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Today's Weekly Update and January schedule
by Ladd, Brent Thomas 09 Jan '23

09 Jan '23

Our EMBRIO Weekly Update for the semester kicks off today at 3pm ET with a research talk by Dr. Krishna Jayant, Assistant Professor, Biomedical Engineering, Purdue University. Spring Semester Zoom link: https://purdue-edu.zoom.us/j/99819751005?pwd=UVlvWVpxRDB0cDVXbmxBU1NUTEZGZz… January 16, next week, we will observe Martin Luther King, Jr. Day and will not meet. However, please consider volunteering locally. EMBRIO's DEI Director, Anjali Iyer-Pascuzzi and I have organized a food drive for EMBRIO members at Purdue that will benefit patrons of Food Finders in the Lafayette-West Lafayette area. You can donate canned goods at the EMBRIO office in Discovery Learning Research building suite 228c starting tomorrow during regular hours. If the office isn't open, there will be a container just outside the door to place your donation. January 23 meeting will be dedicated to the next session in the Trainee Grants Professional Development Series focused on creating successful Aims Pages. January 30 Dr. Anjali Iyer-Pascuzzi, Assoc. Prof., BPP, Purdue, and EMBRIO DEI Director, will present DEI plans for the Institute and an overview of her Thrust 2 oriented research collaboration. 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 laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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Important EMBRIO Events
by Ladd, Brent Thomas 06 Jan '23

06 Jan '23

[cid:37bfa110-b715-4f93-b091-aaedd7a4f12c] Happy New Year EMBRIO Members! As we all gear up for the spring semester, we have a number of important upcoming dates for the Institute that I'll be sending out calendar invites. Please take a few minutes to read the basic information about each event or deadline below. NSF Site Visit - Friday, March 3, 10 am - 1pm ET Our inaugural NSF site visit is scheduled for Friday, March 3, 10 am - 1 pm ET and conducted virtually (NSF will be sharing the meeting link soon). The purpose is for our NSF Program Officer Wilson Francisco and other officers of the NSF BII program to interact with us and learn about our progress, challenges, and plans moving forward. NSF has specifically focused the site visit on integration, with the requested format of one to two leadership members presenting on behalf of the Institute. The site visit is billed as an interactive discussion expected to take three hours with two 10 min breaks. NSF has asked for as many members as possible to participate in this site visit, as there will be opportunities for everyone to engage in the discussion, as well as gain input and feedback from the BII Program. NSF Annual Report and Yr 3 Budget due to NSF in June An FYI for EMBRIO Investigators - NSF has moved up all BII timelines this year for getting annual reports and budget requests submitted. We will need to start this process in March to ensure we make their new deadline. Summer Trainee Workshop - July 10-12, Notre Dame University, South Bend, Indiana Trainees, mark your calendars July 10-12 for our 2nd annual summer workshop to be hosted this year at Notre Dame. The primary focus of this workshop will be all things imaging related. Trainees will stay on site at Notre Dame starting Sunday evening July 9th. Travel, lodging, and agenda details forthcoming. Following the workshop, we will shuttle or collectively carpool attendees the 2-hour drive down to Purdue for the annual meeting (see below). All-Hands Annual Meeting July 13-14, Purdue University, West Lafayette, Indiana The Institute's All-Hands Annual Meeting will be held in person Thursday and Friday, July 13-14 on Purdue's West Lafayette campus, hosted again by Weldon School of Biomedical Engineering. I'll be communicating the format, agenda, and logistics as those come together, but for now we want to plan on having as many members as possible in person for this event. EMBRIO Purdue Research Experience for Undergraduates, May 22 - August 2. Deadline for Purdue Labs project descriptions for the SURF Application Program is Jan. 13. EMBRIO Purdue Faculty: Please submit your project details (internal online survey<https://forms.gle/yzUQ6hEpFpXcwsN8A>) for mentoring a summer REU student in your lab. It is very beneficial to have your project details in by next Friday, January 13 for first consideration. This will enable prospective students to match up with your project and meet the SURF program<https://engineering.purdue.edu/Engr/Research/EURO/students/about-SURF> application deadlines. All EMBRIO summer REU students will participate in the SURF program. Please complete our internal EMBRIO online survey<https://forms.gle/yzUQ6hEpFpXcwsN8A> to submit your project details, and if you have a student already in mind, their contact information (you don't have to have a student in mind yet). Student Stipend is full-time 40 hrs/wk for 10 wks. Student stipend of $6,000 is split equally 3-ways between 1/3 EMBRIO funds (covering the PI portion), 1/3 SURF/CoE funds, and 1/3 from faculty mentor's Department. For students who are recruited from an underrepresented minority population in science and engineering, EMBRIO will also cover the faculty mentor's departmental contribution. Thrust & Site Leaders Workshop - Feb. 9-10, Indiana University, Bloomington, Indiana. Research Thrust Leaders - I'll be in touch with you on next steps for travel and lodging arrangements. Weekly Research & Education Zoom Meetings 2023 Spring Semester, Monday’s 3 – 4 pm ET. This semester we will maintain the Monday 3 pm (ET) time continuing our Weekly Updates split between research talks, DEI topics, professional development trainings, and a monthly meeting for Thrust and Site Leaders. We will kick off the new year with a research talk this coming Monday, January 9th by Dr. Krishna Jayant, Assistant Professor, Biomedical Engineering, Purdue University. Spring Semester Zoom link: https://purdue-edu.zoom.us/j/99819751005?pwd=UVlvWVpxRDB0cDVXbmxBU1NUTEZGZz… * January 9 – Krishna Jayant, Asst. Prof., BME, Purdue * January 16 – Martin Luther King, Jr. Day – University Holiday, No Meeting, please volunteer locally * January 23 – Trainee Professional Development, Grants Series Session #2 * January 30 – Anjali Iyer-Pascuzzi, Assoc. Prof., BPP, Purdue, DEI Director, EMBRIO * February 6 – Thrust & Site Leads Update Meeting * February 13 – Priyanka Baloni, Asst. Prof, HHS, Purdue * February 20 – Trainee Professional Development, Grants Series Session #3 * February 27 – Bakary Samasa, Mary Mullins Lab * March 6 – Thrust & Site Leads Update Meeting * March 13 – Spring break, no meeting * March 20 – Open * March 27 - Trainee Professional Development * April – May TBD Best, Brent Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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End of week announcements
by Ladd, Brent Thomas 16 Dec '22

16 Dec '22

Dear EMBRIO Members, Wishing you all an enjoyable winter break, safe travels, and may we all be healthy in the New Year. A few announcements and dates to hold on your calendar as we close out the semester. Please hold the following dates for next summer in-person activity: July 10 - 12, Trainee Workshop, Notre Dame University July 13 - 14, All-Hands Annual Meeting, Purdue University Thrust & Site Leads Only - block Feb. 9 and 10 for our workshop at Indiana University NSF Items Our annual report and year 3 budget will be due the end of June to our NSF Program Officer (rather than Sept. 1). This necessitates a much earlier start to the reporting and budget request process. More details are coming in the New Year. Our first official NSF site visit will be virtual, with a yet to be determined date in February or March. Again, more details forthcoming. EMBRIO Purdue campus REU student nominations and project details due Jan. 13 for first consideration. Please complete the online survey<https://forms.gle/yzUQ6hEpFpXcwsN8A> to submit your project details, and student information if you have a student already in mind. Weekly Updates - Spring Semester We will resume Weekly Updates on Monday, January 9th , 3 pm with Dr. Krishna Jayant presenting. Spring Semester Weekly Update Schedule, Monday at 3pm ET & Zoom link: https://purdue-edu.zoom.us/j/99819751005?pwd=UVlvWVpxRDB0cDVXbmxBU1NUTEZGZz… January 9 Krishna Jayant, Asst. Prof., BME, Purdue January 16 Martin Luther King, Jr. Day – No Meeting, please volunteer locally January 23 Trainee Professional Development, Grants Series Session #2 January 30 Anjali Iyer-Pascuzzi, Assoc. Prof., BPP, Purdue, DEI Director, EMBRIO February 6 Thrust & Site Leads Update Meeting February 13 Priyanka Baloni, Asst. Prof, HHS, Purdue February 20 Trainee Professional Development, Grants Series Session #3 February 27 Bakary Samasa, Mary Mullins Lab March 6 Thrust & Site Leads Update Meeting March 13 Spring break, no meeting March 20 DEI Topic March 27 Trainee Professional Development April 3 Thrust & Site Leads Update Meeting April 10 TBD - Research Talk April 17 TBD - Research Talk April 24 Trainee Professional Development May 1 Thrust & Site Leads Update Meeting May 8 Javier Munoz, Doug Brubaker Lab Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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Emergence: Issue 10
by Brent T Ladd 14 Dec '22

