Recent MBL Publications

(as of January 3, 2018)

Chandler, T., Mehta, S., Shroff, H., Oldenbourg, R., & La Riviere, P. J. (2017). Single-fluorophore orientation determination with multiview polarized illumination: modeling and microscope design. OPTICS EXPRESS, 25(25), 31309-31325. doi: 10.1364/OE.25.031309

Crump, B. C., Fine, L. M., Fortunato, C. S., Herfort, L., Needoba, J. A., Murdock, S., & Prahl, F. G. (2017). Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary. LIMNOLOGY AND OCEANOGRAPHY, 62(6), 2713-2731. doi: 10.1002/lno.10601

Hanlon, R., Mathger, L. M., Bell, G. R. R., Kuzirian, A. M., & Senft, S. L. (2017). White reflection from cuttlefish skin leucophores. Bioinspir Biomim. doi: 10.1088/1748-3190/aaa3a9

Medeiros, A. T., Soll, L. G., Tessari, I., Bubacco, L., & Morgan, J. R. (2017). alpha-Synuclein Dimers Impair Vesicle Fission during Clathrin-Mediated Synaptic Vesicle Recycling. FRONTIERS IN CELLULAR NEUROSCIENCE, 11(ARTN 388). doi: 10.3389/fncel.2017.00388

Nelson, F. E., Hollingworth, S., Marx, J. O., Baylor, S. M., & Rome, L. C. (2017). Small Ca2+ releases enable hour-long high-frequency contractions in midshipman swimbladder muscle. J Gen Physiol. doi: 10.1085/jgp.201711760

Sepehri Rad, M., Choi, Y., Cohen, L. B., Baker, B. J., Zhong, S., Storace, D. A., & Braubach, O. R. (2017). Voltage and Calcium Imaging of Brain Activity. Biophys J, 113(10), 2160-2167. doi: 10.1016/j.bpj.2017.09.040

Wang, F. M., Ding, Y. Z., Sayer, E. J., Li, Q. L., Zou, B., Mo, Q. F., Li, Y. W., Lu, X. L., Tang, J. W., Zhu, W. X., & Li, Z. A. (2017). Tropical forest restoration: Fast resilience of plant biomass contrasts with slow recovery of stable soil C stocks. FUNCTIONAL ECOLOGY, 31(12), 2344-2355. doi: 10.1111/1365-2435.12925

Zamponi, E., Buratti, F., Cataldi, G., Caicedo, H. H., Song, Y., Jungbauer, L. M., LaDu, M. J., Bisbal, M., Lorenzo, A., Ma, J., Helguera, P. R., Morfini, G. A., Brady, S. T., & Pigino, G. F. (2017). Prion protein inhibits fast axonal transport through a mechanism involving casein kinase 2. PLOS ONE, 12(12), e0188340. doi: 10.1371/journal.pone.0188340

DeLay, B. D., Corkins, M. E., Hanania, H. L., Salanga, M., Deng, J. M., Sudou, N., Taira, M., Horb, M., & Miller, R. K. (2017). Tissue-specific Gene Inactivation in Xenopus laevis: Knockout of lhx1 in the Kidney with CRISPR/Cas9. Genetics. doi: 10.1534/genetics.117.300468

Fortunato, C. S., Larson, B., Butterfield, D. A., & Huber, J. A. (2017). Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids. Environ Microbiol. doi: 10.1111/1462-2920.14011

Gemmell, B. J., Colin, S. P., & Costello, J. H. (2017). Widespread utilization of passive energy recapture in swimming medusae. J Exp Biol. doi: 10.1242/jeb.168575

Hasegawa, Y., Mark Welch, J. L., Rossetti, B. J., & Borisy, G. G. (2017). Preservation of three-dimensional spatial structure in the gut microbiome. PLOS ONE, 12(11), 1-16. doi: 10.1371/journal.pone.0188257

Huang, W. Y. C., Ditlev, J. A., Chiang, H. K., Rosen, M. K., & Groves, J. T. (2017). Allosteric Modulation of Grb2 Recruitment to the Intrinsically Disordered Scaffold Protein, LAT, by Remote Site Phosphorylation. J Am Chem Soc, 139(49), 18009-18015. doi: 10.1021/jacs.7b09387

Liebeskind, B. J., Hofmann, H. A., Hillis, D. M., & Zakon, H. H. (2017). Evolution of Animal Neural Systems. In D. J. Futuyma (Ed.), (pp. 377-398): ANNUAL REVIEWS.

