Bigelow Laboratory for Ocean Sciences

Publications

This is a selected list of 2007 publications in which Bigelow scientists are either first authors or contributors.

• Allen, M.J, J.M. Martinez, D.C. Schroeder, P.J. Somerfield, and W.H. Wilson. 2007. Use of microarrays to assess viral diversity: from genotype to phenotype. Environmental Microbiology. 9(4) 971-982.
• Andersen, R.A. 2007. Molecular Systematics of the Chrysophyceae and Synurophyceae.Pp. 283-311 in Unraveling the Algae: The Past, Present and Future of Algal Systematics, J.Lewis and J. Brodie, eds. Taylor and Francis, Boca Raton, FL.
• Andersen, R.A. 2007. Heterokontophyta: Synurophyceae. Pp. 235-254 In Algae of Australia: Introduction. P.M. McCarthy and A.E.Orchard, eds. ABRS, Canberra, CSIRO Publishing, Melbourne.
• Baer, K. and D.A. McClellan. 2007. Molecular coevolution of the vertebrate cytochrome c1 and Rieske iron sulfur proteins in the cytochrome bc1 complex. International Journal of Bioinformatics Research and Applications 3:456-470.
• Balch, W.M., J.J. Vaughn, J.I. Goes, J.F. Novotny, D.T. Drapeau, E.S. Booth, and C.L. Vining. 2007. Bio-optical consequences of viral infection of phytoplankton: I. Experiments with the cyanobacterium, Synechococcus sp. Limnology and Oceanography 52:727-738.
• Balch, W.M., D.T. Drapeau, B.C. Bowler, and E.S. Booth. 2007. Prediction of pelagic calcification rates using satellite measurements. Deep -Sea Research II (Chapman Calcification Conference Special Volume). Vol. 54, no. 5-7, Pp. 478-495 DOI:10.1016/J.DSR2.2006.12.006.
• Balch, W.M. 2007. Coccolithophores and the "sea of milk". In Our Changing Planet: The View From Space. M.King, C. Parkinson, K. Partington and R. Williams, eds. Cambridge University Press. Cambridge, U.K.
• Benfield M. C., P. Grosjean, P. Culverhouse, X. Irigoien, M.E. Sieracki, A. Lopez-Urrutia, H.G. Dam, Q. Hu, C.S. Davis, A. Hansen, C.H. Pilskaln, E. Riseman, H. Schultz, P.E. Utgoff, G. Gorsky. 2007. RAPID: Research on Automated Plankton Identification. Oceanography 20:12 - 26.
• Benavides, E., R. Baum, D.A. McClellan, and J.W. Sites. 2007. Molecular phylogenetics of the lizard genus Microlophus (Squamata: Tropiduridae): Aligning and retrieving indel signal from nuclear introns. Systematic Biology 56:776-797.
• Berelson, W.M., W.M. Balch, R. Najjar, R.A. Feely, C. Sabine, and K. Lee. 2007. Relating estimates of CaCO3 production, export and dissolution in the water column to measurements of CaCO3 rain into sediment traps and dissolution on the sea floor: A revised global carbonate budget. Global Biogeochemical Cycles. 21, GB1024, DOI:10.1029/2006GB002803
• Carroll, H.D., M.T.W. Ebbert, M. Clement, Q.O. Snell, W.A. Beckstead, T.D. O'Connor, and D.A. McClellan. 2007. DNA alignment benchmark based on tertiary structure of encoded proteins. Bioinformatics 23:2648-2649.
• Chamala, S., W.A. Beckstead, M.J. Rowe, and D.A. McClellan. 2007. Evolutionary selective pressure on three mitochondrial SNPs in consistent with their influence on metabolic efficiency in Pima Indians. International Journal of Bioinformatics Research and Applications 3:504-522.
• Cleland D., K. Jastrzembski, E. Stamenova, J. Benson, C. Catranis, D. Emerson, and B. Beck. 2007. Growth characteristics of microorganisms on commercially available animal-free alternatives to tryptic soy medium. Journal of Microbiological Methods. 69:345-352.
• Ebbert, M.T.W., T.D. O'Connor, W.A. Beckstead, M.J. Clement, and D.A. McClellan. 2007. Pharmacogenomics: Analyzing SNPs in the CYP2D6 gene using amino acid properties. International Journal of Bioinformatics Research and Applications 3:471-479.
