CQB Seminar- Dr. Samira Murah

Dr. Samira Musah will serve as the next speaker for CQB on Friday, March 22, 2024

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.

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.


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)