Synthetic Biology can be broadly defined as the use of modern technologies and computation to engineer biology to solve problems related to the environment and human health. This is accomplished by adding or enhancing the functionality of existing organisms or cells, or by creating “cell free” biochemical systems that use genetic elements taken from living systems. The approach is inherently multidisciplinary, often consisting of research teams that integrate diverse expertise to discover and apply new design principles for biology. It is a field that is training the next generation of scientists and engineers to explore a new type of biology where basic science and engineering are used in concert to develop principles that aid in our understanding of life. The Synthetic Biology Institute is home to interdisciplinary researchers who are motivated to “join forces” to solve hard problems in biotechnology. They represent the fields of molecular and micro-biology, biochemistry, bioengineering, physics, applied mathematics, and computer science.

Leadership

Nan Hao

Molecular Biology

The Hao laboratory combines quantitative single-cell imaging, microfluidic technology and computational modeling to study how molecular networks govern regulatory responses in the context of stresses, aging, or diseases.

Jeff Hasty

Molecular biology, Bioengineering

Dr. Hasty's laboratory focuses on the use of engineering methods in the theoretical design and experimental construction of synthetic gene regulatory networks.

Lev Tsimring

Synthetic Biology Institute

Dr. Tsimring's group is involved in computational modeling of biological processes on different scales: from subcellular signaling and gene regulation networks to multiucellular dynamics, organismal processes and evolution

Jin Zhang

Pharmacology

Dr. Zhang’s laboratory is interested in understanding the molecular mechanisms and functional roles of signaling enzymes such as protein kinases and phosphatases. We seek a fundamental understanding of spatiotemporal regulation of cell signaling.

Staff

Coreen Davis

Management Services Officer

cwdavis@ucsd.edu 858-534-7207

Gissel Cortes

Research Administrator

glcortes@ucsd.edu

Steering Committee

Eric Allen

Scripps Institution of Oceanography

The research of Dr. Allen centers upon the use of environmentally-derived genome sequence information, or metagenomics, to explore the genetic potential, ecology, and evolution of environmental microbial populations.

Ahmad Badran

Chemistry

The Badran Lab combines principles of chemical biology, bioengineering, directed evolution, genome editing and synthetic biology to (re)engineer highly integrated cellular signaling networks towards researcher-defined function.

Doug Bartlett

Scripps Institution of Oceanography

The Bartlet lab examines the diversity and activity of microbial life in the deep sea to investigate intricate biogeochemical cycles and oceanographic patterns shaping our world.

Cinnamon Bloss

School of Public Health, Psychiatry

Dr. Bloss conducts interdisciplinary and transdisciplinary research focused on social and behavioral phenomena related to emerging information and biotechnologies.

Itay Budin

Chemistry and Biochemistry

The Budin lab uses synthetic and systems biology approaches to understand and engineer the molecular processes that occur on the surfaces of cells and their organelles.

Jack Bui

Pathology

Dr. Bui studies how to initiate innate immune responses to cancer. His basic research lab uses mouse and human model systems to elucidate genes involved in tumor rejection.

Geoffrey Chang

Pharmacology

The Chang lab has been mostly focused on determining the x-ray structures of the four classes of multidrug resistance (MDR) transporters found in nature where the drug binding sites reside in the cell membrane.

Stephanie Fraley

Bioengineering

The Fraley Lab focuses on cancer cell migration research into the third dimension through imaging techniques, three-dimensional matrix engineering, and molecular engineering.

Jack Gilbert

Pediatrics

The Gilbert lab investigates the environmental and medical implications of microbial ecology & biogeochemistry, with a focus on microbiome interactions.

Susan Golden

Molecular Biology

Dr. Golden focuses on circadian rhythms of gene expression in cyanobacteria, functional genomics in S. elongatus, and metabolic engineering of cyanobacteria for the production of molecules of interest.

Neal Deveraj

Chemistry and Biochemistry

The Deveraj group investigates how non-living matter can assemble to form life through looking at aspects of lipid vesicle assemblies, and developing chemical tools to blueprint the structure and function of modern cells.

