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2001

Dickey, T., S. Zedler, X. Yu, S.C. Doney, D. Frye, H. Jannasch, D. Manov, D. Sigurdson, J.D. McNeil, L. Dobeck, T. Gilboy, C. Bravo, D.A. Siegel, and N. Nelson. 2001. Physical and biogeochemical variability from hours to years at the Bermuda Testbed Mooring site: June 1994-March 1998. Deep-Sea Research II, 48: 2105–2140. http://dx.doi.org/10.1016/S0967-0645(00)00173-9

Dixon, J.E., and D.A. Clague. 2001. Volatiles in basaltic glasses from Loihi Seamount, Hawaii: Evidence for a relatively dry plume component. Journal of Petrology, 42: 627–654. http://dx.doi.org/10.1093/petrology/42.3.627

Ducklow, H., C. Carlson, M. Church, D. Kirchman, D. Smith, and G. Steward. 2001. The seasonal development of the bacterioplankton bloom in the Ross Sea, Antarctica, 1994–1997. Deep Sea research II, 48: 4199–4221. http://dx.doi.org/10.1016/S0967-0645(01)00086-8

Ducklow, H.W., D.C. Smith, L. Campbell, M.R. Landry, H.L. Quinby, G.F. Steward, and F. Azam. 2001. Heterotrophic bacterioplankton in the Arabian Sea: Basinwide response to year-round high primary productivity.. Deep-Sea Research II, 48: 1303–1323. http://dx.doi.org/10.1016/S0967-0645(00)00140-5

Dyer, A., K. Soole, and G.I. Matsumoto. 2001. Quantitative TaqMan PCR without a real-time thermal cycler: An assay for fish insulin-like growth factor I messenger RNA. Marine Biotechnology, 3: 16–21. http://dx.doi.org/10.1007/s101260000029

Edgington, D.R., T.C. O'Reilly, D. Davis, R. Henthorn, M.P. McCann, T. Meese, W. Radochonski, M. Risi, B. Roman, and R. Schramm. 2001. "Smart Network" infrastructure for the MBARI Ocean Observatory Observing System. MTS/IEEE Oceans 2001: An Ocean Odyssey: 1276–1282.

Erickson, J., P.G. Brewer, G.E. Friederich, and E.T. Peltzer. 2001. Design and operation of a pressure retaining sampler for sedimentary gases and gas hydrates. MTS/IEEE Oceans 2001: An Ocean Odyssey: 2396–2399.

Freezor, M.D., F.Y. Sorrell, P.R. Blankinship, and J.G. Bellingham. 2001. Autonomous underwater vehicle homing/docking via electromagnetic guidance. Journal of Oceanic Engineering, 26: 515–521.

Freytag, J.K., P.R. Girguis, D.C. Bergquist, J.P. Andras , J.J. Childress, and C.R. Fisher. 2001. A paradox resolved: Sulfide acquisition by roots of seep tubeworms sustains net chemoautotrophy. Proceedings of the National Academy of Science, 98: 13408–13413.

Goffredi, S.K., and J.J. Childress. 2001. Activity and inhibitor sensitivity of ATPases in the hydrothermal vent tubeworm Riftia pachyptila: A comparative approach. Marine Biology, 138: 259–265. http://dx.doi.org/10.1007/s002270000462

Guenther, E.A., K.S. Johnson, and K.H. Coale. 2001. Direct ultraviolet spectrophotmetric determination of total sulfide and iodide in natural waters. Analytical Chemistry, 73: 3481–3487.

Haddock, S.H.D., TJ. Rivers, and B.H. Robison. 2001. Can coelenterates make coelenterazine? Dietary requirement for luciferin in cnidarian bioluminescence. Proceedings of the National Academy of Sciences of the United States of America, 98: 11148–11151. http://dx.doi.org/10.1073/pnas.201329798

Halanych, K.M., R.A. Feldman, and R.C. Vrijenhoek. 2001. Molecular evidence that Sclerolinum brattstromi is closely related to vestimentiferans, no to frenulate pogonophorans (Siboglinidae, Annlida). Biological Bulletin, 201: 65–75.

