Publications – BobTail Squid Database

Publications on the Squid-Vibrio Symbiosis

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2023

Baden, T., John Briseño, Gabrielle Coffing, Sophie Cohen-Bodénès, Amy Courtney, Dominick Dickerson, GülDölen Graziano Fiorito,Camino Gestal, Taryn Gustafson, Elizabeth Heath-Heckman, Qiaz Hua, Pamela Imperadore, Ryosuke Kimbara, Mirela Król, Zdeneˇk Lajbner, Nicolás Lichilín, Filippo Macchi, Matthew J. McCoy, Michele K. Nishiguchi, Spencer V. Nyholm, Eve Otjacques, Pedro Antonio Pérez-Ferrer, Giovanna Ponte, Judit R. Pungor, Thea F. Rogers, Joshua J. C. Rosenthal, Lisa Rouressol, Noelle Rubas, Gustavo Sanchez, Catarina Pereira Santos, Darrin T. Schultz, Eve Seuntjens, Jeremea O. Songco-Casey, Ian Erik Stewart, Ruth Styfhals, Surangkana Tuanapaya, Nidhi Vijayan, Anton Weissenbacher, Lucia Zifcakova, Grace Schulz, Willem Weertman, Oleg Simakov, and Caroline Albertin. 2023. Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology. Integrative and Comparative Biology 1:1-14
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Bongrand, C., Foster, J.S., 2023. Modelled microgravity impacts Vibrio fischeri population structure in a mutualistic association with an animal host. Environmental Microbiology DOI: 10.1111/1462-2920.16522
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Cecere, A.G., Cook, R.A. and Miyashiro, T.I., 2023. A case study assessing the impact of mating frequency on the reproductive performance of the Hawaiian bobtail squid Euprymna scolopes. Laboratory Animal Research, 39(1), 1-8.
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Donnelly AR, Giacobe EJ, Cook RA, Francis GM, Buddle GK, Beaubrun CL, et al. (2023) Quantification of the capacity of Vibrio fischeri to establish symbiosis with Euprymna scolopes. PLoS ONE 18(7): e0287519.
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Essock-Burns, T., Lawhorn, S., Wu, L., McClosky, S., Moriano-Gutierrez, S., Ruby, E.G. and McFall-Ngai, M.J., 2023. Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership. Microbiome, 11(1), pp.1-16.
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Guckes, K.R. and Miyashiro, T.I., 2023. The type VI secretion system of the beneficial symbiont Vibrio fischeri. Microbiology (Reading, England), 169(2).
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Guckes, K.R., Yount, T.A., Steingard, C.H. and Miyashiro, T.I., 2023. Quorum sensing inhibits interference competition among bacterial symbionts within a host. Current Biology, in press.
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McAnulty, S.J., Kerwin, A.H., Koch, E., Nuttall, B., Suria, A.M., Collins, A.J., Schleicher, T.R., Rader, B.A. and Nyholm, S.V., 2023. “Failure To Launch”: Development of a Reproductive Organ Linked to Symbiotic Bacteria. Mbio, 14(1), e02131-22.
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Provencher, E.A.P., Ehrig, M.R., Cecere, A.G., Cousins, S.C., Maybin, M.A., Meredith, T.C. and Miyashiro, T., Inhibition of biofilm formation by a lipopolysaccharide-associated glycosyltransferase in the bacterial symbiont Vibrio fischeri. Frontiers in Bacteriology, 2, 1254305.
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Reardon, S. (2023) Octopuses used in research could receive same protections as monkeys. Nature; September 15, 2023 doi.org/10.1038/d41586-023-02887-w
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Rouressol, L., Briseno, J., Vijayan, N., Chen, G.Y., Ritschard, E.A., Sanchez, G., Nyholm, S.V., McFall-Ngai, M.J. and Simakov, O., 2023. Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid. iScience.
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Surrett, E.D., Guckes, K.R., Cousins, S., Ruskoski, T.B., Cecere, A.G., Ludvik, D.A., Okafor, C.D., Mandel, M.J. and Miyashiro, T.I., 2023. Two enhancer binding proteins activate σ54-dependent transcription of a quorum regulatory RNA in a bacterial symbiont. eLife, 12, e78544.
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2022

Albertin, C.B., Medina-Ruiz, S., Mitros, T., Schmidbaur, H., Sanchez, G., Wang, Z.Y., Grimwood, J., Rosenthal, J.J., Ragsdale, C.W., Simakov, O. and Rokhsar, D.S., 2022. Genome and transcriptome mechanisms driving cephalopod evolution. Nature communications, 13(1), p.2427.
