from Kay Kobak, Assoc. Dir., EURO, Purdue: Hello Undergraduate Research Allies, SURF Post a Research Project Portal<https://engineering.purdue.edu/Engr/Research/EURO/SURF/Research/Y2024/add_r…> is now open for faculty  Program Name Description Student Compensation In-Lab Time Commitment Funding provided by Call for applications* Summer Undergraduate Research Fellowships (SURF)<https://engineering.purdue.edu/Engr/Research/EURO/students/about-SURF> Summer program for both Purdue Internal and external students, full time research experience. A total of $6000 paid over 12 weeks. 30-40 hours/week Cost shared 1:1:1 between EURO, the College, and the lab. (EMBRIO Note: the Institute will pay the PI tab of $2K, plus the $1K housing stipend if a non-Purdue student) Summer 2024 project portal open now. Early deadline is Dec. 1st *if you have already identified a student you wish to work with for a given time period, we still ask you post the project so we can maintain that information for our records. We can expedite the selection process and then close the project to other applicants if you already have someone in mind. Additional opportunities if you're currently hosting undergraduate researchers: EURO Travel Grant<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…>: For Purdue affiliated undergraduates who will be presenting their research at a conference - $500 awarded by EURO OUR Fall Expo<https://www.purdue.edu/undergrad-research/conferences/fall/index.php>: While the abstract deadline has passed for those wishing to give a talk, undergraduate researchers can still request to present virtually or give a poster Nov. 14-21. Other undergrad researcher funding opportunities can be found here<https://www.purdue.edu/undergrad-research/scholarships/grants.php>, here<https://www.purdue.edu/undergrad-research/scholarships/ExtGrants.php>, and here<https://exed.purdue.edu/funding/student.php>. Please feel free to reach out if you have any questions, Kay Kobak, Ph.D. she, her, hers Associate Director, Engineering Undergraduate Research Office DUDL 2526 | o.765-496-2349 | STUDENT LEADERSHIP COUNCIL CORNER The SLC is recruiting new officers to represent your university and your perspective for EMBRIO. Reach out to David Gazzo (dgazzo(a)nd.edu) incoming president, for more information, and log your ideas for future topics or events<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> that the SLC could organize. Access SLC slides and documents<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, and consider signing up to give or receive mentoring<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> for/from EMBRIO trainees in helping support and orient to the EMBRIO mission and interdisciplinary framework. EMBRIO ABIDES (Access, Belonging, Inclusion, Diversity, Equity, Support) Dr. Anjali Iyer-Pascuzzi, EMBRIO ABIDES Director and Professor at Purdue, leads activities for Institute members. A series of mentoring topics have been presented at the beginning of Weekly meetings, and a continuation of the Mentoring Panel topics from the annual retreat was presented October 23rd during the EMBRIO Weekly with a deeper dive into how culture impacts our mentoring and team thinking. BTW, if you missed “The role of culture and communication in mentoring” mini-workshop – view it here,<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> or the previous “mentoring snacks” check out the slides and resources in the ABIDES > Mentoring folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, and listen to “The Secret of Great Teams<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhiddenbra…>” episode of The Hidden Brain podcast. JOURNAL CLUBS Journal Club on Calcium Imaging Techniques meets Monday’s 11am ET Due to the need within our EMBRIO community to process and analyze Ca2+ Images, Dr. Norma Perez Rosas (nperezro(a)purdue.edu<mailto:nperezro@purdue.edu> ) is helping lead this club in discussing papers regarding methods and tools for analyzing calcium imaging. The goal, beyond integrating these techniques, is to write a review paper. The Club is meeting weekly on Mondays at 11am. Please contact Norma about participating. Journal Club on Multimodal Functions of Calcium in Tuning and Regulating Cytoskeleton Networks Please contact Dr. Linlin Li (li2212(a)purdue.edu<mailto:li2212@purdue.edu> ) for information. The club is in the writing stage for organizing and publishing a review paper on the topic. It isn’t too late to join. Here is the link to the current working documents: https://docs.google.com/document/d/1Cpg77yjtioWiIuRmiDMCcAiAd4jNNX_J7s64RQk…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> UPCOMING DEADLINES, IMPORTANT DATES, & INFO EMBRIO All-hands Meeting Schedule, Monday’s 3-4pm ET. Zoom link<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>.Weekly Update Meeting Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Aug 14 Benchling Workshop - SLC (Feyisayo) Aug 21 Student Leadership Council - Grads and Postdocs Only Session Aug 28 Faculty Investigators Only Sept 4 Labor Day no meeting Sept 11 Dr. Linlin Li: Part I: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 18 Dr. Linlin Li: Part II: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 25 Dr. Adrian Buganza Tepole: Part I: Physics informed machine learning Oct 2 Dr. Adrian Buganza Tepole: Part II: Physics informed machine learning Oct 9 Fall Break - no meeting Oct 16 Open Discussion and Thrust Project Breakout Rooms Oct 23 ABIDES: Culture, Mentoring, & Teams Mini Workshop Oct 30 No meeting. Thrust Leads organize own meetings Nov 6 VCell tutorial by Dr. Michael Blinov, Center for Cell Analysis and Modeling, UConn Nov 13 No meeting. Thrust Leads organize own meetings Nov 20 Dr. Weiwei Zhang, Staiger Lab, Thrust 2 Integrations Nov 27 No meeting. Thrust Leads organize own meetings Dec 4 Javier Muñoz (Brubaker/Green Lab) Dec 11 No meeting. Thrust Leads organize own meetings Winter Break December 4, 2023. EMBRIO All-Hands. Systems modeling for Multiomics Analysis Integration in Inflammatory Bowel Disease. This work in the CORE thrust is presented by Javier Muñoz from the Brubaker/Green Lab. Systems modeling for Multiomics AnalysisIntegration in Inflammatory Bowel Disease. Javier Munoz-Briones and Doug Brubaker Crohn’s disease and ulcerative colitis are chronic inflammatory bowel diseases (IBD) with a rising global prevalence, influenced by clinical and demographics factors. The pathogenesis of IBD involves complex interactions betweengut microbiome dysbiosis, epithelial cell barrierdisruption, and immune hyperactivity, which are poorly understood. This necessitates the development of novel approaches to integrate and model multiple clinical and molecular data modalities from patients, animal models, and in vitro systems to discover effectivebiomarkers for diseaseprogression and drug response. For this presentation, my focus is on the lack of understanding of regarding the composition and functional interactions of the gut microbiome in IBD. As sequencing technologies advance, the amount of molecular and compositional data from pairedmeasurements of host and microbiome systems is exploding. While it is become routine to generate such rich, deep datasets, tools for their interpretation lag behind. Here, I presenta computational framework for integrative modelingof microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE combines various types of microbiome multi-omics data using single-omic latent variables (LV) into a structured meta-model to determine the most predictive combinations of multi-omics features predicting an outcome, patient group, or phenotype. I implemented and tested LIVE using publicly available metagenomic and metabolomics data set from Crohn’s Disease(CD) and ulcerative colitis (UC) status patients in the PRISM and LLDeep cohorts. The findings show that LIVE reduced the number of features interactions from the originaldatasets for CD to tractable numbers and facilitated prioritization of biological associations between microbes, metabolites, enzymes, clinical variables, and a disease status outcome. LIVE modeling makes a distinct and complementary contribution to the current methods to integrate microbiome data to predict IBD status because of its flexibility to adapt to different types of microbiome multi-omics data, scalability for large and small cohort studies via reliance on latent variables and dimensionality reduction, and the intuitive interpretability of the meta-model integrating -omic data types. January 2 – 6, 2024. BMES – CMBE Conference. San Juan, Puerto Rico. Conference details: https://www.bmes.org/cmbe2024<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bmes.…> BII Annual Conference - January 22-23, 2024 . NSF is planning a hybrid one and 1/2 day meeting for all Biology Integration Institutes. Most attendees will be virtual, with a team of us in person at NSF headquarters. View the draft agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. February 6-7, 2024. EMBRIO Thrust & Site Leads Retreat. Thrust and site leads, and key investigators, will engage in two days of thrust and project working sessions in person (and yes, actual retreat social activity, as well). Logistics have been shared with all involved. March 6-10, 2024. The Allied Genetics Conference (TAGC24). Washington D.C. (Genetics Society of America). https://genetics-gsa.org/tagc-2024/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenetics-…> Note: EMBRIO is organizing a workshop for this conference. More TBA. Hot Off the Press: New EMBRIO Journal Papers Let us know about new papers you want to highlight for the EMBRIO community! 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.” Awards Congrats to Feyisayo Akande (Staiger Lab, Purdue) for passing her thesis defense: Investigating the role of atpiezo as a possible mechanoreceptor during plant defense. Feyisayo will be continuing her research career at the University of Missouri in the plant sciences Ph.D. program. We wish you continued success, Feyi! 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://app.box.com/s/frd9275xc069gmgtbe3y1osoz1j7ssk7<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> ) Submit your items for the next newsletter by Dec. 8 to Brent (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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Next All-hands seminar Dec. 6th
by Ladd, Brent Thomas 27 Nov '23

