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
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
Hana El Samad
Altos
Galit Lahav
Harvard Medical School
Wendell Lim
UCSF
Olga Troyanskaya
Princeton
Albert P. Pisano
CSD
Kit Pogliano
UCSD
MICROFLUIDICS
DEEP TISSUE IMAGING
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.
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.
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.
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.
11th Annual Winter q-Bio conference
February 19-23, 2024 — Four Seasons Oahu at Ko Olina, Hawaii
The 11th 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
Elementary School Science Partnership
For many of us, elementary school science was a forgettable experience. Dry textbooks and staid examples did nothing to incite our natural curiosity. Here at UCSD, we want to change that. We take brilliant graduate students, professors and all the resources that a world-class research institute offers, and put them in front of an elementary-school audience who can truly appreciate it. Our message is simple: the world is a wondrous place, and worth learning about! We invite you to look at the incredible things our students and teachers have done together, and we hope you’ll lend us a hand in making better futures for our kids.
What We Do
What was the most fun thing you ever did, in your years of science education? What experiment sticks with you to this very day? More than anything, we want to bring the magic for our students every week. We encourage crazy experiments, we make messes, and we’re lucky enough to have the resources to be able to do most anything.
Purpose
In order to attempt to improve public science education at the local level, we have initiated an ”Elementary School Partnership” program within the Synthetic Biology Institute at UCSD. We currently work with Lafayette Elementary in the Clairemont area of the San Diego Unified School District. Lafayette Elementary serves 247 students in grades K-5, with the BioCircuits Elementary School Partnership working closely with grades 3-5. Lafayette was designed and built for general education students and the District’s DHH program, meeting the needs of its very diverse population. They are designated a Title 1 school based on the number of students who qualify for free or reduced lunch and/or whose parents have less than a high school education.
Each graduate student is responsible for a different grade level, and teaches in the same classroom each week, giving one-on-one attention to students and directing classroom experiments. Coordinators and students plan experiments based on the science curriculum for the week, and graduate students supplement classroom materials with scientific equipment brought from their respective lab.
More information is available at the Biocircuits Outreach Website.
Volunteers
Sarah Hasty
UCSD Synthetic Biology Institute Elementary Science Outreach Coordinator
Kristina Chan
Volunteer
Alyssa Chiang
Volunteer
Austin Doughty
Volunteer
Philip Emmanuele
Volunteer
Shayna Holness
Volunteer
Mitchell Kong
volunteer
Shalni Kumar
Volunteer
Benjamin Liang
Volunteer
Zahra Mousavi Karimi
Volunteer
Chloe Nguyen
Volunteer
Katie O'Connor
Volunteer
Jon Price
Volunteer
Sekou Rowe
Volunteer
Diva Sansanwal
Volunteer
Paige Steppe
Volunteer
Joanna Zhang
Volunteer