14 Dec '22

[cid:0ec0fb87-20bc-4369-8a8c-fe2aaf011d2f] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 10: December 14, 2022 DIRECTORS’ NOTE This is our last issue of the year – we hope your semester has been full of discovery, learning, and fruitful collaborations. Wishing good tidings to everyone in the EMBRIO community and a restful and regenerative winter break! We’ve had a solid series of research and education talks this year, and we want to especially recognize the 20 graduate students and postdocs who have presented their research-in-progress to the Institute this past summer and fall. Speaking of our awesome trainees, the next session in our Grants Professional Development series is scheduled for January 23, 3pm ET: De-Mystifying the Craft of Creating an Aims Page. A reminder for Spring semester 2023: we will maintain the Monday 3pm (ET) time continuing Weekly Updates split between research talks, DEI topics, professional development trainings, and a monthly meeting for Thrust and Site Leaders. A calendar invite with a new Zoom link was emailed on 11/18 and is available in the Upcoming Deadlines and Dates section of this issue. And, speaking of future dates, we are very close to securing dates and venues for our annual summer trainee workshop and all-hands annual meeting. More on this is to come soon, but please hold July 10-12 for a training workshop at Notre Dame followed by our All-Hands Annual Meeting July 13-14 at Purdue. The Member Spotlight introduces two affiliate members we are excited to welcome into the EMBRIO family: Dr. Priyanka Baloni, Health & Human Sciences, Purdue, and Dr. Greg Reeves, Chemical Engineering, TAMU. Please welcome them to our community. Dr. Reeves presented his research on December 5th, and Dr. Baloni will present on February 13th. EMBRIO Purdue campus REU student nominations and project details are due January 13 for first consideration (and to enable students to meet the SURF program application deadlines). Please complete the online survey<https://forms.gle/yzUQ6hEpFpXcwsN8A> to submit your project details, and if you have a student already in mind, their contact information. We want to hear about your news and announcements. Send them to Brent (laddb(a)purdue.edu<mailto:laddb@purdue.edu>) by January 13 for inclusion in the next issue of Emergence. David, Chris, Stephanie, and Brent Quotable Quote: “As always in life, people want a simple answer... and it’s always wrong.” — Baroness Susan Greenfield<https://www.ageing.ox.ac.uk/people/view/26>, Neuroscientist QUICK LINKS Schedule Your One-on-One Interview with Soumi<https://www.when2meet.com/?16968903-R8veS> RAISING A RESILIENT SCIENTIST<https://www.training.nih.gov/workshops_and_trainings_for_extramural_princip…> NIH series EMBRIO TRAINEE PROFESSIONAL DEVELOPMENT GRANTS SERIES For trainees that missed the Grants session panel discussion Nov. 28th, the video recording and chat file are available on our Box account > Weekly Meeting Recordings > 2022-11-28_EMBRIO Weekly Update_Grants-Series_Prof-Dev_Session 1. Direct link: https://app.box.com/s/3py70qibjqbbzywss3zc95y8qksav2ib Thank you to the panelists for sharing your insights and experience! Drs. Jason Cannon, Alejandra Magana, and Chris Staiger. The next session in the series is scheduled for January 23, 3pm ET: De-Mystifying the Craft of Creating an Aims Page November 28th : The Grants Process and Federal Granting Agencies – Faculty Panel January 23rd : De-Mystifying the Craft of Creating an Aims Page February 20th : Students present draft Aims page for Peer-Feedback (Jazzmin Owens and Peter Brumm share their aims pages) March 27th: TBD MEMBER SPOTLIGHT: Priyanka Baloni [cid:43840e45-962e-4a43-8ebd-5fd7109146b7] Dr. Priyanka Baloni is an Assistant Professor in the School of Health Sciences here at Purdue with expertise in computational biology, neuroscience, oncology, reproductive sciences, and infectious diseases. She is joining EMBRIO as an affiliate member contributing to the CORE Thrust. We sat down with Priyanka recently to learn more about her research and teaching activities. She will present her research to EMBRIO on February 13th during our regular Weekly Update. You can read more about Dr. Baloni’s scholarship at her lab website<https://hhs.purdue.edu/directory/priyanka-baloni/>. Hello Priyanka! You recently arrived at Purdue. Can you tell us more about your career up to this point? I received my Ph.D. from the Indian Institute of Science(IISc), India, working on the host-pathogen interactions in tuberculosis infection. In 2016, I began my postdoctoral position at the Institute for Systems Biology (ISB) and was mentored by Drs. Leroy Hood and Nathan Price. During my research experience at ISB, I collaborated and led computational efforts in various projects focusing on the metabolic signatures in neurodegenerative disorders, pregnancy, and cancer. As a tenure-track faculty in the School of Health Sciences at Purdue, my lab’s research focus is in exploring mechanisms underlying adverse outcomes of environmental exposure on human health using high-throughput data and computational approaches. I think my broad expertise in computational biology, multi-omics analyses, and predictive modeling is a great fit to the research being done in the Core Thrust at EMBRIO, leading to potential collaborations across different labs and paving way for translational research. In your brief time at Purdue, you’ve hit the ground running. What are some of the collaborations you’ve been involved in and the investigations you have going now? I am a co-Investigator on four NIH-funded projects and was an MPI for an R01 funded by the National Institute of Child Health and Human Development (NICHD). My funding from NIH R01s has allowed me to collaborate with researchers from Johns Hopkins University, Duke University, Indiana University, University of Florida, Cincinnati Children’s Hospital Medical Center, and Weill Cornell Medicine. I collaborated on a project with Amgen Inc., in which I generated the genome-scale metabolic model of rat liver to explore the effects of diet restriction and chemical compounds and predict the metabolic outcome. I have used my expertise on metabolic networks for the COVID-19 research at ISB and investigated the metabolic reprogramming of immune cells in COVID-19 patients. Going forward, I will perform systems-level analysis using genomics and multi-omics data, along with information available from various databases, and leverage the metabolic and transcriptional regulatory networks for rigorous dissection of molecular mechanisms, leading to new insights for improving public health using these data-driven models. This data-driven approach can lead to the generation of testable hypotheses and the development of personalized models predicting the effect of environmental exposure. You’ve also been active in teaching, mentoring others, and supporting diverse learners. Can you tell us more about those activities? In addition to research, I value and enjoy teaching and mentoring. I developed many of my core teaching principles during the Science Teaching Experience for Postdocs (STEP) fellowship program, through the University of Washington, where I designed and taught a semester-long course on personalized medicine and wellness with two other postdocs. During this fellowship I learned skills in inquiry-based teaching approaches, curriculum and syllabus development, lesson planning, classroom management and student evaluations. This unique experience provided me with a platform to develop my teaching skills with weekly evaluations and discussions to improve my teaching effectiveness. My interest in education also extends outside of the classroom, where I have placed a priority on mentoring undergraduate students from diverse economic, racial, ethnic and educational backgrounds. As a teacher and mentor for students, the best way I can contribute to supporting diversity is by supporting students who are at a disadvantage when starting their academic career as an undergraduate or have struggled with challenges throughout their careers. I will identify opportunities for funding and lead in the writing of grants to support equity and inclusion efforts within the Institute. Thank you for sharing your enthusiasm, research, and teaching experiences. We are excited to have you join EMBRIO as an affiliate member! Thank you! Being a part of EMBRIO,I foresee opportunities to collaborate with several groups at the Institute as the computational models can be used for studying infectious diseases, host-microbiome interactions, neurotoxins and other conditions. The collaborations can lead to potential funding opportunities and publications. I look forward to being a part of the Core Thrust at EMBRIO and bring in my expertise to complement the ongoing research at EMBRIO. MEMBER SPOTLIGHT: Gregory Reeves [cid:d3d23d58-b76d-4e20-a92c-a400a2da34bc] Dr. Greg Reeves is an Associate Professor of Chemical Engineering at Texas A&M University and a member of the Faculty of the Interdisciplinary Graduate Program in Genetics. He is joining EMBRIO as an affiliate member, contributing to the Thrust 1 and 2 areas of the Institute. He recently presented his research to the EMBRIO