James McCarthy, Staff Scientist

Dr. James K. “Flip” McCarthy is a Postdoctoral Fellow in Andrew Allen’s lab at the J. Craig Venter Institute studying nitrate assimilation in the marine diatom Phaeodactylum tricornutum. Flip received his BA in English at Union College. For his doctorate in Microbiology and Molecular Genetics from Rutgers University, he focused on the directed evolution of cellulolytic enzymes of the marine hyperthermophile, Thermotoga neapolitana. Flip then moved to Scripps Institution of Oceanography to pursue postdoctoral studies in Dr. Bradley Tebo’s lab. His research at SIO, lead to the genome sequencing of the marine bacterium, Pseudomonas putida sp. GB-1, and the identification of the gene(s) required for manganese oxidation in GB-1.

Research Interests:

  • Nitrate reductase (NR) localization in the cell
  • Physiological and molecular mechanisms that drive vacuolar storage of nitrate: the probability of NR and vacuolar transport protein complexes
  • Using transcriptomic, proteomics and phosphoproteomics to describe an NR regulon

Flip is interested in determining if diatom NR is in proximity to, or localized on, the vacuolar membrane under N-source and life-cycle conditions that drive NR from a cytosolic localization. His current research aims to identify the vacuolar transport proteins in P. tricornutum that have been shown in plants to pump NO3 into and out of the vacuole. Flip is also interested in identifying a cohort of proteins that identifies diatoms’ response to nitrate replete vs. deplete conditions. To that end, he is currently using a transcriptomic expression cluster of NR-related genes, derived from a time-course experiment, to query the proteomic data set, from the same experiment, for proteins that either do or do not sync to the transcriptome cohorts’ expression patterns. Most recently, he is analyzing a phospho-peptide data set, drawn from the time course, to identify discreet and shared peptides, and expression patterns, that may help describe a shared phosphoryl-response to extra- and intracellular nitrate availability.

Selected Publications:

Veluchamy, A. and Rastogi, A. and Lin, X. and Lombard, B. and Murik, O. and Thomas, Y. and Dingli, F. and Rivarola, M. and Ott, S. and Liu, X. and Sun, Y. and Rabinowicz, P. D. and McCarthy, JK, and Allen, A. E. and Loew, D. and Bowler, C. and Tirichine, L. 2015. An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum. Genome Biol. 16:102. 10.1186/s13059-015-0671-8

Weyman PD, Beeri K, Lefebvre SC, Rivera J, McCarthy JK, Heuberger AL, Peers G, Allen AE, Dupont CL. 2015. Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis. Journal of Plant Biotechnology 13(4): 460-70.

Geszvain K, McCarthy JK, Tebo BM. 2013. Elimination of manganese (II,III) oxidation in Pseudomonas putida GB-1 by a double knockout of two putative multicopper oxidase genes. Applied and Environmental Microbiology. 79(1): 357-66.

Dick GJ, Podell S, Johnson HA, Rivera-Espinoza Y, Bernier-Latmani R, McCarthy JK, Torpey JW, Clement BG, Gaasterland T, Tebo BM. 2008. Applied and Environmental Microbiology. 74(9): 2646-58.

Tebo BM, Johnson HA, McCarthy JK, Templeton AS. 2005. Geomicrobiology of manganese(II) oxidation. Trends in Microbiology. 13(9): 421-8.

McCarthy JK, Uzelac A, Davis DF, Eveleigh DE. 2004. Improved catalytic efficiency and active site modification of 1,4-beta-D-glucan glucohydrolase A from Thermotoga neapolitana by directed evolution. Journal of Biological Chemistry 19; 279(12): 11495-502

McCarthy JK, O’Brien CE, Eveleigh DE. 2003. Thermostable continuous coupled assay for measuring glucose using glucokinase and glucose-6-phosphate dehydrogenase from the marine hyperthermophile Thermotoga maritima. Analytical Biochemistry. 15; 318(2):196-203.

Yernool DA, McCarthy JK, Eveleigh DE, Bok JD. 2000. Cloning and characterization of the glucooligosaccharide catabolic pathway beta-glucan glucohydrolase and cellobiose phosphorylase in the marine hyperthermophile Thermotoga neapolitana. Journal of Bacteriology. 182 (18):5172-9.