Publications

January - May 2011

Adey, A; Morrison, HG; Asan; Xun, X; Kitzman, JO; Turner, EH; Stackhouse, B; MacKenzie, AP; Caruccio, NC; Zhang, XQ; Shendure, J. 2010. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biology. 11 (12): Art. No. R119.

Agogue H; Lamy D; Neal PR; Sogin ML; Herndl GJ. 2011. Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing. Molecular Ecology. 20 (2): 258-274.

Algar, CK; Boudreau, BP; Barry, MA. 2011. Initial rise of bubbles in cohesive sediments by a process of viscoelastic fracture. Journal of Geophysical Research B: Solid Earth. 116: Art. No. B04207.

Algar, CK; Boudreau, BP; Barry, MA. 2011. Release of multiple bubbles from cohesive sediments. Geophysical Research Letters. 38: Art. No. L08606.

Alliegro MC. 2011. The centrosome and spindle as a ribonucleoprotein complex. Chromosome Research. 19 (3): 367-376.

Amaral-Zettler, LA; Zettler, ER; Theroux, SM; Palacios, C; Aguilera, A; Amils, R. 2011. Microbial community structure across the tree of life in the extreme Rio Tinto. ISME Journal. 5 (1): 42-50.

Beaulieu, JJ; Tank, JL; Hamilton, SK; Wollheim, WM; Hall, RO; Mulholland, PJ; Peterson, BJ; Ashkenas, LR; Cooper, LW; Dahm, CN; Dodds, WK; Grimm, NB; Johnson, SL; McDowell, WH; Poole, GC; Valett, HM; Arango, CP; Bernot, MJ; Burgin, AJ; Crenshaw, CL; Helton, AM; Johnson, LT; O'Brien, JM; Potter, JD; Sheibley, RW; Sobota, DJ; Thomas, SM. 2011. Nitrous oxide emission from denitrification in stream and river networks. Proceedings of the National Academy of Sciences. 108 (1): 214-219.

Brangwynne, CP; Mitchison, TJ; Hyman, AA. 2011. Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes. Proceedings of the National Academy of Sciences. 108 (11): 4334-4339.

Chafee, ME; Zecher, CN; Gourley, ML; Schmidt, VT; Chen, JH; Bordenstein, SR; Clark, ME; Bordenstein, SR. 2011. Decoupling of Host-Symbiont-Phage Coadaptations Following Transfer Between Insect Species. Genetics. 187 (1): 203-215.

Chiao CC; Wickiser JK; Allen JJ; Genter B; T Hanlon R. 2011. Hyperspectral imaging of cuttlefish camouflage indicates good color match in the eyes of fish predators. Proceedings of the National Academy of Sciences. 108 (22): 9148-9153.

Cummins, SF; Boal, JG; Buresch, KC; Kuanpradit, C; Sobhon, P; Holm, JB; Degnan, BM; Nagle, GT; Hanlon, RT. 2011. Extreme Aggression in Male Squid Induced by a beta-MSP-like Pheromone. Current Biology. 21 (4): 322-327.

Dittami, GM; Rajguru, SM; Lasher, RA; Hitchcock, RW; Rabbitt, RD. 2011. Intracellular calcium transients evoked by pulsed infrared radiation in neonatal cardiomyocytes. Journal of Physiology London. 589 (6): 1295-1306.

Edgcomb VP; Breglia SA; Yubuki N; Beaudoin D; Patterson DJ; Leander BS; Bernhard JM. 2011. Identity of epibiotic bacteria on symbiontid euglenozoans in O2-depleted marine sediments: evidence for symbiont and host co-evolution. ISME Journal. 5 (2):231-43.

Fussell, KC; Udasin, RG; Gray, JP; Mishin, V; Smith, PJS; Heck, DE; Laskin, JD. 2011. Redox cycling and increased oxygen utilization contribute to diquat-induced oxidative stress and cytotoxicity in Chinese hamster ovary cells overexpressing NADPH-cytochrome P450 reductase. Free Radical Biology and Medicine. 50 (7): 874-882.