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Bongrand, C., Koch, E., Mende, D., Romano, A., Lawhorn, S., McFall-Ngai, M., DeLong, E.F. and Ruby, E.G., 2022. Evidence of genomic diversification in a natural symbiotic population within its host. Frontiers in Microbiology, 13.
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Cecere, A.G. and Miyashiro, T.I., 2022. Impact of transit time on the reproductive capacity of Euprymna scolopes as a laboratory animal. Laboratory Animal Research, 38(1), pp.1-9.
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Fidopiastis, P.M., Childs, C., Esin, J.J., Stellern, J., Darin, A., Lorenzo, A., Mariscal, V.T., Lorenz, J., Gopan, V., McAnulty, S. and Visick, K.L., 2022. Vibrio fischeri possesses Xds and Dns nucleases that differentially influence phosphate scavenging, aggregation, competence, and symbiotic colonization of squid. Applied and Environmental Microbiology, 88(22), pp.e01635-22.
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Lynch, J.B., Bennett, B.D., Merrill, B.D., Ruby, E.G. and Hryckowian, A.J., 2022. Independent host-and bacterium-based determinants protect a model symbiosis from phage predation. Cell reports, 38(7), p.110376.
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Lynch, J.B., James, N., McFall-Ngai, M., Ruby, E.G., Shin, S. and Takagi, D., 2022. Transitioning to confined spaces impacts bacterial swimming and escape response. Biophysical Journal, 121(13), pp.2653-2662.
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Marino, A., Kizenko, A., Wong, W.Y., Ghiselli, F. and Simakov, O., 2022. Repeat age decomposition informs an ancient set of repeats associated with coleoid cephalopod divergence. Frontiers in Genetics, p.421.
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McFall-Ngai, M., 2022. Building a career during a revolution in biology. Nature Microbiology, 7(3), pp.347-348.
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Medina, M., Baker, D.M., Baltrus, D.A., Bennett, G.M., Cardini, U., Correa, A., Degnan, S.M., Christa, G., Kim, E., Li, J. and Nash, D.R., 2022. Grand challenges in coevolution. Frontiers in Ecology and Evolution, 9, p.916.
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Pipes, B.L. and Nishiguchi, M.K., 2022. Nocturnal Acidification: A Coordinating Cue in the Euprymna scolopes–Vibrio fischeri Symbiosis. International Journal of Molecular Sciences, 23(7), p.3743.
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Suria, A.M., Smith, S., Speare, L., Chen, Y., Chien, I., Clark, E.G., Krueger, M., Warwick, A.M., Wilkins, H. and Septer, A.N., 2022. Prevalence and diversity of type VI secretion systems in a model beneficial symbiosis. Frontiers in Microbiology, 13, p.988044.
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Vroom, M.M., Troncoso-Garcia, A., Duscher, A.A. and Foster, J.S., 2022. Modeled microgravity alters apoptotic gene expression and caspase activity in the squid-vibrio symbiosis. BMC microbiology, 22(1), p.202.
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Yount, T.A., Murtha, A.N., Cecere, A.G. and Miyashiro, T.I., 2022. Quorum sensing facilitates interpopulation signaling by Vibrio fischeri within the light organ of Euprymna scolopes. Israel Journal of Chemistry, p.e202200061.
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2021

Chavez-Dozal, A., Soto, W. and Nishiguchi, M.K., 2021. Identification of a transcriptomic network underlying the wrinkly and smooth phenotypes of Vibrio fischeri. Journal of Bacteriology, 203(3).
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Cohen, J.J., Eichinger, S.J., Witte, D.A., Cook, C.J., Fidopiastis, P.M., Tepavčević, J. and Visick, K.L., 2021. Control of competence in Vibrio fischeri. Applied and Environmental Microbiology, 87(6).
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Dial, C.N., Eichinger, S.J., Foxall, R., Corcoran, C.J., Tischler, A.H., Bolz, R.M., Whistler, C.A. and Visick, K.L., 2021. Quorum sensing and cyclic di-GMP exert control over motility of Vibrio fischeri KB2B1. Frontiers in microbiology, 12.
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Dial, C.N., Speare, L., Sharpe, G.C., Gifford, S.M., Septer, A.N. and Visick, K.L., 2021. Para-Aminobenzoic Acid, Calcium, and c-di-GMP Induce Formation of Cohesive, Syp-Polysaccharide-Dependent Biofilms in Vibrio fischeri. Mbio, 12(5), pp.e02034-21.
