BME MONDAY ROUNDTABLE

December 5, 2022

 

HEADS NOTE

This week we have a BME Faculty Coffee Chat for Grad Students with Deva Chan that I’m sure will be engaging and informative.  I’m also excited to welcome Dr. Henry Lam for our Distinguished Seminar Series.  Henry Lam is Associate Head and Professor in Chemical and Biological Engineering from HKUST in Hong Kong. 

 

UPCOMING IMPORTANT DATES

 

Week of December 5

Tues., Dec. 6: MJIS Passenger Elevator DOWN from 7:00 a.m. – until 1:00 p.m. for required maintenance/repair. Analog stairwells and freight elevator will remain fully functional and available.

Tues., Dec. 6: BME PhD Preliminary Exam Announcement for Aditya Shanghavi (A. Sereno and B. Duerstock, co-advisors), 1:30 p.m. in MJIS 2001 and via Zoom. Title of presentation:  A Study of Tremor in Parkinson’s Disease Using Signals From Wrist-Worn IMU Sensors

Wed., Dec. 7: BME Distinguished Seminar Series, 9:30 a.m., MJIS 1001 and via Zoom. Henry H.N. Lam, Associate Head and Professor, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology will present “Proteomics and its applications in antibiotic tolerance research.”

Wed., Dec. 7: Frontiers in Biophysics Seminar, 1:30 p.m., MJIS 1001 and via Zoom. Cheng Zhu, Georgia Institute of Technology will present “Mechanosensing through immunoreceptors.” The seminar series is co-sponsored by Structural and Computational Biology & Biophysics in the Department of Biological Sciences and the NIGMS-funded Molecular Biophysics Training Program in partnership with the Departments of Biomedical Engineering, Biochemistry, Physics and Astronomy, Chemistry, and Medicinal Chemistry and Molecular Pharmacology and the following Institutes: PI4D, PCCR, and PIDD. Zoom link: https://purdue-edu.zoom.us/meeting/register/tJUtd-2rrTlqEt28s1D20iZPi-9RRDGj76V5

Thurs., Dec. 8: BME Faculty Coffee Chats for Grad Students, 2:00-3:00 p.m., MJIS 2041. Faculty host: Deva Chan. Potential discussion topics: AMA work-life, teaching & diversity statements, time management

 

Holiday Updates

Purdue University will be closed beginning Friday, December 23rd and will reopen on Tuesday, January 3rd. This means all offices, labs and buildings will be closed. This translates to no mail or package delivery, so (hopefully) you haven’t ordered anything perishable that will languish until your return on Tuesday, January 3rd.. We will also be closing and locking the student club room (MJIS 1051) over this time. Any food left in the refrigerator as of 5:00 p.m. on Thursday, December 22nd will be put in the trash.

 

REMINDER:  users of the Club Room on the 1st floor ARE RESPONSIBLE FOR CLEANING UP YOUR OWN MESSES. Lately, there has been an exponential increase in splattered food not being wiped out of the microwave, and other food debris left on the table surfaces, which has led to an influx of mice (and mice droppings) in this room. If you use the club room, YOU are responsible for cleaning up your mess. We don’t want to be forced to shut this area down, but if it continues to be left dirty, with unlabeled food in the refrigerator, we may have to take more drastic measures for everyone’s health safety.

 

Researchers also need to make note that for the Winter Recess – The ordering deadline for research materials (animals, chemicals, drugs, etc.) will be noon on Wednesday, December 14, 2022, for delivery dates of December 19  – 22, 2022.  There will be no deliveries of any kind on campus from December 22, 2022 through January 3, 2023. This same schedule will be followed for Drug Distribution Center orders. Please plan accordingly.

 

Upcoming important deadlines and info.

Mon., Dec. 12: BME PhD Preliminary Exam Announcement for Li Fang (F. Huang, advisor), 2:30 p.m., MJIS 2001 and via Zoom. Title: Molecular localization of single molecule switching sequences with deep learning.

