Bio Catalyst
Vatsan Raman on Protein Allostery and Bacteriophages

Vatsan Raman on Protein Allostery and Bacteriophages

November 25, 2021

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 as 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) -- allosteric behavior in other protein families

(12:45) -- going beyond single mutation restoration experiments 

(13:32) -- challenges and opportunities of bacteriophages

(14:50) -- deep mutational scanning for engineering bacteriophages 

(18:06) -- translatability of phage therapy 

(20:43) -- bacteriophages in space

(22:38) -- influence of Vatsan’s mentors

(24:03) -- big vs. small labs

(26:32) -- qualities of a good synthetic biologist

Prachee Avasthi on Cytoskeleton and Academic Publishing

Prachee Avasthi on Cytoskeleton and Academic Publishing

September 25, 2021

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 preprints 

(24:45) -- open reviews

(29:02) -- crowd sourced peer review

(32:48) -- need for journals 

Nigel Goldenfeld on the Genetic Code

Nigel Goldenfeld on the Genetic Code

August 7, 2021

In this episode, I speak with Prof. Nigel Goldenfeld. 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/physics 

(40:56) -- biology as a reverse engineering problem

Allan Drummond on Protein Evolution (and a lot more)

Allan Drummond on Protein Evolution (and a lot more)

May 19, 2021

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 molecular evolution translates to phenotypic changes

(26:51) -- cultural evolution

(28:45) -- overemphasis on molecular mechanisms?

(39:00) -- role of storytelling in science

(45:00) -- employee bootcamps

(54:03) -- Allan’s journey to becoming a professor at UChicago

(70:03) -- non-traditional paths in science

(74:30) -- mentorship 

Mohammed AlQuraishi on Machine Learning and Structural Biology

Mohammed AlQuraishi on Machine Learning and Structural Biology

April 23, 2021

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) -- predicting higher energy states in conformational space

(15:46) -- is structure overrated?

(18:10) -- protein localization prediction

(20:37) -- pitfalls of having a programmatic view of a cell

(23:34) -- why individuals with quantitative backgrounds may find biology interesting

Anders Hansen on 3D Genome Organization

Anders Hansen on 3D Genome Organization

March 28, 2021

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

(9:18) -- genome organization as a function of organism complexity

(11:54) -- mechanism of loop formation in genome

(15:25) -- RNA binding regions and their role in CTCF function

(20:45) -- role of chemistry background in Anders’ research 

(22:55) -- importance of de novo design of genomes

Gautam Dey on Nuclear Remodelling

Gautam Dey on Nuclear Remodelling

March 13, 2021

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

(11:47) -- future experimental plans

(13:06) -- impact of covid on science

(14:45) -- science in US vs Europe

(17:33) -- influence of theatre on Gautam 

(19:15) -- evolutionary origin of eukaryotic cells

(23:13) -- favorite idea in evolutionary biology

Janet Iwasa on Molecular Animations

Janet Iwasa on Molecular Animations

February 28, 2021

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 

(11:13) -- common visualization mistakes

(12:00) -- Pixar

(13:27) -- role of VR in visualization

(15:26) -- future of animations

 

 

Paul Robustelli on Molecular Dynamics Simulations

Paul Robustelli on Molecular Dynamics Simulations

February 11, 2021

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 simulations

(26:40) -- disordered proteins and drug discovery

 

Liam Holt on Cellular Crowding

Liam Holt on Cellular Crowding

December 25, 2020

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 crowding 

(14:05) -- Ribosomes role in crowding

(17:00) -- Cell size and function

(19:58) -- Modular evolution 

(24:37) -- Villages vs. NYC

(25:35) -- Science Sketches

(29:47) -- Inspire Science

(31:43) -- Evolutionary biology as a powerful lens

(32:43) -- Role of abstraction in biology 

(36:01) -- Tool development 

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