mit synthetic biology phd

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Synthetic Biology

Synthetic Biology is an emerging field of research where researchers construct new biological systems and redesign existing biological systems. Faculty in BE are studying synthetic biology from the foundational level of developing a programming language for cells to the applied level of engineering viruses to secrete enzymes that breakdown harmful bacterial biofilms. 

Jessica Stark, PhD

Anders sejr hansen, phd, laurie a. boyer, phd, james j. collins, phd, amy e. keating, phd, ron weiss, phd, alan jasanoff, phd, ed boyden, phd, christopher a. voigt, phd, eric alm, phd.

Media Arts & Sciences Synthetic Neurobiology

Your brain mediates everything that you sense, feel, think, and do. The brain is incredibly complex—each cubic millimeter of your brain contains perhaps a hundred thousand cells, connected by a billion synapses, each operating with millisecond precision. The MIT Synthetic Neurobiology group , led by Ed Boyden, develops tools that enable the mapping of the molecules and wiring of the brain, the recording and control of its neural dynamics, and the repair of its dysfunction. They distribute their tools as freely as possible to the scientific community, and also apply them to the systematic analysis of brain computations, aiming to reveal the fundamental mechanisms of brain function, and yielding new, ground-truth therapeutic strategies for neurological and psychiatric disorders.

Learn more about Synthetic Neurobiology .

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A new control system for synthetic genes

Posted: .

Researchers have developed a technique that could help fine-tune the production of monoclonal antibodies and other useful proteins.

Credits:  Cell image: Matthew Daniels, edited by MIT News

• Bioengineering and Neuroengineering

• ACS Synthetic Biology

MIT has a long-standing tradition of excellence in microbiological research, and there are over 50 faculty from several different departments and divisions who study or use microbes in significant ways in their research.

Research in microbiology is going on throughout MIT and includes more than 50 faculty. These faculty are from several departments and divisions in both the Schools of Science and Engineering, including: Biology; Biological Engineering; Chemical Engineering; Chemistry; Civil and Environmental Engineering; Earth, Atmospheric and Planetary Sciences; Electrical Engineering and Computer Science; Materials Sciences and Engineering; and Physics. Many labs take multiple approaches to studying and manipulating microbial systems and the expertise and research covers a wide range of areas, including biochemistry, biotechnology, cell and molecular biology, chemical and biological engineering, computational biology, ecology, environmental biology, evolutionary biology, genetics, genomics, geobiology, immunology, pathogenesis, structural biology, synthetic biology, systems biology and virology.

The program integrates educational resources across the participating departments, to build connections among faculty with shared interests from different units, and to build an educational community for training students in the study of microbial systems.

The graduate training program aims to attract and train a talented group of students interested in a range of aspects of microbiology. The program will provide students a broad exposure to underlying elements of modern microbiological research and engineering, and will provide depth in specific areas of microbiology during the student‘s thesis work. Students completing this program will be prepared and able to go into a range of fields in microbial science and engineering. Students with interdisciplinary training in microbiology are in increasing demand in both public and private sectors. With the broad interdisciplinary training and high quality in-depth research experience, students from this program will have excellent career options in academic, industrial, and government settings.

Microbiology is fundamental to the life sciences

The study of microbes has been critical in our current understanding of basic biological processes, evolution, and the functions of the biosphere and has contributed to numerous fields of engineering. Microbes have the amazing ability to grow in extreme conditions, to grow slowly or rapidly, and to readily exchange DNA. They are essential for life as we know it, but can also be agents of disease. They are instrumental in shaping the environment, in evolution, and in modern biotechnology. They are amenable to virtually all modern approaches in science and engineering. They provide natural engineering laboratories for creating new capabilities for industry (e.g., pharmaceuticals, chemicals, energy), and are the foundation of pioneering efforts in synthetic biology – i.e. building life from its component parts. Effective study of microbes and their applications demands multiple interdisciplinary approaches that cross all scales of biological organization, from molecules to vast ecosystems.

Microbiology and Energy

Microbes have tremendous potential for use in energy generation. They are able to synthesize materials useful for producing energy and their remarkable metabolic processes can be harnessed for energy generation. One of the hallmarks of the microbial world is the ability of microorganisms to catalyze diverse and challenging chemical reactions as part of their metabolism. Complex processes such as photosynthesis, nitrogen fixation, conversion of methane to methanol, lignocellulose degradation, ethanol production, and electron transfer to solid substrates (to name just a few) can potentially be harnessed for the purpose of energy generation. Over billions of years, microbes have evolved sophisticated catalytic machinery for energy generation that has actively shaped the geochemistry of the Earth. Today, we can study how their catalytic abilities manifest their effects in various environments, including the world’s oceans and terrestrial habitats. Many labs at MIT are focused on understanding the diverse cellular and metabolic processes of microbes and using this basic information for purposes of energy production.

Initial financial support for the Microbiology Graduate Program came from the School of Science, the School of Engineering, the Provost’s Office, and the Departments of Biological Engineering, Biology, Chemical Engineering, Chemistry and Astra Zeneca. Current financial support comes from the School of Science, the School of Engineering, and the Departments of Biological Engineering, Biology, Chemical Engineering and Civil & Environmental Engineering.

