Sakshi’s undergraduate honor’s thesis entitled “Novel Methodology for Determining Dihedral Angles of Intrinsically Disordered Proteins in Various Contexts” received “Major Honors with Distinction” from the school of Natural Sciences and Mathematics at the University of Texas at Dallas.
Dominique wins “best student talk” and Shoyab wins “best post-doc poster” at the 5th annual Biophysics retreat
Graduate student Dominique Lagasca’s talk about studying the intrinsically disordered regions of proteins was recognized with the “best student talk” award. Post-doc Shoyab Ansari’s poster about selective amplification of amyloid fibril inside cells was recognized with the “best post-doc poster” award. And! Rania Dumarieh’s poster about isotopic labeling strategies and peak shape analysis was recognized with the “best staff poster runner up” award. An exciting close to the 5th Annual Molecular Biophysics Departmental retreat in Texoma!
Poster madness! Eric and Sakshi
Eric Tong presented a poster on his work at the STARS poster session this morning on campus at UTSouthwestern and Sakshi Krishna presented a poster on her work at the Summer Platform for Undergraduate Research poster session on the University of Texas at Dallas campus this afternoon.
Eric Tong joins the lab through the STARS summer research program
Eric Tong, a junior at the ASPIRE Academy at Grapevine High School joins us through the STARS summer research program for high school students at UT Southwestern. Welcome, Eric!
Pre-Print! DNP-assisted solid-state NMR enables detection of proteins at nanomolar concentrations in fully protonated cellular environments
DNP increases the sensitivity of NMR to the point where detection of isotopically labeled proteins at very low concentrations is possible, concentrations so low that the amount of NMR visible carbon from natural abundance (which is only 1,1%) may be larger than the protein that we want to see. We determined which experimental conditions enable specific detection of nanomolar concentrations of an isotopically labeled protein when it is inside a cell. Whitney Costello lead this work with contributions from Yiling Xiao and Jaka Kragelj from our group and Fred Mentink-Vigier at the National High Magnetic Field Lab in Tallahassee. Check out this pre-print on bioRxiv!
Green Fellow Sakshi Krishna joins the group
Sakshi Krishna, a junior at the University of Texas at Dallas, joins our group through the UT Dallas/UT Southwestern Green Fellows program which provides a semester-long fully-paid undergraduate research fellowship for UT Dallas students. Welcome Sakshi!
Rupam Ghosh defends his thesis!
Rupam Ghosh successfully defended his this about “Structural biology in cellular environments using sensitivity enhanced NMR”. Congratulations!!
Pre-print! The conformational ensemble of an intrinsically disordered protein explains peak shapes under DNP conditions
While DNP increases the sensitivity of NMR to the point where detection of proteins at endogenous levels inside cells is possible, it also typically requires that such samples are frozen. This results in broad lines, especially for regions of intrinsic disorder. However, because of the relationship between chemical shift and dihedral angles, the peak shapes can – and do! – report on the sampled conformations at each site. In this pre-print, we describe an approach to predict and interpret peak shapes of frozen regions of intrinsic disorder. Post-doc Jaka Kragelj lead this work with contributions from Rania Dumarieh and Yiling Xiao. Check out this pre-print on bioRxiv!
Carla Madrid selected for a travel award to the SACNAS conference
Graduate student Carla Madrid was honored with a travel award to attend the 2022 SACNAS National Diversity in STEM conference in San Juan, Puerto Rico!
Rupam selected at the Tau Leadership Fellow by the Rainwater Charitable Foundation
From the Center Times:
August 18, 2022 • Rachel Stowe Master
Rupam Ghosh, a fifth-year student in the Biological Chemistry Graduate Program, has been named a 2022 Tau Leadership Fellow by the Rainwater Charitable Foundation, an honor bestowed on early-career postdoctoral researchers and graduate students whose work has the potential to be a breakthrough in the field of tau-related pathologies. The award carries a monetary prize of $10,000.
“I have been working with tau for a couple of years now, and this award provides a lot of encouragement at this stage,” Mr. Ghosh said. “Being an international student, there are limited options of grants and fellowships for me, so an opportunity like this is great. Also, the competition was quite tough as graduate students and postdocs were competing in a single group.”
In the lab of Kendra Frederick, Ph.D., Assistant Professor of Biophysics, Mr. Ghosh studies how the tau protein causes Alzheimer’s disease from a structural biology point of view.
“Alzheimer’s disease pathology is highly variable across different patients and stages of the disease even though the causing agent – tau protein – remains the same. The mystery I’m trying to address is to figure out how a single protein can cause multiple pathologies. Understanding this will be very helpful to design specific and targeted therapeutic strategies,” he said.
Studying an intrinsically disordered protein like tau in its native cellular environment may reveal unique insights that would be useful in understanding physiological and pathological processes of conformational diseases, such as neurodegenerative diseases, he added.
“Rupam has been intimately involved in developing the technology to apply a cutting-edge structural biology technique – sensitivity-enhanced NMR (nuclear magnetic resonance) spectroscopy – to biological systems to establish a platform to determine structures at atomic resolution for proteins inside of living cells,” said Dr. Frederick, who holds an additional appointment in the Center for Alzheimer’s and Neurodegenerative Diseases. “This methodology will be critical to bridge a current gap in our ability to determine structures of the proteins at the center of many neurodegenerative disorders in relevant biological contexts, such as in genetic backgrounds that include genetic risk factors for disease or in the presence and absence of potential therapeutics.”
Last year, Mr. Ghosh was selected for the Peter O’Donnell Jr. Brain Institute’s Neural Scientist Training Program. He received an integrated Bachelor-Master of Science degree with majors in biological sciences and minors in chemical sciences from the Indian Institute of Science Education and Research Bhopal, in India.
“One of the best things that attracted me to UT Southwestern was the possibility of collaboration with a world-class hospital,” he said. “In addition, the freedom to do lab rotations across different departments, world-class faculties, the very diverse and collaborative research culture, wonderful student center and clubs, and great Texan food, were the other factors that helped me choose UT Southwestern over other U.S. institutions.”
Frederick Lab 