BME7900 Seminar Series - Adam Arkin, PhD




For our next speaker, we welcome Dr. Adam Arkin. He is the Dean A. Richard Newton Memorial Professor from the Department of Bioengineering at UC Berkeley. Along with his role in Bioengineering, Dr. Arkin is also a Senior Faculty Scientist at the Lawrence Berkeley National Laboratory. Dissecting mechanisms of metabolism and predation in environmental microbial communities Abstract: One of the central biological engineering challenges in the next century will be engineering to mitigate the progression and impact of climate change and large scale human industries on the environment. These solutions will likely involve, in part, the systems engineering of plants, microbes and their communities along with good land- and water-use practice. The communities of organisms that provide services in the environment are complex and are often exceptionally uncharacterized. Here we will discuss progress on developing scientific and technological approaches to understanding these communities in situ and bringing critical components into the laboratory for deep dissection and recovery of elements useful for intervening in environmental processes. In specific, we will discuss how we are deploying advanced field measurements, metagenomics, and high-throughput genetics to understand microbial community assembly and activity within a metal and nitrate contaminated watershed amplified by our work building an open and extensible systems biology platform- the DOE Systems Biology Knowledgebase. Bio: Dr. Arkin and his laboratory develop experimental and computational technologies for discovery, prediction, control and design of microbial and viral functions and behaviors in environmental contexts. His work spans synthetic and systems biology, genomics, metagenomics, and physiology. He is the chief scientist of the Department of Energy Scientific Focus Area, ENIGMA, designed to understand, at a molecular level, the impact of microbial communities on their ecosystems with specific focus on terrestrial communities in contaminated watersheds. He also directs the Department of Energy Systems Biology Knowledgebase program, an open platform for comparative functional genomics, systems and synthetic biology for microbes, plants and their communities, and for sharing results and methods with other scientists. He is director of the Center for Utilization of Biological Engineering in Space which seeks microbial and plant-based biological solutions for in situ resource utilization that reduce the launch mass and improves reliability and quality of food, pharmaceuticals, fuels and materials for astronauts on a mission to Mars.