Harbison, G.R., G.I. Matsumoto, and B.H. Robison. 2001. Lampocteis cruentiventer gen. nov., sp. nov.: A new mesopelagic lobate ctenophore, representing the type of a new family (Class Tentaculata, Order Lobata, Family Lampoctenidae, fam. nov.). Bulletin of Marine Science, 68: 299–311.

Jannasch, H.W., P.R. McGill, M. Zdeblick, and J. Erickson. 2001. Integrated microanalyzers with frozen plug valves. Micro Total Analysis Systems 2001: 526–530.

Johnson, K.S. 2001. Iron supply and demand in the upper ocean: Is extraterrestrial dust a significant source of bioavailable iron? Global Biogeochemical Cycles, 15: 61–63.

Johnson, K.S., F.P. Chavez, V.A. Elrod, S.E. Fitzwater, J.T. Pennington, K.R. Buck, and P.M. Walz. 2001. The annual cycle of iron and the biological response in central California coastal waters. Geophysical Research Letters, 28: 1247–1250. http://dx.doi.org/10.1029/2000gl012433

Karner, M.B., E.F. Delong, and D.M. Karl. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature, 409: 507–510. http://dx.doi.org/10.1038/35054051

Kirkwood, W.J., D. Au, D. Gashler, M. Greise, R. McEwen, E. Mellinger, T. O'Reilly, F. Shane, G. Thurmond, and K. Streitlien. 2001. MBARI/MIT ducted propeller control system developed for autonomous underwater vehicles. Underwater Intervention 2001.

Kirkwood, W.J., D. Gashler, H. Thomas, T.C. O'Reilly, R. McEwen, N. Tervalon, F. Shane, D. Au, M. Sibenac, T. Konvalina, A. Bahlavouni, and J.G. Bellingham. 2001. Development of a long endurance autonomous underwater vehicle for ocean science exploration. MTS/IEEE Oceans 2001: An Ocean Odyssey: 1504–1512.

Kirkwood, W.J., H. Thomas, M. Sibenac, N. Tervalon, R. McEwen, F. Shane, R. Henthorn, D. Gashler, E. Mellenger, D. Au, T. O'Reilly, and J.G. Bellingham. 2001. An autonomous underwater vehicle system for Arctic operations. Arctic Instrumentation Workshop.

Kirkwood, W.J., J.G. Bellingham, J. Stannard, P. Stein, and J. Overland. 2001. Development of Dorado/ALTEX vehicle and subsystems. Society for Underwater Techonolgy - AUV Masterclass Symposium.

Kleinberg, R.L., and P.G. Brewer. 2001. Probing gas hydrate deposits. American Scientist, 89: 244–251.

Land, L.A., and C.K. Paull. 2001. Thermal gradients as a tool for estimating groundwater advective rates in a coastal estuary: White Oak River, North Carolina, USA. Journal of Hydrology, 248: 198–215. http://dx.doi.org/10.1016/S0022-1694(01)00405-X

Liu, S.C., J. Kramer, D. Edgington, and T. Delbruck. 2001. Making direction selective cells using AER retina and spiking neurons. 2001 Workshop on Neuromorphic Engineering: 94–96.

Maffei, A.R., A.D. Chave, G. Massion, S.N. White, J. Bailey, S. Lerner, A. Bradley, D. Yoerger, H. Frazier, and R. Buddenberg. 2001. NEPTUNE gigabit ethernet submarine cable system. MTS/IEEE Oceans 2001: An Ocean Odyssey: 1303–1310.

MBARI Mapping Team. 2001. MBARI Northern California and Oregon Margin Multibeam Survey, CD-ROM, MBARI Digital Data Series.

MBARI Mapping Team. 2001. MBARI Northern California and Oregon Margin Multibeam Survey, CD-ROM.

