BME WEEKLY ROUNDTABLE

MAY 6, 2024

COMMENCEMEN WEEK!

INTERIM HEAD’S NOTE

For all Spring Full Term and Second Eight Week classes, Grade entry ends at 5 p.m. Tuesday, May 7. This includes all graduate and undergraduate research students. This is a kind reminder from me in addition to the one sent by Cindy a hour ago.

We had quite some fun last Friday at Lafayette County Club. 30+ faculty and staff attended it. We were assigned randomly to teams, and all learned a bit about Indiana, West Lafayette, Purdue University, BME, and MJIS through quiz questions. The last question was the height difference between me and Zach Edey. To spice it up a bit, each team was asked to place a bet instead of just getting the normal 1 point for the correct answer. Judging by the noise we made, it was a success.

Another friendly reminder, the commencement ceremony, the BME Graduation Celebration will be held on May 11st, 9 – 11:30 am in the MJIS Atrium. It is open to all the faculty and staff. Please come out to send your best wishes to all graduates and greet their parents. It is time for celebration.

The following undergraduate students won awards in this awards season. Congratulations to them and their faculty and staff nominators and supporters.

Kyle Heaton and Sarah Staller received the Havel-Decker Outstanding Biomedical Engineering scholarship for juniors.
Joshua Sexton and Winston Ngo received the Haselby Outstanding Biomedical Engineering scholarship for Seniors
Matthew Margraf and Sarah Staller received the Grubbs Summer Fellowship
Owen Jones and Nicole Nagel received the Weldon Senior Class Scholarship
Deniz Eksioglu, Kara McCrindle, Nathan Petrucci and Samantha Stebbings receive the Charles Wayne Sullivan Scholarship.
More to come

UPCOMING IMPORTANT DATES

Week of May 6

Tues., May 7: Grade entry ends at 5 p.m.

Tues., May 7: BME PhD Defense Announcement for Vidhya Vijayakrishnan Nair (Yunjie Tong, advisor). Everyone is invited to attend the public presentation beginning at 9:00 AM in MJIS 2001 and via Zoom. Research title: Human Cerebrospinal Fluid Movement across Wake and Sleep States – A Multimodal Imaging Study

Wed., May 8: BME PhD Defense Announcement for Yilun Li (Fang Huang, advisor). Everyone is invited to attend the public presentation beginning at 10:00AM EST in FLEX B038 or via Zoom. Title: A user-centric cloud computation platform for super-resolution imaging reconstruction.

Thurs., May 9: IBSC-BME Preliminary Exam Announcement for Eric J. Tan (Tamara Kinzer-Ursem, advisor), 2:30 p.m., MJIS 2001. This preliminary exam is open only to those who have signed the Lilly NDA. Title: Developing ultrasensitive point-of-care detection of hyper-phosphorylated tau in patients with preclinical Alzheimer’s disease. Committee: Tamara L. Kinzer-Ursem, Chair; Jacqueline Linnes; Jean-Christophe Rochet; Scott C. Bolton

Fri., May 10: Deadline for Registration for 2024 Hitchhiker’s Guide to the Biomolecular Galaxy, to be held Thursday, May 23-Friday, May 24 in Armstrong Hall. ! Please register using this link. If you would like to present an oral presentation or poster, please submit an abstract when registering. Awards will be given to the Top 3 posters and oral presentations, with a People’s Choice award at the end of the second day.

MJIS END OF SEMESTER ALERTS/REMINDERS

Just a quick reminder of a few MJIS policies as we approach the chaos that is the end of the semester.

(1) Do not give access (e.g., open a door, prop a door) to anyone you do not know into the secure lab block or any office or meeting room. If there is someone you do not recognize, feel free to call/text Susan Hardy and let her know. Vendors or service personnel should always be invited and escorted by a BME staff or faculty member, and should not be in the building after (or before) normal working hours. Purdue service personnel should always identify themselves and their purpose for being in MJIS.

(2) Do not leave office doors unlocked or personal items (backpacks, purses, laptops) unattended.

