News and Announcements
Bryan Ryder, mentored by Dr. Lukasz Joachimiak, successfully defended his dissertation titled “Architecture and Function of the J-Domain Chaperone DNAJB8”. Bryan combined a cross-linking mass spectrometry-based approach with other multi-disciplinary methods in biophysics, biochemistry, and cell biology to study the disordered J-domain protein chaperone DNAJB8. As a result, Bryan’s research uncovered a Hsp70 auto-inhibitory function in the DNAJB8 C-terminal domain Nat. Commun. (2020), a minimal phenylalanine-driven motif that drives DNAJB8 self-assembly, and seed-competent tau protein as a substrate of DNAJB8. Following graduation, Bryan will be starting a postdoctoral position in the lab of Dr. Jason Gestwicki at UCSF, studying the mechanisms of proteosome activation and its consequences for proteome remodeling.
The Molecular Biophysics Graduate Program held its annual symposium on May 6 after a two year break. We had a lovely day at the Dallas Arboretum with 5 student talks, 5 postdoc talks, a lively poster session and an exceptional keynote talk by Dr. Janet Iwasa of University of Utah on “Animating Molecular Machines.” Congratulations to Jenny Jiou (Lab of Dr. Yuh Min Chook) and Michael Cotten (Lab of Dr. Michael Rosen) for winning best talk awards, and Rupam Ghosh (Lab of Dr. Kendra Frederick) and newly admitted student, Alex Wosztyl, working in the Joachimiak Lab, for the best poster awards!
Karolina Paulina Stepien, mentored by Jose Rizo-Rey, successfully defended her thesis titled ‘Munc18-1 is a master orchestrator of synaptic SNARE assembly’. Munc18-1 is a protein that regulates neurotransmitter release, a reaction required for proper brain functions. Karo’s work demonstrated that Munc18-1 is essential to overcome inhibition of synaptic membrane fusion imposed by another protein called αSNAP (Nature Com 2019) and to support fusion driven by a few neuronal SNAREs (PNAS 2021). In the recently submitted publication, she reported two cryo-electron microscopy structures that provide visualization of how Munc18-1 facilitates and controls SNARE zippering required for triggering neurotransmitter release. After completion of Karolina’s work in the Rizo-Rey lab, she will look for positions in industry in Poland.
Thuy Nguyen, mentored by Dr. Kimberly Reynolds, successfully defended her dissertation titled "The Structural Distribution of Epistasis in a Pair of Essential Metabolic Enzymes". In her thesis work, she characterized the growth rate effects of nearly 10,000 mutation combinations in a pair of metabolic enzymes. Achieving this required a combination of high-throughput experiments and computational data analysis. These data provide a view of how interactions between metabolic enzymes shape protein sequence. Her data provide a springboard for future quantitative metabolic modeling efforts, and a test set for validating computational prediction algorithms. In the last year of her thesis work, Thuy was awarded an Archer public policy fellowship, and completed a summer internship at The Center for Security and Emerging Technology at Georgetown University. Thuy will apply her scientific training towards a career in industry or in public service.
Sean Rogers, mentored by Dr. Mike Henne, successfully defended his dissertation titled “Metabolic regulation at sub-organelle length scales: inter-organelle contacts and lipid droplets”. During his graduate work, Sean investigated how the organization of enzymes and lipids within organelles can influence metabolism. Sean discovered an important metabolic enzyme, HMG-CoA Reductase, spatially partitions at an inter-organelle contact site during nutrient stress, which serves to finely tune the production of a key sterol precursor, mevalonate (eLife). Genetic ablation of this inter-organelle contact site prevented spatial partitioning of the enzyme and had negative consequences on organismal adaptation to stress states. He also found that lipid droplets, vital lipid storage organelles, can alter the organization of sterol-derived lipids within their core, which leads to dramatic changes in the protein composition of lipid droplets (bioRxiv). You can read more about Sean’s work in JOVE, EMBO Reports, and JCB. Sean is now a postdoctoral fellow at Washington University-St. Louis with Dr. David Pagliarini.