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Essock-Burns, T., Bennett, B.D., Arencibia, D., Moriano-Gutierrez, S., Medeiros, M., McFall-Ngai, M.J. and Ruby, E.G., 2021. Bacterial Quorum-Sensing Regulation Induces Morphological Change in a Key Host Tissue during the Euprymna scolopes–Vibrio fischeri Symbiosis. Mbio, 12(5), pp.e02402-21.
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Fernández-Álvarez, F.Á., Sánchez, P. and Villanueva, R., 2021. Morphological and molecular assessments of bobtail squids (Cephalopoda: Sepiolidae) reveal a hidden history of biodiversity. Frontiers in Marine Science, 7 (632261)
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Fidopiastis, P.M., Mariscal, V., McPherson, J.M., McAnulty, S., Dunn, A., Stabb, E.V. and Visick, K.L., 2021. Vibrio fischeri amidase activity is required for normal cell division, motility, and symbiotic competence. Applied and Environmental Microbiology, 87(3).
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Funk MA. 2021. Light conversation. Science 372:251.3–252.
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Heath-Heckman, E. and Nishiguchi, M.K., 2021. Leveraging Short-Read Sequencing to Explore the Genomics of Sepiolid Squid. Integrative and comparative biology, 61(5), pp.1753-1761.
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Ludvik, D.A., Bultman, K.M. and Mandel, M.J., 2021. Hybrid histidine kinase BinK represses Vibrio fischeri biofilm signaling at multiple developmental stages. Journal of Bacteriology, pp.JB-00155.
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McFall-Ngai, M. and Bosch, T.C., 2021. Animal development in the microbial world: the power of experimental model systems. Current topics in developmental biology, 141, p.371.
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McFall-Ngai, M. and Ruby, E., 2021. Getting the message out: the many modes of host-symbiont communication during early-stage establishment of the squid-vibrio partnership. Msystems, 6(5), pp.e00867-21.
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Moriano-Gutierrez, S., Ruby, E.G. and McFall-Ngai, M.J., 2021. MicroRNA-mediated regulation of initial host responses in a symbiotic organ. Msystems, 6(3), pp.e00081-21.
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Nourabadi, N. and Nishiguchi, M.K., 2021. pH Adaptation drives diverse phenotypes in a beneficial bacterium-host mutualism. Frontiers in Ecology and Evolution, 9, p.14.
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Nyholm, S.V. and McFall-Ngai, M.J., 2021. A lasting symbiosis: how the Hawaiian bobtail squid finds and keeps its bioluminescent bacterial partner. Nature Reviews Microbiology, 19(10), pp.666-679.
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Øresland, V. and G. Oxby, 2021. A photo-illustrated dissection guide for bobtail squids. Diverse and Scientists West Coast Sweden, Guide No. 1, pp. 122.
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Ruby, E., 2021. Getting to know our microbial friends by dropping into their neighbourhood. Environmental Microbiology Reports, 13(1), pp.27-30.
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Soto, W. and Nishiguchi, M.K., 2021. Environmental stress selects for innovations that drive vibrio symbiont diversity. Frontiers in Ecology and Evolution, 9, p.383.
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Speare, L., Woo, M., Bultman, K.M., Mandel, M.J., Wollenberg, M.S. and Septer, A.N., 2021. Host-like conditions are required for T6SS-mediated competition among Vibrio fischeri light organ symbionts. Msphere, 6(4), pp.e01288-20.
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Tischler, A.H., Vanek, M.E., Peterson, N. and Visick, K.L., 2021. Calcium-Responsive Diguanylate Cyclase CasA Drives Cellulose-Dependent Biofilm Formation and Inhibits Motility in Vibrio fischeri. Mbio, 12(6), pp.e02573-21.
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Visick, K.L., Stabb, E.V. and Ruby, E.G., 2021. A lasting symbiosis: how Vibrio fischeri finds a squid partner and persists within its natural host. Nature Reviews Microbiology, 19(10), pp.654-665.
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Vroom, M.M., Rodriguez-Ocasio, Y., Lynch, J.B., Ruby, E.G. and Foster, J.S., 2021. Modeled microgravity alters lipopolysaccharide and outer membrane vesicle production of the beneficial symbiont Vibrio fischeri. npj Microgravity, 7(1), pp.1-10.
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Wasilko, N.P., Ceron, J.S., Baker, E.R., Cecere, A.G., Wollenberg, M.S. and Miyashiro, T.I., 2021. Vibrio fischeri imports and assimilates sulfate during symbiosis with Euprymna scolopes. Molecular Microbiology, 116(3), pp.926-942.
