Publications

Spring - Summer, 2010

Allen, JJ; Mathger, LM; Barbosa, A; Buresch, KC; Sogin, E; Schwartz, J; Chubb, C; Hanlon, RT. 2010. Cuttlefish dynamic camouflage: responses to substrate choice and integration of multiple visual cues. Proceedings of the Royal Society of London B. 277 (1684): 1031-1039.

Alliegro, MA; Henry, JJ; Alliegro, MC. 2010. Rediscovery of the nucleolinus, a dynamic RNA-rich organelle associated with the nucleolus, spindle, and centrosomes. Proceedings of the National Academy of Sciences. 107 (31): 13718-13723.

Angueyra, JM; Pulido, C; Malagon, G; Nasi, E; Gomez, MD. 2010. Role of Intracellular Calcium Mobilization in Melanopsin-mediated Light Signalling in Amphioxus. Journal of General Physiology. 136 (1): 5A.

Auger, H; Sasakura, Y; Joly, JS; Jeffery, WR. 2010. Regeneration of oral siphon pigment organs in the ascidian Ciona intestinalis. Developmental Biology. 339 (2): 374-389.

Bahn, M; Reichstein, M; Davidson, EA; Grunzweig, J; Jung, M; Carbone, MS; Epron, D; Misson, L; Nouvellon, Y; Roupsard, O; Savage, K; Trumbore, SE; Gimeno, C; Yuste, JC; Tang, J; Vargas, R; Janssens, IA. 2010. Soil respiration at mean annual temperature predicts annual total across vegetation types and biomes. Biogeosciences. 7 (7): 2147-2157.

Barrett, SL; Albertini, DF. 2010. Cumulus cell contact during oocyte maturation in mice regulates meiotic spindle positioning and enhances developmental competence. Journal of Assisted Reproduction and Genetics. 27 (1): 29-39.

Bathe, M; Chang, F. 2010. Cytokinesis and the contractile ring in fission yeast: towards a systems-level understanding. Trends in Microbiology. 18 (1): 38-45.

Bernhard, AE; Landry, ZC; Blevins, A; de la Torre, JR; Giblin, AE; Stahl, DA. 2010. Abundance of Ammonia-Oxidizing Archaea and Bacteria along an Estuarine Salinity Gradient in Relation to Potential Nitrification Rates. Applied and Environmental Microbiology. 76 (4): 1285-1289.

Birkeland SR; Preheim SP; Davids BJ; Cipriano MJ; Palm D; Reiner DS; Svärd SG; Gillin FD; McArthur AG. 2010. Transcriptome analyses of the Giardia lamblia life cycle. Molecular and Biochemical Parasitology. 174 (1): 62-65.

Bodaker, I; Sharon, I; Suzuki, MT; Feingersch, R; Shmoish, M; Andreishcheva, E; Sogin, ML; Rosenberg, M; Maguire, ME; Belkin, S; Oren, A; Beja, O. 2010. Comparative community genomics in the Dead Sea: an increasingly extreme environment. ISME Journal. 4 (3): 399-407.

Bokhorst, S; Bjerke, JW; Melillo, J; Callaghan, TV; Phoenix, GK. 2010. Impacts of extreme winter warming events on litter decomposition in a sub-Arctic heathland. Soil Biology & Biochemistry. 42 (4): 611-617.

Brazelton, WJ; Sogin, ML; Baross, JA. 2010. Multiple scales of diversification within natural populations of archaea in hydrothermal chimney biofilms. Environmental Microbiology Reports. 2 (2): 236-242.

Briggs, MA; Gooseff, MN; Peterson, BJ; Morkeski, K; Wollheim, WM; Hopkinson, CS. 2010. Surface and hyporheic transient storage dynamics throughout a coastal stream network. Water Resources Research. 46: Art. No. W06516.

Brin, LD; Valiela, I; Goehringer, D; Howes, B. 2010. Nitrogen interception and export by experimental salt marsh plots exposed to chronic nutrient addition. Marine Ecology Progress Series. 400: 3-17.

Cai, WJ; Luther, GW; Cornwell, JC; Giblin, AE. 2010. Carbon Cycling and the Coupling Between Proton and Electron Transfer Reactions in Aquatic Sediments in Lake Champlain. Aquatic Geochemistry. 16 (3): 421-446.