MBARI Mapping Team. 2001. MBARI West Coast Seamounts and Ridges Multibeam Survey, CD–ROM.

MBARI Mapping Team. 2001. Santa Barbara Multibeam Survey, CD–ROM.

McEwen, R., and K. Streitlien. 2001. Modeling and Control of a Variable-Length AUV. International Symposium on Unmanned Untethered Submersible Technology.

McGillicuddy Jr., D.J., V.K. Kosnyrev, J.P. Ryan, and J.A. Yoder. 2001. Covariation of mesoscale ocean color and sea-surface temperature patterns in the Sargasso Sea. Deep-Sea Research II, 48: 1823–1836.

McNutt, M.K. 2001. Engineering the ocean. The invisible Future: The seamless Integration of Technology in Everyday Life: 27–42.

McNutt, M.K., and R.D. Ballard. 2001. Two case studies of collaborations between aquariums and resesarch institutions in exploration and education. Marine Technology Society Journal, 35: 76–85.

Meese, T., D.R. Edgington, W. Radochonski, K. Headley, and S. Jensen. 2001. A new mooring controller platform: An evolution of the OASIS instrument controller toward a distributed ocean observing system. MTS/IEEE Oceans 2001: An Ocean Odyssey: 1296–1302.

Mellinger, E., T. Aabo, A. Bowen, C. Katz, and R.A. Petitt Jr. 2001. High voltage testing of an ROV electro-optical tether cable. MTS/IEEE Oceans 2001: An Ocean Odyssey: 1145–1150.

MUSE Project Team. 2001. MUSE Data August 2000: MOOS Upper-Water-Column Science Experiment, CD-ROM.

Noble, R.T., and G.F. Steward. 2001. Estimating viral proliferation in aquatic samples. Methods in Microbiology: Marine Microbiology, 30: 67–84.

O'Reilly, T., and D. Edgington. 2001. Software infrastructure for the MBARI Ocean Observing System. International Workshop on Autonomous Measurements of Biogeochemical parameters in the Ocean.

Orphan, V.J., C.H. House, K.U. Hinrichs, K.D. McKeegan, and E.F. DeLong. 2001. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science, 293: 484–487. http://dx.doi.org/10.1126/science.1061338

Orphan, V.J., Hinrichs, K.U., W. Ussler III, C.K. Paull, L.T. Taylor, S.P. Sylva, J.M. Hayes, and E.F. DeLong. 2001. Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Applied and Environmental Microbiology, 67: 1922–1934. http://dx.doi.org/10.1128/AEM.67.4.1922-1934.2001

Pasteris, J.D., J.J. Freeman, S.K. Goffredi, and K.R. Buck. 2001. Raman spectroscopic and laser scanning confocal microscopic analysis of sulfur in living sulfur-precipitating marine bacteria. Chemical Geology, 180: 3–18. http://dx.doi.org/10.1016/S0009-2541(01)00302-3

Paull, C.K., and W. Ussler III. 2001. History and significance of gas sampling during DSDP and ODP drilling associated with gas hydrates. Natural gas hydrates: Occurrence, distribution, and detection, 124: 53–65.

Paull, C.K., S. Stratton, M. Conway, K Brekke, Dawe, T. Craig, N. Maher, and W. Ussler III. 2001. Deep sea vibracoring system improves ROV sampling capability. EOS, Transactions, 82: 325–326.

Pennington, J.T, and S.A. Stricker. 2001. Phylum Brachiopoda. Atlas of Marine Invertebrate Larval Forms, 441–461.

Plafker, G., H.G. Greene, N.M. Maher, and C. Synolakis. 2001. The destructive 1994 submarine landslide and tsunami at Skagway, Alaska: An example of a near shore submarine failure. NATO Advanced Workshop on Submarine Underwater Ground Failures on Tsunami Generation, Modeling, Risk, and Mitigation.