Mitchison, T. J., & Field, C. M. (2017). Spindle-to-Cortex Communication in Cleaving Frog Eggs. Cold Spring Harb Symp Quant Biol. doi: 10.1101/sqb.2017.82.033654

Nguyen, P. A., Field, C. M., & Mitchison, T. J. (2017). Prc1E and Kif4A control microtubule organization within and between large xenopus egg asters. Mol Biol Cell. doi: 10.1091/mbc.E17-09-0540

Criswell, K. E., Coates, M. I., & Gillis, J. A. (2017). Embryonic origin of the gnathostome vertebral skeleton. Proc Biol Sci, 284(1867). doi: 10.1098/rspb.2017.2121

Gillis, J. A., Alsema, E. C., & Criswell, K. E. (2017). Trunk neural crest origin of dermal denticles in a cartilaginous fish. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1713827114

Huntingford, C., Atkin, O. K., Martinez-de la Torre, A., Mercado, L. M., Heskel, M. A., Harper, A. B., Bloomfield, K. J., O’Sullivan, O. S., Reich, P. B., Wythers, K. R., Butler, E. E., Chen, M., Griffin, K. L., Meir, P., Tjoelker, M. G., Turnbull, M. H., Sitch, S., Wiltshire, A., & Malhi, Y. (2017). Implications of improved representations of plant respiration in a changing climate. Nat Commun, 8(1), 1602. doi: 10.1038/s41467-017-01774-z

Lu, X., Cheng, X., Li, X., & Tang, J. (2017). Opportunities and challenges of applications of satellite-derived sun-induced fluorescence at relatively high spatial resolution. Sci Total Environ, 619-620, 649-653. doi: 10.1016/j.scitotenv.2017.11.158

Schmidt, V., Gomez-Chiarri, M., Roy, C., Smith, K., & Amaral-Zettler, L. (2017). Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish. mSystems, 2(6). doi: 10.1128/mSystems.00133-17

Sturdivant, E. J., Lentz, E. E., Thieler, E. R., Farris, A. S., Weber, K. M., Remsen, D. P., Miner, S., & Henderson, R. E. (2017). UAS-SfM for Coastal Research: Geomorphic Feature Extraction and Land Cover Classification from High-Resolution Elevation and Optical Imagery. Remote Sensing, 9(10). doi: 10.3390/rs9101020

Wu, Y., Kumar, A., Smith, C., Ardiel, E., Chandris, P., Christensen, R., Rey-Suarez, I., Guo, M., Vishwasrao, H. D., Chen, J., Tang, J., Upadhyaya, A., La Riviere, P. J., & Shroff, H. (2017). Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy. Nat Commun, 8(1), 1452. doi: 10.1038/s41467-017-01250-8

Zheng, Y. S., Tarozo, R., & Huang, Y. S. (2017). Optimizing chromatographic resolution for simultaneous quantification of long chain alkenones, alkenoates and their double bond positional isomers. Organic Geochemistry, 111, 136-143. doi: 10.1016/j.orggeochem.2017.06.013

Spira, F., Cuylen-Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., Oldenbourg, R., Sixt, M., & Gerlich, D. W. (2017). Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. Elife, 6. doi: 10.7554/eLife.30867

Tully, B. J., Wheat, C. G., Glazer, B. T., & Huber, J. A. (2017). A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. ISME J. doi: 10.1038/ismej.2017.187

Vallecillo-Viejo, I. C., Liscovitch-Brauer, N., Montiel-Gonzalez, M. F., Eisenberg, E., & Rosenthal, J. J. C. (2017). Abundant off-target edits from site-directed RNA editing can be reduced by nuclear localization of the editing enzyme. RNA Biol, 0. doi: 10.1080/15476286.2017.1387711

Anderson, R. E., Reveillaud, J., Reddington, E., Delmont, T. O., Eren, A. M., McDermott, J. M., Seewald, J. S., & Huber, J. A. (2017). Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. Nat Commun, 8(1), 1114. doi: 10.1038/s41467-017-01228-6

Carbone, C. B., Kern, N., Fernandes, R. A., Hui, E., Su, X., Garcia, K. C., & Vale, R. D. (2017). In vitro reconstitution of T cell receptor-mediated segregation of the CD45 phosphatase. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1710358114

Chafee, M., Fernàndez-Guerra, A., Buttigieg, P. L., Gerdts, G., Eren, A. M., Teeling, H., & Amann, R. I. (2017). Recurrent patterns of microdiversity in a temperate coastal marine environment. ISME J. doi: 10.1038/ismej.2017.165

Delmont, T. O., & Eren, A. M. (2017). Simulations predict microbial responses in the environment? This environment disagrees retrospectively. Proc Natl Acad Sci U S A, 114(43), E8947-E8949. doi: 10.1073/pnas.1712186114