community (Dec. 5). You can learn more about Dr. Reeves’ research at his lab website<https://reeveslab.engr.tamu.edu/>. We asked Greg to tell us more about his background, research, and academic activities. Hi Greg! Thanks for your recent presentation to the Institute. We are excited for you to collaborate with us in EMBRIO. Not long ago you moved your lab to Texas A&M. Can you tell us more about your career up to this point? Yes, in the middle of the pandemic I moved my lab in the Fall of 2020 to Texas A&M. Prior to that, I worked at NC State University in the Chemical and Biomolecular Engineering Department for 10 years. I received my Ph.D. in Chemical Engineering from Princeton University – in the same lab that Jeremy Zartman got his Ph.D. Broadly, my research addresses the question of how cells make reliable decisions in a multicellular context, especially in the face of dynamic signals between cells. My goal is to synergistically use quantitative, in vivo imaging experiments and predictive, mechanistic modeling to deduce the rules of how signaling pathways dictate cellular decision making in tissue development and stem cell differentiation. Our systems biology approach is required to untangle the complexity and dynamics of development. What are some of the collaborations you’ve been involved in and the investigations you have going now? We specialize in quantitative imaging in live tissues, including raster image correlation spectroscopy (RICS), which allows us to measure the mobility, binding, and concentration of fluorescently tagged signaling proteins. Our imaging data constrain mechanistic models of these signaling pathways, which in turn allow us to design future experiments. Our primary model system is the 1-3 h old Drosophila melanogaster (fruit fly) embryo. We used modeling and experiment synergistically to make novel discoveries of the spreading and cellular interpretation of the Dorsal-mediated signal. These discoveries have revealed previously unknown mechanisms behind the robustness of NF-κB signaling. Dorsal signaling also restricts the expression of the gene dpp to the dorsal half of the embryo, and dpp codes for the BMP ligand Dpp. We are also studying how the dynamics of Dpp signaling on the dorsal half of the embryo relates to Dpp target gene expression. Our initial work suggests that there are genes that are activated specifically by a transient exposure of Dpp signaling yet have sustained expression due to an unknown memory mechanism. Our work on Dpp signaling in the early embryo also translates to studying Dpp signaling in female germ line stem cell specification, in which Dpp signaling from nearby cells to the germline stem cell represents self-renewal signal. We are studying how the dynamics of the intracellular portion of the Dpp pathway results in robust stem cell decisions. My research aligns directly with Thrusts 1 and 2 of EMBRIO. My work on Dorsal is both intracellular and intercellular, and thus spans both Thrusts. Similarly, my work on Dpp signaling in the embryo aligns with Thrust 2, while my work in the germline stem cells aligns with Thrust 1. I have been working on proposals with EMBRIO Institute members David Umulis and Jeremiah Zartman. The proposal focuses on engineering principles found in the BMP/Smad pathway in four model systems. As an outgrowth of the proposed ideas, we are working on a computational study to make predictions of these engineering principles. You’ve also been active in broadening participation in STEM and supporting diverse learners. Can you tell us more about those activities? At the high school level, I ran enrichment summer camps at NCSU titled “Bioengineering in the High School Classroom,” specifically targeting high schools from underprivileged areas. At TAMU, I’m integrating the material from the summer camp into STEM summer outreach programs in collaboration with the Spark! PK-12 Engineering Education Outreach and AggieSTEM programs. At the undergraduate level, I’ve been partnering with TAMU's First-Generation Engineering Students (FGEn) Mentoring Program. TAMU is a federally designated Hispanic Serving Institution (the general population of Texas is close to 40% Hispanic), and many Hispanics in the College of Engineering are first-gen. Data suggest that first-gen students have low retention rates, and that retention rate can be greatly improved by increasing motivation through undergraduate research. At the grad student level, my group composition has always reflected a commitment to female representation (between 50 and 60% female) in a largely male-dominant field (chemical engineering is roughly 2/3rds male). On the institutional side, the Core Facilities at TAMU are planning to offer pipeline facility workshops that target students at local HBCUs in which I will participate and teach RICS methods. URG students attending HBCUs have less access to state-of-the-art core facilities, and these facility workshops are an opportunity for training in cutting edge research methods. Thank you for sharing your motivations, research, and supporting diversity. We are excited to have you join EMBRIO as an affiliate member! Thanks – I am definitely looking forward to integrating into this exciting community of scientists and opening up more opportunities for collaboration. Weekly Update Zoom Breakout Rooms: Are you looking for a collaborator? Would you like to get conversation started about a specific research topic with other EMBRIO members? Email me (Brent, laddb(a)purdue.edu<mailto:laddb@purdue.edu>) with your breakout room topics for upcoming Weekly Update sessions. INSTITUTE EVALUATION: SIGN UP FOR YOUR ONE-ON-ONE INTERVIEW (hint: it’s mandatory) “My name is Soumi Mukherjee, and I am a Graduate Student at the Department of Biological Sciences at Purdue. Along with my advisor Dr. Stephanie Gardner, I will be conducting an institute wide evaluation study as a part of Thrust 4 initiative. The process will help in capturing your experiences as a member of EMBRIO, which will be utilized to create a formative evaluation report for NSF at the end of each year. Your participation will not only aid in furthering the goals of the institute for providing an interdisciplinary collaborative environment essential for promoting knowledge integration across all the four thrusts, but also enable us to structure activities catered towards your own professional development. If you are a member of the EMBRIO institute currently doing a research project, we would like to invite you for participating in this study. Participation in the evaluation process is MANDATORY for all the members of the institute. As a part of the evaluation process, you will take part in an online session (via Zoom), which includes an interview and a brief survey, and the entire process should be completed in less than an hour. Interviews will be conducted annually for the total duration of your participation in the institute and the session would not exceed an hour and would be completed in a day. Please fill in all the times you may be available for our interviews using the link below with either your name or email address. This information is requested so that we may contact you to set up an online session, but we will use a randomly generated 4-digit code in place of your name to identify all your information for the data collection and analysis. https://www.when2meet.com/?16968903-R8veS Your participation will not affect any aspect of your association with the EMBRIO institute. If you have any doubts regarding the evaluation process, please reach out to me at mukher42(a)purdue.edu<mailto:mukher42@purdue.edu>.” With Regards Soumi NIH Raising a Resilient Scientist Series The NIH OITE is pleased to offer the RAISING A RESILIENT SCIENTIST<https://www.training.nih.gov/workshops_and_trainings_for_extramural_princip…> series for faculty, staff scientists, and administrators who mentor students and postdoctoral fellows in the biomedical, behavioral, and social sciences. The goal of the Raising a Resilient Scientist series is to promote the mental health and well-being of the academic research community by supporting faculty and administrators to develop self-management, relationship-management, and mentoring skills. Raising a Resilient Scientists Units Workshop Date Registration Communication Skills to Build Trainee Resilience Nov 9, 2022 12:00-2:15 pm ET https://nih.zoomgov.com/meeting/register/ vJIsdeyhrjwsG3qSl89jFlF9zUdzoYlz4Vw<https://nih.zoomgov.com/meeting/register/vJIsdeyhrjwsG3qSl89jFlF9zUdzoYlz4Vw> Promoting Trainee Resilience Dec 14, 2022 12:00-2:15 pm ET https://nih.zoomgov.com/meeting/register/vJIsc-uvpzovGbw2kGLBSbihRcERfN2raTc<https://nih.zoomgov.com/meeting/register/%20vJIsc-uvpzovGbw2kGLBSbihRcERfN2…> Building a Welcoming and Inclusive Research Group Jan 11, 2023 12:00-2:15 pm ET https://nih.zoomgov.com/meeting/register/ vJItcOurqjojGtH9Y_zDJPVHhg2Nm6zWNb0<https://nih.zoomgov.com/meeting/register/%20vJItcOurqjojGtH9Y_zDJPVHhg2Nm6z…> Difficult Conversations, Conflict, and Feedback Feb 8, 2023 12:00-2:15 pm ET https://nih.zoomgov.com/meeting/register/vJIsc-CgrTsiHfcOa91MnLLQ-_REQmdOQ2I<https://nih.zoomgov.com/meeting/register/%20vJIsc-CgrTsiHfcOa91MnLLQ-_REQmd…> The Mental