Congratulations to Karolina (Karo) Stepien, Molecular Biophysics Graduate Program student and recipient of the 36th Annual Ida M. Green Award! This award, established in 1987 by a bequest from Mrs. Green to Southwestern Medical Foundation with the encouragement of her husband, Cecil Green, recognizes a female graduate student who has demonstrated research excellence, exceptional community service, and outstanding commitment to the well-being and success of other graduate students.
Karo first came to UT Southwestern Medical Center in 2014 as part of an exchange program with Wroclaw University and other top universities in Poland supervised by Jose Rizo-Rey, PhD, Professor of Biophysics. After working as a visiting student in the Rizo-Rey lab, Karo matriculated to UT Southwestern Graduate School in 2016 and joined Dr. Rizo-Rey’s lab for her dissertation research. Karo has been highly productive in the lab. Her research has yielded important new insights into the molecular mechanism of neurotransmitter release, work that has contributed to first-author publications in PNAS USA and Nature Communications and co-authorships on five additional papers in high-impact journals. Karo has also had an outstanding record of service to her fellow graduate students and the UTSW community overall. She chaired her department’s social committee, had leadership roles promoting career strategies with the Graduate Career Development Office, led numerous science outreach activities with United to Serve and Science on Tap, and served on the Board of Directors of the Dallas chapter of the Fulbright Association to promote international exchanges. These accomplishments make Karo very deserving of the 2021 Ida M. Green Award.
Wenmin Xing, mentored by Dr. Michael Rosen, successfully defended her dissertation titled “Quantitative studies of composition and formation of yeast P bodies.” Wenmin developed quantitative methods and generated a quantitative inventory of yeast P body proteins including their absolute concentrations, partition coefficient and dynamics. The work demonstrated that there are only 7 highly concentrated P body proteins indicating composition of natural P bodies could be simpler. It also provided a framework to understand compositions of natural biomolecular condensates. Additionally, she showed that P bodies in yeast are formed through phase separation. Wenmin’s work was published in eLife (2020). Read more about Wenmin’s work during her graduate studies, Science (2016), and eLife (2017). Following her graduation, Wenmin will move back to China and start a job in venture capital firm.
Jing Zhang, mentored by Dr. Nick Grishin, successfully defended her dissertation titled “Butterfly genomics of complete continent.” Jing investigated the relationship between phenotype and genotype and the possible mechanism for speciation using butterflies as model organism. Jing’s work was published in Human Mutation, PNAS and Proceedings of the Royal Society B.
Anna Lee completed her dissertation “Translational Repression of G3BP in Cancer and Germ Cells Suppresses Stress Granules and Enhances Stress Tolerance” under the supervision of Dr. P. Ryan Potts. During her graduate studies, Anna characterized the first RNA-binding Melanoma Antigen (MAGE) protein, MAGE-B2. She demonstrated that the testis-specific protein MAGE-B2 increases stress tolerance by suppressing stress granule formation through translational inhibition of the stress granule nucleator G3BP. In addition, she found that knockout of the MAGE-B2 mouse ortholog or overexpression of G3BP confers hypersensitivity of the male germline to heat stress in vivo, thereby suggesting that the selective expression of MAGE-B2 in testes provides the highly thermosensitive germline cells with an enhanced stress tolerance to maintain fertility in the face of fluctuating environmental temperatures (Mol Cell, 2020). Anna is now studying the role of RNA-binding proteins in the initiation and progression of leukemia as a postdoctoral fellow in the laboratory of Dr. Iannis Aifantis at the New York University School of Medicine.
Katelyn Doxtader, mentored by Dr. Yunsun Nam, successfully defended her dissertation, “Structures and Regulation of the N6 methyladenosine Methyltransferase, METTL16.” Katelyn investigated the mechanisms by which METTL16 catalyzes methylation of RNA, and controls SAM homeostasis, using a combination of biochemistry and structural biology. Katelyn's work was published in Molecular Cell (2016 and 2018). Now, Katelyn is a postdoctoral fellow at Ionis Pharmaceuticals.
