Author: Xavier Larkin

CQB Seminar- Jim Collins, PhD- MIT

Dr. Jim Collins will serve as the guest speaker on Friday, March 8, 2024. This seminar is hosted by CQB, CAGT, and CBTE.

 

 

 

 

 

 

 

 

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:

Synthetic biology is bringing together engineers, physicists and
biologists to model, design and construct biological circuits out of
proteins, genes and other bits of DNA, and to use these circuits to
rewire and reprogram organisms.  These re-engineered organisms are
going to change our lives in the coming years, leading to cheaper
drugs, rapid diagnostic tests, and synthetic probiotics to treat
infections and a range of complex diseases.  In this talk, we
highlight recent efforts to create synthetic gene networks and
programmable cells, and discuss a variety of synthetic biology
applications in biotechnology and biomedicine

Save the Date: Dr. Alex Holehouse | CQB Seminar

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

CQB Seminar: Nathan Crook, Ph.D

Dr. Nathan Crook received his B.S. in Chemical Engineering from the California Institute of Technology in 2009, and his Ph.D. in Chemical Engineering from the University of Texas at Austin in 2014, studying under Dr. Hal Alper.  He pursued postdoctoral studies in Pathology and Immunology at Washington University in Saint Louis School Medicine from 2014-2017 in the lab of Dr. Gautam Dantas.  Dr. Crook joined the department of Chemical and Biomolecular Engineering at NCSU in January 2018, and his lab focuses on how to engineer microbial communities.  He received an NSF CAREER award and NIH New Innovator Award in 2023, and mentors 10 amazing graduate students and 3 amazing postdocs.

Abstract: The large intestine is the site of many human diseases yet is difficult to access with orally- or intravenously delivered drugs.  At the same time, the gut provides a habitat for a numerous and diverse population of microbes (viral, prokaryotic, and eukaryotic) that perform important, health-relevant chemistries using host- and diet-derived carbohydrates as a feedstock.  Therefore, there has been a rising interest in genetically engineering these gut microbes to produce therapeutic molecules in the gut, ultimately improving drug delivery and reducing drug costs. Saccharomyces boulardii (Sb) is a widely used yeast probiotic, demonstrating effectiveness against various gastrointestinal disorders.

As a yeast, Sb exhibits high rates of protein secretion, is tolerant to low pH, can be freeze-dried, and low (if any) rates of horizontal gene transfer.  Sb is therefore a promising chassis for development of personalized engineered probiotic medicines. In this talk, I will discuss our lab’s recent progress in tuning four key parameters of Sb’s efficacy as a drug delivery vehicle.  First, I will present the development of a constitutive Sb promoter library, and how we applied this library to synthesize β-carotene in the mouse gut.  Then, I will introduce how sensing of extracellular metabolites may be achieved through repair of Sb’s defective mating pathway and the expression of human adenosine and melatonin G protein-coupled receptors. I will next detail our efforts to enhance Sb’s in vivo residence time through both rational and screening-based approaches.

Finally, I will discuss some new work from our lab focusing on the engineering and optimization of protein secretion titers in Sb, culminating in a quadruple knockout strain with a 10-fold increase to recombinant peptide production. Taken together, this work establishes Sb as a genetically tractable commensal fungus and demonstrates the tunable delivery of small-molecule and protein therapeutics during colonization.

Sticking together: How bacterial collectives (re)shape themselves with Dr. Sujit Datta

On behalf of the Duke Center for Quantitative Biodesign, we would like to thank Dr. Sujit Datta for his incredible presentation to our seminar class last week. At Princeton University, his lab conducts extremely interesting and innovative research at the nexus of quantitative biology, materials, and fluid dynamics, focusing on, specifically, the self-organization of living systems (what he calls “squishy” materials).

His work has led to novel insights into how the material properties (e.g., transport and mechanics of porous hydrogels) critically contribute to the control of cell physiology and drive their collective behavior. These insights suggest new ways of controlling cellular behavior for practical applications in bioremediation and medicine.