Unfortunately, this is the time of year when individuals come on to our campus to take advantage of distractions associated with the semester ending. We have had personal items stolen in the past. Don’t become a victim!

Upcoming important deadlines and information

Tues., May 14: BME Master's Defense Announcement for Natalie Romick (L. Solorio, advisor). Everyone is invited to attend the public presentation beginning at 1:00 PM in MJIS 2001. Title of research: Evaluation of Biodegradable in situ Forming Implant Components to Advance Extended Release ISFI Treatment for Opioid Use Disorder.

Wed., May 15: IBSC-BME PhD Preliminary Examination Announcement for Worapat Sawatwong (D. Little and D. Chan, co-advisors). Everyone is invited to attend the public presentation beginning at 10:00 AM in LYNN 1192. Research title: Influences on Bone Mechanosensitivity: Mechanical Load Distribution History and Alterations in the Gut-Bone Axis

Wed., May 15: National NIH K12 DiabDocs Career Development Session, 3:00 p.m., via Zoom. This monthly presentation features world-renowned experts via Zoom. This month’s speaker is Juan Carlos Espinoza Salomon, MD, Chief Research Informatics Officer, Stanley Manne Children’s Research Institute, Feinberg School of Medicine, speaking on “Use of AI in Diabetes Research.”

Thurs., May 16: Indiana O’Brien Center for Advanced Renal Imaging and Molecular Analysis Online Symposium, 11 a.m.-4 p.m., via Zoom. “Large-Scale 3D Microscopy as a Tool in Renal Research.” The symposium will be presented online via Zoom. Attendance is free, but requires registration at https://iu.zoom.us/webinar/register/WN_5ZUge4PnTX6DC6eJOAF_WA#/registration

Thurs., May 23-Fri., May 24: 2024 Hitchhiker’s Guide to the Biomolecular Galaxy, Armstrong Hall. Registration is officially open for the 2024 Hitchhiker’s Guide to the Biomolecular Galaxy! Please register using this link. Hitchhiker's Guide to the Biomolecular Galaxy Symposium brings together undergraduate students, graduate students, post-doctorates, and faculty throughout the Midwest who are all striving to share and gain more insight into various biophysical approaches. Registration is completely free with breakfast, lunch, coffee, and snacks provided both days. The symposium will include a keynote address given by Dr. Jin Zhang from the University of California San Diego. Dr. Zhang’s research lab developed a series of molecular tools and fluorescence imaging technologies to understand the spatiotemporal regulation of cell signaling.

Fri., June 7: Indiana Human-Centered Design for Health Seminar Series, 12:00 p.m. via Zoom. Lean about research and best practices in HCD and health, promote the diverse HCD expertise in Indiana, and build a community of HCD researchers and practitioners focused on health, in Indiana and beyond. The speaker will be Youngbok Hon, Professor, Herron School of Art and Design, IUPUI. Register and learn about upcoming seminars at healthtechquitylab.org/hcd-seminar

Resources and further information

Tues., May 7: BME PhD Defense Announcement for Vidhya Vijayakrishnan Nair (Yunjie Tong, advisor). Everyone is invited to attend the public presentation beginning at 9:00 AM in MJIS 2001 and via Zoom. Research title: Human Cerebrospinal Fluid Movement across Wake and Sleep States – A Multimodal Imaging Study. Thesis Committee Members: Dr. Yunjie Tong (Chair), Dr. A.J. Schwichtenberg, Dr. Vitaliy L. Rayz, Dr. Yu-Chien Wu.

