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PALENIK, BRIAN

Professor of Marine Biology

Education Director Ocean Biology Program

Degrees:

• B.S.E., Princeton University
• Ph.D., Massachusetts Institute of Technology, Woods Hole Oceanographic Institution

Research Interests:

• Marine genomics and metagenomics
• Phytoplankton diversity and evolution
• Adaptations of phytoplankton to their physical and chemical environments, especially nutrient limitation and metal toxicity
• Algal biofuels

Courses Recently Taught:

• BIMM127: Marine Microbiology Lab
• ESYS101: Environmental Biology
• SIO 126: Marine Microbiology
• SIO278: Seminar in Ocean Biosciences
• SIO282: Phytoplankton Diversity

Honors and Awards:

• NSF Research Fellowship in Marine Biotechnology, 1989-1991 Darbaker Prize, Botanical Society of America 2010

Mentoring:

• Paz Yepes, Javier (Post Doc; 2011-)
• Wang, Shuyi (Post Doc; 2011-)
• Stuart, Rhona (Graduate; 2006-2012)
• Landry, Dori (Graduate; 2000-2006)
• Davis, Aubrey (Graduate; 1999-2005)
• Toledo, Gerardo (Graduate; 1995-2000)
• Dyhrman, Sonya (Graduate; 1994-1999)
• , (Graduate; -)
• Collier, Jackie (Post Doc; -)
• Daniels, Emy (Masters; -)
• Dupont, Chris (Graduate; -)
• Ferris, Mike (Post Doc; -)
• Johnson, Todd (Graduate; -)
• Lambert, William (Masters; -)
• Ma, Yingfei (Post Doc; -)
• Tai, Vera (Graduate; -)
• Worden, Alex (Post Doc; -)

Palenik, B., 1994. Cyanobacterial community structure as seen from RNA polymerase gene sequence analysis. Appl. Environ. Micro. 60: 3212-3219.

Palenik, B. and J. A. Koke, 1995. Characterization of a nitrogen-regulated protein identified by cell surface biotinylation of a marine phytoplankton. Appl. Environ. Micro. 61: 3322-3315.

Palenik, B. and H. Swift, 1996. Cyanobacterial evolution and prochlorophyte diversity as seen in DNA-dependent RNA polymerase gene sequences. J. Phycol. 32: 638-646.

Dyhrman, S. T. and B. P. Palenik, 1997. The identification and purification of a cell-surface alkaline phosphatase from the dinoflagellate Prorocentrum minimum (Dinophyceae). J. Phycol. 33: 602-612.

Palenik, B. and S. E. Henson, 1997. The use of amides and other organic nitrogen sources by the phyytoplankton Emiliania huxleyi. Limnology and Oceanography 42: 1544-1551.

Toledo, G. and B. Palenik, 1997. Synechococcus diversity in the California Current as seen by RNA polymerase (rpoC1) gene sequences of isolated strains. Applied and Environmental Microbiology 63: 4298-4303.

Ferris, M. J. and B. Palenik, 1998. Niche adaptation in ocean cyanobacteria. Nature 396: 226-228.

Dyhrman, S. T. and B. Palenik, 1999. Phosphate stress in cultures and field populations of the dinoflagellate Prorocentrum minimum detected by a single-cell alkaline phosphatase assay. Appl. Environ. Microbiol. 65: 3205-3212.

Collier, J. L., B. Brahamsha and B. Palenik, 1999. The marine cyanobacterium Synechococcus sp. WH7805 requires urease (urea amidohydrolase, EC 3.5.1.5) to utilize area as a nitrogen source: molecular-genetic and biochemical analysis of the enzyme. Microbiology U.K. 145: 447-459.

Palenik, B., G. Toledo and M. J. Ferris, 1999. Cyanobacterial diversity in marine ecosystems as seen by RNA polymerase (rpoC1) gene sequences, in Marine Cyanobacteria (L. Charpy and A.W.D. Larkum, eds.), Bull. l'Inst. Oceanographique, Monaco, Spec. Issue No. 19, pg. 101-105. Review

Palenik, B., 2000. Why do isolates of eubacterial species have different growth rates under the same conditions, in Microbial Biosystems: New Frontiers (C.R. Bell, M. Brylinsky and P. Johnson-Green, eds.), Proceedings of the 8th International symposium on Microbial Ecology. Atlantic Canada Soc. For Microbial Ecology, Halifax, Canada, pp. 611-616.

Toledo, G., B. Palenik, and B. Brahamsha, 1999. Swimming marine Synechoccus strains with widely different photosynthetic pigment ratios form a monophyletic group. Applied and Environmental Microbiology 65: 5247-5251.

Palenik, B., 2001. Chromatic adaptation in marine Synechococcus strains. Applied and Environmental Microbiology 67: 991-994.

Dyhrman, S. T. and B. Palenik, 2001. A single-cell immunoassay for phosphate stress in the dinoflagellate Prorocentrum minimum (Dinophyceae). J. Phycology 37: 400-410.

Toledo, G. and B. Palenik. 2003. A Synechococcus serotype is found preferentially in surface marine waters. Limnol. Oceanogr. 48: 1744-1755.