Chadwick, WW; Butterfield, DA; Embley, RW; Tunnicliffe, V; Huber, JA; Nooner, SL; Clague, DA. 2010. Axial Seamount. Oceanography. 23 (1): 38-39.

Chiao, CC; Chubb, C; Buresch, KC; Barbosa, A; Allen, JJ; Mathger, LM; Hanlon, RT. 2010. Response to 'Holes in the camouflage'. Journal of Experimental Biology. 213 (17): 3075-3076.

Cleveland, CC; Houlton, BZ; Neill, C; Reed, SC; Townsend, AR; Wang, YP. 2010. Using indirect methods to constrain symbiotic nitrogen fixation rates: a case study from an Amazonian rain forest. Biogeochemistry. 99 (1-3): 1-13.

de Faveri, J; Smolowitz, RM; Roberts, SB. 2009. Development And Validation Of A Real-Time Quantitative Pcr Assay For The Detection And Quantification Of Perkinsus Marinus In The Eastern Oyster, Crassostrea Virginica. Journal of Shellfish Research. 28 (3): 459-464.

Edds-Walton PL; Holstein GR; Fay RR. 2010. gamma-Aminobutyric acid is a neurotransmitter in the auditory pathway of toadfish, Opsanus tau. Hearing Research. 262 (1-2): 45-55.

Espinosa, L; Ramirez, N; Gomez, MD; Nasi, E. 2010. Molecular Identification of Two Isoforms of Arrestin in the Retina of Pecten: Role in Light Response Termination in Ciliary Invertebrate Photoreceptors. Journal of General Physiology. 136 (1): 5A-6A.

Fleeger, JW; Johnson, DS; Carman, KR; Weisenhorn, PB; Gabriele, A; Thistle, D; Barry, JP. 2010. The response of nematodes to deep-sea CO2 sequestration: A quantile regression approach. Deep Sea Research Part I. 57 (5): 696-707.

Fleidervish, IA; Lasser-Ross, N; Gutnick, MJ; Ross, WN. 2010. Na+ imaging reveals little difference in action potential-evoked Na+ influx between axon and soma. Nature Neuroscience. 13 (7): 852-U96.

Galford, GL; Melillo, JM; Kicklighter, DW; Cronin, TW; Cerri, CEP; Mustard, JF; Cerri, CC. 2010. Climate Mitigation and Agricultural Productivity in Tropical Landscapes Special Feature: Greenhouse gas emissions from alternative futures of deforestation and agricultural management in the southern Amazon. Proceedings of the National Academy of Sciences. E-first. 10.1073/pnas.1000780107

Gardiner, JM; Atema, J. 2010. The Function of Bilateral Odor Arrival Time Differences in Olfactory Orientation of Sharks. Current Biology. 20 (13): 1187-1191.

Gatlin, JC; Matov, A; Danuser, G; Mitchison, TJ; Salmon, ED. 2010. Directly probing the mechanical properties of the spindle and its matrix. Journal of Cell Biology. 188 (4): 481-489.

German, CR; Bowen, A; Coleman, ML; Honig, DL; Huber, JA; Jakuba, MV; Kinsey, JC; Kurz, MD; Leroy, S; McDermott, JM; Mercier de Lepinay, B; Nakamura, K; Seewald, JS; Smith, JL; Sylva, SP; Van Dover, CL; Whitcomb, LL; Yoerger, DR. 2010. Diverse styles of submarine venting on the ultraslow spreading Mid-Cayman Rise. Proceedings of the National Academy of Sciences. 107 (32): 14020-14025.

Gilg, IC; Amaral-Zettler, LA; Countway, PD; Moorthi, S; Schnetzer, A; Caron, DA. 2010. Phylogenetic Affiliations of Mesopelagic Acantharia and Acantharian-like Environmental 18S rRNA Genes off the Southern California Coast. Protist. 161 (2): 197-211.

Gladyshev, EA; Arkhipova, IR. 2010. Genome Structure of Bdelloid Rotifers: Shaped by Asexuality or Desiccation?. Journal of Heredity. 101 (suppl_1): S85-S93.

