March 2024 - Bmegradstudents-list

BME PhD Defense Announcement for Hui Ma (Jacqueline Linnes and Tamara Kinzer-Ursem, Co-Chairs)
by May, Sandra M 29 Mar '24

29 Mar '24

BME PhD Defense Announcement for Hui Ma (Jacqueline Linnes and Tamara Kinzer-Ursem, Co-Chairs) Everyone is invited to attend the public presentation beginning at 10:00 am. Dissertation title: Computational and Experimental Investigation of Microfluidics into Biophysical Interaction. Date: April 10, 2024 Time: 10 am Location: MJIS 2001 Zoom link (no password): https://purdue-edu.zoom.us/j/3601666168?omn=93108263752<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Committee: Dr. Jacqueline C. Linnes (Co-Chair), Dr. Tamara L. Kinzer-Ursem (Co-Chair), Dr. Arezoo M. Ardekani, and Dr. Steven T. Wererley Abstract: Protein-protein interaction plays a key role in biological, biomedical and pharmaceutical research. The technical development of biosensors, new drugs and vaccines, and disease diagnostics heavily rely on the characterization of protein-protein interaction kinetics. The current gold standard assays for measuring protein-protein interaction are surface plasmon resonance (SPR), and bio-layer interferometry (BLI). These commercial devices are accurate but expensive, however. Microfluidic techniques have been widely adopted in biomedical research due to the precise control of fluids, small volume requirement, low cost and etc, and have boosted the development of biomolecular interaction analysis, point-of-care diagnostics, and biosensors. Here, I have developed new microfluidic techniques and models in protein-protein interaction kinetics measurement, rotational diffusion coefficient modeling, electrochemical impedance spectroscopy-based biosensors, and two-phase porous media flow models. Firstly, I applied particle diffusometry (PD) in the streptavidin-biotin binding kinetics measurement, utilizing a Y-junction microchannel. Secondly, to reduce solution volumes used in an analysis experiment, I designed a low-volume chip and coupled it with PD to measure the binding kinetics of human immunodeficiency virus p24 antibody-antigen interactions. Thirdly, considering the Brownian motion of the non-symmetric particles, I developed a new model to efficiently compute particles' rotational diffusion coefficients. Fourthly, to make economic biosensors to detect multiple biomarkers, I created a new chip, enabling hundreds of tests in a single droplet (~ 50 μL) on one chip. Finally, to understand the liquid flow in porous media, such as nitrocellulose in lateral flow assays, I built a new two-phase porous media flow model based on the Navier-Stokes equation and compared it with experiments. These techniques and models underwent rigorous experimental and computational validation, demonstrating their effectiveness and performance.

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BME-IBSC PhD Defense Announcement for Emeka Nwanochie (Jacqueline Linnes and Tamara Kinzer-Ursem, Co-Chairs)
by May, Sandra M 29 Mar '24