Thurs., Dec. 15 The BME Senior Design Expo will be from 3:30 - 5:30pm in MJIS 1097, 1001, and Atrium. There will be 24 projects presented followed by awards ceremony. Stay tuned for additional details.

Fri., Dec. 23 through Mon., Jan. 2: Winter Recess. No classes, all university offices and buildings closed. Purdue will reopen Tuesday, January 3.

 

PURDUE ADVERSE WINTER WEATHER POLICY

If adverse weather conditions necessitate that a wind chill, snow or ice emergency be declared for the West Lafayette campus, special procedures pertaining to classes, operations, parking, pay and/or attendance will become effective. Jay Wasson, vice president for physical facilities and chief public safety officer, describes procedures for adverse winter weather in this memo.

 

Committee Updates

 

IUPUI-Purdue Integration Update

 

As you have seen in the Provost updates, the IUPUI-Purdue integration continues to gain momentum. We were happy that our work in BME is being highlighted. Central to all discussions and planning are our core values of respect, belonging, and excellence. Our particular focus in academic programs is providing a rigorous and inclusive training environment for our students; with a culture of respect and belonging such that each student attains their highest potential of excellence. The joint IUPUI-Purdue team share these values and a strong collaborative spirit that led to many positive and productive discussions thus far. The Weldon School meet with IUPUI BME colleagues for a day-long workshop on Nov 4.day.Undergraduate programs integration team focused on programmatic learning outcomes and identifying similarities and differences among the two curriculum. The graduate programs team also focused at the programmatic level on which degrees to offer on the two campuses and on impact on students already in the IUPUI programs.  Attached are the notes from the meeting with many, many more details. The UG and Grad integration teams are continuing to meet at least every other week as we work toward a detailed teach-out plan that is due on Jan 31.  

 

Academic Programs Update

 

Please make note of the grading deadline for all research students (grad & undergrad) and your Fall classes: Grade entry began at 8 a.m. December 2 and ends at 5 p.m. December 20. Faculty at West Lafayette not meeting the submission deadline for their reporting window will be required to submit via the Grade change workflow found in their myPurdue portal.

 

Undergraduate Programs Update

 

The BME Senior Design Expo will be Thursday, December 15 from 3:30 - 5:30pm in MJIS 1097, 1001 and Atrium. There will be 24 projects presented followed by awards ceremony. Stay tuned for additional details.

 

Graduate Office Update

 

It is officially Three Minute Thesis (3MT®) competition season! To increase academic representation in our 3MT® competition, we are asking that West Lafayette graduate faculty members nominate talented graduate student(s) to represent their academic units. This is an exciting year to participate, as we have increased the cash prizes, which include $5,000 for first place, $3,000 for second place, and $2,000 for the People’s Choice Award winner. Nominees must be current Purdue graduate students studying at the West Lafayette campus. Each nominee will be contacted by Graduate School staff and encouraged to register for the competition. Nominations are not required for students to submit a draft video; they are simply intended to help the Graduate School identify and encouraged talented students to participate. The link to the nomination form below, as well as some additional information about the Graduate School’s 3MT® competition. Please email me, Allison Loy (Loy2@purdue.edu), with any questions!

Virtual 3MT® 2023 Nomination Form:

https://purdue.ca1.qualtrics.com/jfe/form/SV_204r4KOtt2fUIbI

What is 3MT®?

Three Minute Thesis (3MT®) is a research communication competition that helps graduate students develop academic, presentation, and research communication skills so that they can effectively explain their research to a non-specialist audience. During each competition, graduate students will have three minutes to present a compelling discussion on their research topic, including its significance and relevance, to the general public. This is a fast-paced competition where the top 10 finalists compete by summarizing their two to three-plus years of research in only three minutes with only one slide. The cash awards for this year’s competition have been increased substantially, including $5,000 for first place, $3,000 for second place, and $2,000 for the People’s Choice Award winner. The first-place winner will also be invited to compete in the Midwestern Association of Graduate School’s (MAGS) annual 3MT® competition.