Adam Engler

Bioengineering

The Engler lab is focused on the mechanobiology of cardiovascular diseases, cancer, and aging. We develop microfabricated technologies and biomaterials to examine how how cell behavior is directed by the extracellular matrix (ECM), a 3-dimensional fibrillar scaffold to which cells adhere.

Rob Knight

Pediatrics, Bioengineering, and Computer Science & Engineering

The Knight Lab uses and develops state-of-the-art computational and experimental techniques to ask fundamental questions about the evolution of the composition of biomolecules, genomes, and communities in different ecosystems, including the complex microbial ecosystems of the human body.

Alexis Komor

Chemistry and Biochemistry

The Komor Lab has initiated a research program aimed at developing new laboratory-based strategies and systems to study how mutations in DNA repair genes (our area of expertise) affect enzymatic activity, cellular function, and ultimately human health.

Prashant Mali

bioengineering

The Mali Lab focuses on the development of molecular toolsets for genome, transcriptome, and proteome engineering and their application to systematic genome interpretation and gene therapy applications; along with the study and engineering of cell fate specification during development utilizing human pluripotent stem cells as the core model system.

Brad Moore

Scripps Institution of Oceanography

Research in the Moore group is focused on the biosynthesis and bioengineering of marine microbial natural products and in the discovery of new enzyme biocatalysts.

Bernhard Palsson

Bioengineering & pediatrics

The Palsson Lab studies the complexity of cellular life using experimental and computational methods that span the genome to the phenotype. Developing, integrating, and applying new methods allow us to gain a systems view of life - from bacterial to human.

Joe Pogliano

Molecular Biology

The Pogliano Lab focuses on discovery of the phage nucleus and spindle along with Antibiotic discovery and mechanism of action.

Julian Schroeder

Biology

The Schroeder Lab's research is directed at the signal transduction mechanisms and pathways that mediate resistance to environmental (“abiotic”) stresses in plants, in particular responses to elevated CO2, drought, salinity stress, and heavy metal stress.

Lingyan Shi

Bioengineering

The Shi Lab's goal is to develop and apply new ultrafast laser scanning optical imaging and spectroscopic technologies, such as stimulated Raman scattering (SRS), second harmonic generation (SHG), and multiphoton fluorescence (MPF) microscopy for visualizing metabolic dynamics in living organisms in situ with subcellular resolution.

Gurol Suel

Molecular Biology

The Suel Lab's goal is to understand how dynamics at the cellular and population level improve bacterial fitness. We typically develop and utilize quantitative biology approaches to inform and constrain mathematical modeling.

Amir Zarrinpar

health Sciences

The Zarrinpar Lab is interested in the intersection of circadian biology, gut physiology, and the gut microbiome and how the three interact to cause obesity, diabetes, steatohepatitis, and other gut-mediated diseases.

Karsten Zengler

Pediatrics & Bioengineering

The Zengler lab studies the complex interactions of microorganisms. Interactions between microbes, their environment, or their host are essential for global cycles and play a crucial role in health and disease.

External Advisory Board

Galit Lahav

Harvard Medical School

Olga Troyanskaya

Princeton

MICROFLUIDICS

The use of microfluidic technology has become widely popular in the field of synthetic biology and beyond. Microfluidics facilitates the study of cellular behavior because it provides the necessary tools for recreating in vivo-like cellular microenvironments. We use microfluidic devices to observe cellular development within dynamic microenvironments, and design devices to generate thermal or chemical gradients or incorporate large-scale networks of fluidic channels for high-throughput cellular analysis. With these devices, we can generate single-cell expression profiles for a large number of cells, or for a library of strains, which is essential to understanding the roles of regulatory motifs within native and synthetic gene networks.

DEEP TISSUE IMAGING

Cells organize to form intricate 3D biological structures that are closely related to their physiological functions. It is critical to assess their structural and functional correlations at an organ-wide scale when study metabolic activities. We are developing novel deep tissue imaging technologies using stimulated Raman scattering (SRS) and multiphoton fluorescence (MPF) microscopy to better understand structural functional interactions in biological systems.
In particular, we developed a novel isotope-probed multiplex stimulated Raman scattering (ipm-SRS) microscopy imaging platform for visualizing deep
tissue metabolism and drug delivery in living organisms. It combines (1)
bioorthogonal labeling to examine the uptake and synthesis activity in
tissues, and (2) label-free SRS and MPF of endogenous signals to examine
cell structure, chemical composition, and biomolecular trafficking.

