Lab Info

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General Information About the lab

TPP

A rough, outdated guide:

http://tools.proteomecenter.org/wiki/index.php?title=TPP:Installing_on_Mac_OSX

Some tips:

Makefile.incl has most of the user configurable stuff. Commented lines allow choice of macports or fink. Only macports work for me.

expat, gd2, boost, boost-jam from mac ports

Edit Makefile, and delete -Werror (throw errors on warn)

Make symbolic link to fix someone's booboo: ln -s /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/bin/ /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/../bin/

In src/cgi/Makefile remove 'u' from 'cp -rfu' line. OS X doesn't have 'u'

Contact Us!


Contact Gabrielle Rocap
Email: rocap {AT} ocean.washington.edu
Office Phone: (206) 685-9994
Lab Phone: (206) 543-9858
FAX: (206) 685-6651

Contact Webmaster
Email: cmckay {AT} uw.edu 

Campus address:
Benjamin Hall Interdisciplinary Research Building
Gabrielle: Room 318
Lab: Room 306
See the Ben Hall IRB on a campus map

Mailing Address (US & Campus Mail):
School of Oceanography
Box 357940
University of Washington
Seattle, WA 98195-7940

Shipping Address (Packages and overnight deliveries):

Benjamin Hall IRB, Room 306
616 NE Northlake Place
Seattle, WA 98105

Publications

 

Sohm, J. A., Ahlgren, N. A., Thomson, Z., Williams, C., Moffett, J.W., Saito, M.A., Webb, E.A., and G. Rocap. Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients, and iron. ISME Journal in press doi: 10.1038/ismej.2015.115

Saunders, J. K. and G. Rocap. Arsenic detoxification strategies vary with environmental phosphate concentrations in global Prochlorococcus populations. ISME Journal in press doi:10.1038/ismej.2015.85

Guannel, M. L., Haring, D, Twiner, M.J., Wang, Z., Noble, A., Lee, P., Saito, M.A., and G. Rocap. 2015. Toxigenicity and biogeography of the diatom Pseudo-nitzschia across distinct environmental regimes in the South Atlantic Ocean. Marine Ecology Progress Series 526:67-87 doi:10.3354/meps11027

Gruber, A., G. Rocap, P. G. Kroth, E. V. Armbrust and T. Mock.  2015. Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage. The Plant Journal 81: 519-528 DOI: 10.1111/tpj.12734

Ahlgren, N. A., Noble A., Patton, A.P., Roache-Johnson, K., Jackson, L., Robinson, D., McKay, C., Moore, L.R., Saito, M.A. and G. Rocap. 2014. The unique trace metal and mixed layer conditions of the Costa Rica upwelling dome support a distinct and dense community of Synechococcus. Limnology and Oceanography 59(6), 2014, 2166-2184 | DOI: 10.4319/lo.2014.59.6.2166

Biller, S.J., Berube, P. M., Berta-Thompson, J. W., Kelly, L., Roggensack, S.E., Awad, L., Roache-Johnson, K. H., Ding, H., Giovannoni, S. J., Rocap, G., Moore, L.R. and S. W. Chisholm. 2014. Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus Scientific Data 1, Article number: 140034 ​doi:10.1038/sdata.2014.34

Starkenburg, S.R., Kwon, K.J., Jha, R.A., McKay, C., Jacobs, M. Chertkov, O., Twary, S., Rocap, G. and Cattolico, R.A. 2014. A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes. BMC Genomics, 15:212  (2014) doi:10.1186/1471-2164-15-212

Nahas Reistetter, E., Krumhardt, K., Callnan, K., Roache-Johnson, K., Saunders, J. Moore, L. R. and G. Rocap. 2013. Effects of phosphorus starvation versus limitation on the marine cyanobacterium Prochlorococcus MED4 II: gene expression. Environmental Microbiology doi:10.1111/1462-2920.12129 (pdf)

Krumhardt, K., Callnan, K., Roache-Johnson, K., Swett, T., Robinson, D., Nahas Reistetter, E., Saunders, J. Rocap, G. and L. R. Moore. 2013. Effects of phosphorus starvation versus limitation on the marine cyanobacterium Prochlorococcus MED4 I: Uptake Physiology. Environmental Microbiology doi:10.1111/1462-2920.12079 (pdf)

Rodríguez-Martínez, R., G. Rocap, G. Salazar and R. Massana. 2013. Biogeography of the uncultured marine picoeukaryote MAST-4: temperature-driven distribution patterns. ISME Journal doi:10.1038/ismej.2013.53 (pdf)

Curtis, B. et al. 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492:59-65 doi:10.1038/nature11681 (pdf)

Ahlgren, N.A. and G. Rocap. 2012 Diversity and distribution of marine Synechococcus: multiple gene phylogenies for consensus classification and development of qPCR assays for sensitive measurement of clades in the ocean Frontiers in Aquatic Microbiology doi: 10.3389/fmicb.2012.00213

Rodríguez-Martínez, R., G. Rocap, R. Logares, S. Romac and R. Massana. 2012 Low Evolutionary Diversification in a Widespread and Abundant Uncultured Protist (MAST-4). Molecular Biology and Evolution 29 (5): 1393-1406. doi: 10.1093/molbev/msr303 (pdf)

Guannel, M. L., M. C. Horner-Devine and G. Rocap.  2011. Bacterial community composition differs with species and toxigenicity of the diatom Pseudo-nitzschia Aquatic Microbial Ecology, 64: 117-133. doi:10.3354/ame01513 (pdf)