Health and Well-being of Your Trainees Mar 8, 2023 12:00-2:15 pm ET https://nih.zoomgov.com/meeting/register/ vJIscuCpqT4pEzjHEmDI2E604ncYzhOrhm4<https://nih.zoomgov.com/meeting/register/%20vJIscuCpqT4pEzjHEmDI2E604ncYzhO…> There is no charge for participation, but advanced registration is required. For more information, and to register, please visit their webpage<https://www.training.nih.gov/workshops_and_trainings_for_extramural_princip…>. Participation in the entire series is recommended but is not required. Resource: US Software Engineers Association New Community Resource via EMBRIO alumnus Matt Thompson: "A professional community known as US Research Software Engineers Association<https://us-rse.org/> is worth joining. From the community call I sat in on last week and resources they have available online, I can tell it will be a big help with professional support, networking, and development. They welcome students, postdocs, faculty, and anyone engaged in any level of software development to do research." UPCOMING DEADLINES, IMPORTANT DATES, & INFO Weekly Research & Education Zoom Meetings Spring Semester, Monday’s 3 – 4 pm. Spring Semester new Zoom link: https://purdue-edu.zoom.us/j/99819751005?pwd=UVlvWVpxRDB0cDVXbmxBU1NUTEZGZz… · January 9 – Krishna Jayant, Asst. Prof., BME, Purdue · January 16 – Martin Luther King, Jr. Day – No Meeting, please volunteer locally · January 23 – Trainee Professional Development, Grants Series Session #2 · January 30 – Anjali Iyer-Pascuzzi, Assoc. Prof., BPP, Purdue, DEI Director, EMBRIO · February 6 – Thrust & Site Leads Update Meeting · February 13 – Priyanka Baloni, Asst. Prof, HHS, Purdue · February 20 – Trainee Professional Development, Grants Series Session #3 · February 27 – Bakary Samasa, Mary Mullins Lab · March 6 – Thrust & Site Leads Update Meeting · March 13 – Spring break, no meeting · March 20 – Open · March 27 - Trainee Professional Development · April – May TBD Nov. 9, 2022 – March 8, 2023. NIH RAISING A RESILIENT SCIENTIST<https://www.training.nih.gov/workshops_and_trainings_for_extramural_princip…> series. Jan. 2 – 6, 2023: The BMES Cellular and Molecular Bioengineering Special Interest Group is seeking abstracts for the BMES Conference (CMBE)<https://www.bmes.org/2023-cmbe-conference> in Indian Wells, CA. Jan. 13, 2023: EMBRIO REU Purdue campus student nominations and project details due for first consideration. Please complete the online survey<https://forms.gle/yzUQ6hEpFpXcwsN8A> to submit your project details, and student information if you have a student already in mind. July 10-12, 2023. Please hold for EMBRIO Trainees Workshop, Notre Dame University. More information forthcoming. July 13-14, 2023. Please hold for EMBRIO All-Hands Annual Meeting, Purdue University. More information forthcoming. Hot Off the Press: New EMBRIO Journal and Conference Papers Let us know about new papers you want to highlight for the EMBRIO community! REMINDER: EMBRIO Acknowledgement for Scholarly Papers. 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.” Conference Presentations: Let us know about your conference presentations. Awards Let us know about awards that you want to highlight. Open Positions Postdoctoral Fellow Position in Interdisciplinary Biomedical Research and Data Science, Purdue University A full-time postdoctoral fellow position is available immediately for interdisciplinary research in computational systems biology and collaborative data science at Purdue University. The postdoctoral position is associated with EMBRIO (Emergent Mechanisms in Biology of Robustness, Integration, and Organization), an NSF Biology Integration Institute with six university partners. The postdoctoral fellow will be broadly involved in the EMBRIO Institute, with efforts engaged in computational systems modeling and simulation research, as well as building expertise, guidance, and collaboration support and research in data management and data analysis for EMBRIO teams. The postdoctoral fellow will conduct research under the guidance of Dr. Elsje Pienaar (https://engineering.purdue.edu/PienaarLab ) and be co-advised by Dr. Adrian Buganza Tepole (https://engineering.purdue.edu/tepolelab/ ). As part of the work with the Pienaar lab the fellow would build and calibrate computational models of Calcium signaling in multicellular environments and its diverse downstream effects. Together with the Tepole lab the fellow would work to leverage machine learning (ML) tools to speed up and automate model evaluation, and to complement closed-form models with multi-modality ML metamodels for improved accuracy. The work is highly interdisciplinary and highly integrative across multiple systems. The fellow will work closely with experimental experts in zebrafish, plant and tissue culture biology within the EMBRIO Institute to build and parameterize the models. The fellow will also have opportunities to work closely with other computational faculty, staff and students on innovating new ways to integrate and analyze models and data across biological scales and systems. As these specific projects progress, the postdoctoral fellow will have the opportunity to collaborate with investigators and interdisciplinary teams to research and deliver secure systems of data collection, storage, sharing, and analysis to produce new and actionable knowledge. This work will research and provide regular guidance and training in data science best practices and serve as a point of contact for all things data related. The postdoctoral fellow will have the opportunity to co-write proposals and to develop research components around the data-rich interdisciplinary modeling and simulation environment of EMBRIO. A Ph.D. degree in Data Science, Computer Science, Biomedical Engineering, Chemical Engineering, Mechanical Engineering, Mathematics, Physics or related fields is required. Previous experience in computational modeling, systems biology, stochastic modeling, numerical methods, and associated statistical analysis, data science, or research data management is desired. Successful applicants will be detail oriented, eager to learn new methods, and enthusiastic about computationally rigorous modeling, collaborating across disciplines, working with experimental biologists and chemists, and advancing and supporting the research data realm of EMBRIO Institute. Salary to be negotiated. To apply for this position, please submit to Dr. Pienaar (epienaar(a)purdue.edu<mailto:epienaar@purdue.edu>) and Dr. Buganza Tepole (abuganza(a)purdue.edu) (1) your CV, (2) a cover letter explaining your background, interest and qualifications for the position, and (3) contact information for three references, including your relationship to the reference, their phone number, email address, and mailing address. Please contact Dr. Pienaar (epienaar(a)purdue.edu) for formal inquiries. Postdoctoral Fellow Position in Interdisciplinary Biochemical Cancer Research, University of Notre Dame A full-time postdoctoral fellow position is available immediately for Multidisciplinary Cancer Research at the University of Notre Dame, affiliated with the Harper Cancer Research Institute, the Notre Dame Warren Drug Delivery Center and Notre Dame Institute for Precision Health. The perspective candidate will conduct an interdisciplinary research on projects studying the basic molecular mechanisms of multiple birth defects, cancer progression and neurodegeneration and developing novel therapies to combat them. The postdoctoral fellow will receive crossdisciplinary training in biochemistry, cell biology, synthetic organic chemistry, and drug discovery utilizing a broad range of biochemical assays related to phenotypic screening and protein-protein interactions. The postdoctoral fellow will conduct research under the guidance of a mentoring team, including Dr. Jeremiah Zartman (http://sites.nd.edu/zartmanlab/) and Dr. Brandon Ashfeld (https://ashfeldlab.nd.edu/) A Ph.D. or M.D. degree in cell or molecular biology, genetics, biochemistry, chemistry or a related discipline, is required. Previous experience in genetics, screening technologies and associated statistical analysis, synthetic chemistry, imaging or mouse modeling is desired. Successful applicants will be detail oriented, eager to learn new techniques, and enthusiastic about biology, exploring the interface between chemistry and biology, and working in an academic lab environment. Salary is commensurate with experience. To apply this position, please submit: (1) your CV, (2) a cover letter explaining your background, interest and qualifications for the position, and (3) contact information for three references, including your relationship to the reference, their phone number, email address, and mailing address. Please contact Dr. Jeremiah Zartman (jzartman(a)nd.edu) or Dr. Brandon Ashfeld (bashfeld(a)nd.edu) for formal inquiries. 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 ), 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 Jan.13 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 laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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Today's Weekly Update: Data Storage and Sharing for the Institute
by Brent T Ladd 12 Dec '22

