Lawrence Berkeley National Lab
Biological Systems and Engineering
Dr. Mukhopadhyay’s work is centered in the Environmental Atlas, focused on understanding membrane transport, signaling, stress response, and tolerance phenotypes in environmental microbes. She utilizes a wide variety of microbiological, biochemical, and systems biology tools to examine environmentally important organisms such as sulfate and metal-reducing bacteria as well as cyanobacteria. She has a specific interest in signaling mechanisms in novel non-model organisms like Pseudomonas stuzeri, Desulfovibrio vulgaris. Her latest work characterizes plasmids isolated from the field site, evaluating these environmental plasmids’ role in the microbial community and their use as biodesign tools, to genetically manipulate isolates from ORR and other bacteria of interest. She is also interested in using viral DNA as a predictor of
She plans to examine signaling systems and mobile genetic elements and evaluate their ecological significance. In order to examine signaling systems, we will primarily focus on response regulators that act via transcriptional activation and implement the DAP-seq approach. We will explore mobile genetic elements, spanning both plasmids and viruses, in samples collected from the OR FRC, by implementing our plasmidome assay. We will evaluate functional genes on these mobile genetic elects in the context of the ecology of the site and we will mine the plasmids tools development, such as creating a library of natural vectors for the isolate collection.
A successful outcome of this work is key publications outlining the signaling and regulatory systems for a select group of Pseudomonas and Rhodanobacter strains in the isolate collection. Further, we will have conducted and published 2-3 plasmidomics studies to compare samples across nitrate, pH gradients, and groundwater vs. sediment. We will also establish an origins library and determine a selection of isolates and model bacteria that can be transformed using them.