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Zink, K.E., Ludvik, D.A., Lazzara, P.R., Moore, T.W., Mandel, M.J. and Sanchez, L.M., 2021. A small molecule coordinates symbiotic behaviors in a host organ. Mbio, 12(2), pp.e03637-20.
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2020

Bennett, B.D., Essock-Burns, T. and Ruby, E.G., 2020. HbtR, a heterofunctional homolog of the virulence regulator TcpP, facilitates the transition between symbiotic and planktonic lifestyles in Vibrio fischeri. Mbio, 11(5).
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Bongrand, C., Moriano-Gutierrez, S., Arevalo, P., McFall-Ngai, M., Visick, K.L., Polz, M. and Ruby, E.G., 2020. Using colonization assays and comparative genomics to discover symbiosis behaviors and factors in Vibrio fischeri. Mbio, 11(2).
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Burgos, H.L., Burgos, E.F., Steinberger, A.J., Suen, G. and Mandel, M.J., 2020. Multiplexed competition in a synthetic squid light organ microbiome using barcode-tagged gene deletions. Msystems, 5(6).
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Christensen, D.G., Marsden, A.E., Hodge‐Hanson, K., Essock‐Burns, T. and Visick, K.L., 2020. LapG mediates biofilm dispersal in Vibrio fischeri by controlling maintenance of the VCBS‐containing adhesin LapV. Molecular Microbiology, 114(5), pp.742-761.
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Christensen, D.G., Tepavčević, J. and Visick, K.L., 2020. Genetic manipulation of Vibrio fischeri. Current Protocols in Microbiology, 59(1), p.e115.
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Christensen, D.G. and Visick, K.L., 2020. Vibrio fischeri: laboratory cultivation, storage, and common phenotypic assays. Current protocols in microbiology, 57(1), p.e103.
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Cohen, S.K., Aschtgen, M.S., Lynch, J.B., Koehler, S., Chen, F., Escrig, S., Daraspe, J., Ruby, E.G., Meibom, A. and McFall‐Ngai, M., 2020. Tracking the cargo of extracellular symbionts into host tissues with correlated electron microscopy and nanoscale secondary ion mass spectrometry imaging. Cellular Microbiology, 22(4), p.e13177.
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Essock-Burns, T., Bongrand, C., Goldman, W.E., Ruby, E.G. and McFall-Ngai, M.J., 2020. Interactions of symbiotic partners drive the development of a complex biogeography in the squid-vibrio symbiosis. Mbio, 11(3).
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Guckes, K.R., Cecere, A.G., Williams, A.L., McNeil, A.E. and Miyashiro, T., 2020. The bacterial enhancer binding protein VasH promotes expression of a type VI secretion system in Vibrio fischeri during symbiosis. Journal of bacteriology, 202(7), pp.e00777-19.
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Koch, E.J., Bongrand, C., Bennett, B.D., Lawhorn, S., Moriano-Gutierrez, S., Pende, M., Vadiwala, K., Dodt, H.U., Raible, F., Goldman, W. and Ruby, E.G., 2020. The cytokine MIF controls daily rhythms of symbiont nutrition in an animal–bacterial association. Proceedings of the National Academy of Sciences, 117(44), pp.27578-27586.
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Koch, E.J., Moriano-Gutierrez, S., Ruby, E.G., McFall-Ngai, M. and Liebeke, M., 2020. The impact of persistent colonization by Vibrio fischeri on the metabolome of the host squid Euprymna scolopes. Journal of Experimental Biology, 223(16).
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Moriano-Gutierrez, S., Bongrand, C., Essock-Burns, T., Wu, L., McFall-Ngai, M.J. and Ruby, E.G., 2020. The noncoding small RNA SsrA is released by Vibrio fischeri and modulates critical host responses. PLoS Biology, 18(11), p.e3000934.
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Speare, L., Smith, S., Salvato, F., Kleiner, M. and Septer, A.N., 2020. Environmental viscosity modulates interbacterial killing during habitat transition. Mbio, 11(1).
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Suria, A.M., Tan, K.C., Kerwin, A.H., Gitzel, L., Abini-Agbomson, L., Bertenshaw, J.M., Sewell, J., Nyholm, S.V. and Balunas, M.J., 2020. Hawaiian bobtail squid symbionts inhibit marine bacteria via production of specialized metabolites, including new bromoalterochromides BAC-D/D′. mSphere, 5(4).