29 Mar '24

BME-IBSC PhD Defense Announcement for Emeka Nwanochie (Jacqueline Linnes and Tamara Kinzer-Ursem, Co-Chairs) Everyone is invited to attend the public presentation beginning at 10:00 AM. Title: TOWARDS QUANTITATIVE MOLECULAR ISOTHERMAL AMPLIFICATION FOR POINT-OF-CARE HIV VIRAL LOAD MONITORING Date: April 12, 2024 Time: 10 AM Location: Purdue Graduate Student Center (PGSC) Room 105 A and B Zoom Link: https://purdue-edu.zoom.us/my/jlinnes<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> (open to all) Committee: 1. Dr. Jacqueline Linnes (Co-Chair) Weldon School of Biomedical Engineering 1. Dr. Tamara Kinzer-Ursem (Co-Chair) Weldon School of Biomedical Engineering 1. Dr. J. Paul Robinson (Member) Weldon School of Biomedical Engineering 1. Dr. Aman Russom (Member) Department of Nanobiotechnology KTH Royal Institute of Technology, Stockholm, Sweden Abstract: The quantification of viral load in people with HIV (PLHIV) is crucial for assessing the effectiveness of antiretroviral therapy and evaluating transmission risk. However, in 2022, 11.3 million PLHIV had still not achieved viral suppression and may become susceptible to both HIV transmission and a variety of opportunistic infections. Nucleic acid amplification tests (NAATs) have emerged as potent tools for monitoring viral load with reverse transcription quantitative polymerase chain reaction (RT-qPCR) being recognized as the benchmark due to its sensitivity and ability for real-time quantification enabled by fluorescence signal emission. Nevertheless, RT-qPCR is burdened by drawbacks including extended processing times, high operational costs, and the requirement for specialized laboratory facilities. In this study, we propose a novel method for HIV-1 viral load monitoring by integrating reverse-transcriptase loop-mediated isothermal amplification (RT-LAMP) with real-time particle diffusometry (PD). By monitoring changes in diffusivity during RT-LAMP amplification of HIV-1, real-time PD allows for the generation of quantitative data embedded within PD plots. Additionally, to address challenges related to amplification inhibition in complex human specimens, we developed a power-free sample processing system specifically designed for extracting HIV-1 RNA from both whole blood and plasma. Ultimately, we incorporated the real-time quantitative PD-RT-LAMP assay onto a field-compatible handheld portable platform suitable for field use, featuring built-in quality control measures. These innovations aim to facilitate quick and comprehensive viral load determination, offering promise for enhanced HIV management and patient care.

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BME PhD Defense Announcement for Han Nguyen (Chien-Chi Lin and Julie Liu, co-advisors)
by May, Sandra M 29 Mar '24

29 Mar '24

BME PhD Defense Announcement for Han Nguyen (Chien-Chi Lin and Julie Liu, co-advisors) Everyone is invited to attend the public presentation beginning at 2:00 PM EST. Title: DESIGNING TUNABLE VISCOELASTIC HYDROGELS FOR STUDYING PANCREATIC CANCER CELL FATE Date: April 11th, 2024 Time: 2:00 PM EST Location: IUPUI SL 220 A Zoom Link: https://purdue-edu.zoom.us/j/7085972423<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Committee: Chien-Chi Lin, Co-Chair; Julie C. Liu, Co-Chair; Hiroki Yokota; Sungsoo Na Abstract: Pancreatic ductal adenocarcinoma (PDAC) is the most common and lethal pancreatic cancer subtype. The silent tumor progression and aggressive development of chemoresistance are the primary factors behind the dismal 13% 5-year survival rate. The tumor microenvironment (TME) has been the focus of many pancreatic cancer research since the TME actively interacts with cancer cells to promote tumor growth, drug resistance, and invasion. A thorough comprehension of PDAC cell and TME interaction is crucial to uncover the mechanism and key regulators behind PDAC's rapid progression, high propensity for metastasis, and exceptional resistance to cancer therapeutics. Hydrogels have emerged as invaluable tools for investigating cell-matrix communication in three-dimensional (3D) environments, as their chemical and mechanical properties can be easily tuned to mimic the dynamic nature of native tissue. However, current biomimetic hydrogels used in PDAC models are elastic and often lack tissue-relevant viscoelastic properties, such as hysteresis and stress-relaxation. Stress-relaxation influences various cellular processes, including differentiation, proliferation, and cancer progression. This dissertation aims to address this gap by introducing viscoelasticity and fast stress relaxation into existing hydrogel platforms to more accurately replicate PDAC tissue mechanics. Specifically, we employ two chemistries-thiol-norbornene photopolymerization and boronic ester dynamic bonding-to fabricate gelatin-based hydrogels. Gels formed solely via irreversible thiol-norbornene chemistry exhibit elasticity and slow stress-relaxation, while gels formed with both thiol-norbornene and reversible boronic ester bonds display viscoelastic properties and stress-relaxation. Cell-laden hydrogels with varying mechanical properties (low vs high stiffness, slow vs fast relaxation) were used as tools to explore the effects of matrix stiffening and viscoelasticity in promoting cancer aggressiveness. Results from these studies describe our recent progress in understanding the mechanism by which viscoelastic substrates facilitate cancer development and how cellular functions can be controlled via modulating cell receptor-matrix binding.