Gomez, MD; Nasi, E. 2010. On the Transduction Gain of Melanopsin-mediated Light Signalling in Amphioxus: Single-Photon, Unitary, and Early Receptor Currents. Journal of General Physiology. 136 (1): 6A.

Gray, JP; Heart, E. 2010. Usurping the mitochondrial supremacy: Extramitochondrial sources of reactive oxygen intermediates and their role in beta cell metabolism and insulin secretion. Toxicology Mechanisms and Methods. 20 (4): 167-174.

Greenan G; Brangwynne CP; Jaensch S; Gharakhani J; Jülicher F; Hyman AA. 2010. Centrosome Size Sets Mitotic Spindle Length in Caenorhabditis elegans Embryos. Current Biology. 20 (4): 353-358.

Greenwood, AK; Peichel, CL; Zottoli, SJ. 2010. Distinct startle responses are associated with neuroanatomical differences in pufferfishes. Journal of Experimental Biology. 213 (4): 613-620.

Hasegawa, Y; Welch, JLM; Valm, AM; Rieken, C; Sogin, ML; Borisy, GG. 2010. Imaging Marine Bacteria with Unique 16S rRNA V6 Sequences by Fluorescence in situ Hybridization and Spectral Analysis. Geomicrobiology Journal. 27 (3): 251-260.

Hegaret, H; Smolowitz, RM; Sunila, I; Shumway, SE; Alix, J; Dixon, M; Wikfors, GH. 2010. Combined effects of a parasite, QPX, and the harmful-alga, Prorocentrum minimum on northern quahogs, Mercenaria mercenaria. Marine Environmental Research. 69 (5): 337-344.

Helmke, P; Neuer, S; Lomas, MW; Conte, M; Freudenthal, T. 2010. Cross-basin differences in particulate organic carbon export and flux attenuation in the subtropical North Atlantic gyre. Deep Sea Research Part I. 57 (2): 213-227.

Hoang, QV; Qian, HH; Ripps, H. 2010. Functional analysis of hemichannels and gap-junctional channels formed by connexins 43 and 46. Molecular Vision. 16 (145-50): 1343-1352.

Huber, JA; Cantin, HV; Huse, SM; Welch, DBM; Sogin, ML; Butterfield, DA. 2010. Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts. FEMS Microbiology Ecology. 73 (3): 538-549.

Huse SM; Welch DM; Morrison HG; Sogin ML. 2010. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental Microbiology. 12 (7): 1889-1898.

Hutt, KJ; Shi, ZQ; Petroff, BK; Albertini, DF. 2010. The Environmental Toxicant 2,3,7,8-Tetrachlorodibenzo-p-Dioxin Disturbs the Establishment and Maintenance of Cell Polarity in Preimplantation Rat Embryos. Biology of Reproduction. 82 (5): 914-920.

Janssens, IA; Dieleman, W; Luyssaert, S; Subke, J-A; Reichstein, M; Ceulemans, R; Ciais, P; Dolman, AJ; Grace, J; Matteucci, G; Papale, D; Piao, SL; Schulze, E-D; Tang, J; Law, BE. 2010. Reduction of forest soil respiration in response to nitrogen deposition. Nature Geoscience. 3 (5): 315-322.

Jaqaman, K; King, EM; Amaro, AC; Winter, JR; Dorn, JF; Elliott, HL; Mchedlishvili, N; McClelland, SE; Porter, IM; Posch, M; Toso, A; Danuser, G; McAinsh, AD; Meraldi, P; Swedlow, JR. 2010. Kinetochore alignment within the metaphase plate is regulated by centromere stiffness and microtubule depolymerases. Journal of Cell Biology. 188 (5): 665-679.

Karpinets, TV; Obraztsova, AY; Wang, YB; Schmoyer, DD; Kora, GH; Park, BH; Serres, MH; Romine, MF; Land, ML; Kothe, TB; Fredrickson, JK; Nealson, KH; Uberbacher, EC. 2010. Conserved synteny at the protein family level reveals genes underlying Shewanella species' cold tolerance and predicts their novel phenotypes. Functional & Integrative Genomics. 10 (1): 97-110.