27 Nov '23

Hello EMBRIOphytes, I hope you all enjoyed a long holiday weekend. A reminder to use the 3-4pm scheduled time today for your project/thrust meetings. We will have our next all-hands meeting Monday Dec. 6th with Ph.D. Candidate and EMBRIO member, Javier Muñoz (Brubaker/Green Labs) presenting his thesis research that includes a computational framework for integrative modeling of multi-omics data titled: Systems modeling for Multiomics Analysis Integration in Inflammatory Bowel Disease. Javier Munoz-Briones and Doug Brubaker Crohn’s disease and ulcerative colitis are chronic inflammatory bowel diseases (IBD) with a rising global prevalence, influenced by clinical and demographics factors. The pathogenesis of IBD involves complex interactions between gut microbiome dysbiosis, epithelial cell barrier disruption, and immune hyperactivity, which are poorly understood. This necessitates the development of novel approaches to integrate and model multiple clinical and molecular data modalities from patients, animal models, and in vitro systems to discover effective biomarkers for disease progression and drug response. For this presentation, my focus is on the lack of understanding of regarding the composition and functional interactions of the gut microbiome in IBD. As sequencing technologies advance, the amount of molecular and compositional data from paired measurements of host and microbiome systems is exploding. While it is become routine to generate such rich, deep datasets, tools for their interpretation lag behind. Here, I present a computational framework for integrative modeling of microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE combines various types of microbiome multi-omics data using single-omic latent variables (LV) into a structured meta-model to determine the most predictive combinations of multi-omics features predicting an outcome, patient group, or phenotype. I implemented and tested LIVE using publicly available metagenomic and metabolomics data set from Crohn’s Disease(CD) and ulcerative colitis (UC) status patients in the PRISM and LLDeep cohorts. The findings show that LIVE reduced the number of features interactions from the original datasets for CD to tractable numbers and facilitated prioritization of biological associations between microbes, metabolites, enzymes, clinical variables, and a disease status outcome. LIVE modeling makes a distinct and complementary contribution to the current methods to integrate microbiome data to predict IBD status because of its flexibility to adapt to different types of microbiome multi-omics data, scalability for large and small cohort studies via reliance on latent variables and dimensionality reduction, and the intuitive interpretability of the meta-model integrating -omic data types. 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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Congrats Feyisayo Akande!
by Ladd, Brent Thomas 22 Nov '23

22 Nov '23

Dear EMBRIO Community, A note to celebrate that Feyisayo Akande in the Staiger Lab successfully defended her MS thesis yesterday. Congrats Feyi! We wish her continued success as she enters the PhD program in Plant Pathology at the University of Missouri. She will work on a plant-nematode interactions project and soybean pathology. For all who are entering prelims and thesis defenses, please reach out and let me know about them, so that we can share the talks and successes with the EMBRIO community. Wishing you all a healthy, safe, and thankful holiday this week, Brent ps. I'm out today hosting a family thanksgiving, so will be slow to respond to emails until next week [cid:b7b9c9c0-2cb4-4ef3-bb69-0b9963fc6fa0] 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 Research Seminar Today at 3pm: Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response.
by Ladd, Brent Thomas 20 Nov '23