• Eckard R.S., P.J. Hernes, B.A. Bergamaschi, R. Stepanauskas, and C. Kendall. 2007. Landscape scale controls on the vascular plant component of dissolved organic carbon across a freshwater delta. Geochemica et Cosmochemica Acta 71:5968-5984.
• Emerson, D., J.A. Rentz, T.G. Lilburn, R.E. Davis, H. Aldrich, C. Chan, and C.L. Moyer. 2007. A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities . PLOSOne. 2(8): e667. doi:10.1371/ journal.pone.0000667
• Emerson, D., and J. Tang. 2007. Media and Nutrition. In Manual of Methods for General and Molecular Microbiology, 3rd Edition. C.A. Reddy, et al [eds.] American Society of Microbiology Press. pp 200-214.
• Evans, C., S.V. Kadner, L.J. Darroch, W.H. Wilson, P. Liss, and G. Malin. 2007. The relative significance of viral lysis and microzooplankton grazing as pathways of dimethylsulfoniopropionate (DMSP) cleavage: An Emiliania huxleyi culture study. Limnology and Oceanography 52:1036-1045.
• Fields, D.M. , M.J. Weissburg, and H. Browman. 2007. Chemoreception in the salmon louse Lepeophtheirus salmonis: an electrophysiology approach. Disease of Aquatic Organisms 78:161-168.
• Fogarty, Incze, Wahle, and Mountain, 2007. Marine Center White Paper, Union of Concerned Scientists Northeast Climate Impacts Assessment synthesis report, Global Environmental Program, UCS, Cambridge, MA.
• Hackett, J.D., H.S. Yoon, N.J. Butterfield, M.J. Sanderson, and D.Bhattacharya. 2007. Plastid endosymbiosis: sources and timing of the major events. In: Evolution of Primary Producers in the Sea, P. Falkowski and A. Knoll, eds. Academic Press.Pp109-133.
• Hoef-Emden, K., F.C. Küpper. and R.A. Andersen. 2007. Meeting Report: Sloan Foundation Workshop to Resolve Problems Relating to the Taxonomy of Microorganisms and to Culture Collections Arising from the Barcoding Initiatives; Portland ,ME, November 6-7, 2006. Protist 158:135-137.
• Kegel, J., M.J. Allen, K. Metfies, W.H. Wilson, D.Wolf-Gladrow, and K. Valentin. 2007. Pilot study of an EST approach of the coccolithophorid Emiliania huxleyi during a virus infection. Gene 406: 209-216
• Kimmance, S.A., W.H. Wilson, and S.D. Archer. 2007. Modified dilution technique to estimate viral versus grazing mortality of phytoplankton: limitations associated with method sensitivity in natural waters. Aquatic Microbial Ecology, 49(3), 207-222.
• Llewellyn, C.A., C. Evans, R.L. Airs, I. Cook, N. Bale, and W.H. Wilson. 2007. The response of carotenoids and chlorophylls during virus infection of Emiliania huxleyi (Prymnesiophyceae). Journal of Experimental Marine Biology and Ecology. 344(1), 101-112.
• Lohr, J., C.B. Munn,. and W.H. Wilson. 2007. Characterisation of a Latent Virus-like Infection of Symbiotic Zooxanthellae. Applied and Environmental Microbiology 73:2976-2981.
• Matondkar, S.G.P., H. Gomes, S.G. Parab, S. Pednekar and J.I. Goes. 2007. Phytoplankton diversity, biomass, and production. In The Mandovi and Zuari Estuaries. S.R. Shetye, M. Dileep Kumar, and D. Shankar, eds. Pp. 99-104 .National Institute of Oceanography, India.
• Martinez, J.M., D.C. Schroeder, A. Larsen, G. Bratbak, and W.H. Wilson. 2007. Molecular Dynamics of Emiliania huxleyi and Cooccurring Viruses during Two Separate Mesocosm Studies. Applied and Environmental Microbiology 73: 554-562
• Matrai, P.A., M. Vernet, and P. Wassmann. 2007. Relating temporal and spatial patterns of DMSP in the Barents Sea to phytoplankton biomass and productivity, Journal of Marine Systems 67(1-2): 87-101.
• Matrai, P.A., L. Tranvik, C. Lek, and J. Knulst. 2007. Are high Arctic microlayers a potential source of aerosol organic precursors? Marine Chemistry. 108:109–122.
