Synthetic and Systems Biology
Berkeley is a pioneer in synthetic biology, which involves the design and construction of parts, devices and systems from biological components, generally at the cellular and molecular scale. Frequently this involves editing the genome of a microorganism to produce a desired chemical compound, or changing their behavior to fight diseases inside the body.
Systems biology approaches living systems as dynamic networks rather than collections of individual units, and aims to understand and use these networks to model and design systems which perform valued functions.
A primary application of these closely-related fields is using microbes to manufacture medications, flavorings, dyes and other chemicals in bulk in a cost-effective and environmentally friendly way. Other uses include the design of new medications and specialized chemicals, the creation of advanced tools for organism customization and safety, and road maps for sustainable agriculture and biomanufacturing communities.
Research in synthetic and systems biology has real-world impact in areas like:
Biosafety and ethics, the Environment, gene editing, manufacturing.
Adam Arkin
For more information, see: https://arkinlab.bio/
The Arkin Lab focus is how microbes transform, clean, and improve soils, soils that are currently degrading due to climate change, pollution, and poor water use. Near close-loops, low-energy, low-input biomanufacturing programs for food, pharmaceuticals, and building materials at “small village” scale, which are initially designed for a deep-space crewed Mars mission but have applications here on Earth for supporting sustainable agriculture. Another interest is to develop engineering approaches for microbiomes so we can control communities of microbes that drive the earth’s mineral cycles, support our plants and efficiency and stress responses, and impact the health and food-efficiency of a good many living creatures including ourselves.
Iain Clark
For more information, see: http://clarklab.berkeley.edu/
The Clark Lab develops microfluidic and molecular methods for the high throughput analysis of single cells. We use these techniques to study HIV latency in CD4 T cells and profile cellular interactions during central nervous system inflammation.
Irina Conboy
For more information, see: https://conboylab.berkeley.edu/
Our work has been focused on establishing new paradigms in multi-tissue stem cell aging, rejuvenation and regulation by conserved morphogenic signaling pathways. One of our goals is to define pharmacology for enhancing maintenance and repair of adult tissues in vivo. The spearheaded by us heterochronic parabiosis and blood apheresis studies have established that the process of aging is reversible through modulation of circulatory milieu. Our synthetic biology method of choice focuses on bio-orthogonal non-canonical amino acid tagging (BONCAT) and subsequent identification of age-imposed and disease-causal changes in mammalian proteomes in vivo. Our drug delivery reg medicine projects focus on CRISPR/Cas9 based therapeutics for more effective and safer gene editing.
John Dueber
For more information, see: https://dueberlab.berkeley.edu/
The Dueber Lab develops strategies for introducing designable, modular control over living cells. We are particularly interested in generating technologies for improving engineered metabolic pathway efficiency and directing flux. Our projects have applications in the development of biofuels, specialty chemicals, and environmentally friendly processes.
Leah Guthrie
For more information, see: https://www.theguthrielab.com/
The Guthrie lab investigates the principles that govern microbial metabolism and signaling in the context of kidney homeostasis and disease using mass spectrometry, chemoinformatics, and molecular biology approaches.
Patrick Hsu
For more information, see: http://patrickhsulab.org/
The Hsu Lab aims to understand and manipulate the genetic circuits that control brain and immune cell function to improve human health. We explore the rich biological diversity of nature to create new molecular technologies, perturb complex cellular processes at scale, and develop next-generation gene and cell therapies. To do this, our group draws from a palette of experimental and computational techniques including CRISPR-Cas systems, single cell genomics, engineered viruses, brain organoids, and pooled genetic screens. Current interests include 1) inventing novel approaches for editing the postmitotic genome, 2) developing engineered vehicles for therapeutic macromolecule delivery, and 3) leveraging library screens and brain organoids to interrogate human neuroscience at scale.
Jay Keasling
For more information, see: https://keaslinglab.lbl.gov/
Metabolic engineering, environmental biotechnology, and biochemical engineering.