Galford, GL; Melillo, J; Mustard, JF; Cerri, CEP; Cerri, CC. 2010. The Amazon Frontier of Land-Use Change: Croplands and Consequences for Greenhouse Gas Emissions. Earth Interactions. 14: Art. No. 15.

Gasparini, S. 2011. Distance- and activity-dependent modulation of spike back-propagation in layer V pyramidal neurons of the medial entorhinal cortex. Journal of Neurophysiology. 105 (3): 1372-1379.

Gast, RJ; Moran, DM; Dennett, MR; Wurtsbaugh, WA; Amaral-Zettler, LA. 2011. Amoebae and Legionella pneumophila in saline environments. Journal of Water and Health. 9 (1): 37-52.

Gilbert, JA; Field, D; Swift, P; Thomas, S; Cummings, D; Temperton, B; Weynberg, K; Huse, S; Hughes, M; Joint, I; Somerfield, PJ; Muhling, M. 2010. The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A 'Multi-Omic' Study of Seasonal and Diel Temporal Variation. PLoS One. 5 (11): Art. No. e15545.

Gomez, MD; Espinosa, L; Ramirez, N; Nasi, E. 2011. Arrestin in Ciliary Invertebrate Photoreceptors: Molecular Identification and Functional Analysis In Vivo. Journal of Neuroscience. 31 (5): 1811-1819.

Gooseff, MN; Benson, DA; Briggs, MA; Weaver, M; Wollheim, W; Peterson, B; Hopkinson, CS. 2011. Residence time distributions in surface transient storage zones in streams: Estimation via signal deconvolution. Water Resources Research. 47: Art. No. W05509.

Gribble, KE; Snell, T; Welch, DBM. 2011. Gene and protein structure of the mate recognition protein gene family in Brachionus manjavacas (Rotifera). Hydrobiologia. 662 (1): 35-42.

Guizetti, J; Schermelleh, L; Mantler, J; Maar, S; Poser, I; Leonhardt, H; Muller-Reichert, T; Gerlich, DW. 2011. Cortical Constriction During Abscission Involves Helices of ESCRT-III-Dependent Filaments. Science. 331 (6024): 1616-1620.

Harmon, ME; Bond-Lamberty, B; Tang, JW; Vargas, R. 2011. Heterotrophic respiration in disturbed forests: A review with examples from North America. Journal of Geophysical Research G: Biogeosciences. 116: Art. No. G00K04.

Hayhoe, SJ; Neill, C; Porder, S; McHorney, R; Lefebvre, P; Coe, MT; Elsenbeer, H; Krusche, AV. 2011. Conversion to soy on the Amazonian agricultural frontier increases streamflow without affecting stormflow dynamics. Global Change Biology. 17 (5): 1821-1833.

Liang, N; Hirano, T; Zheng, ZM; Tang, J; Fujinuma, Y. 2010. Soil CO2 efflux of a larch forest in northern Japan. Biogeosciences. 7 (11): 3447-3457.

Loranty, MM; Goetz, SJ; Rastetter, EB; Rocha, AV; Shaver, GR; Humphreys, ER; Lafleur, PM. 2011. Scaling an Instantaneous Model of Tundra NEE to the Arctic Landscape. Ecosystems. 14 (1): 76-93.

Luo, YQ; Melillo, J; Niu, SL; Beier, C; Clark, JS; Classen, AT; Davidson, E; Dukes, JS; Evans, RD; Field, CB; Czimczik, CI; Keller, M; Kimball, BA; Kueppers, LM; Norby, RJ; Pelini, SL; Pendall, E; Rastetter, E; Six, J; Smith, M; Tjoelker, MG; Torn, MS. 2011. Coordinated approaches to quantify long-term ecosystem dynamics in response to global change. Global Change Biology. 17 (2): 843-854.