20 Nov '23

Friendly reminder about our all-hands research seminar will be live at 3pm EST: Join Zoom Meeting https://purdue-edu.zoom.us/j/95112137034?pwd=cklTUS8zWmtra0w1UWp3eU5XdUJqUT…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> November 20, 2023. EMBRIO All-Hands. Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response. This work in Thrust 2 that Dr. Zhang is presenting includes collaborations with multiple EMBRIO labs that are working with the Staiger lab to develop data analysis tools and mathematical models. Abstract Plants have evolved conserved molecular mechanisms to recognize microbe-associated or damage-associated molecular patterns (MAMPs or DAMPS), mechanical perturbation, and/or cell wall integrity changes to initiate the first layer of defense response known as pattern-triggered immunity or PTI. During the first few minutes of PTI, several hallmark cellular responses occur including influxes of Ca2+ into the cytosol, accumulation of the signaling lipid phosphatidic acid, a transient reactive oxygen species (ROS) burst, and remodeling of the actin cytoskeleton. Among these hallmark events, cytosolic Ca2+ signals are recognized as a key early signaling element as they are highly specific in duration, amplitude, and frequency, and therefore encode specific information and trigger distinct downstream signaling pathways in response to different stimuli. Despite their obvious importance, Ca2+ signatures and how they spread in space and time in response to different stimuli during PTI have not been carefully characterized nor are the molecular mechanisms encoding these spatiotemporal Ca2+ signatures well understood. In this work, we developed an image acquisition and analysis pipeline to study plant defense related Ca2+ dynamics in Arabidopsis cotyledon epidermal cells using the live cell calcium biosensor R-GECO1. We characterized both single-cell Ca2+ signatures as well as intercellular Ca2+ wave patterns in response to two types of stimuli that mimic pathogen attack: global chemical stimulation with MAMPs and local mechanical stimulation by single-cell laser ablation. In addition, we show that pre-disruption of the cortical actin cytoskeleton resulted in altered single-cell Ca2+ signatures and increased calcium signaling durations, suggesting a negative feedback mechanism between the actin cytoskeleton and calcium signaling during PTI. Our work will help understand the calcium signaling mechanisms as well as the spatial spread of immune signals across a tissue during plant defense against pathogens. 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 26: November 17, 2023
by Ladd, Brent Thomas 20 Nov '23

