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James K. “Flip” McCarthy is a staff scientist in Andrew E. Allen’s lab at the J. Craig Venter Institute. Dr. McCarthy’s long-term research centers on how marine diatoms, specifically the model organism, Phaeodactylum tricornutum, assimilate nitrate under the nitrate replete and depleted conditions encountered in the marine environment. Focusing on the expression of the genes and cognate proteins, involved in the transport, reduction and storage of nitrate, as well as the ultimate integration of nitrate with assimilated carbon, his current research seeks to unravel the mechanisms involved in the regulation of nitrate assimilation. Dr. McCarthy’s recent work produced a nitrate reductase mutant strain of P. tricornutum, described how the loss of function affected the morphology and viability of the cell and pointed to physiological and molecular mechanisms that drive vacuolar storage of nitrate and the possibility of nitrate reductase–vacuolar transport protein complexes.
Prior to joining JCVI, Dr. McCarthy was a post-doctoral fellow at Scripps Institution of Oceanography (UC San Diego) where he made the gene knockout of the first manganese (Mn) oxidase identified in Pseudomonas putida, GB-1, initiated the sequencing of the P. putida, GB-1 genome and helped characterize Mn-oxidation in two Pseudomonads.
Dr. McCarthy received his B.A in English from Union College, Schenectady, NY. He then pursued a career as a cameraman, producer and writer for documentary and educational films and videos. Eventually, his keen interest in municipal-scale composting and alternative fuels led him to a Ph.D. in Microbiology and Molecular Genetics from Rutgers University.
Research Priorities
Components of the nitrate interactome in Phaeodactylum tricornutum
- Cohort of metabolites critical to the cellular response to nitrate flux
- Localization and activity of dual nitrite reductases and putative vacuolar nitrate transporters
- Protein-protein interactions/complexes that streamline nitrate assimilation
Distribution of lipids in P. tricornutum wild type vs. knockout cell lines
- Variation in lipid fractions, between whole cells and organelles: chloroplasts and vacuoles, are mediated by nitrate availability
Laboratory model for “luxury uptake” of nitrate by marine diatoms
- In the ocean environment, diatoms outcompete other planktonic species in response to nitrate-rich upwelling conditions by taking up and storing nitrate beyond their immediate needs – “luxury uptake”.
Publications
Research Priorities
Components of the nitrate interactome in Phaeodactylum tricornutum
- Cohort of metabolites critical to the cellular response to nitrate flux
- Localization and activity of dual nitrite reductases and putative vacuolar nitrate transporters
- Protein-protein interactions/complexes that streamline nitrate assimilation
Distribution of lipids in P. tricornutum wild type vs. knockout cell lines
- Variation in lipid fractions, between whole cells and organelles: chloroplasts and vacuoles, are mediated by nitrate availability
Laboratory model for “luxury uptake” of nitrate by marine diatoms
- In the ocean environment, diatoms outcompete other planktonic species in response to nitrate-rich upwelling conditions by taking up and storing nitrate beyond their immediate needs – “luxury uptake”.