Podar, M., S.H.D. Haddock, M.L. Sogin, and G.R. Harbison. 2001. A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes. Molecular Phylogenetics and Evolution, 21: 218–230. http://dx.doi.org/10.1006/mpev.2001.1036

Polito, P.S., Ryan, J.P., W.T. Liu, and F.P. Chavez. 2001. Oceanic and atmospheric anomalies of tropical instability waves. Geophysical Research Letters, 28: 2233–2336. http://dx.doi.org/10.1029/2000gl012400

Purcell, J.E., D.L. Breitburg, M.B. Decker, W.M. Graham, M.J. Youngbluth, and K.A. Raskoff. 2001. Pelagic cnidarians and ctenophores in low dissolved oxygen environments: A review. Coastal hypoxia: Consequences for living resources and ecosystems, 58: 77–100.

Raskoff, K.A. 2001. The ecology of the mesopelagic cnidarians in Monterey Bay: 267.

Rau, G.H., F.P. Chavez, and G.E. Friederich. 2001. Plankton 13C/12C variations in Monterey Bay, California: Evidence of non-diffusive inorganic carbon uptake by phytoplankton in an upwelling environment. Deep Sea Research Part I: Oceanographic Research Papers, 48: 79–94.

Rau, G.H., S. Ralston, J.R. Southon, and F.P. Chavez. 2001. Upwelling and the condition and diet of juvenil rockfish: A study using 14C, 13C, and 15N natural abundances. Limnology and Oceanography, 46: 1565–1570.

Rehder, G., and E. Suess. 2001. Methane and pCO2 in the Kuroshio and the South China Sea during maximum summer surface temperatures. Marine Chemistry, 75: 89–108.

Robison, B.H. 2001. Water column life. Atlas of the ocean: the deep frontier: 98–99.

Rodgers, D.H., A. Maffei, P.M. Beauchamp, G. Massion, A.D. Chave, T.M. McGinnis, and S. Gauder. 2001. NEPTUNE regional observatory system design. MTS/IEEE Oceans 2001: An Ocean Odyssey: 1356–1365.

Ryan, J.P., J.A. Yoder, and D.W. Townsend. 2001. Influence of a Gulf Stream warm-core ring on water mass and chlorophyll distributions along the southern flank of Georges Bank. Deep-Sea Research II, 48: 159–178. http://dx.doi.org/10.1016/S0967-0645(00)00117-X

Salamy, K.A., M. Chaffey, J. Erickson, D. Au, T.C. O'Reilly, and D. Stakes. 2001. Rock coring technology on the Juan de Fuca plate with the MBARI ROV Tiburon. Oceanology International.

Sayles, F.L., W.R. Martin, Z. Chase, and R.F. Anderson. 2001. Benthic remineralization and burial of biogenic SiO2, CaCO3, organic carbon, and detrital material in the Southern Ocean along a transect at 170º West. Deep-sea Research II, 48: 4323–4383.

Seibel, B.A., and D.B. Carlini. 2001. Metabolism of pelagic cephalopods as a function of habitat depth: A reanalysis using phylogenetically independent contrasts. Biological Bulletin, 201: 1–5. http://dx.doi.org/10.2307/1543519

Singh, H., J.G. Bellingham, F. Hover, S. Lerner, B. Moran, K. vonDerHeydt, and D. Yoerger. 2001. Docking for an autonomous ocean sampling network. Journal of Oceanic Engineering, 26: 498–514. http://dx.doi.org/10.1109/48.972084

Stakes, D., B. Romanowicz, P.R. McGill, D. Neuhauser, K.S. Johnson, H.W. Jannasch, and C.G. Wheat. 2001. Multidisciplinary observatory development in Monterey Bay. Joint Ocean Hemisphere Network Project/International Ocean Network (OHP/ION) Symposium.

Steward, G.F. 2001. Fingerprinting viral assemblages by Pulsed Field Gel Electrophoresis (PFGE). Methods in Microbiology: Marine Microbiology, 30: 85–103.