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Synthetic biology

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Prof. Ritu Raman has developed centimeter-scale robots that use biological muscle, reports Liam Drew for Nature . “Raman is now developing muscle systems connected to neurons that can trigger contraction, just as they exist in animals,” writes Drew. “In the longer term, she aims to use networks of biological neurons that can sense external stimuli as well, enabling them to move in response to environmental cues.”

The Boston Globe

Boston Globe reporter Robert Weisman spotlights Integrated Biosciences, a startup co-founded by MIT researchers that is using artificial intelligence to identify anti-aging drug candidates. “We’re trying to go after aging and aging-associated disorders,” says postdoc Felix Wong. “We all know loved ones who have suffered from some of these conditions.”

Ginkgo Bioworks, a biotech company founded by Jason Kelly BS ’03, PhD ’08, Reshma Shetty PhD ‘08, Barry Canton PhD ’08, Austin Che PhD ’08 and Professor Tom Knight, is working to develop synthetic fragrances, reports Scott Kirsner for The Boston Globe .

Scientific American

Prof. Ritu Raman speaks with Scientific American about her work “building machines that we call bio-hybrid because they're part biological and part made out of synthetic materials. The biological robots that we're building are powered by muscle tissue so that every time the muscle contracts, you could get something that looks like movement.”

Asimov - an MIT spinout co-founded by Prof. Christopher Voigt, Alec Nielsen PhD ’16, Raja Srinivas PhD ’16, and Boston University Prof. Douglas Densmore - is a biotechnology company developing tools to design living systems, reports John Cumbers for Forbes . “Every cell is capable of computing. Perceiving environmental signals, information processing, turning genes on and off,” says Nielsen. “The ability to engineer this gift of evolution is, in my view, going to be the most meaningful and impactful technology that humans have ever developed.”

Scientists from MIT, Georgia Institute of Technology, Sun Yat-sen University and Beijing-based AI startup Galixir have developed a deep-learning toolkit that can predict biosynthetic pathways for natural products, which are a primary source of clinical drug discovery, reports Xinhua Net . “The researchers presented a toolkit called Bionavi-NP to propose NP biosynthetic pathways from simple building blocks in an oprtimal fashion, which requires no already-known biochemical rules,” writes Xinhua Net .

MIT startup Volta Labs is developing a new instrument that can automate the processes used to prepare genetic samples, reports Emma Betuel for TechCrunch . CEO and co-founder Udayan Umapathi ’17 is confident that with the right programming, the platform could allow “liquids to be manipulated in even more complex ways, like using magnetic fields to draw certain molecules out of samples for further analysis,” writes Betuel.

Smithsonian Magazine

Researchers from MIT and the Smithsonian Conservation Biology Institute are developing a probiotic to cure amphibian chytrid fungus in frogs, reports Jennifer Zoon for Smithsonian Magazine .

New York Times

New York Times reporter Steve Lohr spotlights the origin and history of MIT startup Gingko Bioworks, a synthetic biology company founded with a “shared belief that biology could be made more like computing with reusable code and standard tools instead of the bespoke experiments of traditional biology." Jason Kelly ’03, PhD ’08, one of the founders of MIT startup Ginkgo Bioworks and the company’s chief executive, explains that “the ultimate goal for Ginkgo is to make it as easy to program a cell as it is to program a computer.”

Ginkgo Bioworks founders Jason Kelly PhD ’08, S.B. ’03 and Reshma Shetty PhD ’08 speak with Boston Globe reporter Scott Kirsner about the inspiration for and growth of the company, which is focused on manipulating genetic material to get living cells to perform new jobs. Shetty notes that the Ginkgo Bioworks team is “dedicated to making biology easier to engineer."

New Scientist

New Scientist reporter Layal Liverpool writes that a new study co-authored by MIT researchers finds that “synthetic cells made by combining components of  Mycoplasma  bacteria with a chemically synthesised genome can grow and divide into cells of uniform shape and size, just like most natural bacterial cells.”

Prof. Kristala L. J. Prather speaks with Korie Grayson of C&EN about her career path and her work harnessing the synthetic power of microbial systems. Of the importance of mentorship, Prather notes, “The exponential way in which you can actually have a positive impact is by taking good care of the people who are placed into your academic and intellectual trust. That’s how we make a difference.”

Marketplace

Prof. James Collins speaks with Molly Wood of Marketplace about his work developing a faster, cheaper and more accurate Covid-19 diagnostic. Collins explains that his research group is “using synthetic biology to create highly sensitive, low-cost diagnostics, some that are now approved for use in clinical diagnostics labs, and now we’re moving towards point-of-care diagnostics, as well as at-home diagnostics.”

Forbes reporter Amy Feldman spotlights MIT startup Ginkgo Bioworks, which aims to “design, modify and manufacture organisms to make existing industrial processes cheaper and entirely new processes possible.” Feldman notes that the promise of synthetic biology is “not just a proliferation of new products, but also a reduction of the environmental harm that comes from our heavy reliance on petrochemicals.”

Guardian reporter Ian Sample writes that MIT startup Synlogic are developing a “living” medicine” made from genetically modified bugs. “By engineering these bacteria, we are able to control how they operate in the human gastrointestinal tract,” says Caroline Kurtz of Synlogic. “It allows us to think about many other diseases where you may need to produce something beneficial, or remove something that is toxic for the patient.”

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