Keeling, PJ; Corradi, N; Morrison, HG; Haag, KL; Ebert, D; Weiss, LM; Akiyoshi, DE; Tzipori, S. 2010. The Reduced Genome of the Parasitic Microsporidian Enterocytozoon bieneusi Lacks Genes for Core Carbon Metabolism. Genome Biology and Evolution. 2: 304-309.

Lasek-Nesselquist E; Welch DM; Sogin ML. 2010. The identification of a new Giardia duodenalis assemblage in marine vertebrates and a preliminary analysis of G. duodenalis population biology in marine systems. International Journal for Parasitology. 40 (9): 1063-1074.

Lee, H-S; Komarova, YA; Nadezhdina, ES; Anjum, R; Peloquin, JG; Schober, JM; Danciu, O; van Haren, J; Galjart, N; Gygi, SP; Akhmanova, A; Borisy, GG. 2010. Phosphorylation Controls Autoinhibition of Cytoplasmicer Protein-170. Molecular Biology of the Cell. 21 (15): 2661-2673.

Lico, DTP; Rosa, JC; Degiorgis, JA; de Vasconcelos, EJR; Casaletti, L; Tauhata, SBF; Baqui, MMA; Fukuda, M; Moreira, JE; Larson, RE. 2010. NOVEL 65 kDa RNA-BINDING PROTEIN IN SQUID PRESYNAPTIC TERMINALS. Neuroscience. 166 (1): 73-83.

Luo, YW; Friedrichs, MAM; Doney, SC; Church, MJ; Ducklow, HW. 2010. Oceanic heterotrophic bacterial nutrition by semilabile DOM as revealed by data assimilative modeling. Aquatic Microbial Ecology. 60 (3): 273-287.

Lv, P; Rodriguez-Contreras, A; Kim, HJ; Zhu, J; Wei, DG; Choong-Ryoul, S; Eastwood, E; Mu, KR; Levic, S; Song, HT; Yevgeniy, PY; Smith, PJS; Yamoah, EN. 2010. Release and Elementary Mechanisms of Nitric Oxide in Hair Cells. Journal of Neurophysiology. 103 (5): 2494-2505.

Mathger, LM; Roberts, SB; Hanlon, RT. 2010. Evidence for distributed light sensing in the skin of cuttlefish, Sepia officinalis. Biology Letters. 6 (5): 600-603.

McLellan, SL; Huse, SM; Mueller-Spitz, SR; Andreishcheva, EN; Sogin, ML. 2010. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environmental Microbiology. 12 (2): 378-392.

Montes-Hugo, M; Sweeney, C; Doney, SC; Ducklow, H; Frouin, R; Martinson, DG; Stammerjohn, S; Schofield, O. 2010. Seasonal forcing of summer dissolved inorganic carbon and chlorophyll a on the western shelf of the Antarctic Peninsula. Journal of Geophysical Research C: Oceans. 115: Art. No. C03024.

Mooney, TA; Lee, WJ; Hanlon, RT. 2010. Long-duration anesthetization of squid (Doryteuthis pealeii). Marine and Freshwater Behaviour and Physiology. 43 (4): 297-303.

Moran, XAG; Lopez-Urrutia, A; Calvo-Diaz, A; Li, WKW. 2010. Increasing importance of small phytoplankton in a warmer ocean. Global Change Biology. 16 (3): 1137-1144.

Morf, L; Spycher, C; Rehrauer, H; Fournier, CA; Morrison, HG; Hehl, AB. 2010. The transcriptional response to encystation stimuli in Giardia lamblia is restricted to a small set of genes. Eukaryotic Cell. E-first. 10.1128/EC.00100-10

Olsen YS; Fox SE; Kinney EL; Teichberg M; Valiela I. 2010. Differences in urbanization and degree of marine influence are reflected in delta(13)C and delta(15)N of producers and consumers in seagrass habitats of Puerto Rico. Marine Environmental Research. 69 (3): 198-206.

Olsen, YS; Valiela, I. 2010. Effect of Sediment Nutrient Enrichment and Grazing on Turtle Grass Thalassia testudinum in Jobos Bay, Puerto Rico. Estuaries and Coasts. 33 (3): 769-783.