Mathger, LM; Lohmann, KJ; Limpus, CJ; Fritsches, KA. 2011. An unsuccessful attempt to elicit orientation responses to linearly polarized light in hatchling loggerhead sea turtles (Caretta caretta). Philosophical Transactions of the Royal Society B: Biological Sciences. 366 (1565): 757-762.

Melillo JM; Butler S; Johnson J; Mohan J; Steudler P; Lux H; Burrows E; Bowles F; Smith R; Scott L; Vario C; Hill T; Burton A; Zhou YM; Tang J. 2011. Soil warming, carbon-nitrogen interactions, and forest carbon budgets. Proceedings of the National Academy of Sciences. 108 (23): 9508-9512.

Menachery, A; Graham, D; Messerli, SM; Pethig, R; Smith, PJS. 2011. Dielectrophoretic tweezer for isolating and manipulating target cells. IET Nanotechnology. 5 (1): 1-7.

Middleton, JW; Kiritani, T; Pedersen, C; Turner, JG; Shepherd, GMG; Tzounopoulos, T. 2011. Mice with behavioral evidence of tinnitus exhibit dorsal cochlear nucleus hyperactivity because of decreased GABAergic inhibition. Proceedings of the National Academy of Sciences. 108 (18): 7601-7606.

Minc N; Burgess D; Chang F. 2011. Influence of cell geometry on division-plane positioning. Cell. 144 (3): 414-426.

Miyata, H; Noda, N; Fairbairn, DJ; Oldenbourg, R; Cardullo, RA. 2011. Assembly of the Fluorescent Acrosomal Matrix and Its Fate in Fertilization in the Water Strider, Aquarius remigis. Journal of Cellular Physiology. 226 (4): 999-1006.

Nuzzio, DB; Zettler, ER; Aguilera, A; Amaral-Zettler, LA. 2011. A direct in situ fingerprinting method for acid rock drainage using voltammetric techniques with a single renewable gold microelectrode. Science of the Total Environment. 409 (10): 1984-1989.

Olsen, YS; Fox, SE; Teichberg, M; Otter, M; Valiela, I. 2011. delta N-15 and delta C-13 reveal differences in carbon flow through estuarine benthic food webs in response to the relative availability of macroalgae and eelgrass. Marine Ecology Progress Series. 421: 83-96.

Pekkurnaz, G; Fera, A; Zimmerberg-Helms, J; DeGiorgis, JA; Bezrukov, L; Blank, PS; Mazar, J; Reese, TS; Zimmerberg, J. 2011. Isolation and Ultrastructural Characterization of Squid Synaptic Vesicles. Biological Bulletin. 220 (2): 89-96.

Pommier, T; Neal, PR; Gasol, JM; Coll, M; Acinas, SG; Pedros-Alio, C. 2010. Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA. Aquatic Microbial Ecology. 61 (3): 212-224.

Qian, HH; Alexander, KR; Ripps, H. 2010. Harmonic analysis of the cone flicker ERG of rabbit. Experimental Eye Research. 91 (6): 811-817.

Rajguru, SM; Richter, CP; Matic, AI; Holstein, GR; Highstein, SM: Dittami, GM; Rabbitt, RD. 2011. Infrared photostimulation of the crista ampullaris. Journal of Physiology London. 589 (6): 1283-1294.

Rastetter, EB. 2011. Modeling coupled biogeochemical cycles. Frontiers in Ecology and the Environment. 9 (1): 68-73.

Ren, W; Tian, HQ; Xu, XF; Liu, ML; Lu, CQ; Chen, GS; Melillo, J; Reilly, J; Liu, JY. 2011. Spatial and temporal patterns of CO2 and CH4 fluxes in China's croplands in response to multifactor environmental changes. Tellus Series B. 63 (2): 222-240.