Alex Partin, mentored by Dr. Yunsun Nam, successfully defended his dissertation, “Understanding Recognition of Primary MicroRNAs by Human Drosha/DGCR8.” Alex investigated the mechanisms by which microRNA biogenesis is initiated by the Microprocessor complex, using a combination of biochemistry and structural biology. Alex's work was published in Molecular Cell (2020) and Nature Communications (2017).
Andrew Schober, mentored by Dr. Kimberly Reynolds, successfully defended his dissertation, “A Two Enzyme Adaptive-unit within Bacterial Folate Metabolism.” Andrew is moving to the University of Chicago as a Yen Postdoctoral Fellow in the lab of Dr. Michael Rust.
Our very own Whitney Costello (lab of Dr. Kendra Frederick) attended the 69th Lindau Nobel Laureate Meeting which took place June 30-July 5, 2019.The meeting, dedicated to physics, engaged 39 Nobel Laureates and 580 young scientists from all over the world in vibrant scientific discussion intended to bridge generations and cultures. Following the meeting, Whitney visited the Max Planck Institute of Biophysics and gave a talk titled “Structural studies of the yeast prion protein via Dynamic Nuclear Polarization NMR.”
Congratulations to Dailu Chen in Dr. Lukasz Joachimiak’s lab! Dailu has just published a first-author paper in Nature Communication titled “Tau local structure shields an amyloid-forming motif and controls aggregation propensity.”
Jordan Baumhardt (lab of Dr. Yuh Min Chook) is undertaking a summer fellowship with Flagship Pioneering. Jordan has joined the Flagship Fellowship program to foster experiences in developing disruptive life science companies, and to build skills and networks essential to his future career goals.
Yusuf Tamer, mentored by Dr. Erdal Toprak, successfully defended his dissertation titled “Exploiting Evolutionary Trade-offs to Fight Antibiotic Resistance Evolution.” Yusuf investigated biophysical and biochemical constraints driving evolution of trimethoprim resistance in pathogenic bacteria. His work led to development of novel drug molecules that can specifically inhibit antibiotic resistant bacteria. Yusuf’s work was published in Molecular Biology and Evolution (2019), Molecular Cell (2017), and PLOS Biology (2016). Following his graduation, Yusuf will move to Dr. Milo Lin’s lab for his postdoctoral studies.
The 2019 Molecular Biophysics Graduate Program Research Symposium was held on May 3, 2019. The talks and posters raised the bar even more this year! Congratulations to Anant Gharpure (Molecular Biophysics student, Dr. Ryan Hibbs’ lab) and Dr. Emiko Uchikawa (research scientist, lab of Dr. Xiaochen Bai) for winning best talk and to Dagimhiwat Legesse (Molecular Biophysics student, Dr. Ryan Hibbs’ lab) and Dr. Nagesh Peddada (postdoctoral researcher, Dr. Jan Erzberger’s lab) for receiving the best poster award.
We are looking forward to the contributions our seven new Molecular Biophysics Graduate Program students will make to our community here at UT Southwestern, and the scientific community at large. Our heartiest welcome to Charis Springhower (lab of Dr. Yuh Min Chook); Umang Goswami (lab of Dr. Ryan Hibbs); Sofia Bali (lab of Dr. Lukasz Joachimiak): Yang Liu (lab of Dr. Xiaochun Li); Kamil Sekulski (lab of Dr. Jan Erzberger); Jesus Vega-Lugo (lab of Dr. Khuloud Jaqaman); and Xuemeng Zheng (lab of Dr. Michael Rosen.)
Shreoshi Majumdar, mentored by Dr. Luke Rice, successfully defended her dissertation titled “An Isolated CLASP TOG Domain Suppresses Microtubule Catastrophe and Promotes Rescue.” To read more about Shreoshi’s work during her graduate studies, please see her 2018 paper in Molecular Biology of the Cell. Shreoshi has moved on to a job in management consulting.