Strutton, P.G., J.P. Ryan, and F.P. Chavez. 2001. Enhanced chlorophyll associated with tropical instability waves in the equatorial Pacific. Geophysical Research Letters, 28: 2005–2008. http://dx.doi.org/10.1029/2000gl012166

Stutzmann, E., J.P. Montagner, A. Sebai, W.C. Crawford, J.L. Thirot, P. Tarits, D. Stakes, B. Romanowicz, J.F. Karczewski, J.C. Koening, J. Savary, D. Neuhauser, and S. Etchemendy. 2001. MOISE: A prototype multiparameter ocean-bottom station. Bulletin of the Seismological Society of America, 91: 885–892. http://dx.doi.org/10.1785/0120000035

Suzuki, M.T., C.M. Preston, F.P. Chavez, and E.F. DeLong. 2001. Quantitative mapping of bacterioplankton populations in seawater: Field tests across an upwelling plume in Monterey Bay. Aquatic Microbial Ecology, 24: 117–127. http://dx.doi.org/10.3354/ame024117

Suzuki, M.T., O. Béjà, L.T. Taylor, and E.F. DeLong. 2001. Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environmental Microbiology, 3: 323–331.

Takahashi, H., C.E. Braby, and A.R. Grossman. 2001. Sulfur economy and cell wall biosynthesis during sulfur limitation of Chlamydomonas reinhardtii. Plant Physiol, 127: 665–673.

Tervalon, N., and W. Kirkwood. 2001. Ice profiling sonar for an AUV: an approach for obtaining SCICEX quality draft data. AUV Sensor Workshop.

Torres, M.E., J.P. Barry, D.A. Hubbard, and E. Suess. 2001. Reconstructing the history of fluid flow at cold seep sites from Ba/Ca ratios in vesicomyid clam shells. Limnology and Oceanography, 46: 1701–1708.

Trieloff, M., J. Kunz, D.A. Clague, D. Harrison, and C.J. Allegre. 2001. Reply to comment on "The nature of pristine noble gases in mantle plumes," by C.J. Ballentine, D. Porcelli, and R. Weiler. Science, 291: 2269.

Tyrrell, J.V., P.R. Bergquist, P.L. Bergquist, and C.A. Scholin. 2001. Detection and enumeration of Heterosigma akashiwo and Fibrocapsa japonica (Raphidophyceae) using rRNA-targeted oligonucleotide probes. Phycologia, 40: 457–467. http://dx.doi.org/10.2216/i0031-8884-40-5-457.1

Van Slyke, R.J., J.M. Morgan, T.S. Leach, and S.A. Etchemendy. 2001. SWATH research vessel hull strength upgrade. Marine Technology, 38: 177–185.

Vecchione, M., R.E. Young, A. Guerra, D.J. Lindsay, D.A. Clague, J.M. Bernhard, W.W. Sager, A.F. Gonzalez, F.J. Rocha, and M. Segonzac. 2001. Worldwide observations of remarkable deep-sea squids. Science, 294: 2505–2506. http://dx.doi.org/10.1126/science.294.5551.2505

W. Ussler, III., and C.K. Paull. 2001. Ion exclusion associated with marine gas hydrate deposits. Natural gas hydrates: Occurrence, distribution, and detection, 124: 41–51.

Wilcox, J.S., J.G. Bellingham, Y. Zhang, and A.B. Baggeroer. 2001. Oceanographic surveys with autonomous underwater vehicles: Performance metrics and survey design. Journal of Oceanic Engineering, 26: 711–725.

Xu, W., R.P. Lowell, and E.T. Peltzer. 2001. Effect of seafloor temperature and pressure variations on methane flux from a gas hydrate layer: Comparison between current and late Paleocene climate conditions. Journal of Geophyiscal Research, 106: 26413–26423. http://dx.doi.org/10.1029/2001jb000420

Zhang, Y., A.B. Baggeroer, and J.G. Bellingham. 2001. Spectral feature classification of oceanographic processes using an autonomous underwater vehicle. IEEE Journal of Oceanic Engineering, 26: 726–741. http://dx.doi.org/10.1109/48.972115

2000

Barry, J.P., and N. Maher. 2000. Observation of the prickly shark, Echinorhinus cookei, from the oxygen minimum zone in Santa Barbara Basin, California. California Fish and Game, 86: 213–215.

