June 2024 - Bmegradstudents-list

BME Master's Defense Announcement for Ashley Kayabasi (M. Verma, advisor)
by May, Sandra M 28 Jun '24

28 Jun '24

BME Master's Defense Announcement for Ashley Kayabasi (M. Verma, advisor) Everyone is invited to attend the public presentation beginning at 11:00am. Title: Devices for On-Field Quantification of Bacteroidales for Risk Assessment in Fresh Produce Operations Exam day details: Friday, July 12th at 11am in ABE 1164 or through Zoom (https://purdue-edu.zoom.us/j/92130331747<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>) Committee members: Dr. Mohit Verma (chair), Dr. Leopold Green, and Dr. Haley Oliver Abstract: The necessity for on-farm, point-of-need (PON) nucleic acid amplification tests (NAATs) arises from the prolonged turnaround times and high costs associated with traditional laboratory equipment. This thesis aims to address these challenges by developing devices and a user-interface application designed for the efficient, accurate, and rapid detection of Bacteroidales as an indicator of fecal contamination on fresh produce farms. Initially, I collaborated with others to engineer a field-applicable heater-imager platform compatible with paper-based biosensors using loop-mediated isothermal amplification (LAMP). This compact, energy-efficient device is user-friendly and capable of real-time heat generation. Subsequently, I led the fabrication of a microfluidic sample processing tool suitable for field applications. This tool enables high-throughput fluid delivery to paper-based biosensors without necessitating a laboratory or extensive training. Both devices underwent rigorous testing through a series of in-lab or on-field experiments to either validate their efficacy in detecting fecal contamination on fresh produce farms or their ability to simplify experimental procedures with an on-farm application. A crucial aspect of device development is ensuring that results are easily interpretable by users. To this end, I developed a Python-based image analysis codebase to quantify the percent positivity of samples for fecal contamination. This program also generates an equation to quantify the concentration of field samples, utilizing calculus-based mathematics combined with image analysis factors. Additionally, I developed a graphical user interface in Python that defines a prediction model for the concentration of Bacteroidales based on local weather patterns and conditions. This thesis encompasses the development of hardware devices for on-field quantification and the creation of a user-interface application for assessing the risk of fecal contamination on fresh produce farms. The integration of these devices with a user-interface application facilitates the acquisition of rapid results directly on the farm. This capability enables the interpretation of results and the development of effective strategies to ensure safety in fresh produce operations.

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IBSC-BME PhD Defense Announcement for Paula Ivey (Tamara Kinzer-Ursem and Kevin Webb, co-advisors)
by May, Sandra M 28 Jun '24

28 Jun '24

IBSC-BME PhD Defense Announcement for Paula Ivey (Tamara Kinzer-Ursem and Kevin Webb, co-advisors) Everyone is invited to attend the public presentation beginning at 10:30 am. Title: Investigating Protein Aggregation in Neurodegenerative Diseases Using Fluorescence Lifetime Imaging Microscopy Date: July 9th Time: 10:30 am Location: BHEE 317 Committee members: Prof. Kevin Webb (Co-chair), Prof. Tamara Kinzer-Ursem (Co-chair), Prof. Jean-Christophe Rochet, Prof. Krishna Jayant Abstract: Alpha-synuclein protein aggregation, involving the recruitment of native monomeric protein by fibrillar seeds, has been proposed as the event that precipitates Parkinson's disease pathology. However, the specific molecular processes underlying this aggregation are not fully understood, mirroring the limitations seen in understanding the etiology of other prion-like neurodegenerative diseases. There are proposed mechanisms connecting alpha-synuclein aggregation to endocytic processes involving the escape and retention of fibrillar seeds. Additionally, intracellular protein-membrane interactions may also play a role. However, effective methods to probe the evolution of aggregation states with sufficient sensitivity in the context of these cellular processes are lacking. We used a custom-built fluorescence lifetime imaging microscope to monitor the evolution of seeded aggregation in primary neurons in the context of endocytic processes that have not been well explored. This was enabled by measuring self-quenching-induced fluorescence lifetime changes of alpha-synuclein-fluorophore fusion proteins, providing a sensitive aggregate detection method. Our results indicate that both escape and retention of fibrillar seeds from endocytic compartments are seeding pathways for aggregation. In addition, we developed a novel imaging scheme using fluorescence lifetime measurements of tethered Förster resonance energy transfer (FRET) reporters to probe membrane-induced alpha-synuclein aggregation. Employing this method in neurons enabled us to decipher which intracellular membrane surfaces likely play a role in alpha-synuclein aggregation. Fluorescence lifetime imaging enabled insights into the underlying mechanisms of alpha-synuclein aggregation, which has broader applications to other prion-like neurodegenerative diseases. These insights further understanding of neurodegenerative disease etiology and can inform more effective treatments.