Abstract: The movement of Cerebrospinal Fluid (CSF) within the brain's ventricles and the subarachnoid spaces of both the cranium and spine is crucial for the health and functioning of the central nervous system. Recent research has emphasized CSF movement's importance in metabolic waste clearance and its effect on the pathophysiology of neurodegenerative and neurodevelopmental disorders. Additionally, CSF movement is significantly enhanced during Non-rapid eye movement (NREM) sleep. Despite the critical role of CSF in maintaining brain health, a comprehensive understanding of the mechanisms driving its movement across different states of wakefulness and sleep is lacking. In this work, multimodal imaging was utilized to simultaneously monitor CSF movement and brain hemodynamics via functional Magnetic Resonance Imaging (MRI), neural activity through Electroencephalography (EEG), and non-neuronal systemic physiology via peripheral functional Near-Infrared Spectroscopy (fNIRS). Our findings reveal that CSF movement is influenced by multiple physiological forces concurrently. During wakefulness, both low-frequency vasomotion and respiration interact to regulate CSF movement. Furthermore, systemic physiological changes significantly impact CSF movement during light NREM sleep, even in the presence of autonomic neural activity. Notably, during deep NREM3 sleep, CSF movement magnitude increases independent of the magnitude of brain hemodynamics, suggesting a decrease in impedance to CSF movement and an enhanced exchange between CSF and interstitial fluid (ISF) in the brain. Building on these observations, significant enhancement of CSF movement was also achieved via simple respiratory interventions, thereby demonstrating their potential to be used as clinical protocols across pathologies characterized by reduced CSF movement.

Zoom Meeting Link: https://purdue-edu.zoom.us/j/95341354792?pwd=L2ZBTmJYUEVDRXhDTm03cU9JYlBOUT09

Meeting ID: 953 4135 4792 Passcode: 741481

Committee Members: FANG HUANG (Chair), DANIEL M. SUTER, STEVEN T. WERELEY, XIAOHUI C. SONG

Abstract: Single-molecule localization microscopy (SMLM) leverages the detection and localization of individual fluorescently tagged molecules to visualize cellular and tissue samples at a nanometer resolution. The reconstruction of a super-resolution image via SMLM, however, involves intricate algorithms and large scale computation that may require hours to achieve a single high-quality 3D image. Additionally, the image generation process calls for specialized expertise and resources, such as knowledge of image processing and massively parallel computing. To address these challenges, we are developing an integrated cloud-based SMLM suite named "cloud-SMLM". This suite combines key algorithms from each stage of single molecule analysis, integrating with high levels of parallelization. Deployable on cloud-based computational services like Amazon Web Service (AWS), cloud-SMLM interacts with its users through a dedicated, easy-to-use drag-and-drop webpage. This design eliminates the prerequisite for hardware such as GPU and reduces the knowledge barrier for users of single molecule nanoscopy. Accessible from any web-browser equipped device, it enables users to initiate and modify data reconstruction. Furthermore, it provides visualization and data mining tools for users to explore the reconstructed three-dimensional ultra-high-resolution cellular and tissue volumes. We expect that this project will democratize existing and new single molecule super-resolution imaging capacities by integrating them into computational pipelines for a wide range of biological model systems. We believe that the success of cloud-SMLM will represent a significant step towards unlocking the full potential of ultra-high resolution optical imaging in biological and biomedical research.

Join Zoom Meeting
https://purdue-edu.zoom.us/j/91595672410?pwd=c2lyTzVSTXpuTTA1R3o2aWR4Y1l2UT09

Meeting ID: 915 9567 2410
Passcode: 730694

Tues., May 14: BME Master's Defense Announcement for Natalie Romick (L. Solorio, advisor). Everyone is invited to attend the public presentation beginning at 1:00 PM in MJIS 2001. Title of research: Evaluation of Biodegradable in situ Forming Implant Components to Advance Extended Release ISFI Treatment for Opioid Use Disorder.