Ridgway, ID; Richardson, CA; Enos, E; Ungvari, Z; Austad, SN; Philipp, EER; Csiszar, A. 2011. New Species Longevity Record For The Northern Quahog (=Hard Clam), Mercenaria Mercenaria. Journal of Shellfish Research. 30 (1): 35-38.

Rietsma, CS; Monteiro, RO; Valiela, I. 2011. Plant Cover, Herbivory, and Resiliency in a Cape Cod Salt Marsh: Multi-year Responses and Recovery Following Manipulation of Nutrients and Competition. Estuaries and Coasts. 34 (1): 198-210.

Rocha, AV; Shaver, GR. 2011. Burn severity influences postfire CO2 exchange in arctic tundra. Ecological Applications. 21 (2): 477-489.

Rosengaus, RB; Zecher, CN; Schultheis, KF; Brucker, RM; Bordenstein, SR. 2011. Disruption of termite gut-microbiota and its prolonged fitness consequences. Applied and Environmental Microbiology. E-first. 10.1128/AEM.01886-10

Rosenthal, GG; Fitzsimmons, JN; Woods, KU; Gerlach, G; Fisher, HS. 2011. Tactical Release of a Sexually-Selected Pheromone in a Swordtail Fish. PLoS One. 6 (2): Art. No. e16994.

Shanks OC; Kelty CA; Archibeque S; Jenkins M; Newton RJ; McLellan SL; Huse SM; Sogin ML. 2011. Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations. Applied and Environmental Microbiology. 77 (9): 2992-3001.

Shapiro, OH; Hatzenpichler, R; Buckley, DH; Zinder, SH; Orphan, VJ. 2011. Multicellular photo-magnetotactic bacteria. Environmental Microbiology Reports. 3 (2): 233-238.

Shashar, N; Johnsen, S; Lerner, A; Sabbah, S; Chiao, CC; Mathger, LM; Hanlon, RT. 2011. Underwater linear polarization: physical limitations to biological functions. Philosophical Transactions of the Royal Society B: Biological Sciences. 366 (1565): 649-654.

Shribak, M. 2011. Complete polarization state generator with one variable retarder and its application for fast and sensitive measuring of two-dimensional birefringence distribution. Journal of the Optical Society of America A. Optics, Image Science and Vision. 28 (3): 410-419.

Skogen, KA; Holsinger, KE; Cardon, ZG. 2011. Nitrogen deposition, competition and the decline of a regionally threatened legume, Desmodium cuspidatum. Oecologia. 165 (1): 261-269.

Smith, HA; Welch, DBM; Snell, TW. 2011. Molecular evolution of the membrane associated progesterone receptor in the Brachionus plicatilis (Rotifera, Monogononta) species complex. Hydrobiologia. 662 (1): 99-106.

Staudinger, MD; Hanlon, RT; Juanes, F. 2011. Primary and secondary defences of squid to cruising and ambush fish predators: variable tactics and their survival value. Animal Behaviour. 81 (3): 585-594.

Straza, TRA; Ducklow, HW; Murray, AE; Kirchman, DL. 2010. Abundance and single-cell activity of bacterial groups in Antarctic coastal waters. Limnology and Oceanography. 55 (6): 2526-2536.

Theroux, S; D'Andrea, WJ; Toney, J; Amaral-Zettler, L; Huang, YS. 2010. Phylogenetic diversity and evolutionary relatedness of alkenone-producing haptophyte algae in lakes: Implications for continental paleotemperature reconstructions. Earth and Planetary Science Letters. 300 (3-4): 311-320.

Tian, HQ; Melillo, J; Lu, CQ; Kicklighter, D; Liu, ML; Ren, W; Xu, XF; Chen, GS; Zhang, C; Pan, SF; Liu, JY; Running, S. 2011. China's terrestrial carbon balance: Contributions from multiple global change factors. Global Biogeochemical Cycles. 25: Art. No. GB1007.