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[Bmeroundtable-list] TODAY: Special BME Research Seminar - Fri., June 28, 3:30 p.m., MJIS 2001
by Gelfand, Johanna K 28 Jun '24

28 Jun '24

[cid:image001.jpg@01DAC8A2.E3CC11B0] SPECIAL BME RESEARCH SEMINAR Friday, June 28, 2024 3:30 - 4:30 pm, MJIS 2001 "Supercontinuum intrinsic fluorescence imaging microscopy" [cid:image002.jpg@01DAC8A2.E3CC11B0] Geng Wang Vadim Backman Lab, Biomedical Engineering, Northwestern University Abstract: Multiphoton fluorescence microscopy is a powerful tool for revealing complex biological systems with high contrast, minimal out-of-focus bleaching, and deep penetration. However, clinical applications face challenges such as the need for stable, tunable laser sources, comprehensive biological information, phototoxicity, and the development of universal quality control tools. Here, we developed supercontinuum intrinsic fluorescence imaging (SCIFI) microscopy. This technique enables co-registered label-free 4-photon (tryptophan), 3-photon (NAD(P)H), 2-photon (FAD, porphyrin/lipofuscin), second harmonic generation (collagen), third harmonic generation (optical heterogeneity), and fluorescence lifetime imaging with single-shot, single-band excitation near 1110 nm. Our laser source features a tunable wavelength range of 950-1150 nm, pulse repetition rates of 1-10 MHz, and pulse widths of 40-400 fs, maintaining stability over 2000 hours. We explored the mechanisms of phototoxicity in nonlinear imaging, identified safe imaging parameters, and developed a universal tool for objective imaging performance comparison. SCIFI maximizes the information obtained from fluorescence microscopy while minimizing harm, paving the way for clinical translation. ~ BME Host: Fang Huang ~ -- 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 Chun-Yi Chang (Chien-Chi Lin and Luis Solorio, advisors)
by May, Sandra M 27 Jun '24

27 Jun '24

BME PhD Defense Announcement for Chun-Yi Chang (Chien-Chi Lin and Luis Solorio, advisors) Everyone is invited to attend the public presentation beginning at 10:00 AM. Title: DEVELOPMENT OF HYDROGEL-BASED MODELS TO INVESTIGATE PANCREATIC CANCER CELL AND CANCER-ASSOCIATED FIBROBLAST RESPONSE TO THE STIFFNESS CUE IN PANCREATIC DUCTAL ADENOCARCINOMA TUMOR MICROENVIRONMENT Date: July 16, 2024 Time: 10:00 AM Location: In-person (SL220A @ Purdue Indy) and virtual via Zoom (https://purdue-edu.zoom.us/j/7696799519?omn=91352110780<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>) Meeting ID: 769 679 9519 Committee members: Dr. Chien-Chi Lin (Chair) Dr. Luis Solorio Dr. Hiroki Yokota Dr. Sungsoo Na Dr. Taimoor H. Qazi Abstract: Pancreatic ductal adenocarcinoma (PDAC), the most common type of pancreatic cancer, is a highly metastatic cancer that has a low survival rate. It is histologically characterized by a thick desmoplastic stroma. Counterintuitively, pancreatic cancer cells can still manage to survive in such a restrictive environment and even metastasize to distant organs. Over the years, efforts have been made to find out the mechanisms underlying these perplexing behaviors. However, questions about the role of ECM accumulation and enhanced stiffness in pancreatic cancer cell dissemination remained unanswered. In this dissertation, we aim to advance the material design for tumor modeling, and propose an explanation for the malignant cell behavior in the PDAC tumor microenvironment (TME). This is achieved through the use of hydrogel-based tumor models that recapitulate the elevated stiffness of the tumor tissue. Specifically, hydrogel stiffness was tuned to mimic the PDAC TME to understand how pancreatic cancer cells and cancer-associated fibroblasts (CAFs) respond to various substrate stiffnesses temporally. Next, we employ bio-orthogonal click chemistries to create hydrogels with on-demand stiffening capabilities, as well as hyaluronic acid deposition in the hydrogel, to investigate the effect of dynamic change in matrix stiffness and composition on PDAC cells and CAFs. Lastly, by leveraging thiol-norbornene, aldehyde-hydrazide, and tetrazine-norbornene click chemistries, we created a microporous hydrogel system with a conformation that combines both the advantage of 3D cell culture and the non-restricting nature of 2D cell culture. Additionally, the system allows the application of modularized user-defined factors, including, but not limited to stiffness and hyaluronic acid (HA) deposition to the system. Stiff gel in 2D facilitated cell spreading of Pa03C in the presence of CAF. Despite being more restrictive on cell spreading, stiff gelatin gel in 3D induced cytokines that promote matrix remodeling and spreading cell morphology can be restored by stiffening with HA. Overall, this dissertation demonstrated that ECM component (i.e., HA), culture dimensionality, and cell-cell interaction play a huge role in cell behavior, and these factors may interact with each other and result in synergistic effects.