Morris, R. M., B. Nunn, C. Frazar, D. Goodlett, Y.S. Ting and G. Rocap. 2010. Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction ISME Journal 4:673-685 (pdf)

Ong, H. C., S. W. Wilhelm, C. J. Gobler, G. Bullerjahn, M. A. Jacobs, J. McKay, E. H. Sims, W. G. Gillett, Y. Zhou, E. Haugen, G. Rocap, R. A. Cattolico. 2010 Analyses of the complete chloroplast genome sequences of two members of the Pelagophyceae:  Aureococcus anophagefferens CCMP1984 and Aureoumbra lagunensis CCMP1507 Journal of Phycology 46:602-615  (pdf)

Collins, R. E., G. Rocap, J. Deming. 2010. Persistence of bacterial and archaeal communities in sea ice through an Arctic winter. Environmental Microbiology 12:1828-1841 (pdf)

Adams, N. G., V. L. Trainer, G. Rocap, R.P. Herwig. L. Hauser. 2009. Genetic population structure of Pseudo-nitzschia (Bacillariophyceae) from the Pacific Northwest and the North Sea.  Journal of Phycology 45:1037-1045. (pdf)

Cattolico, R.A. M. A. Jacobs, Y. Zhou, J. Chang, M. Duplessis, T. Lybrand, J. McKay, H.C. Ong, E. Sims, and G. Rocap. 2008.  Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES 293 (West Pacific) strains BMC Genomics 9:211 doi:10.1186/1471-2164-9-211  (pdf)

Hubbard, K. A. G. Rocap and E. V. Armbrust. 2008  Inter- and intra-specific community structure within the diatom genus Pseudo-nitzschia (Bacillariophyceae).  Journal of Phycology 44: 637-649 (pdf)

Collins, R.E. and G. Rocap. 2007 REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis.  Nucleic Acids Research 35 (Web server issue): W58-W62; (pdf)

Ahlgren, N. A. and G. Rocap. 2006. Culture isolation and culture-independent clone libraries reveal new marine Synechococcus ecotypes with distinctive light and N physiologies. Applied and Environmental Microbiology 72: 7193-7204. PDF file (752 kb)

Fuchsman, C. A. and G. Rocap. 2006. Whole genome reciprocal BLAST analysis reveals Planctomycetes do not share an unusually high number of genes with Eukarya and Archaea. Applied and Environmental Microbiology 72:6841-6844 PDF file (214 kb)

Van Mooy, B.A.S., G. Rocap, H. F. Fredricks, C. T. Evans and A. H. Devol. 2006. Sulfolipids dramatically decrease phosphorus demand by picocyanobacteria in oligotrophic marine environments. PNAS. 103:8607-8612. PDF file (856 kb)

Ahlgren, N. A., G. Rocap, and S. W. Chisholm. 2005. Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies Environmental Microbiology 8: 441-454 PDF file (257 kb)

Saito, M. A., G. Rocap, and J. W. Moffett. 2005. Production of Cobalt Binding Ligands in a Synechococcus Feature at the Costa Rica Upwelling Dome. Limnology and Oceanography 50: 279-290. PDF file (380 kb)

Rocap, G., F. W. Larimer, J. Lamerdin, S. Malfatti, P. Chain, N. A. Ahlgren, A. Arellano, M. Coleman, L. Hauser, W. R. Hess, Z. I. Johnson, M. Land, D. Lindell, A. F. Post, W. Regala, M. Shah, S. L. Shaw, C. Steglich, M. B. Sullivan, C. S. Ting, A. Tolonen, E. A. Webb, E. R. Zinser and S. W. Chisholm. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047. PDF file (430 kb)
Supplementary Information (418 kb)

Rocap, G., D. L. Distel, J. B.Waterbury and S. W. Chisholm. 2002. Resolution of Prochlorococcus and Synechococcus ecotypes using 16S-23S rRNA internal transcribed spacer (ITS) region sequences. Applied and Environmental Microbiology, 68: 1180-1191. PDF file (362 kb)

Ting, C. S., G. Rocap, J. King and S. W. Chisholm. 2002. Cyanobacterial Photosynthesis in the Oceans: Origins and Significance of Divergent Light Harvesting Strategies. Trends in Microbiology. 10:134-142. PDF file (136 kb)

Moore, L. R., A. F. Post, G. Rocap and S. W. Chisholm. 2002. Differential nitrogen utilization of the marine cyanobacteria Prochlorococcus and Synechococcus. Limnology and Oceanography 47: 989-996. PDF file (178 kb).

Hess, W. R., G. Rocap, C. S. Ting, F. W. Larimer, S. Stilwagon, J. Lamerdin and S. W. Chisholm. 2001. The photosynthetic apparatus of Prochlorococcus - a genomic perspective. Photosynthesis Research, 70:53-71. PDF file (717 kb)

Ting, C., G. Rocap, J. King and S. W. Chisholm. 2001. Phycobiliprotein genes of the marine prokaryote Prochlorococcus: Evidence for rapid evolution of genetic heterogeneity. Microbiology 147: 3171-3182. PDF file (1.6 Mb)

Rocap, G., L. R. Moore and S. W. Chisholm. 1999. Molecular Phylogeny of Prochlorococcus ecotypes. in Marine Cyanobacteria, L. Charpy and A. W. D. Larkum ed. Bulletin de líInstitute Océanographique, Monaco, special issue No. 19. pp. 107-116. PDF file (548 kb)

Moore, L. R., G. Rocap and S. W. Chisholm. 1998. Physiology and Molecular Phylogeny of Coexisting Prochlorococcus ecotypes. Nature 393: 464-467. PDF file (345 kb)

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