12 Dec '22

ALL EMBRIO members, Plan to join us today, Dec. 12th , 3pm (ET) we will focus on data storage and sharing options for the Institute. This is a critical piece of integration for EMBRIO. Lev Gorenstein, Senior Computational Scientist with the Rosen Center for Advanced Computing at Purdue, will provide an overview of the Data Depot storage system and answer questions, followed by discussion for establishing a system of storing and sharing EMBRIO research data. Zoom link: https://purdue-edu.zoom.us/j/96053485465?pwd=elVnY20wcm9kaFRtVUdPcmFHaGl1UT… We will break for winter holidays and reconvene Monday, January 9th at 3pm ET with a research presentation by Krishna Jayant, Assistant Professor, Weldon School of Biomedical Engineering at Purdue and the Nano Neurotechnology Lab<https://nanoneurotech.com/lab-members/krishna-jayant/>. Please note the new Zoom link for the Weekly Updates next semester. This was shared as a calendar invite for the series: https://purdue-edu.zoom.us/j/99819751005?pwd=UVlvWVpxRDB0cDVXbmxBU1NUTEZGZz… Thanks, Brent Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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End of Week Reminders
by Brent T Ladd 09 Dec '22

09 Dec '22

Dear EMBRIO Community, ALL members, please plan to join us this next Monday Dec. 12th at 3pm (ET) we will focus on data storage and sharing options for the Institute. This is a critical piece of integration for EMBRIO. Lev Gorenstein, Senior Computational Scientist with the Rosen Center for Advanced Computing at Purdue, will provide an overview of the Data Depot storage system and answer questions, followed by discussion for establishing a system of storing and sharing EMBRIO research data. Zoom link: https://purdue-edu.zoom.us/j/96053485465?pwd=elVnY20wcm9kaFRtVUdPcmFHaGl1UT… Next Monday will be the last Weekly Update of the semester. We will reconvene Monday, January 9th at 3pm ET with a research presentation by Krishna Jayant, Assistant Professor, Weldon School of Biomedical Engineering at Purdue and the Nano Neurotechnology Lab<https://nanoneurotech.com/lab-members/krishna-jayant/>. Please note the new Zoom link for the Weekly Updates next semester. This was shared as a calendar invite for the series: https://purdue-edu.zoom.us/j/99819751005?pwd=UVlvWVpxRDB0cDVXbmxBU1NUTEZGZz… Reverse Engineering Cellular Systems Workshop TODAY Today is the Virtual Notre Dame - Mexico Symposium 2022: Reverse Engineering Cellular Systems: Patterning and Morphogenesis. Registration to participate: https://forms.gle/KZurTw5rwxyCdYxE9<https://urldefense.com/v3/__https:/forms.gle/KZurTw5rwxyCdYxE9__;!!IBzWLUs!…> REU EMBRIO Student Nominations We want to start planning now for another successful summer EMBRIO cohort of undergraduate research experiences. It is highly encouraged that EMBRIO Purdue summer interns apply to the SURF REU program<https://engineering.purdue.edu/Engr/Research/EURO/students/about-SURF>. SURF program deadline is Feb. 10, so we want to identify EMBRIO REU students early. Please complete this form<https://forms.gle/yzUQ6hEpFpXcwsN8A> for each student you request support. Deadline for first consideration is January 13. Note that in addition to Purdue undergraduate students, there may be an opportunity to request support to mentor a student from our Partners UPR-M (contact Clara Isaza, email<mailto:clara.isaza@upr.edu>) or Morehouse College (contact Juana Mendenhall, email<mailto:juana.mendenhall@morehouse.edu>). Graduate Student Recruitment Resource: Ignacio Camarillo, Outreach & Recruitment Lead for EMBRIO, has provided curated lists of candidates representing minoritized populations interested in pursuing graduate school in domains relevant to our Institute (as well as some undergraduates seeking summer research internships). EMBRIO Institute is committed to increasing and supporting diversity and inclusion at all levels. You can access the recruitment lists on our shared Box account directly here<https://app.box.com/s/k9firxkxc3mhsrnl5c2qba03fi1e966h>, or via login and folders at EMBRIO Institute > Recruitment > 2022 Recruitment Lists. Please contact Ignacio directly (email<mailto:ignacio@purdue.edu>) for more information about specific students you are interested in recruiting. He may be able to provide an abstract of their recent research presentation from SACNAS or ABRCMS. Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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Today's Weekly and seminar Dec. 7
by Brent T Ladd 05 Dec '22

05 Dec '22

Hello EMBRIO Members, For our Weekly Update Today at 3 pm ET, December 5th, we feature guest speaker and our first affiliate member, Dr. Gregory Reeves<https://engineering.tamu.edu/chemical/profiles/reeves-gregory.html>, Chemical Engineering, Texas A&M University. Zoom link<https://purdue-edu.zoom.us/j/96053485465?pwd=elVnY20wcm9kaFRtVUdPcmFHaGl1UT…> Everyone is invited to the Watch Party tomorrow, December 6, 10:30am - 12:30pm(ET) Quantitative Systems Biology course student presentations. In person: PURDUE, Room MJIS 2001. Zoom link<https://purdue-edu.zoom.us/j/98100711659?pwd=Z3FrYkJCL241aGRXU0s0WTBDbkFIZz…> Seminar, Wed. Dec. 7., 1:30 pm ET. Mechanosensing through Immunorecepters. Dr. Cheng Zhu, Georgia Tech and Emory Univ. (flyer attached) In person: Purdue, MJIS 1001. Zoom Link<https://purdue-edu.zoom.us/meeting/register/tJUtd-2rrTIqEt28s1D20iZPi-9RRDG…> [https://purdue-edu.zoom.us/w_p/91004339089/bc7fad82-8932-4135-86fc-c2953220…]<https://purdue-edu.zoom.us/meeting/register/tJUtd-2rrTIqEt28s1D20iZPi-9RRDG…> Welcome! You are invited to join a meeting: Frontiers in Biophysics Seminar Series | Purdue University. After registering, you will receive a confirmation email about joining the meeting.<https://purdue-edu.zoom.us/meeting/register/tJUtd-2rrTIqEt28s1D20iZPi-9RRDG…> Dear Purdue Community and Guests, We thank you for joining for the Frontiers in Biophysics Seminar Series (FBSS) that is co-sponsored by the Structural and Computational Biology & Biophysics research area within the Department of Biological Sciences and the NIH-funded Molecular Biophysics Training Program (MBTP). The seminars will be on Wednesdays @ 1:30 PM. Faculty and trainees of SCBB and the MBTP continue to work together to prepare an impressive lineup of exciting speakers for the FBSS, bringing world-renowned and leading researchers each semester to our Purdue campus. We hope to see you at each of the FBSS seminars throughout the semester! Cheers, On behalf of the FBSS Organizers Structural and Computational Biology & Biophysics, Biological Sciences https://www.bio.purdue.edu/structural/index.html Molecular Biophysics Training Program https://molbiophys.science.purdue.edu/ === purdue-edu.zoom.us Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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End of Week Reminders
by Brent T Ladd 02 Dec '22

02 Dec '22

Dear EMBRIO Community, Weekly Update For our Weekly Update next Monday, December 5th, we feature guest speaker and our first affiliate member, Dr. Gregory Reeves<https://engineering.tamu.edu/chemical/profiles/reeves-gregory.html>, Chemical Engineering, Texas A&M University. Zoom: https://purdue-edu.zoom.us/j/96053485465?pwd=elVnY20wcm9kaFRtVUdPcmFHaGl1UT… Watch Party All EMBRIO members are invited to a Watch Party next Tuesday, Dec. 6, 10:30-12:30 ET featuring student presentations in the Quantitative Systems Biology course taught by Drs. Umulis and Linlin Li. please RSVP<https://purdue.ca1.qualtrics.com/jfe/form/SV_0HFcMbnm00lzEyy> by the end of today, Friday Dec. 2, so that we can plan for enough pizza available. In person: PURDUE, Room MJIS 2001 Watch Party Zoom: https://purdue-edu.zoom.us/j/98100711659?pwd=Z3FrYkJCL241aGRXU0s0WTBDbkFIZz… Meeting ID: 981 0071 1659 Passcode: 918890 Symposium Dec. 9 Taking place next Friday, Dec. 9, 9am - 5pm: Virtual Notre Dame - Mexico Symposium 2022: Reverse Engineering Cellular Systems: Patterning and Morphogenesis. https://forms.gle/KZurTw5rwxyCdYxE9<https://urldefense.com/v3/__https:/forms.gle/KZurTw5rwxyCdYxE9__;!!IBzWLUs!…> New DEI Director & Thrust 2 Investigator If you missed our interview with Dr. Anjali Iyer-Pascuzzi, new DEI Director for EMBRIO and Thrust 2 investigator, you can read it in the recent issue of Emergence<https://www.purdue.edu/research/embrio/files/newsletters/embrio-news-update…>. Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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Emergence newsletter Issue 9
by Brent T Ladd 30 Nov '22