Olsrud, M; Carlsson, BA; Svensson, BM; Michelsen, A; Melillo, JM. 2010. Responses of fungal root colonization, plant cover and leaf nutrients to long-term exposure to elevated atmospheric CO2 and warming in a subarctic birch forest understory. Global Change Biology. 16 (6): 1820-1829.

Parfrey, LW; Grant, J; Tekle, YI; Lasek-Nesselquist, E; Morrison, HG; Sogin, ML; Patterson, DJ; Katz, LA. 2010. Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life. Systematic Biology. E-first. 10.1093/sysbio/syq037

Pasapera, AM; Schneider, IC; Rericha, E; Schlaepfer, DD; Waterman, CM. 2010. Myosin II activity regulates vinculin recruitment to focal adhesions through FAK-mediated paxillin phosphorylation. Journal of Cell Biology. 188 (6): 877-890.

Pautzke, SM; Mather, ME; Finn, JT; Deegan, LA; Muth, RM. 2010. Seasonal Use of a New England Estuary by Foraging Contingents of Migratory Striped Bass. Transactions of the American Fisheries Society. 139 (1): 257-269.

Piontek, J; Lunau, M; Handel, N; Borchard, C; Wurst, M; Engel, A. 2010. Acidification increases microbial polysaccharide degradation in the ocean. Biogeosciences. 7 (5): 1615-1624.

Rabbitt, RD; Boyle, R; Highstein, SM. 2010. Mechanical amplification by hair cells in the semicircular canals. Proceedings of the National Academy of Sciences. 107 (8): 3864-3869.

Rastetter, EB; Williams, M; Griffin, KL; Kwiatkowski, BL; Tomasky, G; Potosnak, MJ; Stoy, PC; Shaver, GR; Stieglitz, M; Hobbie, JE; Kling, GW. 2010. Processing arctic eddy-flux data using a simple carbon-exchange model embedded in the ensemble Kalman filter. Ecological Applications. 20 (5): 1285-1301.

Ripps, H. 2010. Light to sight: milestones in phototransduction. FASEB Journal. 24 (4): 970-975.

Saffo, MB; McCoy, AM; Rieken, C; Slamovits, CH. 2010. Nephromyces, a beneficial apicomplexan symbiont in marine animals. Proceedings of the National Academy of Sciences. E-first. 10.1073/pnas.1002335107

Sarkar, IN; Schenk, R; Miller, H; Norton, CN. 2009. LigerCat: Using “MeSH Clouds” from Journal, Article, or Gene Citations to Facilitate the Identification of Relevant Biomedical Literature. AMIA Annual Symposium Proceedings. 2009: 563-567.

Schmitz MH; Held M; Janssens V; Hutchins JR; Hudecz O; Ivanova E; Goris J; Trinkle-Mulcahy L; Lamond AI; Poser I; Hyman AA; Mechtler K; Peters JM; Gerlich DW. 2010. Live-cell imaging RNAi screen identifies PP2A-B55alpha and importin-beta1 as key mitotic exit regulators in human cells. Nature Cell Biology. 12: 886–893.

Schofield, O; Ducklow, HW; Martinson, DG; Meredith, MP; Moline, MA; Fraser, WR. 2010. How Do Polar Marine Ecosystems Respond to Rapid Climate Change?. Science. 328 (5985): 1520-1523.

Searchinger, TD; Hamburg, SP; Melillo, J; Chameides, W; Havlik, P; Kammen, DM; Likens, GE; Obersteiner, M; Oppenheimer, M; Robertson, GP; Schlesinger, WH; Lubowski, R; Tilman, GD. 2010. Bioenergy: Counting on Incentives--Response. Science. 327 (5970): 1200-a.

Shah, MR; Alexander, KR; Ripps, H; Qian, HH. 2010. Characteristics of period doubling in the rat cone flicker ERG. Experimental Eye Research. 90 (2): 196-202.

Shanklin, DR. 2010. On the pulmonary toxicity of oxygen: III. The induction of oxygen dependency by oxygen use. Experimental and Molecular Pathology. 89 (1):36-45.

Smith PJ; Collis LP; Messerli MA. 2010. Windows to cell function and dysfunction: Signatures written in the boundary layers. Bioessays. 32 (6):514-23.