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IBSC-BME Preliminary Exam Announcement for Eric J. Tan (Tamara Kinzer-Ursem, advisor)
by May, Sandra M 29 Mar '24

29 Mar '24

IBSC-BME Preliminary Exam Announcement for Eric J. Tan (Tamara Kinzer-Ursem, advisor) 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 Date: April 11,, 2024 Time: 10:30 am Location: MJIS 2001 Committee: Tamara L. Kinzer-Ursem, Chair; Jacqueline Linnes; Jean-Christophe Rochet; Scott C. Bolton

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[Bmeroundtable-list] FW: 2024 Hitchhiker’s Guide to the Biomolecular Galaxy Pre-Symposium Survey
by Gelfand, Johanna K 28 Mar '24

28 Mar '24

Hello, My name is Kadidia Samassekou and I am a fifth-year Ph.D. candidate in the Department of Chemistry at Purdue University. This year I am co-chairing a completely student-run conference called Hitchhiker's Guide to the Biomolecular Galaxy (HG2BG). This symposium has been put on for >10 years and brings together undergraduate students, graduate student, post-doctorates, and faculty throughout the Midwest who are all striving to share and gain more insight into various biophysical approaches. I was wondering if you could please share the email below to your department. I will send another email when registration opens. Thank you in advance for your help! Best, Kadidia Samassekou [cid:image001.png@01DA7C5C.E09D1F80] Calling all astronauts and control center personnel, Prepare for liftoff of the 2024 Hitchhiker’s Guide to the Biomolecular Galaxy symposium<https://hitchhikers.science.purdue.edu/2024/index.html>! Please fill out this quick, pre-symposium survey (link<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqualtrics…>) and let us know if you plan on attending the symposium, what interests you, and ideas you may have for the committee to discuss. Note: This is NOT registration. This survey is used to gauge interest and seek information about how to improve the symposium this year. The 9th annual Hitchhiker’s Guide to the Biomolecular Galaxy (HG2BG) symposium will be held on Thursday-Friday, May 23rd & 24th 2024 and we hope to see you there. HG2BG brings graduate and undergraduate students, post-doctoral researchers, research scientists, and faculty together from across the Midwest who have a passion for biophysical research. The symposium will include a keynote address given by Dr. Jin Zhang from the University of California San Diego. Dr. Zhang’s research contributions were recognized by numerous awards. Her lab developed a series of molecular tools and fluorescence imaging technologies to understand the spatiotemporal regulation of cell signaling. Dr. Zhang’s lab website<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjinzhangl…> There will be a reception and poster session where graduate students, postdoctoral fellows, undergraduates, faculty, and visitors can share their work, as well as seminar-style lectures and workshops on topics related to career development and technological developments. Lastly, we will also be hosting pre-symposium events on Wednesday, May 22nd 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! 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) Link to survey<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fqualtrics…> Kadidia Samassekou PhD Candidate | Lyon Lab Department of Chemistry WTHR 327, 560 Oval Drive, West Lafayette, IN 47907 ksamasse(a)purdue.edu<mailto:ksamasse@purdue.edu> | www.chem.purdue.edu/lyon<http://www.chem.purdue.edu/lyon/> Lab: (765) 494-5292 [cid:image002.png@01DA7C5C.E09D1F80]<https://www.purdue.edu/?utm_source=signature&utm_medium=email&utm_campaign=…> -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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BME PhD Defense Announcement for Homeira Kafi (Hari Bharadwaj, advisor)
by May, Sandra M 26 Mar '24