B. Palenik, B. Brahamsha, F.W. Larimer, M. Land, L. Hauser, P. Chain, J. Lamerdin, W. Regala, E. A. Allen, J. McCarren, I. Paulsen, A. Dufresne, F. Partensky, E. A. Webb, J. Waterbury. 2003. The genome of a motile marine Synechococcus. Nature 424:1037-42.

J. Collier and B. Palenik, 2003. Phycoerythrin-containing picoplankton in the Southern California Bight. Deep Sea Research. Part II. 50:2405-2422.

S. T. Dyhrman and B. Palenik. 2003. Characterization of ectoenzyme activity and phosphate-regulated proteins in the coccolithophorid Emiliania huxleyi . J. Plankton Res. 25: 1215-1225.

Z. Su, P. Dam, X. Chen, V. Olman, T. Jiang, B. Palenik, Y. Xu. 2003. Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102. Genome Information. 14:3-13.

A. Z. Worden, J.K.Nolan and B. Palenik. 2004. Assessing the dynamics and ecology of marine picophytoplankton: The importance of the eukaryotic component. Limnol. Oceanogr. 49:168-179.

E.V. Armbrust, J.A. Berges, C. Bowler et al (Palenik). 2004. The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 306: 79-86.

X. Chen, Z. Su, P. Dam, B. Palenik, Y. Xu, and T. Jiang. 2004. Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome. Nucleic Acids Research. 32: 2147-2157. .

A.K. Davis, M. Hildebrand, B. Palenik. 2005. A stress-induced protein associated with the girdle band region of the diatom Thalassiosira pseudonana. J. Phycol. 41:577-589.

Z.C. Su, M. Fenglou, P. Dam, H.W. Wu, V. Olman, I.T. Paulsen, B. Palenik, Y. Xu. 2006 Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH8102. Nucleic Acids Research. 34:1050-1065.

A.K. Davis, M. Hildebrand, B. Palenik. 2006. Gene expression induced by copper stress in the diatom Thalassiosira pseudonana. Eukaryotic Cell. 5:1156-1168.

D Landry, T. Gaasterland, B. Palenik. 2006. A Cell Surface Protein Induced by Phosphate Limitation in E. huxleyi. J. Phycol. 42:814-821.

Brian Palenik, Qinghu Ren, Chris L. Dupont, Garry S. Myers, John F. Heidelberg, Jonathan H. Badger, Ramana Madupu, William C. Nelson, Lauren M. Brinkac, Robert J. Dodson, A. Scott Durkin, Sean C. Daugherty, Stephen A. Sullivan, Hoda Khouri, Yasmin Mohamoud, Rebecca Halpin, and Ian T. Paulsen. 2006. The genome of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proc. National Academy of Sciences. 103:13555-13559.

Chris L. Dupont, Song Yang, B. Palenik, P. Bourne. 2006. Modern Proteomes Contain Putative Imprints of Ancient Shifts in Trace Metal Geochemistry Proc. National Academy of Sciences. 103 (47): 17822-17827.

Denis de la Broise, B. Palenik 2007.. Immersed in situ microcosms: a tool for the assessment of pollution impact on phytoplankton. JEMBE. 341:274-281.

Brian Palenik, Jane Grimwood, Andrea Aerts, Pierre Rouzé, Asaf Salamov, Nicholas Putnam, Chris Dupont, Richard Jorgensen, Evelyne Derelle, Stephane Rombauts, Kemin Zhou, Robert Otillar, Sabeeha S. Merchant, Sheila Podell, Terry Gaasterland, Carolyn Napoli, Karla Gendler, Andrea Manuell, Vera Tai, Olivier Vallon, Gwenael Piganeau, Séverine Jancek, Marc Heijde, Kamel Jabbari, Chris Bowler, Martin Lohr, Steven Robbens, Gregory Werner, Inna Dubchak, Gregory J. Pazour, Qinghu Ren, Ian Paulsen, Chuck Delwiche, Jeremy Schmutz, Daniel Rokhsar, Yves Van de Peer, Hervé Moreau, and Igor V. Grigoriev. 2007. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc. National Academy of Sciences. 104: 7705-7710.

C. L. Dupont, K. Barbeau, B. Palenik. 2008. Ni uptake and limitation in marine Synechococcus strains. Appl. Environ. Micro. 74:23-31.

A. K. Davis and B. Palenik. 2008. Characterization of a modular, cell-surface protein and identification of a new gene family in the diatom Thalassiosira pseudonana. Protist. 159: 195-207.

C.L. Dupont, K. Neupane, J. Shearer, B. Palenik. 2008. Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases. Environ. Microbiol.10: 1831-1843.

A. Dufresne, M. Ostrowski, D.J. Scanlan, L. Garczarek, S. Mazard, B.P. Palenik, I.T. Paulsen, N.T. de Marsac , P. Wincker, C. Dossat, S. Ferriera, J. Johnson, A.F. Post, W.R. Hess, F. Partensky. 2008. Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biology, 9(5):R90.

B. Palenik, Q. Ren, V. Tai, I. T. Paulsen. 2008 Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environmental Microbiology. November. Online Available.