Eric Prinslow, mentored by Dr. Jose Rizo-Rey, successfully defended his dissertation titled “Dissecting Roles for the Macromolecular Machinery Involved in Neurotransmitter Release.” In his graduate work, Eric investigated the mechanism by which neurotransmitters send messages between neurons as a specific model system to study the general mechanism of intracellular membrane fusion. Specifically, he showed that multiple factors such as Munc18, Munc13, Complexin, and Synaptotagmin contribute to maintaining assembled trans-SNARE complexes in the presence of NSF-αSNAP using fluorescence spectroscopy (eLife 2019). Additionally, he investigated the inhibitory role of Complexin and solved a controversy over conflicting ITC data (eLife 2017). Eric plans to pursue a career in biochemistry/biophysics and would like to develop therapies that are at the cutting edge of drug discovery. Eric is now a scientist at Johnson and Johnson.
Bradley Quade, mentored by Dr. Jose Rizo-Rey, successfully defended his dissertation titled “Mechanistic Insights Into The Role of Munc13 In Synaptic Vesicle Docking, Priming, And Fusion.” During his graduate work, Brad used various biophysical techniques to characterize the role that Munc13 plays in interneuronal communication, ultimately showing that Munc13 is critical for synaptic vesicle docking. (ELife 2019) Brad will begin a postdoctoral research position in Dr. Xiaochen Bai’s lab where he will perform structural studies on receptor tyrosine kinases to further understand the mechanisms driving receptor tyrosine kinase signaling.
Anthony Vega, mentored by Dr. Khuloud Jaqaman, successfully defended his dissertation, “Computer Vision to Characterize Protein Interactions at the Cell Membrane.” In his graduate work, Anthony developed a novel computational approach to detect transient changes in molecular mobility as well as developing quantitative approaches to study composition-dependent microcluster-actin interactions during T-cell activation. Anthony will continue on to his postdoctoral research in the labs of Dr. Marc Diamond and Dr. Satwik Rajaram at UT Southwestern. To read more about Anthony’s work during his graduate studies, please see his March, 2018 paper in Biophysical Journal, as well as in Cell and Journal of Cell Science.
Lindsay Clark, mentored by Dr. Dan Rosenbaum, successfully defended her dissertation, “Structural Studies of Integral Membrane Proteins Involved in GPCR Signaling and Sterol Homeostasis.” Lindsay developed and applied de novo isotopic labeling strategies to wild-type G protein-coupled receptors in order to facilitate NMR spectroscopic measurements connecting ligand efficacy to protein dynamics (Clark et al. 2017. eLife Oct 6;6. 10.7554/eLife.28505.) Also, in collaboration with the Radhakrishnan lab and the Brown and Goldstein labs, Lindsay used cryo-Electron Microscopy and X-ray crystallography to understand the allosteric changes involved in cholesterol sensing by membrane proteins in the SREBP pathway, a step toward a deeper understanding of this pathway and its role in disease. Lindsay will continue on to her postdoctoral research in the Lab of Dr. Tom Rapoport at Harvard Medical School, continuing her multidisciplinary approach to understand the structure-function of membrane proteins in the endoplasmic reticulum. To further explore Lindsay’s scientific achievements, please see her work in the Journal of Biomolecular NMR and Methods in Enzymology.
Elisabeth (Beth) Geyer, mentored by Dr. Luke Rice, successfully defended her dissertation titled “Mechanistic Analysis of Microtubule Dynamics and Regulation.” Beth has accepted a position as a scientist in the Antibody Engineering/Bispecifics Group at Janssen Pharmaceuticals (Johnson & Johnson). Beth’s main thesis project in the Rice Lab centered on dissecting the mechanism of a microtubule polymerase using a combination of protein engineering, quantitative biochemistry, and in vitro reconstitution monitored by time lapse two color TIRF microscopy. To read more about Beth’s work, please see her publications in Developmental Cell (2017), Journal of Cell Biology (2017), and eLife in 2018, 2017, and 2015.