3MT® Timeline

Learn more about the Purdue University Graduate School’s 3MT® competition here: https://www.purdue.edu/gradschool/professional-development/competitions/3mt/index.php

 

 

Graduate Admissions Update

 

Fall 2022 (Fall 2023 Admit Term) BME Graduate Admissions

DateDATE

Activity

Now

Research Areas create a plan and potentially agree on dates to meet ranking deadlines.

December 19th—All Fellowship Nominations Due

Dec 19

DUE: All Fellowship Nominations and Additional Invite Lists

Dec 20

Grad office to process admission for all fellowship-nominated applicants to the Purdue Graduate School and any additional applicants you would like to admit from the open house invitation list.

Dec 20

Tammy to send invitations to invited students to participate in our virtual open house.

Jan 3

Deadline for students to respond to Open House RSVP (hotels released today).

Jan 26

Agendas for all invited students due from faculty to Tammy and sent to student.

Feb 2-4

Weldon School Visitation Days (Hybrid)

Feb 8

Last chance for Research Areas / Faculty to remove students from fellowship consideration

Feb 10

Fellowship offers announced and complete rankings list made available to BME faculty; BME Graduate Office will notify students by email (offer letters distributed as soon as signed by BME Head and COE Dean)

Mar 10

DUE: All Master’s students to be decisioned as either admit, deny or hold

Mar 31

Due: All PhD students to be decisioned as either admit, deny or hold

April 15

Graduate applicant acceptance deadline

 

 

Resources, attachments, further information

 

BME PhD Preliminary Exam Announcement for Aditya Shanghavi (A. Sereno and B. Duerstock, co-advisors), Tues., Dec. 6, 1:30 p.m. in MJIS 2001 and via Zoom. Title of presentation:  A Study of Tremor in Parkinson’s Disease Using Signals From Wrist-Worn IMU Sensors.

Advisory Committee: Anne B. Sereno, Co-Chair; Bradley S. Duerstock, Co-Chair; Craig J. Goergen; Satyajit S. Ambike

Abstract: Parkinson’s Disease (PD) is the second most common neurodegenerative disorder with resting tremor (RT) being its most common motor symptom. The literature has revealed that the need for lengthy, clinic-based subjective evaluation by trained neurologists of treatment effects in PD creates challenges for monitoring the progression of the disease and titrating optimal therapeutic therapies. Preliminary studies have shown that features of a power spectral density (PSD) analysis of wrist velocity and acceleration can be used as objective, reliable, and sensitive detectors of RT. Replacing the neurologist’s judgement on the progression of the disease is not feasible, yet some aspects of tracking the disorder and treatment may profit from more frequent remote sensor measurements. There is an opportunity to improve patient-care by introducing non-invasive, sensor-based objective measurements of RT using wrist movements that can aid the neurologist with the MS- UPDRS evaluation in the diagnostic process. Success in objectively quantifying RT with such a method would allow physicians to more frequently and remotely monitor patients to change the treatment plan as needed to reduce the severity of harmful side effects of PD medication.

Virtual Link: https://purdue-edu.zoom.us/j/4520252995

 

BME Distinguished Seminar Series, Wed., Dec. 7, 9:30 a.m., MJIS 1001 and via Zoom. Henry H.N. Lam, Associate Head and Professor, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology will present “Proteomics and its applications in antibiotic tolerance research” on Wednesday, December 7, at 9:30 a.m. in MJIS 1001 and via Zoom.