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[Bmeroundtable-list] Special BME Research Seminar - Fri., June 27, 3:30 p.m., MJIS 2001
by Gelfand, Johanna K 27 Jun '24

27 Jun '24

[cid:image001.jpg@01DAC8A2.E3CC11B0] SPECIAL BME RESEARCH SEMINAR Friday, June 27, 2024 3:30 - 4:30 pm, MJIS 2001 "Supercontinuum intrinsic fluorescence imaging microscopy" [cid:image002.jpg@01DAC8A2.E3CC11B0] Geng Wang Vadim Backman Lab, Biomedical Engineering, Northwestern University Abstract: Multiphoton fluorescence microscopy is a powerful tool for revealing complex biological systems with high contrast, minimal out-of-focus bleaching, and deep penetration. However, clinical applications face challenges such as the need for stable, tunable laser sources, comprehensive biological information, phototoxicity, and the development of universal quality control tools. Here, we developed supercontinuum intrinsic fluorescence imaging (SCIFI) microscopy. This technique enables co-registered label-free 4-photon (tryptophan), 3-photon (NAD(P)H), 2-photon (FAD, porphyrin/lipofuscin), second harmonic generation (collagen), third harmonic generation (optical heterogeneity), and fluorescence lifetime imaging with single-shot, single-band excitation near 1110 nm. Our laser source features a tunable wavelength range of 950-1150 nm, pulse repetition rates of 1-10 MHz, and pulse widths of 40-400 fs, maintaining stability over 2000 hours. We explored the mechanisms of phototoxicity in nonlinear imaging, identified safe imaging parameters, and developed a universal tool for objective imaging performance comparison. SCIFI maximizes the information obtained from fluorescence microscopy while minimizing harm, paving the way for clinical translation. ~ BME Host: Fang Huang ~ -- 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] PLEASE return the cart to the dock
by Gelfand, Johanna K 25 Jun '24

25 Jun '24

Whoever borrowed a cart from the MJIS dock last week (Wednesday evening/Thursday morning) needs to return it ASAP. Otherwise, we will have to contact the police department to check the video feed to see who has it. We don't mind you using the cart within MJIS, but it is never to leave the building, and should not be missing for over 24 hours. There are others who need it. It is clearly labeled "MJIS dock". Thank you for your cooperation and the quick return of our missing cart. -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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FW: Postdoc Recruitment Opportunity in Augustin Luna's Lab at NIH
by Gelfand, Johanna K 25 Jun '24