Tian, HQ; Xu, XF; Lu, CQ; Liu, ML; Ren, W; Chen, GS; Melillo, J; Liu, JY. 2011. Net exchanges of CO2, CH4, and N2O between China's terrestrial ecosystems and the atmosphere and their contributions to global climate warming. Journal of Geophysical Research G: Biogeosciences. 116: Art. No. G02011.

Townsend-Small, A; McClelland, JW; Holmes, RM; Peterson, BJ. 2011. Seasonal and hydrologic drivers of dissolved organic matter and nutrients in the upper Kuparuk River, Alaskan Arctic. Biogeochemistry. 103 (1-3): 109-124.

Valm AM; Mark Welch JL; Rieken CW; Hasegawa Y; Sogin ML; Oldenbourg R; Dewhirst FE; Borisy GG. 2011. Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proceedings of the National Academy of Sciences. 108 (10): 4152-4157.

Wollert, T; Patel, A; Lee, YL; Provance, DW; Vought, VE; Cosgrove, MS; Mercer, JA; Langford, GM. 2011. Myosin5a Tail Associates Directly with Rab3A-containing Compartments in Neurons. Journal of Biological Chemistry. 286 (16): 14352-14361.

Yilmaz, P; Kottmann, R; Field, D; Knight, R; Cole, JR; Amaral-Zettler, L; Gilbert, JA; Karsch-Mizrachi, I; Johnston, A; Cochrane, G; Vaughan, R; Hunter, C; Park, J; Morrison, N; Rocca-Serra, P; Sterk, P; Arumugam, M; Bailey, M; Baumgartner, L; Birren, BW; Blaser, MJ; Bonazzi, V; Booth, T; Bork, P; Bushman, FD; Buttigieg, PL; Chain, PSG; Charlson, E; Costello, EK; Huot-Creasy, H; Dawyndt, P; DeSantis, T; Fierer, N; Fuhrman, JA; Gallery, RE; Gevers, D; Gibbs, RA; Gil, IS; Gonzalez, A; Gordon, JI; Guralnick, R; Hankeln, W; Highlander, S; Hugenholtz, P; Jansson, J; Kau, AL; Kelley, ST; Kennedy, J; Knights, D; Koren, O; Kuczynski, J; Kyrpides, N; Larsen, R; Lauber, CL; Legg, T; Ley, RE; Lozupone, CA; Ludwig, W; Lyons, D; Maguire, E; Methe, BA; Meyer, F; Muegge, B; Nakielny, S; Nelson, KE; Nemergut, D; Neufeld, JD; Newbold, LK; Oliver, AE; Pace, NR; Palanisamy, G; Peplies, J; Petrosino, J; Proctor, L; Pruesse, E; Quast, C; Raes, J; Ratnasingham, S; Ravel, J; Relman, DA; Assunta-Sansone, S; Schloss, PD; Schriml, L; Sinha, R; Smith, MI; Sodergren, E; Spor, A; Stombaugh, J; Tiedje, JM; Ward, DV; Weinstock, GM; Wendel, D; White, O; Whiteley, A; Wilke, A; Wortman, JR; Yatsunenko, T; Glockner, FO. 2011. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29 (5): 415-420.

Zakon, HH; Jost, MC; Lu, Y. 2011. Expansion of voltage-dependent Na+ channel gene family in early tetrapods coincided with the emergence of terrestriality and increased brain complexity. Molecular Biology and Evolution. 28 (4): 1415-1424.

Zottoli SJ; Wong TW; Agostini MA; Meyers JR. 2011. Axon cap morphology of the sea robin (prionotus carolinus) mauthner cell is correlated with the presence of 'signature' field potentials and a C-type startle response. Journal of Comparative Neurology. 58 (5): 590-614.

Zylinski, S; How, MJ; Osorio, D; Hanlon, RT; Marshall, NJ. 2011. To Be Seen or to Hide: Visual Characteristics of Body Patterns for Camouflage and Communication in the Australian Giant Cuttlefish Sepia apama. American Naturalist. 177 (5): 681-690.