Hubbard, C. J., Brock, M. T., van Diepen, L. T., Maignien, L., Ewers, B. E., & Weinig, C. (2017). The plant circadian clock influences rhizosphere community structure and function. ISME J. doi: 10.1038/ismej.2017.172

Kirby, A., Lewbart, G. A., Hancock-Ronemus, A., & Papich, M. G. (2017). Pharmacokinetics of enrofloxacin and ciprofloxacin in Atlantic horseshoe crabs (Limulus polyphemus) after single injection. J Vet Pharmacol Ther. doi: 10.1111/jvp.12462

Liang, L. L., Arcus, V. L., Heskel, M. A., O’Sullivan, O. S., Weerasinghe, L. K., Creek, D., Egerton, J. J. G., Tjoelker, M. G., Atkin, O. K., & Schipper, L. A. (2017). Macromolecular Rate Theory (MMRT) Provides a Thermodynamics Rationale to Underpin the Convergent Temperature Response in Plant Leaf Respiration. Glob Chang Biol. doi: 10.1111/gcb.13936

Mark Welch, J. L., Hasegawa, Y., McNulty, N. P., Gordon, J. I., & Borisy, G. G. (2017). Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice. Proc Natl Acad Sci U S A, 114(43), E9105-E9114. doi: 10.1073/pnas.1711596114

Nunez, I., Rodriguez Pino, M., Wiley, D. J., Das, M. E., Chen, C., Goshima, T., Kume, K., Hirata, D., Toda, T., & Verde, F. (2016). Spatial control of translation repression and polarized growth by conserved NDR kinase Orb6 and RNA-binding protein Sts5. Elife, 5. doi: 10.7554/eLife.14216

Peirson, B. R. E., Bottino, E., Damerow, J. L., & Laubichler, M. D. (2017). Quantitative Perspectives on Fifty Years of the Journal of the History of Biology. J Hist Biol. doi: 10.1007/s10739-017-9499-2

Perez, T., Rodriguez, F., Fernandez, M., Albornoz, J., & Dominguez, A. (2017). Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus. Gene, 628, 63-71. doi: 10.1016/j.gene.2017.07.035

Swaminathan, V., Kalappurakkal, J. M., Mehta, S. B., Nordenfelt, P., Moore, T. I., Koga, N., Baker, D. A., Oldenbourg, R., Tani, T., Mayor, S., Springer, T. A., & Waterman, C. M. (2017). Actin retrograde flow actively aligns and orients ligand-engaged integrins in focal adhesions. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(40), 10648-10653. doi: 10.1073/pnas.1701136114

Walton, P. L., Christensen-Dalsgaard, J., & Carr, C. E. (2017). Evolution of Sound Source Localization Circuits in the Nonmammalian Vertebrate Brainstem. Brain Behavior and Evolution, 90(2), 131-153. doi: 10.1159/000476028

He, H., Cheng, X., Li, X., Zhu, R., Hui, F., Wu, W., Zhao, T., Kang, J., & Tang, J. (2017). Aerial photography based census of Adélie Penguin and its application in CH4 and N2O budget estimation in Victoria Land, Antarctic. Sci Rep, 7(1), 12942. doi: 10.1038/s41598-017-13380-6

Perez, T., Rodriguez, F., Fernandez, M., Albornoz, J., & Dominguez, A. (2017). Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus. Gene, 628, 63-71. doi: 10.1016/j.gene.2017.07.035

Pikul, J. H., Li, S., Bai, H., Hanlon, R. T., Cohen, I., & Shepherd, R. F. (2017). Stretchable surfaces with programmable 3D texture morphing for synthetic camouflaging skins. SCIENCE, 358(6360), 210-214.doi: 10.1126/science.aan5627

Tcherkez, G., Gauthier, P., Buckley, T. N., Busch, F. A., Barbour, M. M., Bruhn, D., Heskel, M. A., Gong, X. Y., Crous, K. Y., Griffin, K., Way, D., Turnbull, M., Adams, M. A., Atkin, O. K., Farquhar, G. D., & Cornic, G. (2017). Leaf day respiration: low CO2 flux but high significance for metabolism and carbon balance. New Phytol. doi: 10.1111/nph.14816

Tkacz, R., Abedin, M. J., Sheath, P., Mehta, S. B., Verma, A., Oldenbourg, R., & Majumder, M. (2017). Phase Transition and Liquid Crystalline Organization of Colloidal Graphene Oxide as a Function of pH. PARTICLE & PARTICLE SYSTEMS CHARACTERIZATION, 34(9). doi: 10.1002/ppsc.201600391