30 Nov '22

[cid:54e7ae4f-e644-4d25-aed2-56819ae76987] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 9: November 30, 2022 DIRECTORS’ NOTE As we bid farewell to November, we hope everyone had an enjoyable break last week and will have a positive wrap up to the Fall semester in the coming weeks. For our Weekly Update next Monday, December 5th, we feature guest speaker and our first affiliate member, Dr. Gregory Reeves<https://engineering.tamu.edu/chemical/profiles/reeves-gregory.html>, Chemical Engineering, Texas A&M University. The following Monday, on Dec. 12th, we will focus on data storage and sharing options for the Institute. This is a critical piece of integration for EMBRIO. Lev Gorenstein, Sr. Computational Scientist with the Rosen Center for Advanced Computing at Purdue, will provide an overview of the Data Depot storage system and answer questions, followed by discussion and next steps for establishing a system of storing and sharing EMBRIO research data. The Member Spotlight in this issue introduces Dr. Anjali Iyer-Pascuzzi<https://www.purdue.edu/btny/iyer-pascuzzilab/>. We are thrilled to announce that Anjali is joining EMBRIO as DEI Director for the Institute and will be engaged in collaborations within Thrust 2. She will work closely with Dr. Ignacio Camarillo who leads outreach and recruiting efforts and the next leader, to be determined, of the EMBRIO Undergraduate research experiences program. Dr. Iyer-Pascuzzi will present her plans for DEI along with her research in Thrust 2 during the January 30th Weekly Update. We sat down with Anjali to ask her about her plans and her research. Read all about it in this issue’s Member Spotlight. This week in our Monday afternoon meeting slot we kicked off a trainee professional development series centered on grants. In this series trainees learn about funding agencies, the components and uses of a well-crafted aims page, and will draft and engage in peer review of their own aims page! The next session will be January 23rd (see details below) so mark your calendars to attend this valuable professional development opportunity. A reminder that for Spring semester 2023, we will maintain our Monday 3pm (ET) time continuing Weekly Updates split between research talks, DEI topics, professional development trainings, and a monthly meeting for Thrust and Site Leaders. A calendar invite with a new Zoom link was emailed on 11/18. The schedule for January and February Weekly Updates is presented in this issue. All EMBRIO members are invited to a Watch Party on Dec. 6 10:30-12:30 featuring student presentations in the Quantitative Systems Biology course taught by Drs. Umulis and Linlin Li. Details are in this issue. We want to hear about your news and announcements. Send them to Brent (laddb(a)purdue.edu<mailto:laddb@purdue.edu>) by 12/9 for inclusion in the next issue of Emergence. David, Chris, Stephanie, and Brent Quotable Quote: “Nothing in life is to be feared, it is only to be understood. Now is the time to understand more, so that we may fear less.” ~ Marie Curie<https://en.wikipedia.org/wiki/Marie_Curie> QUICK LINKS Schedule Your One-on-One Interview with Soumi<https://www.when2meet.com/?16968903-R8veS> Reverse Engineering Cellular Systems Workshop<https://forms.gle/KZurTw5rwxyCdYxE9> Propose Breakout Room Topics during Weekly Updates (Email Brent: Laddb(a)purdue.edu<mailto:Laddb@purdue.edu> ) RAISING A RESILIENT SCIENTIST<https://www.training.nih.gov/workshops_and_trainings_for_extramural_princip…> NIH series EMBRIO WATCH PARTY On behalf of Prof. Umulis and Dr. Li, All EMBRIO members are invited to the Watch Party, December 6, 10:30am - 12:30pm(ET) Quantitative Systems Biology course student presentations. For Purdue students and faculty (not already in the course) who will attend in person, please RSVP<https://purdue.ca1.qualtrics.com/jfe/form/SV_0HFcMbnm00lzEyy> by Friday Dec. 2, so that we can plan for enough pizza available. Santa hats optional. In person: PURDUE, Room MJIS 2001 Join Zoom Meeting: https://purdue-edu.zoom.us/j/98100711659?pwd=Z3FrYkJCL241aGRXU0s0WTBDbkFIZz… Meeting ID: 981 0071 1659 Passcode: 918890 EMBRIO RELATED 1-Day WORKSHOP: Reverse Engineering Cellular Systems: Patterning and Morphogensis Virtual Notre Dame - Mexico Symposium 2022: Reverse Engineering Cellular Systems: Patterning and Morphogenesis December 9, 2022 Co-organized by EMBRIO faculty Jeremy Zartman at Notre Dame, this is a virtual 1-day symposium of potential interest to members of the EMBRIO community. Registration and call for abstracts: https://forms.gle/KZurTw5rwxyCdYxE9<https://urldefense.com/v3/__https:/forms.gle/KZurTw5rwxyCdYxE9__;!!IBzWLUs!…> Registration is free and abstracts are being accepted for short talks on topics related to patterning and morphogenesis. The symposium highlights several researchers from across Mexico and includes a talk from Bomyi Lim, who works on gene regulation at our partner U Penn. EMBRIO TRAINEE PROFESSIONAL DEVELOPMENT GRANTS SERIES For trainees that missed the Grants session panel discussion Nov. 28th, the video recording and chat file are available on our Box account > Weekly Meeting Recordings > 2022-11-28_EMBRIO Weekly Update_Grants-Series_Prof-Dev_Session 1. Direct link: https://app.box.com/s/3py70qibjqbbzywss3zc95y8qksav2ib Thank you to the panelists for sharing your insights and experience! Drs. Jason Cannon, Alejandra Magana, Chris Staiger. The next session in the series is scheduled for January 23, 3pm ET: De-Mystifying the Craft of Creating an Aims Page November 28th : The Grants Process and Federal Granting Agencies – Faculty Panel January 23rd : De-Mystifying the Craft of Creating an Aims Page February 20th : Students present draft Aims page for Peer-Feedback (Jazzmin Owens and Peter Brumm) MEMBER SPOTLIGHT: Anjali Iyer-Pascuzzi [cid:9693bedb-09a6-45ff-be64-1654b633e1c6] Dr. Anjali Iyer-Pascuzzi is an Associate Professor in the Botany and Plant Pathology Department at Purdue University. Dr. Iyer-Pascuzzi has joined EMBRIO in a leadership role as Diversity, Equity, and Inclusion Director for the Institute. She brings expertise in research collaboration in Thrust 2 exploring how pathogen manipulation of cytoskeleton dynamics leads to changes in root tissues and enhanced disease. We sat down with Anjali to discuss her new position with the Institute. How have you been involved in DEI efforts at Purdue and beyond? I’ve served on the American Society for Plant Biology (ASPB)’s Equity, Diversity, and Inclusion committee (EDIC) since October 2020. In this capacity I’ve developed and led DEI-based workshops at the annual ASPB meeting, designed inclusive rubrics for evaluating trainee travel award proposals, and broadened awareness of DEI within the plant biology community. Prior to this work I was a member of the College of Agriculture Diversity Action Team in Agriculture (DATA) committee, where I contributed to organizing activities for MLK Day in the College. My program also plays a major role in a summer outreach with the Felege Hiywot Center (FHC) in Indianapolis. FHC serves low-income urban youth and aims to generate confidence through engagement in urban farming. I’m also the PI of a National Needs Graduate Training Fellowship grant from the USDA that aims to comprehensively train students in plant-microbe interactions and data analysis. As part of this, I’ve lead grad student recruitment and mentoring, and organized lab rotations and journal club. What are some of your ideas for leading DEI activities for EMBRIO? As the leader of the DEI and Broader Participation Activities of EMBRIO, I will leverage my previous experiences and work with the leadership to develop DEI programming, encourage inclusion across EMBRIO and lower barriers to participation by all scientists. In the first year, I have the following goals: Build trust in the DEI position within the EMBRIO community, particularly with early career scientists. I envision twice per semester lunches with graduate students and postdocs to listen to their experiences, learn what is going well and what can be improved in the DEI space. Active listening is a critical component of DEI work, and I will aim to ensure that all voices are heard. Promote student and postdoc leadership within the center. Senior graduate students can be excellent ambassadors for diversity and inclusion, and I hope to engage these students as leaders in DEI and mentoring activities. This will include encouraging short workshops held by senior students that introduce junior graduate students to different aspects of graduate school (prelims or proposal writing, for example), or promoting student writing groups within the Institute. Understand current opinions about DEI within the Institute through an anonymous survey, which will also include demographic information. I will work with other members of the EMBRIO leadership team and the Purdue Discovery Learning Center to conduct surveys about inclusivity and collect demographic data on a yearly basis. Further inclusion and a sense of community: Good mentorship is a component of inclusion. I will introduce Individual Development Plan (IDPs) and/or mentorship compacts for post-docs and graduate students within the institute. I will promote the use of a short ‘personal slide’ at the beginning of research presentations to showcase the range of backgrounds and paths to success. I will also encourage the use of alternative text for presentations and posters. Develop an action plan for challenging situations: During the first year, I will work with other EMBRIO faculty to develop a response plan if members of the EMBRIO community are victims of racial, sexual or gender-based harassment. Your research lab brings expertise to the Institute contributing to Thrust 2 activity. Can you tell us more about your research and collaborations in this space? Scientifically, my research is well-aligned with the mission of EMBRIO. My program aims to understand how soil microbes manipulate plant root physiology and development to cause plant disease or promote plant health. I am particularly interested in (1) how microbial perception in specific root cell types is signaled to surrounding tissues, and how those signals are integrated into phenotypic changes across the entire root system, and (2) how the bacterial pathogen manipulates host cell physiology to promote disease. My group has recently discovered a bacteria effector protein which interacts with the plant cytoskeleton and promotes pathogen virulence. In a collaborative project with Dr. Chris Staiger, we are exploring how pathogen manipulation of cytoskeleton dynamics leads to changes in root tissues and enhanced disease. Research in my program takes a multi-scale approach, from the molecular and cellular scale to organ level. Imaging and image analysis is a major component of our work. To this end, I have collaborated with colleagues in engineering, math, and physics for nearly 15 years, both as a faculty member at Purdue and as a postdoc at Duke. I am excited about the possibility of working with EMBRIO and continuing to collaborate with Dr. Staiger and others in this area. >From the EMBRIO Leadership: “We are excited to have Dr. Iyer-Pascuzzi join the Institute in this leadership role as our new DEI Director, and the expertise she will bring to Thrust 2 activity. Please welcome her to the Institute!” Weekly Update Zoom Breakout Rooms: Are you looking for a collaborator? Would you like to get conversation started about a specific research topic with other EMBRIO members? Email me (Brent, laddb(a)purdue.edu<mailto:laddb@purdue.edu>) with your breakout room topics for upcoming Weekly Update sessions. INSTITUTE EVALUATION: SIGN UP FOR YOUR ONE-ON-ONE INTERVIEW (hint: it’s mandatory) “My name is Soumi Mukherjee, and I am a Graduate Student at the Department of Biological Sciences at Purdue. Along with my advisor Dr. Stephanie Gardner, I will be conducting an institute wide evaluation study as a part of Thrust 4 initiative. The process will help in capturing your experiences as a member of EMBRIO, which will be utilized to create a formative evaluation report for NSF at the end of each year. Your participation will not only aid in furthering the goals of the