Thesis Committee: Luis Solorio (Chair), Kinam Park, Andrew Otte

Abstract: Opioid use disorder (OUD) presents a challenging and nuanced condition with potential for debilitating social and physical consequences. Patients with OUD have access to treatment options, but they may encounter issues such as diversion, invasiveness, or poor adherence. With over 2.5 million adults in the US experiencing OUD as of 2021, the need for an OUD treatment that overcomes these challenges is clear. One available treatment method is Sublocade®, a PLGA-based in situ forming implant (ISFI) that releases buprenorphine. This treatment shows promise due to its physician administered extended release design, which addresses many current issues in OUD treatment. However, the practicality of this treatment remains a challenge due to its monthly injection requirement. To address this, we investigated how altering ISFI components impacts the timeframe of buprenorphine release from a PLGA-based ISFI. Our focus was on evaluating factors that lead to extended buprenorphine release while maintaining zero-order release. We varied polymer-to-solvent ratios, drug content, and solvent type, assessing their effects through drug release studies. We also conducted SEM imaging and swelling/erosion studies to evaluate polymer behavior and implant microstructure, gaining further insights into drug release mechanisms. Our drug release studies revealed that higher buprenorphine content in the implant significantly reduced total drug release and linearized drug release patterns. Decreasing the polymer-to-solvent ratio similarly linearized drug release and reduced drug burst, although the overall amount of drug released over time remained similar. Introducing Triacetin (TA) as a solvent helped reduce drug burst and maintain release linearity in lower drug content implants. In higher drug content implants, TA appeared to increase drug release over time, likely due to degradation processes indicated by high swelling and increased degradation observed in SEM imaging. Erosion studies showed less implant erosion with higher drug loading, aligning with release study observations. In conclusion, solvent type and drug content significantly influence buprenorphine release in ISFI systems and should be carefully considered when designing extended release systems similar to Sublocade®.

Wed., May 15: IBSC-BME PhD Preliminary Examination Announcement for Worapat Sawatwong (D. Little and D. Chan, co-advisors). Everyone is invited to attend the public presentation beginning at 10:00 AM in LYNN 1192. Research title: Influences on Bone Mechanosensitivity: Mechanical Load Distribution History and Alterations in the Gut-Bone Axis

Thesis Committee members: Dr. Dianne Little (co-chair, BMS), Dr. Deva Chan (co-chair, BME), Dr. Timothy Lescun (VCS), Dr. Andrew Brightman (BME), Dr. Glen Niebur (University of Notre Dame)

Abstract: Osteoporosis is a bone disease that affects over 20% of the global elderly population. It is characterized by reduced bone mass and strength, leading to increased fracture susceptibility due to diminished responsiveness to mechanical stimuli. Understanding how bones sense and respond these mechanical signals is crucial, as it directly relates to osteoporosis severity and fracture risk. There remains a critical need to identify the key factors influencing bone mechanosensation to develop effective interventions for osteoporosis patients. Tissue-level mechanical strain directs bone adaptation. Non-physiological strain distributions can induce bone formation even under normal strain levels, highlighting the significant impact of strain distribution on bone mechanosensitivity. Physiological strain is influenced by daily locomotion patterns, which vary across species. For instance, sprawling locomotion in reptiles with distinct stances and load distributions from quadrupedal mammals, may establish novel bone mechanosensitivity pathways. Additionally, systemic perturbations like disrupted gut microbiome (GM) diversity – dysbiosis, alter bone homeostasis through inflammatory changes, affecting bone quality. Antibiotic use disrupts long-term GM diversity and may influence bone adaptation and mechanosensation, while exercise may offer restoration. However, specific responses of osteocytes to different strain modes, the impact of locomotion stance on bone mechanosensitivity, and the interplay between GM dysbiosis and exercise on bone health remain unclear. We hypothesize that these mechanical load experience and systemic interference impact bone metabolism. Aim 1 will assess the effects at the level of gene expression of different strain distribution patterns during loading using two external mouse tibia loading models on bone cells. Aim 2 will investigate bone remodeling responses in sprawling hindlimb gait quadrupeds using iguana models. Aim 3 will study the interplay between antibiotic-induced GM dysbiosis and treadmill exercise on long-term bone homeostasis using mouse forelimb bones. Understanding the factors influencing changes in bone mechanosensation is essential for developing new drug targets and mechanical stimulation for osteoporosis patients. Completion of this project will help me develop the skills necessary for my long-term goal of becoming an independent researcher in musculoskeletal biology, osteoporotic disease, and sport sciences.