DYNOMICS

Genome-scale technologies have enabled mapping of the complex molecular networks that govern cellular behavior. An emerging theme in the analyses of these networks is that cells use many layers of regulatory feedback to constantly assess and precisely react to their environment. The importance of complex feedback in controlling the real-time response to external stimuli has led to a need for the next generation of cell-based technologies that enable both the collection and analysis of high-throughput temporal data. Toward this end, we have developed a microfluidic platform capable of monitoring temporal gene expression from over 2,000 promoters. By coupling the “DynOMICS” platform with deep neural network (DNN) and associated explainable artificial intelligence (XAI) algorithms, we can assess patterns in transcriptional data on a genome scale and identify which genes contribute to these patterns. DynOMICS platform can be used as a field-deployable real-time biosensor of heavy metals in urban water, based on the the dynamic transcription profiles of 1,807 unique Escherichia coli promoters.

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MICROBIOME

The human body harbors an estimated ten times as many microbial cells as human cells. By studying these microbes, we can learn more about ourselves, as microbial communities may record traces of what we’ve eaten, where we’ve lived, and who we’ve been in contact with, and also influence our health. Our ultimate goal is not just to read out our microbiome and look at predispositions but be able to change it for the better.

Our studies of  microbiota rely on robust, high-throughput molecular and microbiological techniques. To support our projects, there are on-going development efforts to establish and augment existing pipelines. An important component of our research is the development of new bioinformatic tools and resources to facilitate processing, analysis, and visualization of large data sets.

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SYNTHETIC BIOLOGY OF AGING

Aging is a defining factor in diseases such as cancer, diabetes, and neurodegenerative disorders. Innovative approaches to mitigate age-related diseases demand a better understanding of the basic biology of aging. Studies in model organisms have been critical in defining individual genes that influence aging. The emerging challenge is to understand how these genes interact and how these interactions drive the dynamics of the aging process. The traditional reductionist approach cannot address the totality of such complexity. Instead, new strategies that integrate multi-dimensional stochastic and nonlinear systems with large data sets are required. Our multidisciplinary team integrates high-throughput dynamic measurements with computational modeling to characterize and quantify the dynamic behaviors of aging-related molecular networks and how they regulate the aging processes in yeast S. cerevisiae. Using this knowledge and synthetic biology approaches we aim to design new intervention strategies to promote longevity.

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ENGINEERING BACTERIAL COMMUNITIES

Making synthetic gene circuits in bacteria is one thing, but making them stable under selective pressure with high mutation rates is another. We addressed this problem with an ecological strategy in which they created three strains of bacteria, each of which could kill or be killed by one of the other strains. Once the first strain of bacteria hosting the engineered circuit underwent mutations that decreased function, the system could be “rebooted” by addition of another strain that killed the first but also contained the desired synthetic circuit, allowing its function to proceed unperturbed. This strategy provides a way to control synthetic ecosystems and maintain synthetic gene circuits without using traditional selection to maintain plasmids with antibiotics.

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10th Annual Winter q-Bio conference

February 19-24, 2023  —  Frenchman’s Reef, St. Thomas, Caribbean ISLANDS

The 10th annual Winter q-bio meeting will bring together scientists and engineers who are interested in all areas of Quantitative Biology. Technology is driving revolutionary changes in biology. Systems Biology has arisen as the deduction of interaction networks from -omics data generated in the wake of remarkable technological achievements. Likewise, DNA synthesis technologies are driving the development of Synthetic Biology, whereby engineered circuitry and even entire genomes can be reconstituted from chemical building blocks. These two emerging areas have catalyzed the growth of Quantitative Biology, whereby the central goal is the deduction of quantitative principles that can be used to construct predictive models for biological phenomena. 

More information is available at the conference website