Left to right: Katie Duncker(Graduate student), Dr. Sujit Datta, and Zhou (Joe) Zhengquing (Graduate student)

 

4th Annual Mid-Atlantic Synthetic Biology Network Symposium (MASBNS)- January 11th-12th, 2024

ICYMI:

Last Thursday and Friday, the Duke Center for Quantitative Biodesign had the incredible honor of co-hosting the 4th Annual Mid-Atlantic Synthetic Biology Network Symposium right here at Duke University, alongside our partners at the NC Biotechnology Center. It was a two-day filled symposium with excitement as we warmly welcomed researchers, educators, entrepreneurs, and leaders from academia, government, and the private sector – all united by a shared passion for synthetic biology and its groundbreaking technologies.

This special NSF-sponsored symposium showcased the latest regional synthetic biology research and created a vibrant space for connection and collaboration. From engaging platform presentations and thought-provoking discussion panels to a lively poster session and reception, the event was more than just a symposium – it was a gathering of minds, ideas, and endless networking opportunities.

Distinguished Guest Speakers for Spring 2024 Seminar Series

We’re elated to announce the first half of our distinguished guest speakers for the Spring 2024 semester: Frontiers in Biodesign Seminar Series.

Please join us in welcoming the following:

  • Dr. Sujit Datta- Associate Director of Chemical and Biological Engineering at Princeton University
  • Dr. Nathan Crook- Assistant Professor, Chemical and Biomolecular Engineering at North Carolina State University
  • Dr. Alex Holehouse- Assistant Professor, Department of Biochemistry and Molecular Biophysics at Washington University in St. Louis

Please stay tuned for the second half of guest speakers.

CQB Seminar: Sujit Datta, Ph.D.

The Duke Center for Quantitative BioDesign welcomes Professor Datta

Dr. Sujit Datta is an Associate Professor and Director of Graduate Studies of Chemical and Biological Engineering at Princeton University. He earned a BA in Mathematics and Physics and an MS in Physics in 2008 from the University of Pennsylvania, and then a PhD in Physics in 2013 from Harvard, where he studied fluid dynamics and instabilities in soft and disordered media with Dave Weitz. His postdoctoral training was in Chemical Engineering at Caltech, where he studied the biophysics of the gut with Rustem Ismagilov. Datta joined Princeton in 2017, where his lab (http://dattalab.princeton.edu) studies the dynamics, self-organization, and applications of complex, soft (“squishy”), and living systems.

Datta’s research has revealed and shed new light on the fascinating behaviors manifested by complex fluids and bacterial populations in complex environments, guiding the development of new approaches to environmental remediation, energy production, agriculture, water security, and biotechnology. He also actively leads outreach efforts in STEM to bring together diverse perspectives and provide access to researchers from traditionally under-represented groups in studies of soft and living systems. Datta’s scholarship has been recognized by awards from a broad range of different communities, reflecting its multidisciplinary nature, including through the AIChE 35 Under 35 Award, ACS Unilever Award, Camille Dreyfus Teacher-Scholar Award, three awards from the APS (Early Career Award in Biological Physics, Andreas Acrivos Award in Fluid Dynamics, and the Apker Award), the Arthur Metzner of the Society of Rheology, Pew Biomedical Scholar Award, NSF CAREER Award, and multiple commendations for teaching.

Abstract: Bacteria are arguably the simplest form of life; and yet, as multi-cellular collectives, they perform complex functions critical 
to environment, food, health, and industry. What principles govern how complex behaviors emerge in bacterial collectives? And how can we harness them to control bacterial behavior? In this talk, I will describe my group’s work addressing these questions using tools from soft matter engineering, 3D imaging, and biophysical modeling. We have developed the ability to (i) directly visualize bacteria from the scale of a single cell to that of an entire multi-cellular collective, (ii) 3D-print precisely structured collectives, and (iii) model their large-scale motion and growth in complex environments. I will describe how, using this approach, we are developing new ways to predict and control how bacterial collectives — and potentially other forms of “active matter” — spread large distances, adapt shape to resist perturbations, and self-regulate growth to access more space by processing 
chemical information in their local environments. 

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