The program is funded by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) of the National Institutes of Health under award number K12DK133995. Additional support provided by Stanford University, Indiana University, and a grant from the Leona M. and Harry B. Helmsley Charitable Trust to Stanford University. Program questions can be directed to diabdocsk12@stanford.edu

Brief Bio for Speaker: After completing his undergraduate degree at Washington University in St. Louis, Dr. Espinoza received an Intramural Research Training Award (IRTA) at the Immunotherapy Unit of the National Institute on Aging at the National Institutes of Health. At the NIH, Dr. Espinoza worked on small molecule design, developing therapeutic and research tools. Successively, he attended the USC Keck School of Medicine, earning his MD in 2010. He completed his pediatric residency at Children’s Hospital Los Angeles in 2013, and in 2014 he became an Assistant Professor of Clinical Pediatrics at Children’s Hospital Los Angeles and the USC Keck School of Medicine. During his time at CHLA, Dr. Espinoza’s clinical time focused on complex care coordination and obesity management, while his research focused on informatics, medical devices, health equity, and global health. In 2016, he joined the team at CTIP (The West Coast Consortium for Technology & Innovation Pediatrics) and took over as Director and Principal Investigator in 2018 with a new $6.6 million FDA grant. In addition to CTIP, he held a number of leadership roles in informatics and innovation, including serving as the Co-Director of Clinical Research Informatics Core for the Southern California Clinical and Translational Science Institute, Medical Director of the Children’s Hospital Los Angeles Innovation Studio, Methods and Data Core Director for the Southern California Center for Latino Health, and Research Lead for the International Digital Health Team. In 2023, Dr. Espinoza was recruited to Lurie Children’s Hospital to become the inaugural Chief Research Informatics Officer (CRIO) for Stanley Manne Children’s Research Institute and Associate Director of the Center for Biomedical Informatics and Data Science at Northwestern University Feinberg School of Medicine. Dr. Espinoza’s research portfolio includes health information systems integration, social determinants of health, geocoded contextual data, regulatory science and medical device development, and patient generated health data in diabetes, obesity, and asthma. As a clinician, he will provide inpatient care a member of the Division of Hospital-Based Medicine. His overall goal as a researcher, physician, and advocate is to identify, refine, and innovate approaches to using data and technology to improve health outcomes and narrow the health gap faced by marginalized communities in the United States and abroad. Dr. Espinoza’s academic interests are complemented by his experiences outside of medicine; in 2010 he co-founded a digital media production company that worked with television, film, web, and mobile technologies. In this endeavor he partnered with the entertainment and healthcare industries.

Speakers include:

Matthias Gunzer – Inst. for Experimental Immunology and Imaging, Univ. of Duisburg-Essen Making kidney substructures precisely countable by a combination of clearing, lightsheet imaging and automated image analysis
Sanjay Jain – Kidney Translational Research Center, Washington University Nephro-neurovascular interactions in the human kidney using light sheet fluorescence microscopy
Christian Kurts – Institute for Molecular Medicine and Experimental Immunology, Bonn Determining individual glomerular proteinuria and periglomerular infiltration in a cleared murine kidney by 3D fast-marching algorithm
Lori O’Brien – Department of Cell Biology and Physiology, University of North Carolina Imaging the kidney: 3D microscopy brings organization to light
Chetan (Che) Poudel - Department of Chemistry, Univ of Washington Automated tracking and segmentation of whole nephrons at the organ scale
Victor Puelles – Aarhus University, University Medical Center Hamburg-Eppendorf Optical clearing and advanced light microscopy to characterize glomerular pathophysiology

