Join the CQB on Friday, September 27, 2024 from 3-4pm in Wilkinson 021,  as we kick off our fall 2024 semester with our first guest speaker, Dr. Hernan Garcia, Associate Professor in the Departments of Molecular & Cell Biology and Physics at University of California, Berkeley.

Bio: Hernan G. Garcia is an Associate Professor in the Departments of Molecular & Cell Biology and of Physics at UC Berkeley. As a Physical Biologist, his research aims to uncover the quantitative and predictive principles dictating biological phenomena, with particular emphasis on embryonic development. Hernan is a co-author of the textbook Physical Biology of the Celland has directed several courses at institutions such as the Kavli Institute for Theoretial Physics at UC Santa Barbara, and the Marine Biological Laboratory in Woods Hole, MA.

Abstract: Over the last few decades we have largely identified the repressors and activators that shape gene expression patterns in developing embryos and that, in turn, dictate cellular fates. Yet, despite amassing this great reservoir of knowledge, we are still incapable of predicting how the number, placement and affinity of binding sites for these transcription factors in regulatory DNA dictate gene expression patterns in space and time. Achieving such predictive understanding calls for going beyond molecular parts lists and for obtaining the in vivo biochemical information necessary for fueling theoretical models of transcriptional regulation in developing animals.

In this talk, I will show how we are using physics as a “microscope” to uncover the molecular mechanisms by which activators and repressors dictate transcription in space and time in developing animals. Specifically, using novel quantitative tools that we have developed for precision measurements, I will show that most developmental genes are transcribed in stochastic bursts, and that many transcription factors regulate gene expression by modulating the frequency, duration, and/or amplitude of these bursts. We will then engage in an iterative dialogue between theoretical models and quantitative experiments aimed at revealing the mechanisms underlying this control of transcriptional bursting. Our results challenge the textbook picture of activator and repressor action based on stable protein-protein interactions and call for a description of transcriptional control that acknowledges that the nucleus is not a bag of well-mixed transcription factors. Most importantly, our work sets a path forward for reaching a predictive understanding of cellular decision making and demonstrates how a quantitative dialogue between theory and experiment can shed light on biological mechanisms beyond the reach of even the best super resolution microscopes.

ICYMI: Congratulations to our very own, Dr. Veronica Ciocanel and her group, on their new paper “Minimal Mechanisms of Microtubule Length Regulation in Living Cells.”

The goal was to understand what controls microtubule length in dendrites of Drosophila neurons. We used experimental measurements and a stochastic mathematical model to study mechanisms such as limited tubulin availability and the dependence of shrinking events on microtubule length.

These are needed since experimental parameters predict unbounded growth! They also developed a reduced deterministic model that informed their choices of parameters for the more complex stochastic model. We hope to use this to further understand how microtubules collectively organize into polarized structures in neurons.

Read more here: https://link.springer.com/article/10.1007/s11538-024-01279-z

ICYMI: Congratulations to Lingchong You on his recent press release entitled, “Industrious Communities Can Create Cheaters, Even in Bacteria” that was supported by Office of Naval Research, the National Science Foundation and the National Institutes of Health.

Congratulations to Prof. Lingchong You on his recent paper that was featured in the science journal, Nature Communications , on  “Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria.”

Congratulations to our very own , Prof. Lingchong You, Director of The Center for Quantitative Biodesign and James L. Meriam Distinguished Professor of Biomedical Engineering on the You Lab’s recent press release regarding Copies of Antibiotic Resistance Genes Greatly Elevated in Humans and Livestock.

Congratulations to Prof. Pranam Chatterjee for receiving a donation from the EndAxD Foundation, to study fatal neurological disease.

Dr. Musah received her BS in chemistry at SUNY Binghamton and  completed her PhD at the University of Wisconsin- Madison, where her work focused on material environments for induced pluripotent stem cells.

Dr. Musah’s research focuses on induced pluripotent stem cells (iPS cells), disease mechanisms, regenerative medicine, molecular and cellular basis of human kidney development and disease, organ engineering, patient-specific disease models, biomarkers, therapeutic discovery, tissue, and organ transplantation, microphysiological systems including organs-on-chips and organoids, matrix biology, mechanotransduction, mechanobiology, and disease biophysics.

James J. Collins, PhD., is the Termeer Professor of Medical Engineering & Science and Professor of Biological Engineering at MIT, as well as a Member of the Harvard-MIT Health Sciences & Technology Faculty. He is also a Core Founding Faculty member of the Wyss Institute for Biologically Inspired Engineering at Harvard University, and an Institute Member of the Broad Institute of MIT and Harvard. He is one of the founders of the field of synthetic biology, and his research group is currently focused on using synthetic biology to create next-generation diagnostics and therapeutics.

Professor Collins’ patented technologies have been licensed by over 25 biotech, pharma and medical devices companies, and he has co-founded a number of companies, including Senti Biosciences, Sherlock Biosciences and Cellarity, as well as Phare Bio, a non-profit focused on AI-driven antibiotic discovery. He has received numerous awards and honors, including a MacArthur “Genius” Award and the Dickson Prize in Medicine, and he is an elected member of all three U.S. National Academies – the National Academy of Sciences, the National Academy of Engineering, and the National Academy of Medicine.

Abstract:

Join the Duke Center for Quantitative Biodesign next Friday, February 16, 2024 at 3:00 pm in Wilkinson 021. Our guest speaker, Dr. Alex Holehouse, is an Assistant Professor of Biochemistry and Molecular Biophysics at Washington University in St. Louis where he will be discussing “Mapping from sequence to function in intrinsically disordered regions.”

The Holehouse Lab studies how biological function is encoded into intrinsically disordered proteins and how this goes wrong in disease. They use a combination of physics-based models, bioinformatics, deep learning, and quantitative cell biology.

#CQBSeminar #Biochemistry #DukeBME #MolecularBiophysics

The Center for Quantitative Biodesign would like thank Dr. Nathan Crook for his exceptional presentation on “Combinatorial and Evolutionary Engineering of Probiotic Yeast for In Situ Biomanufacturing” and the work that is conducted in your lab. #CQBSeminar