20 Nov '23

[cid:173c8980-11a3-402e-a76c-57d63f795461] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 26: November 17, 2023 DIRECTORS’ NOTE As we approach the Thanksgiving holiday next week, we wish everyone a relaxing break, and safe travels. However, don’t miss our next EMBRIO seminar this coming Monday, November 20th; Dr. Weiwei Zhang in the Staiger Lab will present a research seminar titled Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response. This work in Thrust 2 that Dr. Zhang is presenting includes collaborations with multiple EMBRIO labs that are working with the Staiger lab to develop data analysis tools and mathematical models. If you missed the all-hands session featuring the intro tutorial on VCell by Dr. Michael Blinov with the Center for Cell Analysis and Modeling at UConn Health, you can access the video in our Box account under the “All-Hands Meetings Recordings” folder (direct link to the VCell session<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>). A note especially to Purdue labs regarding EMBRIO travel funds: For the faculty, staff, and trainees, please complete the Request for Travel Funds application<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> well ahead of your planned conference(s). A new policy and heads-up to trainees: to gain access to EMBRIO travel support funds it is necessary to describe how the conference will aid your professional development, as well as document your participation in Institute activities. Regular and sustained participation in Institute activities is necessary for travel funds approval. There are several upcoming public seminars being presented by trainees from EMBRIO labs. Please check out the Upcoming Deadlines, Important Dates, and Info section below. A thank you to Feyisayo Akande (Staiger Lab) for serving as President of the EMBRIO Student Leadership Council, and hearty shout of support as she presents her thesis research next Tuesday (zoom link available below), Investigating the role of atpiezo as a possible mechanoreceptor during plant defense. If you are new to EMBRIO (or want a refresher), we recommend that you take a look at the resources on the shared Box account in the Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> sub-folder. We will dedicate an all-hands session in the spring to this topic. Purdue labs looking/planning for undergraduate researchers now or next summer (and our partner institutions who have students who want to come to Purdue for a summer research experience), Brent has been in touch with the Engineering Undergraduate Research Office about next steps. See the info from Kay Kobak, their new Assoc. Director in this issue. We want to hear about your news and announcements. Send them to Brent (laddb(a)purdue.edu) by December 1st for inclusion in the next issue of Emergence. David, Chris, Stephanie, Anjali, Janice, Jeremy, and Brent Notable Quote "Any knowledge that doesn’t lead to new questions quickly dies out: it fails to maintain the temperature required for sustaining life. This is why I value that little phrase “I don’t know” so highly. It’s small, but it flies on mighty wings. It expands our lives to include the spaces within us as well as those outer expanses in which our tiny Earth hangs suspended." ~ Polish poet Wisława Szymborska ((July 2, 1923–February 1, 2012); from Nobel Laureates acceptance speech. QUICK LINKS All-Hands Meetings Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> ABIDES Culture and Mentoring resources<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Undergraduate Researchers Opportunities for EMBRIO Labs and Students Note from Kay Kobak, Assoc. Dir., EURO, Purdue: Hello Undergraduate Research Allies, We will also be asking for SURF applications in the coming weeks, so begin to think about your Summer 2024 needs now.  Program Name Description Student Compensation In-Lab Time Commitment Funding provided by Call for applications* Summer Undergraduate Research Fellowships (SURF)<https://engineering.purdue.edu/Engr/Research/EURO/students/about-SURF> Summer program for both Purdue Internal and external students, full time research experience. A total of $6000 paid over 12 weeks. 30-40 hours/week Cost shared 1:1:1 between EURO, the College, and the lab. Summer 2024 cohort proposals to open in November OUR Scholars <https://www.purdue.edu/undergrad-research/students/OUR-Scholars.php> Full-time undergraduate researcher for TWO semesters. $1000 scholarship ($500/semester) By agreement with faculty Cost shared between OUR and the College Fall 2023/Spring 2024 application closed. First Year Investigator's Program (Office of Undergraduate Research)<https://www.purdue.edu/undergrad-research/students/firstyear/index.php> Fall semester program for First-Year students. $15/hour 6-10 hours/week Office of Undergraduate Research Fall 2023 application closed *if you have already identified a student you wish to work with for a given time period, we still ask you post the project so we can maintain that information for our records. We can expedite the selection process and then close the project to other applicants if you already have someone in mind. Additional opportunities if you're currently hosting undergraduate researchers: EURO Travel Grant<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…>: For Purdue affiliated undergraduates who will be presenting their research at a conference - $500 awarded by EURO OUR Fall Expo<https://www.purdue.edu/undergrad-research/conferences/fall/index.php>: While the abstract deadline has passed for those wishing to give a talk, undergraduate researchers can still request to present virtually or give a poster Nov. 14-21. Other undergrad researcher funding opportunities can be found here<https://www.purdue.edu/undergrad-research/scholarships/grants.php>, here<https://www.purdue.edu/undergrad-research/scholarships/ExtGrants.php>, and here<https://exed.purdue.edu/funding/student.php>. Please feel free to reach out if you have any questions, Kay Kobak, Ph.D. she, her, hers Associate Director, Engineering Undergraduate Research Office DUDL 2526 | o.765-496-2349 | STUDENT LEADERSHIP COUNCIL CORNER The SLC is recruiting new officers to represent your university and your perspective for EMBRIO. Reach out to David Gazzo (dgazzo(a)nd.edu) incoming president, for more information, and log your ideas for future topics or events<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> that the SLC could organize. Access SLC slides and documents<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, and consider signing up to give or receive mentoring<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> for/from EMBRIO trainees in helping support and orient to the EMBRIO mission and interdisciplinary framework. EMBRIO ABIDES (Access, Belonging, Inclusion, Diversity, Equity, Support) Dr. Anjali Iyer-Pascuzzi, EMBRIO ABIDES Director and Professor at Purdue, leads activities for Institute members. A series of mentoring topics have been presented at the beginning of Weekly meetings, and a continuation of the Mentoring Panel topics from the annual retreat was presented October 23rd during the EMBRIO Weekly with a deeper dive into how culture impacts our mentoring and team thinking. BTW, if you missed “The role of culture and communication in mentoring” mini-workshop – view it here,<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> or the previous “mentoring snacks” check out the slides and resources in the ABIDES > Mentoring folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, and listen to “The Secret of Great Teams<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhiddenbra…>” episode of The Hidden Brain podcast. JOURNAL CLUBS Journal Club on Calcium Imaging Techniques meets Monday’s 11am ET Due to the need within our EMBRIO community to process and analyze Ca2+ Images, Dr. Norma Perez Rosas (nperezro(a)purdue.edu<mailto:nperezro@purdue.edu> ) is helping lead this club in discussing papers regarding methods and tools for analyzing calcium imaging. The goal, beyond integrating these techniques, is to write a review paper. The Club is meeting weekly on Mondays at 11am. Please contact Norma about participating. Journal Club on Multimodal Functions of Calcium in Tuning and Regulating Cytoskeleton Networks Please contact Dr. Linlin Li (li2212(a)purdue.edu<mailto:li2212@purdue.edu> ) for information. The club is in the writing stage for organizing and publishing a review paper on the topic. It isn’t too late to join. Here is the link to the current working documents: https://docs.google.com/document/d/1Cpg77yjtioWiIuRmiDMCcAiAd4jNNX_J7s64RQk…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> EMBRIO SUMMER WORKSHOP RESOURCES EMBRIO Institute's 2nd Annual Summer Training Workshop took place July 10-12. Workshop Schedule of Sessions<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>. Hosted by Dr. Jeremiah Zartman at the University of Notre Dame with a theme of Image Acquisition, Processing, and Analysis, tutorials and hands-on sessions were specifically aimed at benefiting trainees from both computational and experimental domains. Slides, handouts, and video recordings from this workshop are available on our shared Box account: https://app.box.com/s/mzo5ihlqiq4tfeig2psx2l6rmmdxto0c<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> EMBRIO ALL-HANDS ANNUAL RETREAT MATERIALS EMBRIO Institute’s Annual Retreat was hosted in the Weldon School of Biomedical Engineering on the Purdue University West Lafayette Campus, July 13-14, 2023. The annual retreat brought together the large majority of EMBRIO members in one physical place, with more than 60 of us engaging in research talks, poster presentations, programmatic discussions, and informal gatherings. Slide decks and posters from the annual retreat can be accessed here: https://app.box.com/s/rmsiuvydlsccexzhugyjp2b5v72xlg9l<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> UPCOMING DEADLINES, IMPORTANT DATES, & INFO EMBRIO All-hands Meeting Schedule, Monday’s 3-4pm ET. Zoom link<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>.Weekly Update Meeting Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Aug 14 Benchling Workshop - SLC (Feyisayo) Aug 21 Student Leadership Council - Grads and Postdocs Only Session Aug 28 Faculty Investigators Only Sept 4 Labor Day no meeting Sept 11 Dr. Linlin Li: Part I: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 18 Dr. Linlin Li: Part II: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 25 Dr. Adrian Buganza Tepole: Part I: Physics informed machine learning Oct 2 Dr. Adrian Buganza Tepole: Part II: Physics informed machine learning Oct 9 Fall Break - no meeting Oct 16 Open Discussion and Thrust Project Breakout Rooms Oct 23 ABIDES: Culture, Mentoring, & Teams Mini Workshop Oct 30 No meeting. Thrust Leads organize own meetings Nov 6 VCell tutorial by Dr. Michael Blinov, Center for Cell Analysis and Modeling, UConn Nov 13 No meeting. Thrust Leads organize own meetings Nov 20 Dr. Weiwei Zhang, Staiger Lab, Thrust 2 Integrations Nov 27 No meeting. Thrust Leads organize own meetings Dec 4 Javier Muñoz (Brubaker/Green Lab) Dec 11 No meeting. Thrust Leads organize own meetings Winter Break November 20, 2023. EMBRIO All-Hands. Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response. This work in Thrust 2 that Dr. Zhang is presenting includes collaborations with multiple EMBRIO labs that are working with the Staiger lab to develop data analysis tools and mathematical models. Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response Abstract Plants have evolved conserved molecular mechanisms to recognize microbe-associated or damage-associated molecular patterns (MAMPs or DAMPS), mechanical perturbation, and/or cell wall integrity changes to initiate the first layer of defense response known as pattern-triggered immunity or PTI. During the first few minutes of PTI, several hallmark cellular responses occur including influxes of Ca2+ into the cytosol, accumulation of the signaling lipid phosphatidic acid, a transient reactive oxygen species (ROS) burst, and remodeling of the actin cytoskeleton. Among these hallmark events, cytosolic Ca2+ signals are recognized as a key early signaling element as they are highly specific in duration, amplitude, and frequency, and therefore encode specific information and trigger distinct downstream signaling pathways in response to different stimuli. Despite their obvious importance, Ca2+ signatures and how they spread in space and time in response to different stimuli during PTI have not been carefully characterized nor are the molecular mechanisms encoding these spatiotemporal Ca2+ signatures well understood. In this work, we developed an image acquisition and analysis pipeline to study plant defense related Ca2+ dynamics in Arabidopsis cotyledon epidermal cells using the live cell calcium biosensor R-GECO1. We characterized both single-cell Ca2+ signatures as well as intercellular Ca2+ wave patterns in response to two types of stimuli that mimic pathogen attack: global chemical stimulation with MAMPs and local mechanical stimulation by single-cell laser ablation. In addition, we show that pre-disruption of the cortical actin cytoskeleton resulted in altered single-cell Ca2+ signatures and increased calcium signaling durations, suggesting a negative feedback mechanism between the actin cytoskeleton and calcium signaling during PTI. Our work will help understand the calcium signaling mechanisms as well as the spatial spread of immune signals across a tissue during plant defense against pathogens. November 21, 2023 Investigating the role of atpiezo as a possible mechanoreceptor during plant defense. In-Person WSLR 116, 9:30 AM. Zoom: https://purdue-edu.zoom.us/J/97Ql336OQ27<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Presented by Feyisayo Akande (Staiger Lab), Botany & Plant Pathology Special Seminar (in partial fulfillment of requirements for the Master of Science degree). Abstract: Plants are capable of perceiving and responding to biotic and abiotic stress. They have evolved a variety of mechanisms to help them recognize and trigger rapid responses to both chemical and mechanical stimuli. In this study, we investigated the potential role of PIEZO,a mechanosensitive ion channelthat is responsible for cellularmechanotransduction in both the plant and animal kingdoms, in plant immuneresponses. Publicly available RNAseq data revealed thatP/EZOexpression remainedconstant and unaltered in response to a varietyof phytopathogens or elicitors.We, then, conducted infectious growthassays onpiezomutants inArabidopsis thaliana plants. Our results indicated that piezo mutants, pzo1-1 and pzo1-5, were more susceptible to Pseudomonas syringaepv. tomato (Pst) DC3000 and theP. syringae hrcC -mutantconfirming PIEZO's role in plant defense and PTI. We further explored disease progression with necrotrophic fungi, Alternaria brassisicola and Botrytiscinerea, on Arabidopsis thaliana plants and found enhanced fungal growth compared to the wild type (Col-0) with Botrytis. Building upon these findings, we probed the role of PIEZO in the growth-defense tradeoff using a root growth inhibition assay with flg22 as MAMP elicitor. piezo mutants were less sensitive to flg22 treatment with less reduction in root growth length compared to wild type. In addition, we investigated whether PIEZO is upstreamof the main NADPH-oxidase, RBOHD, and the associated oxidative burst that occursin early defense. There was no significant difference in ReactiveOxygen Species (ROS) production between piezo mutants and the wild type in an apoplastic ROS assay with a MAMP elicitor (flg22). In conclusion, we demonstrated a potential role for PIEZO as a mechanoreceptor and mechanosensitive ion channel in plant immune defense responses and the growth-defense tradeoff. These signals coordinate plant growth, development, and innate immune responses. However, we have limited knowledge about how mechanical signals are perceived and transduced during the plant immune response. November 22, 2023. Dr. Norma Pérez Rosas, EMBRIO Postdoc, will be co-presenting an online webinar for Plantae, American Society of Plant Biologists, titled: “Shifting to a New Species/Research Subject”. 12pm EST. REGISTER for the event<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fus06web.z…> (free). Abstract: Join us for a groundbreaking webinar as we delve into the world of shifting research focus to new species and subjects. In this thought-provoking event, pioneering scientists who have successfully shifted their field of study will share their invaluable insights, experiences, and practical advice. Explore the challenges, opportunities, and ethical considerations involved in this transition, and gain a deeper understanding of how to navigate uncharted territories in your research. Whether you're a seasoned scientist looking to broaden your horizons or a curious explorer of the scientific realm, this webinar will provide you with a unique opportunity to learn from those who have blazed new trails and transformed their scientific journeys. Don't miss this chance to gain fresh perspectives and chart exciting paths in your research endeavors. November 22, 2023. Novel Mechanisms In Regulating Neutrophil Migration. 3:00 PM, LILY 1-117, Biological Sciences Defense Seminar by Tianqi Wang (Deng Lab). Abstract: Tianqi completed his D.VM. and Master's in veterinary medicine at Huazhong Agricultural University in China. He joined Dr. Qing Deng's lab in 2017, where his research focused on neutrophil migration. Throughout his PhD studies, Tianqi made discoveries related to novel mechanisms governing neutrophil chemotaxis and baseline motility. Beyond his rigorous academic pursuits, Tianqi has a passion for photography, gourmet cooking, playing video games, and enjoying time with his family. Following his graduation, he will continue his adventure in neutrophil research in the context of various human diseases at the Wagner lab in Boston Children's Hospital. January 2 – 6, 2024. BMES – CMBE Conference. San Juan, Puerto Rico. Conference details: https://www.bmes.org/cmbe2024<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bmes.…> BII Annual Conference - January 22, 2024 . Details on the agenda will be shared when available. NSF is planning a hybrid one day meeting for all Biology Integration Institutes. Most attendees will be virtual, with a few of us in person at NSF headquarters. February 6-7, 2024. EMBRIO Thrust & Site Leads Retreat. Thrust and site leads, and key investigators, will engage in two days of thrust and project working sessions in person (and yes, actual retreat social activity, as well). Logistics have been shared with all involved. March 6-10, 2024. The Allied Genetics Conference (TAGC24). Washington D.C. (Genetics Society of America). https://genetics-gsa.org/tagc-2024/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenetics-…> Note: EMBRIO is organizing a workshop for this conference. More TBA. Hot Off the Press: New EMBRIO Journal Papers Let us know about new papers you want to highlight for the EMBRIO community! 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.” 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://app.box.com/s/frd9275xc069gmgtbe3y1osoz1j7ssk7<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> ) Submit your items for the next newsletter by Dec. 1 to Brent (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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Next All-hands Monday, November 20th, Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response by Dr. Weiwei Zhang
by Ladd, Brent Thomas 13 Nov '23