• Neubauer, S.C., G. E. Toledo-Dur´n, D.Emerson, J.P.Megonigal. 2007. Returning to their roots: Iron-oxidizing bacteria enhance short-term plaque formation in the wetland-plant rhizosphere. Geomicrobiology Journal 24:65-73.
• O’Donnell, K.P., R.A. Wahle, M.J. Dunnington, and M. Bell. 2007. Spatially referenced trap arrays detect sediment disposal impacts in a New England estuary. Marine Ecology Progress Series . 348: 249–260.
• Porter, M., T. Cronin, D.A. McClellan, and K. A. Crandall. 2007. Molecular characterization of crustacean visual pigments and the evolution of pancrustacean opsins. Molecular Biology and Evolution 24:253-268.
• Poulton, A. J., T.R. Adey, W.M. Balch, and P.M. Holligan. 2007. Relating coccolithophore calcification rates to phytoplankton community dynamics: regional differences and implications for carbon export. Deep-Sea Research II (Chapman Calcification Conference- Special Volume). Vol. 54, no. 5-7, pp. 538-557.
• Rentz, J.A., C. Kraiya, G.W. Luther III, and D. Emerson. 2007 Control of ferrous iron oxidation within circumneutral microbial iron mats by cellular activity and autocatalysis. Environmental Science and Technology 41:6048-6089.
• Roden, E. R. and D. Emerson. 2007. Microbial Metal Cycling in Aquatic Environments. Manual of Environmental Microbiology, 3rd Ed. American Society of Microbiology Press. Washington, D.C. pp, 540-562.
• Roesler, C. S. and E. Boss. 2007. In situ measurement of the inherent optical properties (IOPs) and potential for harmful algal bloom (HAB) detection and coastal ecosystem observations, Chapter 5. In Real-Time Coastal Observing Systems for Ecosystem Dynamics and Harmful Algal Blooms: Thoery, Observation and Modeling. M. Babin, J J. Cullen, and C.S. Roesler, eds. UNESCO Series Monographs on Oceanographic Methodology.
• Saunders. G.W. and R.A. Andersen. 2007. Heterokontophyceae: Pelagophyceae. Pp.228-234. In Algae of Australia: Introduction. P.M. McCarthy and A.E. Orchard, eds. ABRS, Canberra, CSIRO Publishing, Melbourne.
• Selgrath, J., K. Hovel,and R.A. Wahle. 2007. Effects of habitat edges on American lobster abundance & survival. Journal of Experimental Marine Biology and Ecology 353: 253-264
• Steele, J.S. Collie, J.J. Bisagni, D.J. Gifford, M.J. Fogarty, J.S. Link, B.K. Sullivan, M.E. Sieracki, A.R. Beet, D.G. Mountain.
• E.G. Durbin, D. Palka, W.T. Stockhausen. 2007 Balancing end-to-end budgets of the Georges Bank ecosystem. Progress in Oceanography. 74:423-448.
• Stepanauskas, R. and M.E. Sieracki. 2007. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proceedings of the National Academy of Sciences of the United States of America 104:9052–9057.
• Weiss, J.V., J.A. Rentz, T. Plaia, S.C. Neubauer, M.M. Floyd, T. Lilburn, C. Bradburne, J.P. Megonigal, and D. Emerson. 2007. Identification of diverse neutrophilic Fe(II)-oxidizing bacteria isolated from the rhizosphere of wetland plants and description of Ferritrophicum radicicola gen. nov. sp. nov., and Sideroxydans paludicola sp. nov. Geomicrobiology J. 24:559-570.
• Wharam, S.D., M.J. Hall, and W.H. Wilson. 2007. Detection of virus mRNA within infected host cells using an isothermal nucleic acid amplification assay: marine cyanophage gene expression within Synechococcus sp. Virology Journal 4:52.
• Williamson, P., R.A. Andersen, and F.C. Küpper. 2007. Why every protist needs a barcode. Microbiology Today 34(1):46-47.
• Yoon, H.S., J.D. Hackett, S. Li, A. Reyes-Prieto, S.E. Rümmele, and D. Bhattacharya. 2007. Phylogenomic analysis supports the association of “Rhizaria” with chromalveolates and the monophyly of cryptophytes and haptophytes. Molecular Biology and Evolution 24:1702-1713.

This is a selected list of 2007 publications in which Bigelow scientists are authors. (3.24.08)