Smith, KE; Raymond, SL; Valenti, ML; Smith, PJS; Linser, PJ. 2010. Physiological and pharmacological characterization of the larval Anopheles albimanus rectum supports a change in protein distribution and/or function in varying salinities. Comparative Biochemistry & Physiology A. 157 (1): 55-62.

Sokolov, AP; Stone, PH; Forest, CE; Prinn, R; Sarofim, MC; Webster, M; Paltsev, S; Schlosser, CA; Kicklighter, D; Dutkiewicz, S; Reilly, J; Wang, C; Felzer, B; Melillo, JM; Jacoby, HD. 2010. CORRIGENDUM: Probabilistic forecast for twenty-first-century climate based on uncertainties in emissions (without policy) and climate parameters. (vol 22, pg 5175, 2009). Journal of Climate. 23 (8): 2230-2231.

Stock, SP; Bordenstein, SR; Odden, J; Oldenburg, D; Reznikoff, W; Werren, JH; Selosse, MA. 2010. Symbiosis instruction: considerations from the education workshop at the 6th ISS Congress. Symbiosis. 51 (1): 67-73.

Teichberg, M; Fox, SE; Olsen, YS; Valiela, I; Martinetto, P; Iribarne, O; Muto, EY; Petti, MAV; Corbisier, TN; Soto-Jimenez, M; Paez-Osuna, F; Castro, P; Freitas, H; Zitelli, A; Cardinaletti, M; Tagliapietra, D. 2010. Eutrophication and macroalgal blooms in temperate and tropical coastal waters: nutrient enrichment experiments with Ulva spp.. Global Change Biology. 16 (9): 2624-2637.

Tian, HQ; Chen, GS; Zhang, C; Melillo, JM; Hall, CAS. 2010. Pattern and variation of C:N:P ratios in China's soils: a synthesis of observational data. Biogeochemistry. 98 (1-3): 139-151.

Uehara R; Goshima G; Mabuchi I; Vale RD; Spudich JA; Griffis ER. 2010. Determinants of Myosin II Cortical Localization during Cytokinesis. Current Biology. 20 (12): 1080-1085.

Vallino, JJ. 2010. Ecosystem biogeochemistry considered as a distributed metabolic network ordered by maximum entropy production. Philosophical Transactions of the Royal Society B: Biological Sciences. 365 (1545): 1417-1427.

Vargas, R; Baldocchi, DD; Allen, MF; Bahn, M; Black, TA; Collins, SL; Yuste, JC; Hirano, T; Jassal, RS; Pumpanen, J; Tang, JW. 2010. Looking deeper into the soil: biophysical controls and seasonal lags of soil CO2 production and efflux. Ecological Applications. 20 (6): 1569-1582.

Wernegreen, JJ; Kauppinen, SN; Degnan, PH. 2010. Slip into something more functional: Selection maintains ancient frameshifts in homopolymeric sequences. Molecular Biology and Evolution. 27 (4): 833-839.

Weston, NB; Giblin, AE; Banta, GT; Hopkinson, CS; Tucker, J. 2010. The Effects of Varying Salinity on Ammonium Exchange in Estuarine Sediments of the Parker River, Massachusetts. Estuaries and Coasts. 33 (4): 985-1003.

Yamashita, G; Miller, H; Goddard, A; Norton, C. 2010. A model for Bioinformatics training: the marine biological laboratory. Briefings in Bioinformatics. E-first. 10.1093/bib/bbq029

Yanai, RD; Battles, JJ; Richardson, AD; Blodgett, CA; Wood, DM; Rastetter, EB. 2010. Estimating Uncertainty in Ecosystem Budget Calculations. Ecosystems. 13 (2): 239-248.

Yano, Y; Shaver, GR; Giblin, AE; Rastetter, EB; Nadelhoffer, KJ. 2010. Nitrogen dynamics in a small arctic watershed: Retention and downhill movement of 15N. Ecological Monographs. 80 (2): 331-351.

Zhang, Z; Bodznick, D. 2010. The importance of N-methyl-D-aspartate (NMDA) receptors in subtraction of electrosensory reafference in the dorsal nucleus of skates. Journal of Experimental Biology. 213 (15): 2700-2709.