13 Nov '23

Dear EMBRIO Members, A reminder that we won't meet today. For Thrusts that don't already have a standing meeting, please consider using this bi-weekly blocked time of Monday 3-4pm ET. Biweekly dates remaining this semester that we won't hold the all-hands Weekly Nov. 27 Dec. 11 Mark your calendars for our EMBRIO session next Monday, November 20th, Dr. Weiwei Zhang in the Staiger Lab will present a research seminar titled Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response. This work in Thrust 2 that Dr. Zhang is presenting includes collaborations with multiple EMBRIO labs that are working with the Staiger lab to develop data analysis tools and mathematical models. Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response Abstract Plants have evolved conserved molecular mechanisms to recognize microbe-associated or damage-associated molecular patterns (MAMPs or DAMPS), mechanical perturbation, and/or cell wall integrity changes to initiate the first layer of defense response known as pattern-triggered immunity or PTI. During the first few minutes of PTI, several hallmark cellular responses occur including influxes of Ca2+ into the cytosol, accumulation of the signaling lipid phosphatidic acid, a transient reactive oxygen species (ROS) burst, and remodeling of the actin cytoskeleton. Among these hallmark events, cytosolic Ca2+ signals are recognized as a key early signaling element as they are highly specific in duration, amplitude, and frequency, and therefore encode specific information and trigger distinct downstream signaling pathways in response to different stimuli. Despite their obvious importance, Ca2+ signatures and how they spread in space and time in response to different stimuli during PTI have not been carefully characterized nor are the molecular mechanisms encoding these spatiotemporal Ca2+ signatures well understood. In this work, we developed an image acquisition and analysis pipeline to study plant defense related Ca2+ dynamics in Arabidopsis cotyledon epidermal cells using the live cell calcium biosensor R-GECO1. We characterized both single-cell Ca2+ signatures as well as intercellular Ca2+ wave patterns in response to two types of stimuli that mimic pathogen attack: global chemical stimulation with MAMPs and local mechanical stimulation by single-cell laser ablation. In addition, we show that pre-disruption of the cortical actin cytoskeleton resulted in altered single-cell Ca2+ signatures and increased calcium signaling durations, suggesting a negative feedback mechanism between the actin cytoskeleton and calcium signaling during PTI. Our work will help understand the calcium signaling mechanisms as well as the spatial spread of immune signals across a tissue during plant defense against pathogens. 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 <https://www.purdue.edu/research/embrio/>

