Volume 6, Issue 3 | Summer 2021

Science Feature

Jacek Zielonka, PhD, discusses his work toward the direct detection of peroxynitrite in cells.

One of the research avenues pursued by my lab is the development and application of redox probes to study cellular oxidants. In collaboration with Dr. Micael Hardy from Aix-Marseille University (France) and Drs. Adam Sikora and Radosław Podsiadły from the Lodz University of Technology (Poland), we are studying the synthesis of probes and the characterization of their chemical reactivity and the products formed. One of the major limitations of commonly used redox probes is their lack of selectivity and propensity to produce signal under the condition of cell death. Over the last decade, we have studied a new class of redox probes based on the oxidation chemistry of boronic acids, unraveling their reaction mechanisms, stoichiometry, and kinetics. 

Upon oxidation, the probe changes its fluorescence from blue to green. Within this paper, we report the reaction kinetics with selected biological oxidants, structurally characterize the products formed, determine the reaction kinetics, and apply the probe to detect peroxynitrite production by activated macrophages. We propose using a combination of real-time monitoring of probe oxidation (using a fluorescence plate reader), confocal microscopy-based oxidant localization, and liquid chromatography/mass spectrometry-based product identification for the most comprehensive characterization of peroxynitrite production in biological systems. This work, carried out in collaboration with Dr. Podsiadły, was mostly performed by Dr. Aleksandra Grzelakowska, who spent two months here in the Department of Biophysics working on the biological aspect of this project. I believe that the value of this paper lies not only in the development of this particular probe, but also in the tone it sets for a comprehensive characterization of newly reported probes, from reaction mechanism and kinetics to identification of the products formed in biological systems.

Alumni Q&A

Learn about the diverse career paths our alumni have pursued after graduating from the Biophysics Graduate Program.

Rachel Bennett, PhD, Armstrong Teasdale LLP

Q: Since obtaining your PhD here in Biophysics in 2001, share with us your career progression to your current role as a patent/intellectual property attorney.

A: After graduating from MCW, I was an engineer at GE and a faculty member at Johns Hopkins. I became interested in law and decided to go to law school. I chose  to focus on patent law because of my technical background and interest in science, and for opportunities to work with scientists and engineers again. My work experience in technical areas together with my technical background help greatly in my career progression as a patent attorney, especially in understanding the client’s needs and technical issues and in advocating for the client’s interests.

Q: Tell us about your major responsibilities, and what projects, committee service, or other activities you might work on in a typical week.

A: Prepare and prosecute patent applications for large and mid-sized clients, manage client patent portfolios, and supervise a team of attorneys and patent professionals for specific clients.

Q: What aspect of your current job do you find most rewarding, and why?

A: Working with scientists and engineers because I like science and technology and enjoy working with scientists and engineers on the latest technology developments.

Q: What advice do you wish you had been given as a graduate student?

A: Set a long-term career goal, and not just focus on finding a job after graduation. To that end, looking back, I should have taken classes that are interesting, such as chemistry and medical classes, instead of taking practical classes, such as computer classes.

Q: What would you look for if you were in the position to hire a recent graduate from MCW?

A: Interest in patent law.

Seminar Series

Our Fall 2021 Biophysics Graduate Seminar Series takes place virtually most Fridays throughout the semester, from 9:30‐10:30 a.m. For details on joining these virtual events, please visit the
Biophysics Events page.

Department News

Welcome

• Julian Grosskopf (MSTP student, Lerch lab)
• Steven Traeger (research technologist, Vasquez Vivar lab) - starts 8/9/2021

Farewell

• Jillian Ward (research technologist, Vasquez Vivar lab)