Sanjay Kumar
For more information, see: https://kumarlab.berkeley.edu/
Our lab seeks to understand and engineer mechanical and other biophysical communication between cells and materials. In addition to investigating fundamental aspects of this problem with a variety of micro/nanoscale technologies, we are especially interested in discovering how this signaling regulates tumor and stem cell biology in the central nervous system. Recent directions have included: (1) Engineering new tissue-mimetic culture platforms for biophysical studies, molecular analysis, and screening; (2) Exploring mechanobiological signaling systems as targets for limiting the invasion of brain tumors and enhancing stem cell neurogenesis; and (3) Creating new biomaterials inspired by cellular structural networks.
Liana Lareau
For more information, see: http://www.lareaulab.org/
A single genome produces the huge diversity of cells and tissues needed to make a human by regulating gene expression to turn on and off the right genes at the right times. The final, post-transcriptional steps of gene expression — RNA processing and translation — are essential to the proper outcome. Our goal is to understand how these layers of regulation are encoded in gene sequences and how disruptions to this regulation can cause disease. Our research uses machine learning and other computational methods, coupled with high-throughput experiments, to understand how post-transcriptional regulation leads to robust and flexible control of gene expression.
Mohammad Reza Kaazempur Mofrad
For more information, see: https://biomechanics.berkeley.edu/
Molecular and Multiscale Biomechanics; Bioinformatics and Computational Biology; Statistical Machine Learning; Computational Precision Health; Microbiome; Personalized Medicine
Aaron Streets
For more information, see: https://streetslab.com/
The Streets lab is interested in applying lessons from mathematics, physics, and engineering, to invent tools that help us dissect and quantify complex biological systems. Our goal is to uncover laws that govern the interactions of molecules inside the cell and the interactions between cells in a tissue or organism, by making precision measurements on single cells. In pursuit of this goal, we exploit three core technologies; microfluidics, microscopy, and genomics.
News About: Synthetic & Systems Biology
Pivot Bio is using microbial nitrogen to make agriculture more sustainable
Co-founded by BioE alumnus Karsten Temme, Pivot is bringing cleaner nitrogen to American farmland.
Arkin Lab receives ARPA-H award for microbiome engineering
Adam Arkin has been granted an award of over $20 million from the Advanced Research Projects Agency for Health (ARPA-H) to pursue microbiome engineering to create probiotic bacterial communities that prevent and treat lung pathogens.
Could a new medical approach fix faulty genes before birth?
Murthy lab and UC Davis have developed a unique mRNA delivery method for in-utero gene editing for neurodevelopmental conditions.
Revealing the Mysteries Within Microbial Genomes
Adam Arkin’s lab has developed a new technique, barcoded overexpression bacterial shotgun library sequencing (Boba-seq), that will make it much easier for researchers to discover the traits or activities encoded by genes of unknown function in microbes.
Bakar ClimatEnginuity Hub: Berkeley’s new home for climate innovation
Professor David Schaffer will lead the new Bakar ClimatEnginuity Hub, an incubator that will provide resources and support to entrepreneurs in renewable energy and clean technology.
Berkeley’s ecosystem of innovation, entrepreneurship combats climate change
Professors John Dueber and David Schaffer are featured in this article highlighting campus research and entrepreneurship in sustainability.
Bolt Threads going public
Bolt Threads, a company co-founded by BioE PhD alumnus David Breslauer, plans to go public in a SPAC deal that values the one-time unicorn at $250 million. Bolt Threads uses synthetic biology and other techniques to sustainably produce engineered biomaterials, including synthetic spider silk and mushroom-based faux leather.
Uncovering the Secrets of the Smallest Phages
In a new paper in Nature Chemical Biology, Professor Adam Arkin and collaborator Vivek Mutalik report advances in understanding phage biology that bring us closer to using these small predators to fight antibiotic-resistant bacteria.
Bacteria for Blastoff: Using Microbes to Make Supercharged New Rocket Fuel
New research led by Professor Jay Keasling took inspiration from an extraordinary antifungal molecule made by Streptomyces bacteria to develop a totally new type of fuel that has projected energy density greater than the most advanced heavy-duty fuels used today, including the rocket fuels used by NASA.
Best Inventions of 2021: Huue
Congratulations BioE startup Huue and founder PhD alumna Tammy Hsu! Huue’s process for creating environmentally friendly indigo dye through synthetic biology has been named one of Time Magazine’s Best Inventions of 2021.