Iversen, M. M., & Rabbitt, R. D. (2017). Wave Mechanics of the Vestibular Semicircular Canals. Biophysical Journal, 113(5), 1133-1149. doi: 10.1016/j.bpj.2017.08.001

Keikhosravi, A., Liu, Y., Drifka, C., Woo, K. M., Verma, A., Oldenbourg, R., & Eliceiri, K. W. (2017). Quantification of collagen organization in histopathology samples using liquid crystal based polarization microscopy. BIOMEDICAL OPTICS EXPRESS, 8(9), 4243-4256. doi: 10.1364/BOE.8.004243

Kroeger, K. D., Crooks, S., Moseman-Valtierra, S., & Tang, J. (2017). Restoring tides to reduce methane emissions in impounded wetlands: A new and potent Blue Carbon climate change intervention. Sci Rep, 7(1), 11914. doi: 10.1038/s41598-017-12138-4

Miyazaki, K., & Ross, W. N. (2017). Sodium dynamics in pyramidal neuron dendritic spines: synaptically evoked entry predominantly through AMPA receptors and removal by diffusion. J Neurosci. doi: 10.1523/JNEUROSCI.1758-17.2017

Neill, C., Jankowski, K., Brando, P. M., Coe, M. T., Deegan, L. A., Macedo, M. N., Riskin, S. H., Porder, S., Elsenbeer, H., & Krusche, A. V. (2017). Surprisingly Modest Water Quality Impacts From Expansion and Intensification of Large-Sscale Commercial Agriculture in the Brazilian Amazon-Cerrado Region. TROPICAL CONSERVATION SCIENCE, 10. doi: 10.1177/1940082917720669

Quince, C., Delmont, T. O., Raguideau, S., Alneberg, J., Darling, A. E., Collins, G., & Eren, A. M. (2017). DESMAN: a new tool for de novo extraction of strains from metagenomes. Genome Biol, 18(1), 181. doi: 10.1186/s13059-017-1309-9

Schlundt, C., Tegtmeier, S., Lennartz, S. T., Bracher, A., Wee, C. B., Kruger, K., Quack, B., & Marandino, C. A. (2017). Oxygenated volatile organic carbon in the western Pacific convective center: ocean cycling, air-sea gas exchange and atmospheric transport. Atmospheric Chemistry and Physics, 17(17), 10837-10854. doi: 10.5194/acp-17-10837-2017

Chen, X., Zeng, G., Xie, Q., Chen, Y., Huang, Y., Qiu, J., Cai, J., Chen, C., & Tang, J. (2017). A novel combined recirculating treatment system for intensive marine aquaculture. AQUACULTURE RESEARCH, 48(9), 5062-5071. doi: 10.1111/are.13323

Euskirchen, E. S., Bret-Harte, M. S., Shaver, G. R., Edgar, C. W., & Romanovsky, V. E. (2017). Long-Term Release of Carbon Dioxide from Arctic Tundra Ecosystems in Alaska. ECOSYSTEMS, 20(5), 960-974. doi: 10.1007/s10021-016-0085-9

Fan, K., Cardona, C., Li, Y., Shi, Y., Xiang, X., Shen, C., Wang, H., Gilbert, J. A., & Chu, H. (2017). Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields. SOIL BIOLOGY & BIOCHEMISTRY, 113, 275-284. doi: 10.1016/j.soilbio.2017.06.020

Hobbie, E. A., Shamhart, J., Sheriff, M., Ouimette, A. P., Trappe, M., Schuur, E. A. G., Hobbie, J. E., Boonstra, R., & Barnes, B. M. (2017). Stable isotopes and radiocarbon assess variable importance of plants and fungi in diets of arctic ground squirrels. ARCTIC ANTARCTIC AND ALPINE RESEARCH, 49(3), 487-500. doi: 10.1657/AAAR0016-062

Iversen, M. M., & Rabbitt, R. D. (2017). Wave Mechanics of the Vestibular Semicircular Canals. Biophys J, 113(5), 1133-1149. doi: 10.1016/j.bpj.2017.08.001

Toledo-Hernández, C., Ruiz-Diaz, C. P., Díaz-Vázquez, L. M., Santiago-Cárdenas, V., Rosario-Berrios, D. N., García-Almedina, D. M., & Roberson, L. M. (2017). Comparison of chemical compounds associated with sclerites from healthy and diseased sea fan corals (Gorgonia ventalina). PeerJ, 5, e3677. doi: 10.7717/peerj.3677

Brady, S. T., & Morfini, G. A. (2017). Regulation of motor proteins, axonal transport deficits and adult-onset neurodegenerative diseases. NEUROBIOLOGY OF DISEASE, 105, 273-282. doi: 10.1016/j.nbd.2017.04.010