institute for providing an interdisciplinary collaborative environment essential for promoting knowledge integration across all the four thrusts, but also enable us to structure activities catered towards your own professional development. If you are a member of the EMBRIO institute currently doing a research project, we would like to invite you for participating in this study. Participation in the evaluation process is MANDATORY for all the members of the institute. As a part of the evaluation process, you will take part in an online session (via Zoom), which includes an interview and a brief survey, and the entire process should be completed in less than an hour. Interviews will be conducted annually for the total duration of your participation in the institute and the session would not exceed an hour and would be completed in a day. Please fill in all the times you may be available for our interviews using the link below with either your name or email address. This information is requested so that we may contact you to set up an online session, but we will use a randomly generated 4-digit code in place of your name to identify all your information for the data collection and analysis. https://www.when2meet.com/?16968903-R8veS Your participation will not affect any aspect of your association with the EMBRIO institute. If you have any doubts regarding the evaluation process, please reach out to me at mukher42(a)purdue.edu<mailto:mukher42@purdue.edu>.” With Regards Soumi NIH Raising a Resilient Scientist Series The NIH OITE is pleased to offer the RAISING A RESILIENT SCIENTIST<https://www.training.nih.gov/workshops_and_trainings_for_extramural_princip…> series for faculty, staff scientists, and administrators who mentor students and postdoctoral fellows in the biomedical, behavioral, and social sciences. The goal of the Raising a Resilient Scientist series is to promote the mental health and well-being of the academic research community by supporting faculty and administrators to develop self-management, relationship-management, and mentoring skills. Raising a Resilient Scientists Units Workshop Date Registration Communication Skills to Build Trainee Resilience Nov 9, 2022 12:00-2:15 pm ET https://nih.zoomgov.com/meeting/register/ vJIsdeyhrjwsG3qSl89jFlF9zUdzoYlz4Vw<https://nih.zoomgov.com/meeting/register/vJIsdeyhrjwsG3qSl89jFlF9zUdzoYlz4Vw> Promoting Trainee Resilience Dec 14, 2022 12:00-2:15 pm ET https://nih.zoomgov.com/meeting/register/vJIsc-uvpzovGbw2kGLBSbihRcERfN2raTc<https://nih.zoomgov.com/meeting/register/%20vJIsc-uvpzovGbw2kGLBSbihRcERfN2…> Building a Welcoming and Inclusive Research Group Jan 11, 2023 12:00-2:15 pm ET https://nih.zoomgov.com/meeting/register/ vJItcOurqjojGtH9Y_zDJPVHhg2Nm6zWNb0<https://nih.zoomgov.com/meeting/register/%20vJItcOurqjojGtH9Y_zDJPVHhg2Nm6z…> Difficult Conversations, Conflict, and Feedback Feb 8, 2023 12:00-2:15 pm ET https://nih.zoomgov.com/meeting/register/vJIsc-CgrTsiHfcOa91MnLLQ-_REQmdOQ2I<https://nih.zoomgov.com/meeting/register/%20vJIsc-CgrTsiHfcOa91MnLLQ-_REQmd…> The Mental Health and Well-being of Your Trainees Mar 8, 2023 12:00-2:15 pm ET https://nih.zoomgov.com/meeting/register/ vJIscuCpqT4pEzjHEmDI2E604ncYzhOrhm4<https://nih.zoomgov.com/meeting/register/%20vJIscuCpqT4pEzjHEmDI2E604ncYzhO…> There is no charge for participation, but advanced registration is required. For more information, and to register, please visit their webpage<https://www.training.nih.gov/workshops_and_trainings_for_extramural_princip…>. Participation in the entire series is recommended but is not required. Please do not hesitate to email Dr. Milgram if you have any questions. Dr. Sharon L. Milgram (she/her/hers) Director, NIH Office of Intramural Training & Education NIH Office of the Director www.training.nih.gov<http://www.training.nih.gov/> UPCOMING DEADLINES, IMPORTANT DATES, & INFO Weekly Research & Education Zoom Meetings Fall Semester, Monday’s 3 – 4 pm. Zoom link: https://purdue-edu.zoom.us/j/96053485465?pwd=elVnY20wcm9kaFRtVUdPcmFHaGl1UT… · December 5 – Gregory Reeves, Assoc. Prof., Chem. Eng., TAMU · December 12 – Data Platform Session, Lev Gorenstein, Rosen Center for Advanced Computing · Winter Break (no meetings until Spring semester) Spring Semester new Zoom link: https://purdue-edu.zoom.us/j/99819751005?pwd=UVlvWVpxRDB0cDVXbmxBU1NUTEZGZz… · January 9 – Krishna Jayant, Asst. Prof., BME, Purdue · January 16 – Martin Luther King, Jr. Day – No Meeting, please volunteer locally · January 23 – Trainee Professional Development, Grants Series Session #2 · January 30 – Anjali Iyer-Pascuzzi, Assoc. Prof., BPP, Purdue, DEI Director, EMBRIO · February 6 – Thrust & Site Leads Update Meeting · February 13 – Priyanka Baloni, Asst. Prof, HHS, Purdue · February 20 – Trainee Professional Development, Grants Series Session #3 · February 27 – Bakary Samasa, Mary Mullins Lab · March 6 – Thrust & Site Leads Update Meeting · March 13 – Spring break, no meeting March, April, May TBD Nov. 9, 2022 – March 8, 2023. NIH RAISING A RESILIENT SCIENTIST<https://www.training.nih.gov/workshops_and_trainings_for_extramural_princip…> series. Dec. 6 Watch Party, December 6, 10:30am - 12:30pm (ET) Quantitative Systems Biology course student presentations. In person: PURDUE, Room MJIS 2001 Zoom: https://purdue-edu.zoom.us/j/98100711659?pwd=Z3FrYkJCL241aGRXU0s0WTBDbkFIZz… Dec. 9 Virtual Notre Dame - Mexico Symposium 2022: Reverse Engineering Cellular Systems: Patterning and Morphogenesis. Registration and call for abstracts: https://forms.gle/KZurTw5rwxyCdYxE9<https://urldefense.com/v3/__https:/forms.gle/KZurTw5rwxyCdYxE9__;!!IBzWLUs!…> Jan. 2 – 6, 2023: The BMES Cellular and Molecular Bioengineering Special Interest Group is seeking abstracts for the BMES Conference (CMBE)<https://www.bmes.org/2023-cmbe-conference> in Indian Wells, CA. Hot Off the Press: New EMBRIO Journal and Conference Papers Let us know about new papers you want to highlight for the EMBRIO community! REMINDER: EMBRIO Acknowledgement for Scholarly Papers. 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.” Conference Presentations: Let us know about your conference presentations. Awards Let us know about awards that you want to highlight. Open Positions Postdoctoral Fellow Position in Interdisciplinary Biomedical Research and Data Science, Purdue University A full-time postdoctoral fellow position is available immediately for interdisciplinary research in computational systems biology and collaborative data science at Purdue University. The postdoctoral position is associated with EMBRIO (Emergent Mechanisms in Biology of Robustness, Integration, and Organization), an NSF Biology Integration Institute with six university partners. The postdoctoral fellow will be broadly involved in the EMBRIO Institute, with efforts engaged in computational systems modeling and simulation research, as well as building expertise, guidance, and collaboration support and research in data management and data analysis for EMBRIO teams. The postdoctoral fellow will conduct research under the guidance of Dr. Elsje Pienaar (https://engineering.purdue.edu/PienaarLab ) and be co-advised by Dr. Adrian Buganza Tepole (https://engineering.purdue.edu/tepolelab/ ). As part of the work with the Pienaar lab the fellow would build and calibrate computational models of Calcium signaling in multicellular environments and its diverse downstream effects. Together with the Tepole lab the fellow would work to leverage machine learning (ML) tools to speed up and automate model evaluation, and to complement closed-form models with multi-modality ML metamodels for improved accuracy. The work is highly interdisciplinary and highly integrative across multiple systems. The fellow will work closely with experimental experts in zebrafish, plant and tissue culture biology within the EMBRIO Institute to build and parameterize the models. The fellow will also have opportunities to work closely with other computational faculty, staff and students on innovating new ways to integrate and analyze models and data across biological scales and systems. As these specific projects progress, the postdoctoral fellow will have the opportunity to collaborate with investigators and interdisciplinary teams to research and deliver secure systems of data collection, storage, sharing, and analysis to produce new and actionable knowledge. This work will research and provide regular guidance and training in data science best practices and serve as a point of contact for all things data related. The postdoctoral fellow will have the opportunity to co-write proposals and to develop research components around the data-rich interdisciplinary modeling and simulation environment of EMBRIO. A Ph.D. degree in Data Science, Computer Science, Biomedical Engineering, Chemical Engineering, Mechanical Engineering, Mathematics, Physics or related fields is required. Previous experience in computational modeling, systems biology, stochastic modeling, numerical methods, and associated statistical analysis, data science, or research data management is desired. Successful applicants will be detail oriented, eager to learn new methods, and enthusiastic about computationally rigorous modeling, collaborating across disciplines, working with experimental biologists and chemists, and advancing and supporting the research data realm of EMBRIO Institute. Salary to be negotiated. To apply for this position, please submit to Dr. Pienaar (epienaar(a)purdue.edu<mailto:epienaar@purdue.edu>) and Dr. Buganza Tepole (abuganza(a)purdue.edu) (1) your CV, (2) a cover letter explaining your background, interest and qualifications for the position, and (3) contact information for three references, including your relationship to the reference, their phone number, email address, and mailing address. Please contact Dr. Pienaar (epienaar(a)purdue.edu) for formal inquiries. Postdoctoral Fellow Position in Interdisciplinary Biochemical Cancer Research, University of Notre Dame A full-time postdoctoral fellow position is available immediately for Multidisciplinary Cancer Research at the University of Notre Dame, affiliated with the Harper Cancer Research Institute, the Notre Dame Warren Drug Delivery Center and Notre Dame Institute for Precision Health. The perspective candidate will conduct an interdisciplinary research on projects studying the basic molecular mechanisms of multiple birth defects, cancer progression and neurodegeneration and developing novel therapies to combat them. The postdoctoral fellow will receive crossdisciplinary training in biochemistry, cell biology, synthetic organic chemistry, and drug discovery utilizing a broad range of biochemical assays related to phenotypic screening and protein-protein interactions. The postdoctoral fellow will conduct research under the guidance of a mentoring team, including Dr. Jeremiah Zartman (http://sites.nd.edu/zartmanlab/) and Dr. Brandon Ashfeld (https://ashfeldlab.nd.edu/) A Ph.D. or M.D. degree in cell or molecular biology, genetics, biochemistry, chemistry or a related discipline, is required. Previous experience in genetics, screening technologies and associated statistical analysis, synthetic chemistry, imaging or mouse modeling is desired. Successful applicants will be detail oriented, eager to learn new techniques, and enthusiastic about biology, exploring the interface between chemistry and biology, and working in an academic lab environment. Salary is commensurate with experience. To apply this position, please submit: (1) your CV, (2) a cover letter explaining your background, interest and qualifications for the position, and (3) contact information for three references, including your relationship to the reference, their phone number, email address, and mailing address. Please contact Dr. Jeremiah Zartman (jzartman(a)nd.edu) or Dr. Brandon Ashfeld (bashfeld(a)nd.edu) for formal inquiries. 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 ), 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. 9 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 laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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Watch Party date and Grants panel recording
by Brent T Ladd 29 Nov '22

