Columbia University Bio Bytes

In which Adam Bass, oncologist and inaugural director of the Columbia Center for Precision Cancer Medicine, discusses the relevance of genomic science and treatments informed by sequencing in modern cancer medicine. Among other things, Vaibhav and Adam discuss current standards of care involving sequencing, the importance of first-principles understanding and research in advancing medicine, and what the future of precision medicine might look like. 

In which Albert Keung, Assistant Professor in the department of Chemical and Biomolecular Engineering at North Carolina State University, shares many insights on Synthetic Biology. He touches on synthetically perturbing the chemical makeup of chromatin, designing and using DNA databases to store digital information, and the challenges and promise associated with developing cerebral organoids. 

In which Aaron speaks with Zach Abbott, PhD, about his company ZBiotics. ZBiotics is a biotechnology start-up that is focused on engineering microorganisms for consumer benefit. Aaron and Zach talk about the company’s current product, a genetically engineered probiotic designed to breakdown acetaldehyde, a toxic byproduct of alcohol. Additionally, Zach offers insight on his transition from completing a PhD to the biotech start-up space.

In which Vaibhav speaks with Dr. Mohammed AlQuraishi, an Assistant Professor of Systems Biology at the Columbia University Irving Medical Center, about using machine learning to predict protein structure. Among other things, they discuss the direction of algorithmic development in computational structure prediction, from neighborhood-based assembly of peptide fragments to modern applications of Deep Learning in structural modeling. They discuss the features of physical priors and discuss approaches in computationally optimizing protein-energy state predictions, taking into account the difficulties associated with the many local minima in an energy function. Throughout this discussion, Mohammed contextualizes the intuition behind the methods used by Deep Mind with their developments of AlphaFold.

In which Vaibhav speaks with Dr. Alison Taylor, an Assistant Professor of Pathology and Cell Biology at the Columbia University Irving Medical Center, about her research on the role of aneuploidy (abnormal numbers of chromosomes) in cancer. Among other things, they discuss the basic mechanisms of aneuploidy, the ways in which it can favor cancer development, and contemporary approaches in chemically targeting aneuploid cells. Alison explains her group's models for studying aneuploidy and their new computational genomics efforts as well. She concludes by discussing ongoing projects in her lab and some pressing questions about genome integrity in cancer initiation and progression. 

In which Aaron speaks with Alex Chavez, MD-PhD about antiviral drug development. They discuss chemical strategies for protease inhibitor development and the details and rationale of a novel assay that allows for early validation of candidate drugs. Additionally Alex discusses newer collaborations he is engaged in to build cellular resistance to damaging radiation. 

In which Josh speaks with Stavros Thomopoulos, PhD about biomechanical engineering at the tendon-bone interface. Dr. Thomopoulos is the director of the Caroll Laboratories for Orthopedic Surgery and the Vice Chair for Basic Science Research in Orthopedic Surgery at the Columbia University Irving Medical Center. Among other things, they discuss the challenges of attaching a tendon to a bone and stem cell-based regenerative medicine to improve healing in orthopedic injuries, such as those to the rotator cuff.

In which Josh explores the intersection of molecular biology, structural biology, and cardiology with Dr. Andrew Marks. Dr. Marks is the Chairman of the Department of Physiology at Columbia Medical School, the Founding Director of the Wu Center for Molecular Cardiology, and a professor of Physiology and Cellular Biophysics and Medicine. Among other things they discuss his critical development of the rapamycin coated drug eluting stent, his past and current work on Ryanodine receptors, and the multi-system impact of defective Ryanodine receptors. 

In which Vaibhav and Dr. Aaron Viny (a clinician scientist and assistant professor at Columbia) discuss the role of Cohesin complexes in 3D genome organization and how spatiotemporal irregularities in higher order genetic structures lead to blood cancers. They talk about the importance of linage commitment and how a disorganized genome can prevent it. Aaron concludes with a discussion of his experience as a physician-investigator and  meeting (now president-elect) Joe Biden. 

In which Vaibhav and Shawn Liu (The Joan and Paul Marks, MD ’49 Assistant Professor of Physiology and Cellular Biophysics at CUIMC) speak about the specifics of epigenome editing, from selecting the right model cells, to tool design, to loci considerations for editing experiments and much more. They also touch on how neurons are methylated during memory acquisition and the potential for in vivo neuroepigenome editing. Find out more about Shawn's work here: https://epibrain.info