Barry, J.P., K.R. Buck, S.K. Goffredi, and J. Hashimoto. 2000. Ultrastructure studies of two chemosynthetic invertebrate-bacterial symbioses (Lamellibrachia sp. and Acharax sp.) from the Hatsushima cold seeps in Sagami Bay, Japan. JAMSTEC Journal of Deep-Sea Research, 16: 91–99.

Begnaud, M.L., and D.S. Stakes. 2000. Constraining continental margin seismicity by extending on-shore seismograph stations to critical off-shore sites. Bulletin of the Seismological Society of America, 90: 414–424. http://dx.doi.org/10.1785/0119990115

Begnaud, M.L., K.C. McNally, D.S. Stakes, and V.A. Gallardo. 2000. A crustal velocity model for locating earthquakes in Monterey Bay, California. Bulletin of the Seismological Society of America, 90: 1391–1408. http://dx.doi.org/10.1785/0120000016

Béjà, O., L. Aravind, E.V. Koonin, M.T. Suzuki, A. Hadd, L. Nguyen, S.B. Jovanovich, C.M. Gates, R.A. Feldman, J.L. Spudich, E.N. Spudich, and E.F. DeLong. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science, 289: 1902–1906.

Béjà, O., M.T. Suzuki, E.V. Koonin, L. Aravind, A. Hadd, L.P. Nguyen, R. Villacorta, M. Amjadi, C. Garrigues, S.B. Jovanovich, R.A. Feldman, and E.F. DeLong. 2000. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environmental Microbiology, 2: 516–529.

Bellingham, J.G., J. Steitlien, J. Overland, S. Jajan, P. Stein, J. Stannard, W. Kirkwood, and D. Yoerger. 2000. An arctic basic observational capability using AUVs. Oceanography, 13.

Bernhard, J.M., K.R. Buck, M.A. Farmer, and S.S. Bowser. 2000. The Santa Barbara Basin is a symbiosis oasis. Nature, 403: 77–80. http://dx.doi.org/10.1038/47476

Borowski, W.S., and C.K. Paull. 2000. Nitrogen isotopic composition of pore-water ammoniuim, Blake Ridge, site 997, ODP Leg 164, Data Report. Proceeding of the Ocean Drilling Program, Scientific Results, 164: 171–172.

Borowski, W.S., T.M. Hoehler, M.J. Alperin, N.M. Rodriguez, and C.K. Paull. 2000. Significance of anaerobic methane oxidation in methane-rich sediments overlying the Blake Ridge gas hydrates. Proceeding of the Ocean Drilling Program, Scientific Results, 164: 87–99.

Brady, R., B. Wernicke, M.K. McNutt, J.C. Mutter, and G. Correa. 2000. Results of the Basin and Range Geoscientific Experiment (BARGE): A marine-style seismic reflection survey across the eastern boundary of the central Basin and Range province. Geochemistry, Geophysics, Geosystems: G3, 1.

Brewer, P.G. 2000. Chemical oceanography. Introduction to Earth systems: Processes and issues: 182–193.

Brewer, P.G. 2000. Gas hydrates and global climate change. Gas hydrates: Challenges for the future, 912: 195–199.

Brewer, P.G. 2000. Major international programs in Ocean Sciences: Ocean chemistry. 50 years of ocean discovery, 1950–2000: 152–161.

Brewer, P.G., and F.M. Orr Jr. 2000. CO2: The burning issue. Chemistry & Industry: 567–571.

Brewer, P.G., E.T. Peltzer, G. Friederich, I. Aya, and K. Yamane. 2000. Experiments on the ocean sequestration of fossil fuel CO2: pH measurements and hydrate formation. Marine Chemistry, 72: 83–93. https://doi.org/10.1016/S0304-4203(00)00074-8