Congratulations to Katelyn Doxtader in Dr. Yunsun Nam’s lab! Katelyn has just published a first-author paper in Molecular Cell titled “Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor.”
Whitney Costello, Molecular Biophysics graduate student in the Lab of Dr. Kendra Frederick, is awarded the FEBS Journal poster prize for her contribution to the 2018 EUROMAR meeting entitled “Digging into the core: studies of the yeast prion protein via DNP-NMR.” The FEBS journal has a long history of supporting early career scientists and is delighted to recognize their important contributions at this meeting.
We are excited to welcome six new students to the Molecular Biophysics Graduate Program this summer: Jordan Finnell and Michael LaCroix (Marc Diamond lab); Adam Osinski (Vincent Tagliabracci lab); Valerie Perez (jointly mentored by Lukasz Joachimiak and Marc Diamond); Michael Porter (Hamid Mirzaei lab); Alex Treacher (Albert Montillo lab); Mike Trenfield (Milo Lin lab); and Casey Wing (Yuh Min Chook lab). We look forward to hearing about your work!
Our 27th annual Molecular Biophysics Research Symposium was a resounding success! Best Research Presentation prizes were awarded to Lindsay Clark (Dan Rosenbaum lab), Anant Gharpure and Richard Walsh (Ryan Hibbs lab), Andrew Mathis (Kim Reynolds lab), Anthony Vega (Khuloud Jaqaman lab), and Wenmin Xing (Michael Rosen lab).
Claudio Morales-Perez in Dr. Ryan Hibbs’ lab is selected as one of 13 international recipients of the prestigious Harold M. Weintraub Graduate Student Award offered by the Fred Hutchinson Cancer Research Center.
Whitney Costello, Graduate Student in the Lab of Dr. Kendra Frederick, is selected to participate in the National Science Foundation’s East Asia and Pacific Summer Institutes (EAPSI) Program. Whitney is one of only seven graduate students in Texas to be awarded a slot in this program.
MSTP student Tae Kim, in Dr. Luke Rice’s lab, and first year graduate student Sean Rogers, in Dr. Mike Henne’s lab, are chosen to participate in the Molecular Biophysics Predoctoral Training Program via a competitive completion.
The 26th annual Molecular Biophysics Research Symposium took place on May 5 at the Dallas Arboretum and Botanical Garden. Allyson Rice, Lab of Dr. Michael Rosen, and Andrew Schober, Lab of Dr. Kimberly Reynolds, took home awards for the Best Research Talk. Anthony Vega, Lab of Dr. Khuloud Jaqaman, and Lindsay Clark, Lab of Dr. Dan Rosenbaum, were awarded Best Poster Presentation. Well done to Lindsay for winning an award for the third year in a row, and congratulations to all four students for their outstanding work!
We are very pleased to welcome the newest students to join our thriving program: Dailu Chen and Bryan Ryder, Lab of Dr. Lukasz Joachimiak; Michael Cotten, Lab of Dr. Michael Rosen; Abner Gonzalez and Jenny Jiou, Lab of Dr. Yuh Min Chook; Tae Kim, Lab of Dr. Luke Rice; Nathan Egge, Lab of Dr. Peter Douglas; Dagimhiwat Legesse, Lab of Dr. Ryan Hibbs; Nicholas Lesner, Lab of Dr. Prashant Mishra; Leigh Manley and Paul Blazek, Lab of Dr. Milo Lin; Sean Rogers, Lab of Dr. Mike Henne; Karolina Stepien, Lab of Dr. Jose Rizo-Rey; and Yujiao Wu, Lab of Dr. Rama Ranganathan. We look forward to helping these students develop their scientific careers!
New Biophysics faculty member Xiaochen Bai, Ph.D., joins the Molecular Biophysics program. We look forward to the benefit of his expertise in mentoring our excellent students!
Michael Cotten, first year student in Dr. Michael Rosen’s lab, is selected as our newest trainee on the Molecular Biophysics Predoctoral Training Program.