25 Jun '24

I hope this message finds you well. Augustin Luna from the NIH is currently recruiting postdocs for his lab. If you know any potential candidates who might be interested, please forward this email to them. Thank you, Norma Perez ________________________________ From: Luna, Augustin (NIH/NLM/NCBI) [E] <augustin.luna(a)nih.gov<mailto:augustin.luna@nih.gov>> Sent: Monday, June 24, 2024 9:07 AM To: Perez, Norma Citlalcue <perezrosasn(a)hhmi.org<mailto:perezrosasn@hhmi.org>> Subject: Seeking Computational Biology Postdocs for AI/ML in Cancer Precision Medicine External Email: Use Caution Norma, I am recruiting several postdocs to my group at the NIH National Library of Medicine (NLM) and National Cancer Institute (NCI). Work in the group uses machine learning and artificial intelligence for cancer precision medicine. Accepted candidates will be working in a multi-disciplinary team that spans basic and translational science to advance 1) network-based algorithms to understand molecular mechanisms of drug response and drug resistance to achieve precision medicine, and/or 2) applications of artificial intelligence and large-language models as a tool for data analysis, integration, and interpretation. Please see the links below for details, requirements, and information on how to apply: * Pharmacogenomics/ML-Related: https://urldefense.com/v3/__https://www.training.nih.gov/jobs/pdf-ccb-03012…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens…> * Knowledge Retrieval/AI/LLM-Related: https://urldefense.com/v3/__https://www.training.nih.gov/jobs/pdf-dscr-0430…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens…> PS: Please let me know if there of any relevant mailing lists for future job posts for the institutes you are affiliated with. Thank you, Augustin Luna, PhD Investigator Computational Biology Branch, National Library of Medicine & Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health Faculty Page: NCI: https://urldefense.com/v3/__https://ccr.cancer.gov/staff-directory/augustin…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens…> , NLM: https://urldefense.com/v3/__https://www.nlm.nih.gov/research/researchstaff/…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens…>

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[Bmeroundtable-list] New Team Member | Senior Academic Advisor- Darcy Allen
by Render, Darshini N 23 Jun '24

23 Jun '24

Dear Colleagues, I am pleased to announce that we have recruited a new member to our undergraduate education team. Effective July 1, Darcy Allen will join the Weldon School as our Senior Academic Advisor. Darcy, a Purdue alumna, brings extensive experience in student affairs from her time at Ivy Tech Community College and Purdue University. As part of her orientation, Darcy will meet with you to learn more about your roles at the Weldon School. Please join me in welcoming Darcy Allen to our team. Best regards, Darshini Render Associate Director Weldon School of Biomedical Engineering Purdue University -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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BMES Annual Meeting 2024: Student Volunteer Program Application Open!
by May, Sandra M 21 Jun '24

21 Jun '24

For those planning to attend the BMES Annual Meeting this year, you might be interested in the student volunteer opportunity below. ________________________________ ---- External Email: Use caution with attachments, links, or sharing data --- Now accepting applications from students who can help in Baltimore [upscaled-2x-Student_Volunteers_EmailHeader]<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fd5h5zm04.…> Now Accepting: Student Volunteer Applications Volunteers play an extremely important role in the BMES Annual Meeting<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fd5h5zm04.…>'s overall success. With your help, we can ensure our attendees have a great experience at this year's meeting in Baltimore that will leave them excited about returning next year. As a thank you for your service, student volunteers will pay a discounted registration of $150.00 for the full conference. This discounted registration is available to students who commit to work at least 8-10 hours at the meeting. We will do our best to accommodate your volunteer preferences. We have limited volunteer slots, so the more flexible you are, the higher the possibility of being chosen as a BMES 2024 student volunteer. Learn More <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fd5h5zm04.…> APPLICATION DEADLINE: Friday, July 19 [Facebook]<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fd5h5zm04.…> [LinkedIn]<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fd5h5zm04.…> [X]<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fd5h5zm04.…> [Instagram]<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fd5h5zm04.…> BMES, 8201 Corporate Drive, Suite 1125, Landover, MD 20785 Unsubscribe<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhs-448934…> Manage preferences<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhs-448934…>

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[Bmeroundtable-list] In case you missed it - Norvin Bruns
by Gelfand, Johanna K 21 Jun '24

21 Jun '24

Congratulations to our very own Norvin Bruns on this well-deserved honor! Two honored by CSSAC for excellence in support, service [cid:image001.jpg@01DAC3BD.277BF000] https://www.purdue.edu/newsroom/purduetoday/releases/2024/Q2/two-honored-by… -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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