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Next All-hands research seminar Nov. 20th Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response by Dr. Weiwei Zhang
by Ladd, Brent Thomas 10 Nov '23

10 Nov '23

Dear EMBRIOphytes, A reminder of the biweekly dates remaining this semester that we won't hold the all-hands Weekly, and instead Thrust level meetings will be organized separately by the thrust leads are: this coming Monday, Nov. 13 Nov. 27 Dec. 11 For Thrusts that don't already have a standing meeting, please consider using this bi-weekly blocked time of Monday 3-4pm ET. Mark your calendars for our EMBRIO session on November 20th, Dr. Weiwei Zhang in the Staiger Lab will present a research seminar titled Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response. This work in Thrust 2 that Dr. Zhang is presenting includes collaborations with multiple EMBRIO labs that are working with the Staiger lab to develop data analysis tools and mathematical models. Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response Abstract Plants have evolved conserved molecular mechanisms to recognize microbe-associated or damage-associated molecular patterns (MAMPs or DAMPS), mechanical perturbation, and/or cell wall integrity changes to initiate the first layer of defense response known as pattern-triggered immunity or PTI. During the first few minutes of PTI, several hallmark cellular responses occur including influxes of Ca2+ into the cytosol, accumulation of the signaling lipid phosphatidic acid, a transient reactive oxygen species (ROS) burst, and remodeling of the actin cytoskeleton. Among these hallmark events, cytosolic Ca2+ signals are recognized as a key early signaling element as they are highly specific in duration, amplitude, and frequency, and therefore encode specific information and trigger distinct downstream signaling pathways in response to different stimuli. Despite their obvious importance, Ca2+ signatures and how they spread in space and time in response to different stimuli during PTI have not been carefully characterized nor are the molecular mechanisms encoding these spatiotemporal Ca2+ signatures well understood. In this work, we developed an image acquisition and analysis pipeline to study plant defense related Ca2+ dynamics in Arabidopsis cotyledon epidermal cells using the live cell calcium biosensor R-GECO1. We characterized both single-cell Ca2+ signatures as well as intercellular Ca2+ wave patterns in response to two types of stimuli that mimic pathogen attack: global chemical stimulation with MAMPs and local mechanical stimulation by single-cell laser ablation. In addition, we show that pre-disruption of the cortical actin cytoskeleton resulted in altered single-cell Ca2+ signatures and increased calcium signaling durations, suggesting a negative feedback mechanism between the actin cytoskeleton and calcium signaling during PTI. Our work will help understand the calcium signaling mechanisms as well as the spatial spread of immune signals across a tissue during plant defense against pathogens. 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 <https://www.purdue.edu/research/embrio/>

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All-Hands Session Introducing VCell Today at 3pm
by Ladd, Brent Thomas 06 Nov '23

06 Nov '23

Today our All-Hands session for EMBRIO features an Introduction to VCell. To those of you interested in learning more about computational modeling - this seminar is for you! (We are using the same calendar zoom link titled EMBRIO Weekly Update: https://purdue-edu.zoom.us/j/95112137034?pwd=cklTUS8zWmtra0w1UWp3eU5XdUJqUT…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>) There are many different platforms for modeling cell biological events. VCell (short for "Virtual Cell") is a comprehensive platform for modeling cell biological systems. The seminar by Dr. Michael Blinov, one of the faculty associates of VCell, will cover what VCell can do for you -- with the added bonus that VCell can write and solve differential equations for you! Learning Objectives for the Session: 1. Get familiar with kinetic modeling using VCell graphical user interface. 2. Understand different types of modeling techniques (deterministic/stochastic, compartmental/spatial, network/rule-based/network-free). 3. Be able to look for additional modeling resources within VCell framework or elsewhere. Check out these VCell links ahead of today's session for more on the capabilities and models of this tool: 1. VCell website: https://vcell.org/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvcell.org…> 2. Publications that use VCell: https://vcell.org/vcell-published-models<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvcell.org…> 3. VCell help: https://vcell.org/support<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvcell.org…>: 4. Video tutorials: https://www.youtube.com/@compcellbiol8898<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.youtu…> See you All this afternoon! 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 <https://www.purdue.edu/research/embrio/>

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All-Hands session Monday will feature a tutorial on VCell
by Ladd, Brent Thomas 03 Nov '23

03 Nov '23

This coming Monday the 6th our All-Hands session for EMBRIO (formerly titled Weekly Update) will feature a tutorial on VCell. To those of you interested in learning more about computational modeling - this November 6th seminar is for you! There are many different platforms for modeling cell biological events. VCell (short for "Virtual Cell") is a comprehensive platform for modeling cell biological systems. The seminar by Dr. Michael Blinov, one of the faculty associates of VCell, will cover what VCell can do for you -- with the added bonus that VCell can write and solve differential equations for you! Learning Objectives for the Session: 1. Get familiar with kinetic modeling using VCell graphical user interface. 2. Understand different types of modeling techniques (deterministic/stochastic, compartmental/spatial, network/rule-based/network-free). 3. Be able to look for additional modeling resources within VCell framework or elsewhere. Check out these VCell links for more on the capabilities and models of this tool: 1. VCell website: https://vcell.org/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvcell.org…> 2. Publications that use VCell: https://vcell.org/vcell-published-models<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvcell.org…> 3. VCell help: https://vcell.org/support<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvcell.org…>: 4. Video tutorials: https://www.youtube.com/@compcellbiol8898<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.youtu…> 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 <https://www.purdue.edu/research/embrio/>

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Emergence newsletter issue 25: Nov. 1, 2023
by Ladd, Brent Thomas 01 Nov '23

