Vatsan Raman on Protein Allostery and Bacteriophages
Bio Catalyst
by Ishan Taneja
2y ago
In this episode, I speak with Vatsan Raman. Vatsan is an assistant professor in the department of biochemistry at the University of Wisconsin-Madison. Vatsan's research spans a wide variety of areas: this ranges from fundamental questions such as deciphering the mechanisms of protein allostery to tackling real world problems such engineering bacteriophages more effectively and efficiently.   (00:18) -- overview of Vatsan’s lab (02:00) -- protein allostery overview (06:25) -- experimental framework for studying allostery  (09:05) -- key results of allostery experiments  (11:50 ..read more
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Prachee Avasthi on Cytoskeleton and Academic Publishing
Bio Catalyst
by Ishan Taneja
2y ago
In this episode, I speak with Prachee Avasthi. Prachee is an Associate Professor of Biochemistry and Cell Biology at Dartmouth University, and her lab broadly studies cytoskeletal assembly. Prachee is also spearheading efforts to improve the academic publishing system in the life sciences.  (00:34) -- how Prachee got interested in cytoskeletal assembly (2:37) -- algae as a model system (6:31) -- evaluating tradeoffs in model systems (9:45) -- general scientific lessons in genetics and cell biology (15:26) -- issues with the academic publishing system (17:44) -- ASAPbio (21:00) -- rise of ..read more
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Nigel Goldenfeld on the Genetic Code
Bio Catalyst
by Ishan Taneja
3y ago
In this episode, I speak with Prof. Nigel Godenfeld. Nigel is a Professor of Physics at the University of Illinois at Urbana-Champaign. He has tackled some fundamental questions in biology, and he provides some very unique thoughts on how he thinks about biological problems from the perspective of a physicist.    (00:24) -- how Nigel got into biology (03:40) -- overview of the genetic code (21:15) -- genetic code as an innovation protocol  (32:25) -- quantitative approaches in biology (34:55) -- energy vs information centric view of biology (39:10) -- biology as chemistry/physic ..read more
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Allan Drummond on Protein Evolution (and a lot more)
Bio Catalyst
by Ishan Taneja
3y ago
In this episode, I speak with Prof. Allan Drummond. Allan is an associate professor at the University of Chicago in the Department of Biochemistry and Molecular Biology. We touch on quite a few topics related to evolution, and Allan shares some unique thoughts and perspectives he's gained during his unorthodox career path.  00:25 -- biggest misconception about Darwinian evolution 03:55 -- neutral theory vs natural selection 06:15 -- meaning of randomness in evolution 07:58 -- evolvability  10:03 -- how proteins evolve 15:30 -- factors influencing protein evolution 23:10 -- how molecu ..read more
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Mohammed AlQuraishi on Machine Learning and Structural Biology
Bio Catalyst
by Ishan Taneja
3y ago
In this episode, I speak with Prof. Mohammed AlQuraishi. Mohammed is an Assistant Professor in the Department of Systems Biology at Columbia University. Mohammed gives us his unique thoughts and perspectives on a variety of problems that lie at the intersection of machine learning and structural biology.   00:30 -- vision of Mohammed’s lab 02:45 -- importance of abstractions to simulate a cell 04:29 -- conceptual advances in abstractions 06:03 -- protein folding 07:28 -- end-to-end differentiability 10:12 -- representations learned by protein structure deep learning models 14:07 -- predic ..read more
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Anders Hansen on 3D Genome Organization
Bio Catalyst
by Ishan Taneja
3y ago
My guest today is Anders Hansen. Anders is an Assistant Professor of Bioengineering at MIT. His group studies the interplay between genome organization and regulation of gene expression in mammals. Anders gives us a deep dive of his research and delves into some very interesting findings from his latest work.    (00:28) -- motivation for studying 3-d genome organization (1:30) -- tools to study 3d genome organization (03:44) -- scope of biological question that can be tackled via experimental techniques  (5:15) -- live cell imaging (6:30) -- topological features of genome ..read more
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Gautam Dey on Nuclear Remodelling
Bio Catalyst
by Ishan Taneja
3y ago
In this episode, I speak with Prof. Gautam Dey. Gautam is a group  leader at the EMBL and his group studies the evolutionary origins of nuclear organization and architecture. Gautam dives into the details of his latest work and also touches on some other very interesting ideas in evolutionary biology.    (00:25) -- motivation for studying nuclear organization (04:18) -- main mechanisms of nuclear division (05:50) -- how nuclear assembly/disassembly works  (07:20) -- mechanism of nuclear division in fission yeast (10:15) -- putting this mechanism in an evolutionary context ..read more
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Janet Iwasa on Molecular Animations
Bio Catalyst
by Ishan Taneja
3y ago
In this episode, I speak with Prof. Janet Iwasa. Janet is an Assistant Professor in the Biochemistry Department at the University of Utah. She and her lab create animations of diverse molecular and cellular processes, and in this conversation, we get her unique insights on a variety of topics related to animation and visualization.  (0:22) -- molecular animation process (3:05) -- favorite animation (04:18) -- interplay between animation and the research process (06:58) -- importance of animation (09:14) --Janet’s journey to animation (10:21) -- other interesting visualization modalities&n ..read more
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Paul Robustelli on Molecular Dynamics Simulations
Bio Catalyst
by Ishan Taneja
3y ago
In this episode, I speak with Prof. Paul Robustelli. Paul is an assistant professor in the department of chemistry at Dartmouth University. Paul has a pretty unique background, and he provides some very interesting perspectives on molecular dynamics simulations.   (00:35) -- role of MD simulations in science (3:12) -- limitations of MD simulations (7:50) -- force field development  (11:35) -- integration between NMR and simulations (16:30) -- insights gained from having a background in NMR (18:50) -- academia vs. industry research (22:30) -- life in Hanover (24:35) -- future of simul ..read more
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Liam Holt on Cellular Crowding
Bio Catalyst
by Ishan Taneja
3y ago
In this episode, I speak with Prof. Liam Holt. Liam is an assistant professor in the department of biochemistry and molecular pharmacology at NYU. Here are a few interesting ideas we touched on: -why the inside of a cell and NYC have more in common than you think -the role of 'modules' in driving evolution -how being a worse drawer can help you make more instructive illustrations    (00:25) -- Inside the cellular environment (2:10) -- Crowding in vitro  (4:07) -- Biological processes impacted by crowding  (8:05) -- Spatial variation in crowding (8:59) -- Quantifying crowdin ..read more
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