Abstract: Proteomics has witnessed rapid technological advances in the past decade and a half. Despite its obvious promise, proteomics still poses a considerable barrier of entry for the average life scientist, and the adoption of this powerful technology across different areas has been uneven. In this talk, I will present two rather distinct stories that have the same underlying goal, namely, to suggest a roadmap for proteomics to become truly ubiquitous in all life science research. The first is in computational method development. Proteomics is a prototypical "Big Data" field, but it may be surprising to some that despite the rapid accumulation of LC-MS/MS data in public repositories, for the most part all these data have not been meaningfully reused. This unfortunate situation can be traced to how we are used to analyze data in proteomics in isolation without prior knowledge, and how we store and organize the data. I will discuss our ongoing efforts to change this by organizing proteomics data by spectral similarity, and our vision for a simpler and more user-friendly way to analyze proteomics data.  The second is in the application of proteomics to an important problem in microbiology -- the fascinating but annoying ability of bacterial pathogens to survive antibiotic treatment.  Antibiotic tolerance, defined as the ability of a bacterial population to outlive lethal doses of antibiotics in a non-proliferating and non-specific way, is distinct from, and less understood, than antibiotic resistance. I will discuss our recent work in applying proteomics and adaptive laboratory evolution to map the "tolerome" (the set of genes and proteins that affect tolerance) in two organisms, Escherichia coli and Staphylococcus aureus, and some hard-learned lessons of how to reduce distraction when dealing with hundreds of differentially expressed proteins. In doing so, I hope to show an example of what proteomics can and cannot do, and how it enables one to make progress towards addressing open-ended biological questions. 

Bio: Prof. Henry Lam is currently Professor in the Department of Chemical and Biological Engineering in the Hong Kong University of Science and Technology (HKUST). He obtained his Ph. D. (Chemical Engineering) from Massachusetts Institute of Technology in 2005, and received postdoctoral training in the Aebersold group at the Institute for Systems Biology (ISB) in Seattle, Washington. At ISB, he participated in developing data analysis workflows in the then-nascent field of proteomics, some of which have become standard practice today. He has a longstanding interest in making the powerful technology of proteomics more reliable and more accessible to life scientists. Current research in his group focuses on method development in proteomics and metabolomics, particularly in algorithm design and data organization, and applications of proteomics in biological research, particularly in microbiology. 

~BME Host: Young Kim~

NOTE:Students registered for the seminar are expected to attend in-person. 

Zoom link: https://purdue-edu.zoom.us/j/7731446991?pwd=RHdkZTVnRkxTM3J3dnRvY1VLWTlYUT09

 

BME PhD Preliminary Exam Announcement for Li Fang (F. Huang, advisor), Mon., Dec. 12, 2:30 p.m., MJIS 2001 and via Zoom. Title: Molecular localization of single molecule switching sequences with deep learning. Committee members: Dr. Fang Huang, Chair; Dr. Leopold N. Green; Dr. ‪Young L. Kim; Dr. Chongli Yuan

Abstract: Single molecule localization microscopy (SMLM) has become an essential tool in imaging nanoscale biological structures. It breaks the diffraction limit by utilizing photo-switchable or photo-convertible fluorophores to obtain isolated single molecule emission patterns (i.e. PSFs) and subsequently localize the molecule’s position with a precision down to ~ 25 to 80 nm laterally-axially. However, standard SMLM algorithms require sparse activation to minimize emission pattern overlapping, which limits imaging speed and temporal resolution and hinders its application in dynamic live cell imaging. Some multi-emitter fitting algorithms have been developed to analyze higher density data and some methods have shown improved localization precision when utilizing multiple frames. But these methods require an accurate PSF model and prior knowledge of photo-switching behavior and fail to fully extract the information in the sequence data. Here, we propose to develop a high-density single molecule localization algorithm through molecule blinking sequence analysis with deep learning to achieve high localization precision approaching the theoretical limit at high density in three dimensions. We aim to apply the algorithm to resolve nanoscale intracellular structures and fast dynamic processes in live cells with high temporal and spatial resolution.

Virtual link:

https://purdue-edu.zoom.us/j/99210793060?pwd=WnlHbVlSUlNGWE1KaGN4QWRCS0lEUT09

Meeting ID: 992 1079 3060

Passcode: 158594

 

Attachments

 

Nov 4 Academic Programs Integration Workshop – meeting notes_Final