01 Nov '23

[cid:e1cc08b9-1247-47a2-a4d3-b2fbfa0f6642] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 25: November 1, 2023 DIRECTORS’ NOTE November is Native American Heritage Month<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nativ…>, we honor the 19 million veterans who have served in the U.S. military on Veterans Day<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.va.go…> (Nov. 11), celebrate Thanksgiving<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipe…> (Nov. 23), and vote in local elections (don’t forget – Nov. 7th nationally is voting day, and early voting times are open now. Check out who’s on your voting ballet, times and locations to vote<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.vote4…>). Oh, and we “fall behind” on the clocks Nov. 5th – an “extra” hour of rest! (what is daylight saving time and why was it created?<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.reute…>) Thank you to the ABIDES team for organizing and presenting “The role of culture and communication in mentoring” mini-workshop last week that provided us with insights into our own individual leanings regarding our Core Cultural Values (handout<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>) and how this can influence how we mentor and receive mentoring – view the video session here,<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> and check out slides and resources in the ABIDES > Mentoring folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. Next Monday the 6th our All-Hands session (formerly titled Weekly Update) will feature a tutorial on VCell by Dr. Michael Blinov with the Center for Cell Analysis and Modeling at UConn Health. To those of you interested in learning more about computational modeling - this November 6th seminar is for you! There are many different platforms for modeling cell biological events, and LinLin Li covered using Python and MatLab earlier this semester. This Monday's seminar will be about the platform called VCell (short for "Virtual Cell") is a comprehensive platform for modeling cell biological systems. The seminar by Dr. Michael Blinov, one of the faculty associates of VCell, will cover what VCell can do for you -- with the added bonus that VCell can write and solve differential equations for you! Check out these VCell links for more on the capabilities and models of this tool: 1. VCell website: https://vcell.org/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvcell.org…> 2. Publications that use VCell: https://vcell.org/vcell-published-models<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvcell.org…> 3. VCell help: https://vcell.org/support<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvcell.org…>: 4. Video tutorials: https://www.youtube.com/@compcellbiol8898<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.youtu…> Please note the changes in the format and frequency of our regular Weekly update. As the Institute has evolved, we aim to best organize a regular all-hands meeting that reflects the diverse needs of our community. Taking into consideration all the input we’ve gathered, and to best accommodate the need for thrust level meetings that are not already taking place, a regular All-Hands meetup will move to a biweekly schedule (see the remaining schedule in this issue). The two weeks per month that we don’t meet will allow thrust leaders to organize their own meetings for the blocked 3-4pm Monday times. Starting now, we will hold an all-hands online meeting bi-weekly rotating with either a research seminar or professional development offering. Starting Spring semester, we will feature a thrust level progress/collab report-out once a month. This will allow everyone to hear each of the four research thrusts on progress, challenges, upcoming activities once per semester and encourage more cross-thrust discussions. Purdue labs looking/planning for undergraduate researchers now or next summer (and our partner institutions who have students who want to come to Purdue), Brent has been in touch with the Engineering Undergraduate Research Office. See the info from Kay Kobak, their new Assoc. Director in this issue. The graduate students in biology education research at Purdue have organized a seminar series with the next seminar this Friday, November 3rd at 11:30 am ET in Zoom<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. Dr. Emily Holt (U of N. Colorado) and Postdoctoral Scholar Ash Heim (Cornell) will be presenting What Do Teaching Philosophy Statements Tell Us? We want to hear about your news and announcements. Send them to Brent (laddb(a)purdue.edu) by November 10th for inclusion in the next issue of Emergence. David, Chris, Stephanie, Anjali, Janice, Jeremy, and Brent Notable Quote “[No matter what you do, whether it’s science or not], take the time to discover who it is that you are, and then…be true to what that person is,” Dr. Paquita Zuidema, atmospheric scientist at the University of Miami, Florida. (hear the full set of audio interviews on sage advice from scientists to students<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.snexp…>) QUICK LINKS ABIDES Culture and Mentoring resources<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> VCell website<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvcell.org…> Weekly Update Meeting Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> EMBRIO ABIDES (Access, Belonging, Inclusion, Diversity, Equity, Support) Dr. Anjali Iyer-Pascuzzi, EMBRIO ABIDES Director and Professor at Purdue, leads activities for Institute members. A series of mentoring topics have been presented at the beginning of Weekly meetings, and a continuation of the Mentoring Panel topics from the annual retreat was presented October 23rd during the EMBRIO Weekly with a deeper dive into how culture impacts our mentoring and team thinking. BTW, if you missed “The role of culture and communication in mentoring” mini-workshop – view it here,<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> or the previous “mentoring snacks” check out the slides and resources in the ABIDES > Mentoring folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, and listen to “The Secret of Great Teams<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhiddenbra…>” episode of The Hidden Brain podcast. JOURNAL CLUBS Journal Club on Calcium Imaging Techniques meets Monday’s 11am ET Due to the need within our EMBRIO community to process and analyze Ca2+ Images, Dr. Norma Perez Rosas (nperezro(a)purdue.edu<mailto:nperezro@purdue.edu> ) is helping lead this club in discussing papers regarding methods and tools for analyzing calcium imaging. The goal, beyond integrating these techniques, is to write a review paper. The Club is meeting weekly on Mondays at 11am. Please contact Norma about participating. Journal Club on Multimodal Functions of Calcium in Tuning and Regulating Cytoskeleton Networks Please contact Dr. Linlin Li (li2212(a)purdue.edu<mailto:li2212@purdue.edu> ) for information. The club is in the writing stage for organizing and publishing a review paper on the topic. It isn’t too late to join. Here is the link to the current working documents: https://docs.google.com/document/d/1Cpg77yjtioWiIuRmiDMCcAiAd4jNNX_J7s64RQk…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> Undergraduate Researchers Opportunities for EMBRIO Labs and Students Note from Kay Kobak, Assoc. Dir., EURO, Purdue: Hello Undergraduate Research Allies, Thank you to those of you who have already posted a First Time Researcher project<https://engineering.purdue.edu/Engr/Research/EURO/programs/ftr>. We are still inviting faculty project postings but the final date to post is TODAY, WEDNESDAY (11/1). I've maintained a table below of all our opportunities so you can keep them in mind moving forward. We will also be asking for SURF applications in the coming weeks, so begin to think about your Summer 2024 needs now.  Program Name Description Student Compensation In-Lab Time Commitment Funding provided by Call for applications* First Time Undergraduate Researcher (FTR) Fellowship<https://engineering.purdue.edu/Engr/Research/EURO/programs/ftr> Spring Semester program for undergraduate students who haven’t conducted a full semester of college level research before (students you began mentoring this semester are welcome to apply). A total of $1000 scholarship. ~10 hours of in-lab time/week Cost shared 1:1 between EURO and the lab. Accepting project proposals NOW for Spring 2023 here<https://www.purdue.edu/undergrad-research/OURConnect.html.php>. Applications close Wednesday 11/1 Summer Undergraduate Research Fellowships (SURF)<https://engineering.purdue.edu/Engr/Research/EURO/students/about-SURF> Summer program for both Purdue Internal and external students, full time research experience. A total of $6000 paid over 12 weeks. 30-40 hours/week Cost shared 1:1:1 between EURO, the College, and the lab. Summer 2024 cohort proposals to open in November OUR Scholars <https://www.purdue.edu/undergrad-research/students/OUR-Scholars.php> Full-time undergraduate researcher for TWO semesters. $1000 scholarship ($500/semester) By agreement with faculty Cost shared between OUR and the College Fall 2023/Spring 2024 application closed. First Year Investigator's Program (Office of Undergraduate Research)<https://www.purdue.edu/undergrad-research/students/firstyear/index.php> Fall semester program for First-Year students. $15/hour 6-10 hours/week Office of Undergraduate Research Fall 2023 application closed *if you have already identified a student you wish to work with for a given time period, we still ask you post the project so we can maintain that information for our records. We can expedite the selection process and then close the project to other applicants if you already have someone in mind. Additional opportunities if you're currently hosting undergraduate researchers: EURO Travel Grant<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…>: For Purdue affiliated undergraduates who will be presenting their research at a conference - $500 awarded by EURO OUR Fall Expo<https://www.purdue.edu/undergrad-research/conferences/fall/index.php>: While the abstract deadline has passed for those wishing to give a talk, undergraduate researchers can still request to present virtually or give a poster Nov. 14-21. Other undergrad researcher funding opportunities can be found here<https://www.purdue.edu/undergrad-research/scholarships/grants.php>, here<https://www.purdue.edu/undergrad-research/scholarships/ExtGrants.php>, and here<https://exed.purdue.edu/funding/student.php>. Please feel free to reach out if you have any questions, Kay Kobak, Ph.D. she, her, hers Associate Director, Engineering Undergraduate Research Office DUDL 2526 | o.765-496-2349 | STUDENT LEADERSHIP COUNCIL CORNER The SLC is recruiting new officers to represent your university and your perspective for EMBRIO. Reach out to David Gazzo (dgazzo(a)nd.edu) incoming president, for more information, and log your ideas for future topics or events<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> that the SLC could organize. Access SLC slides and documents<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, and consider signing up to give or receive mentoring<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> for/from EMBRIO trainees in helping support and orient to the EMBRIO mission and interdisciplinary framework. EMBRIO SUMMER WORKSHOP RESOURCES EMBRIO Institute's 2nd Annual Summer Training Workshop took place July 10-12. Workshop Schedule of Sessions<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>. Hosted by Dr. Jeremiah Zartman at the University of Notre Dame with a theme of Image Acquisition, Processing, and Analysis, tutorials and hands-on sessions were specifically aimed at benefiting trainees from both computational and experimental domains. Slides, handouts, and video recordings from this workshop are available on our shared Box account: https://app.box.com/s/mzo5ihlqiq4tfeig2psx2l6rmmdxto0c<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> EMBRIO ALL-HANDS ANNUAL RETREAT MATERIALS EMBRIO Institute’s Annual Retreat was hosted in the Weldon School of Biomedical Engineering on the Purdue University West Lafayette Campus, July 13-14, 2023. The annual retreat brought together the large majority of EMBRIO members in one physical place, with more than 60 of us engaging in research talks, poster presentations, programmatic discussions, and informal gatherings. Slide decks and posters from the annual retreat can be accessed here: https://app.box.com/s/rmsiuvydlsccexzhugyjp2b5v72xlg9l<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> UPCOMING DEADLINES, IMPORTANT DATES, & INFO EMBRIO All-hands Meeting Schedule, Monday’s 3-4pm ET. Zoom link<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>.Weekly Update Meeting Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Aug 14 Benchling Workshop - SLC (Feyisayo) Aug 21 Student Leadership Council - Grads and Postdocs Only Session Aug 28 Faculty Investigators Only Sept 4 Labor Day no meeting Sept 11 Dr. Linlin Li: Part I: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 18 Dr. Linlin Li: Part II: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 25 Dr. Adrian Buganza Tepole: Part I: Physics informed machine learning Oct 2 Dr. Adrian Buganza Tepole: Part II: Physics informed machine learning Oct 9 Fall Break - no meeting Oct 16 Open Discussion and Thrust Project Breakout Rooms Oct 23 ABIDES: Culture, Mentoring, & Teams Mini Workshop Oct 30 No meeting. Thrust Leads organize own meetings Nov 6 VCell tutorial by Dr. Michael Blinov, Center for Cell Analysis and Modeling, UConn Nov 13 No meeting. Thrust Leads organize own meetings Nov 20 Dr. Weiwei Zhang, Staiger Lab, Thrust 2 Integrations Nov 27 No meeting. Thrust Leads organize own meetings Dec 4 Javier Muñoz (Brubaker/Green Lab) Dec 11 No meeting. Thrust Leads organize own meetings Winter Break November 3, 2023. Biological Sciences Seminar Series. The graduate students in biology education research at Purdue have organized a seminar series with the next seminar this Friday, November 3rd at 11:30 am ET in Zoom<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. Dr. Emily Holt (U of N. Colorado) and Postdoctoral Scholar Ash Heim (Cornell) will be presenting What Do Teaching Philosophy Statements Tell Us? January 2 – 6, 2024. BMES – CMBE Conference. San Juan, Puerto Rico. Accepting abstracts – deadline September 12. Conference details: https://www.bmes.org/cmbe2024<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bmes.…> BII Annual Conference - January 22nd - Hold the Date. Details on the agenda will be shared when available. NSF is planning a hybrid one day meeting. Expecting most will be virtual, with a few of us in person at NSF headquarters. March 6-10, 2024. The Allied Genetics Conference (TAGC24). Washington D.C. (Genetics Society of America). https://genetics-gsa.org/tagc-2024/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenetics-…> Note: EMBRIO is organizing a workshop for this conference. More TBA. Hot Off the Press: New EMBRIO Journal Papers Let us know about new papers you want to highlight for the EMBRIO community! 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.” 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://app.box.com/s/frd9275xc069gmgtbe3y1osoz1j7ssk7<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> ) Submit your items for the next newsletter by Nov. 10th to Brent (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 <https://www.purdue.edu/research/embrio/>

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