26 Mar '24

BME PhD Defense Announcement for Homeira Kafi (H. Bharadwaj, advisor) Everyone is invited to attend the public presentation beginning at noon EST. Title: Multiple Pathways to Suprathreshold Speech in Noise Deficit in Human Listener Date: 04/11/2024 Time: Noon EST Zoom link: https://pitt.zoom.us/j/97232990469<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpitt.zoom…> Thesis Committee: Hari M. Bharadwaj, Chair Edward L. Bartlett Michael G. Heinz Joshua M. Alexander Abstract: Threshold audiometry, which measures the audibility of sounds in quiet, is currently the foundation of clinical hearing evaluation and patient management. Yet, despite using clinically prescribed state-of-the-art hearing aids that can restore audibility in quiet, patients with sensorineural hearing loss (SNHL) experience difficulty understanding speech in noisy backgrounds (e.g. cocktail party-like situations). This is likely because the amplification provided by modern hearing aids while restoring audibility in quiet, cannot compensate for the degradation in neural coding of speech in noise resulting from a range of non-linear changes in cochlear function that occur due to hearing damage. Furthermore, in addition to robust neural coding, the efficacy of cognitive processes such as selective attention also influences speech understanding outcomes. While much is known about how audibility affects speech understanding outcomes, little is known about suprathreshold deficits in SNHL. Unfortunately, direct measurements of the physiological changes in human inner ears are not possible due to ethical constraints. Here, I use noninvasive tools to characterize the effects of two less-familiar forms of SNHL: cochlear synaptopathy and distorted tonotopy. Results from our experiments showed that age-related CS degrades envelope coding even in the absence of audiometric hearing loss and that these effects can be quantified using non-invasive electroencephalography (EEG)-based envelope-following response (EFRs) metrics. To date, DT has been only studied in laboratory-controlled animal models. Here, I combined psychophysical tuning curves, EFRs, and speech-in-noise measurements to characterize the effects of DT. Our results suggest that low-frequency noise produces a strong masking effect on the coding of speech by the high-frequency portions of the cochlea in individuals with SNHL and that an index of DT (tip-to-tail ratio) obtained from psychophysical tuning curves can account for a significant portion of the large individual variability in listening outcomes among hearing-aid users, over and beyond audibility. Lastly, I propose a machine-learning framework to study the effect of attentional control on speech-in-noise outcomes. Specifically, I introduced a machine-learning model to assess how attentional control influences speech-in-noise understanding, using EEG to link prestimulus neural activity with listening performance. This design allows for examining the influence of top-down executive function on listening outcomes separately from the peripheral effects of SNHL.

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TOMORROW--BME Special Seminar: The M. tuberculosis-macrophage encounter: From basic science discovery to a potential host-directed therapy for tuberculosis”
by Siemers, Tammy R 26 Mar '24

26 Mar '24

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Corrected Zoom link: BME PhD Defense Announcement for Luke Schepers (C. Goergen, advisor)
by May, Sandra M 25 Mar '24

25 Mar '24

Please note the corrected Zoom meeting link below. BME PhD Defense Announcement for Luke Schepers (C. Goergen, advisor) Everyone is welcome to attend the public presentation starting at 12:00pm in MJIS 2001. Title: Photocurable Sealant Development for Hemostasis and Aortic Aneurysm Thrombus Characterization with Ultrasound, Histology, and Microscopy Date: Tuesday, March 26th Time: 12:00pm Location: MJIS 2001 Zoom link: https://purdue-edu.zoom.us/j/96249556476?pwd=UXh0SnBnVVNyK0xQbk4wTTdxNUZCZz…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Thesis Committee: Craig J. Goergen, Chair; Vitaliy L. Rayz; Andrew Otte; Jonathan D. Tune Abstract: Hemorrhage and aortic aneurysms result from external or internal damage to a vessel wall and can be lethal if timely interventions are not made. Blood clotting and thrombus sometimes have a negative connotation in the medical community, but the coagulation cascade is a vital response to hemorrhage and disease. For hemorrhage, the coagulation cascade forms a plug at the injury site providing potentially life-saving hemostasis. In aortic aneurysms, blood coagulates inside the vessel or vessel wall to form intraluminal or intramural thrombus. The role of intraluminal and intramural thrombus in aneurysm rupture remains poorly understood, but past research suggests it may protect against further vessel damage dependent on its location and time of deposition. My dissertation focuses on application of a new photocurable sealant that surrounds a wound and aids in the coagulation cascade during hemorrhage, and analysis of the intramural and intraluminal thrombus that forms in aortic dissections and abdominal aortic aneurysms, respectively. We used volumetric and pulsed-wave Doppler ultrasound to detect changes in hemodynamics, vessel morphology, aneurysm thrombus deposition, and tracked the photocurable sealant's performance and degradation in vivo. We used novel scanning electron microscopy analysis techniques in aortic aneurysm studies to uncover and quantify new information about thrombus structure. Our characterization and in vivo feasibility study with the photocurable sealant can serve as evidence for translation to future use in humans, and our techniques and findings in murine aneurysm models can potentially be used to elucidate the role and structure of thrombus in human aortic aneurysms.