29 Nov '22

EMBRIO Community, EMBRIO Watch Party On behalf of Prof. Umulis and Dr. Li, All EMBRIO members are invited to the Watch Party, December 6, 10:30am - 12:30pm(ET) Quantitative Systems Biology course student presentations. For Purdue students and faculty (not already in the course) who will attend in person, please RSVP<https://purdue.ca1.qualtrics.com/jfe/form/SV_0HFcMbnm00lzEyy> by Friday Dec. 2, so that we can plan for enough pizza available. Santa hats optional. In-person Room: MJIS 2001 Join Zoom Meeting: https://purdue-edu.zoom.us/j/98100711659?pwd=Z3FrYkJCL241aGRXU0s0WTBDbkFIZz… Meeting ID: 981 0071 1659 Passcode: 918890 Trainee Grants Series Session One Recording For trainees that missed the excellent Grants session panel discussion yesterday, the video recording and chat file is available on our Box account > Weekly Meeting Recordings > 2022-11-28_EMBRIO Weekly Update_Grants-Series_Prof-Dev_Session 1. Direct link: https://app.box.com/s/3py70qibjqbbzywss3zc95y8qksav2ib Thank you to the panelists for sharing your insights and experience! Drs. Jason Cannon, Alejandra Magana, Chris Staiger. The next session in the series is scheduled for January 23, 3pm ET: De-Mystifying the Craft of Creating an Aims Page Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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