Thurs., May 23-Fri., May 24: 2024 Hitchhiker’s Guide to the Biomolecular Galaxy, Armstrong Hall. Registration is officially open for the 2024 Hitchhiker’s Guide to the Biomolecular Galaxy! Please register using this link. Hitchhiker's Guide to the Biomolecular Galaxy Symposium brings together undergraduate students, graduate students, post-doctorates, and faculty throughout the Midwest who are all striving to share and gain more insight into various biophysical approaches. Registration is completely free with breakfast, lunch, coffee, and snacks provided both days. The symposium will include a keynote address given by Dr. Jin Zhang from the University of California San Diego. Dr. Zhang’s research lab developed a series of molecular tools and fluorescence imaging technologies to understand the spatiotemporal regulation of cell signaling. We will be hosting pre-symposium events on Wednesday, May 22^nd 2024. Our pre-symposium events are focused on advancing careers with professional development and implementing diversity and inclusion in our field, along with social and networking opportunities with other researchers at Purdue and the Midwest! Each day of the symposium will consist of seminar style lectures where graduate students, postdoctoral fellows, undergraduates, faculty, and visitors can share their work. If you would like to present an oral presentation, please submit an abstract when registering by May 10, 2024.

The first day will also include a two-hour workshop session with four technical workshops:

Easy (and accurate) structure modeling & validation on web server for cryo-EM
An introduction to 3D Molecular movies (PyMOL, Chimera, Blender/Maya)
Figure Making and Ethics
Quantitative proteomics

When registering for the symposium, participants will rank the order of workshops they are interested in (1 being the most likely). Participants will be placed in each workshop on a first-come, first- serve basis upon registering until the workshop reaches maximum capacity.

On the second day of the symposium, we will be hosting a two-hour poster session. If you would like to participate in this poster session, please submit an abstract by May 10, 2024, when registering for the symposium! Awards will be given to the Top 3 posters and oral presentations, with a People’s Choice award at the end of the second day.

Hope to see you all there!

On behalf of the 2024 organizing committee:

Co-Chair, Kadidia Samassekou (Department of Chemistry)

Co-Chair, Vaani Ohri (Department of Biological Sciences)

Kadir Ozcan (Department of Biological Sciences)

Hanna Bovill (Department of Chemistry)

Ketaki Mahurkar (PULSe/Department of Chemistry)

Michelle Bush (Department of Biological Sciences)

Ryan Peters (Department of Biological Sciences)

Hunain Janjua (PULSe/Department of Biological Sciences)

Faculty Mentor: Dr. Lauren Ann Metskas (Department of Biological Sciences and Chemistry)

Postdoctoral Fellow Opportunity – IUSM Emergency Medicine

The laboratory of Dr. Nathan J. Alves, PhD, within the Department of Emergency Medicine at the Indiana University School of Medicine (IUSM), is seeking a highly motivated and independent post-doctoral research fellow. Dr. Alves is a Chemical and Biomolecular Engineer, Associate Professor and the Director of Translational Research for the Department of Emergency Medicine in addition to having an affiliate faculty appointment at Purdue University in Biomedical Engineering. The Alves Lab explores highly interdisciplinary research interests applying engineering and biophysical principles and designs to create translational technologies and treatments in the area of blood coagulation and fibrinolysis. The primary focus of research in the laboratory is to develop targeted clot digesting therapeutic agents to more safely digest clinically relevant blood clots to treat pulmonary embolism (PE, blood clots in the lungs), deep vein thrombosis (DVT), and ischemic stroke. This interdisciplinary research utilizes diverse enzyme assays, chemical synthesis, blood clot formation and digestion assays under shear, and other novel testing/delivery platforms that include multivalent branched molecules and nanoparticle drug delivery systems. Projects Include: (1) Leveraging multivalency to modulate enzyme activity and improve inhibitor selectivity (nanoparticle drug delivery and targeting). (2) Ex-vivo flowing models of clot digestion under shear using in-vivo like fluorescently labeled blood clots from human whole blood. (3) Development of novel fibrinolytic diagnostics tools to assess coagulation state. (4) Mouse models of clot formation/targeting/digestion utilizing intravital microscopy. (5) Study the effects of environmental microplastic exposure on coagulation/fibrinolysis. Projects are funded both externally and internally.

For additional information and to apply, go to: https://indiana.peopleadmin.com/postings/19651