Postdoctoral Scholars

I am broadly interested in microbial physiology, metabolic diversity, and understanding the mechanisms of extracellular electron transfer driven microbial processes and their ecological and evolutionary implications. Currently, my work is focused on characterizing cytochrome c biogenesis in Archaea and understanding the role of multiheme cytochrome c in direct interspecies electron transfer between Archaea and its syntrophic bacteria.

Dr. Dinesh Gupta (he/him)

Email: guptadineshATberkeley DOTedu

Postdoctoral Scholar
November 2020-present

Ph.D., Plant and Microbial Biosciences, Washington University in St. Louis
M.S., Biology, California State University Northridge
B.S., Microbiology, Tribhuvan University, Nepal

I aim to bring expertise from established fields of the Life Sciences, such as cell biology and enzymology, into emerging fields in the intersection of biology, chemistry, and geology, to bridge the gap between different scientific disciplines that will allow tackling questions concerning the past, present, and future impact of microbial life on Earth.
My previous research involved immunological and biochemical analyses of human pathologies, as well as geochemical analyses for mineralogical interpretations. I used this research background to develop two major interdisciplinary projects during my PhD work:
(1) Elaborate new methods to detect and analyze molecular fossils preserved in the geological record by using an antibody-based biomarker visualization approach and by a novel chromatographic separation assay, both methods reminiscent of immunological and analytical chemistry techniques used in cell biology and biochemistry, but this time applied as a geochemical tool to study the fossil record. These novel approaches link sedimentary molecular fossils with their biological provenance to better understand Earth’s biological past.
(2) Developing new methods to detect the field activity of the microbial enzymes urease and carbonic anhydrase, both relevant players in the carbon cycle that have considerable applications in biotechnology. Along with geochemical and metagenomic data, I used these novel field enzymatic assays to in situ test the role of microbes in the formation mechanism of tufas—an alien-looking carbonate rock that may play an important role in carbon sequestration and that may preserve signatures of life on Earth’s geological past and even on other planets. 
In addition, I have recently adapted one of the enzymatic field detection methods to serve as a simple and fun hands-on activity for middle and high school students. Through outreach events in different schools from the Bay Area, I initiated a citizen science project to conduct the first environmental microbial activity survey with data provided by students, which will benefit both science and our local communities alike.       
My current research as a Simons Foundation postdoctoral fellow focuses on understanding the molecular mechanisms by which methanogenic archaea sense their environment and regulate the production of methane. These microorganisms are the major source of Earth’s methane—a soaring greenhouse gas nearly 80-times more potent than carbon dioxide—having a tremendous impact in our present and future climate crisis. We are using a combination of evolutionary, genetic, biochemical, and geochemical tools in an interdisciplinary effort to uncover novel environmental signals and genetic regulators of methanogenesis, which will help us understand the physiology and evolutionary relationships of methanogenic archaea to better predict (and hopefully manage) methane emissions. 

Dr. Fernando Medina Ferrer (he/him)

Email: medinaferrerATberkeley DOTedu

Postdoctoral Scholar
March 2021-present

Ph.D., Earth Sciences-Geobiology. University of Minnesota, Minneapolis, MN, USA.
M.S., Geology, University of Chile, Santiago.
M.S., Biochemistry, University of Chile, Santiago.
B.S., Biochemistry, University of Chile, Santiago.

I am interested in understanding the evolution of energy metabolism in microbes at multiple scales, from the interactions of organisms with their physical environment down to the modifications of individual bioenergetic protein complexes. I focus on organisms that are important sources and sinks of methane on Earth. Much of my previous work was conducted on uncultured organisms in complex environments, allowing us to understand broadly which biogeochemical processes are carried out by which organisms. My work in the Nayak lab at UC Berkeley will focus on the genetic manipulation and physiological studies to produce more mechanistic understanding of energy metabolism in understudied organisms within the Archaea.

Dr. Grayson Chadwick (he/him)

Email: chadwickATberkeley DOTedu

Miller Postdoctoral Scholar
August 2020-present

Ph.D., Geobiology, California Institute of Technology
B.S. with honors, Biology, California Institute of Technology

In my research, I use the stable isotopic composition of methane as a proxy for the activity of methane-producing and consuming microbes. During my Ph.D., I developed metabolic network models of methanogens and methanotrophs, which I combined with enzyme-level isotopic effects to link environmental conditions, metabolic states, and isotopic compositions of methane.
This theme will continue in my postdoctoral research, where I will focus on conducting experiments using genetically-tractable methanogenic strains in the Nayak lab. These will be complemented with bulk and clumped isotopic measurements in the Stolper lab in the EPS Department.

Dr. Jonathan Gropp (he/him)

Email: jaDOTgroppATberkeley DOTedu

Postdoctoral Scholar (joint with the Stolper Lab)
August 2022-present

Ph.D., Chemical Sciences, Weizmann Institute of Science, Israel
M.S., Life Sciences, Weizmann Institute of Science, Israel
B.S., Biotechnology, Tel-Hai College, Israel

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