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[Bmeroundtable-list] UPDATE: 3rd floor printer copier
by Gelfand, Johanna K 25 Mar '24

25 Mar '24

The printer/copier on the 3rd floor has been repaired and is again working. PLEASE NOTE: the door to the copier room is to be shut and locked at all times. We have had to close the door FOUR times today. Jo -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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[Bmeroundtable-list] BME Distinguished Research Seminar - Wed., March 27
by Gelfand, Johanna K 25 Mar '24

25 Mar '24

[cid:image002.jpg@01DA7EC1.4F577310] BME DISTINGUISHED RESEARCH SEMINAR SERIES Wednesday, March 27, 2024 9:30 - 10:20am, MRGN 121 ZOOM LINK: https://purdue-edu.zoom.us/j/95124789878?pwd=S0x0VW5Vd3VaMVc1LytlL0NJU1FYUT…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> *Students registered for the seminar are expected to attend in-person. "Talking to cells: Biomolecular engineering for deep tissue imaging and control of cellular function" [cid:image003.jpg@01DA7EC1.4F577310] Mikhail G. Shapiro, PhD Max Delbruck Professor of Chemical Engineering & Medical Engineering, California Institute of Technology Abstract: The study of biological function in intact organisms and the development of targeted cellular therapeutics necessitate methods to image and control cellular function in vivo. Technologies such as fluorescent proteins and optogenetics serve this purpose in small, translucent specimens, but are limited by the poor penetration of light into deeper tissues. In contrast, most non-invasive techniques such as ultrasound and magnetic resonance imaging - while based on energy forms that penetrate tissue effectively - are not effectively coupled to cellular function. Our work attempts to bridge this gap by engineering biomolecules with the appropriate physical properties to interact with magnetic fields and sound waves. In this talk, I will describe our recent development of biomolecular reporters and actuators for ultrasound. The reporters are based on gas vesicles - a unique class of gas-filled protein nanostructures from buoyant photosynthetic microbes. These proteins produce nonlinear scattering of sound waves, enabling their detection with ultrasound. I will describe our recent progress in understanding the biophysical and acoustic properties of these biomolecules, engineering their mechanics and targeting at the genetic level, developing methods to enhance their detection in vivo, expressing them heterologously as reporter genes, and turning them into dynamic sensors of intracellular molecular signals. In addition to their applications in imaging, gas vesicles can be used to control cellular location and function by serving as receivers of acoustic radiation force or seeding localized bubble cavitation. Additional remote control is provided by thermal bioswitches - biomolecules that provide switch-like control of gene expression in response to small changes in temperature. This allows us to use focused ultrasound to remote-control engineered cells in vivo. Biography: Mikhail Shapiro is the Max Delbrück Professor of Chemical Engineering and Medical Engineering, an HHMI Investigator, and Director of the Center for Molecular and Cellular Medicine at Caltech. The Shapiro laboratory develops biomolecular technologies allowing cells to be imaged and controlled inside the body using noninvasive methods such as ultrasound. These technologies enable the study of biological function in vivo and the development of cell-based and gene-based diagnostic and therapeutic agents. Mikhail received his PhD in Biological Engineering from MIT and his BSc in Neuroscience from Brown. He conducted post-doctoral research at the University of Chicago and the University of California, Berkeley, where he was a Miller Fellow. Mikhail's awards include the NIH Pioneer Award, the Packard Fellowship, the Pew Scholarship, the Vilcek Prize for Creative Promise, the Sontag Foundation Distinguished Scientist Award, the Mark Foundation Emerging Leader Award, the Camille Dreyfus Teacher-Scholar Award, the Carl Hellmuth Hertz Ultrasonics Award and the Roger Tsien Award for Excellence in Chemical Biology. More information about the Shapiro Lab can be found online at shapirolab.caltech.edu<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fshapirolab…>. ~ BME Host: Krishna Jayant ~ -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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