Congratulations

• Gang Cheng was promoted to Assistant Professor in Biophysics.
• Gang Cheng & Balaraman Kalyanaraman published a paper in iScience.
• Gang Cheng, Jacek Zielonka, & Balaraman Kalyanaraman published a paper in iScience.
• James Hyde, Bob Strangeway, & Jason Sidabras published a paper in Applied Magnetic Resonance, as part of the collection Harold M. Swartz: On the Occasion of His 85th Birthday.
• Balaraman Kalyanaraman published a paper in RSC Chemical Biology and a paper in Journal of Biomedical Materials Research - Part B Applied Biomaterials. 
• Shi-Jiang Li published a paper in European Neuropsychopharmacology.
• Karol Subczynski published a paper in Antioxidants.
• Tim Thelaner was promoted to Engineer II.
• Jeannette Vasquez Vivar published a paper in Frontiers in Cell Developmental Biology.
• Jacek Zielonka published a paper in Frontiers in Pharmacology.
• Jacek Zielonka & Balaraman Kalyanaraman published a protocol in the book Mitochondrial Medicine, which is part of the Methods in Molecular Biology book series.

New Biophysics EPR Development Dry Lab

MFRC 2053 was originally built as a state-of-the-art computer room, complete with carpeted walls. It shifted from a computer room to a student cubicle area as computers became more prevalent and even high-powered computers fit on individual desks. Most recently, it housed Tim Thelaner’s office and workshop as well as storage for extra EPR equipment and parts. A remodel (before, during, and after photos below) began in January 2021 and was completed April 2021. The carpet was removed and the room was converted into a modern, fully functional EPR Development Dry Lab. It now has tile floors, painted walls, and lab benches and fits in with the style of other Biophysics wet labs. The room houses a Bruker X-band E600 spectrometer with space to develop novel and enabling EPR technologies. For example, it currently is being used to carry out the aims of an NIH Focused Technology Research and Development R01 (MPIs: Klug/Lerch) to develop two transformative technologies for a variety of basic science and clinical research, a critical first step in driving the National Biomedical EPR Center at MCW into a new era of enabling technology development for the broad scientific community. As the technologies become mainstream, they will transition out of the development lab, and new technologies will be designed and investigated.

Recipe

Soba Salad with Lemon-Miso Vinaigrette

(Yield: serves four. Time: 30 minutes.)

Ingredients

• 2 1⁄2 oz small radicchio leaves
• 2 1⁄2 oz small red leaf lettuce leaves
• 24 small shiso or basil leaves
• 16 small grape tomatoes
• 4 small dill fronds
• 2 small carrots, thinly sliced crosswise
• 1 Persian cucumber, thinly sliced crosswise
• 1 red finger chile
• 1⁄3 cup extra-virgin olive oil
• 3 tbsp fresh lemon juice
• 1 1⁄2 tbsp rice vinegar
• 1 1⁄2 tbsp soy sauce
• 1 tbsp white miso
• 2 tsp toasted sesame oil
• 1⁄2 tsp sugar
• One 2-inch piece ginger, peeled
• Kosher salt and freshly ground black pepper
• 1 tbsp toasted sesame seeds
• 8 oz fresh or dried soba noodles

Instructions

1. In a large bowl, combine radicchio and lettuce leaves with the shiso (or basil), tomatoes, dill, carrots, and cucumber. Using a sharp knife, begin thinly slicing the chile from the tip. When you reach the seeds, stop slicing and discard, or save the remaining chile for another use. Add the sliced chile to the vegetables in the bowl and toss to combine.
2. In a small bowl, whisk the olive oil with the lemon juice, rice vinegar, soy sauce, miso, sesame oil, and sugar. Using a Microplane positioned over a fine sieve set in a bowl, grate the ginger into the sieve, then press on the solids to extract as much juice as possible into the bowl. Add 1 teaspoon of the ginger juice to the bowl of dressing, reserving the rest for another use. Season the dressing with salt and black pepper, and whisk until emulsified. Divide the dressing among four small ramekins and sprinkle each with some of the sesame seeds.
3. In a large pot of boiling water, cook the soba noodles until al dente, about 3 minutes for fresh noodles or 4–6 minutes for dried noodles. Drain into a colander and rinse under cold running water until the water runs clear. Divide the noodles among four serving plates. Divide the vegetables over the noodles, sprinkle with the remaining sesame seeds, and serve immediately with the dressing on the side.

Recipe obtained from Saveur.

Biophysics News is a quarterly MCW departmental newsletter aimed at enhancing departmental engagement through information and good news sharing. Do you have information you’d like to share–news, a photo, a recipe? Send it to Lydia.

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