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Zink, K.E., Tarnowski, D.A., Mandel, M.J. and Sanchez, L.M., 2020. Optimization of a minimal sample preparation protocol for imaging mass spectrometry of unsectioned juvenile invertebrates. Journal of Mass Spectrometry, 55(4), p.e4458.
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2019

Aschtgen, M.S., Brennan, C.A., Nikolakakis, K., Cohen, S., McFall-Ngai, M. and Ruby, E.G., 2019. Insights into flagellar function and mechanism from the squid–vibrio symbiosis. NPJ biofilms and microbiomes, 5(1), pp.1-10.
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Belcaid, M, G Casaburi, SJ McAnulty, H Schmidbau, AM Suria, S Moriano-Gutierrez, MS Pankey, TH Oakley, N Kremer , EJ Koch, AJ Collins, H Nguyen, S Lek, Irina Goncharenko, P Minx, E Sodergren, G Weinstock, D Rokhsar, Margaret McFall-Ngai, O Simakov, JS Foster, SV Nyholm, 2019. Symbiotic organs shaped by distinct modes of genome evolution in cephalopods. Proceedings of the National Academy of Sciences, 116(8), pp.3030-3035.
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Bongrand, C. and Ruby, E.G., 2019. The impact of Vibrio fischeri strain variation on host colonization. Current opinion in microbiology, 50, pp.15-19.
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Bongrand, C. and Ruby, E.G., 2019. Achieving a multi-strain symbiosis: Strain behavior and infection dynamics. The ISME Journal, 13(3), p.698.
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Bosch, T.C., Guillemin, K. and McFall‐Ngai, M., 2019. Evolutionary “Experiments” in Symbiosis: The Study of Model Animals Provides Insights into the Mechanisms Underlying the Diversity of Host–Microbe Interactions. BioEssays, 41(10), p.1800256.
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Bultman, K.M., Cecere, A.G., Miyashiro, T., Septer, A.N. and Mandel, M.J., 2019. Draft Genome Sequences of Type VI Secretion System-Encoding Vibrio fischeri Strains FQ-A001 and ES401. Microbiology resource announcements, 8(20), pp.e00385-19.
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Fuqua, C., Filloux, A., Ghigo, J.M. and Visick, K.L., 2019. Biofilms 2018: A diversity of microbes and mechanisms.
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Guckes, K.R., Cecere, A.G., Wasilko, N.P., Williams, A.L., Bultman, K.M., Mandel, M.J. and Miyashiro, T., 2019. Incompatibility of Vibrio fischeri strains during symbiosis establishment depends on two functionally redundant hcp genes. Journal of bacteriology, 201(19), pp.e00221-19.
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Koehler, S., Gaedeke, R., Thompson, C., Bongrand, C., Visick, K.L., Ruby, E. and McFall‐Ngai, M., 2019. The model squid–vibrio symbiosis provides a window into the impact of strain‐and species‐level differences during the initial stages of symbiont engagement. Environmental microbiology, 21(9), pp.3269-3283.
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Lynch, J.B., Schwartzman, J.A., Bennett, B.D., McAnulty, S.J., Knop, M., Nyholm, S.V. and Ruby, E.G., 2019. Ambient pH Alters the Protein Content of Outer Membrane Vesicles, Driving Host Development in a Beneficial Symbiosis. Journal of bacteriology, 201(20), pp.e00319-19.
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Mandel, M.J., Broderick, N.A., Martens, E.C. and Guillemin, K., 2019. Reports from a Healthy Community: the 7th Conference on Beneficial Microbes. Applied and Environmental Microbiology 85(10): e02562-18
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Moriano-Gutierrez, S., Koch, E.J., Bussan, H., Romano, K., Belcaid, M., Rey, F.E., Ruby, E.G. and McFall-Ngai, M.J., 2019. Critical symbiont signals drive both local and systemic changes in diel and developmental host gene expression. Proceedings of the National Academy of Sciences, 116(16), pp.7990-7999.
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Rotman, E.R., Bultman, K.M., Brooks, J.F., Gyllborg, M.C., Burgos, H.L., Wollenberg, M.S. and Mandel, M.J., 2019. Natural strain variation reveals diverse biofilm regulation in squid-colonizing Vibrio fischeri. Journal of bacteriology, 201(9), pp.e00033-19.
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Sanchez, G., Jolly, J., Reid, A., Sugimoto, C., Azama, C., Marlétaz, F., Simakov, O. and Rokhsar, D.S., 2019. New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis. Communications biology, 2(1), pp.1-15.
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Schwartzman, J.A., Lynch, J.B., Flores Ramos, S., Zhou, L., Apicella, M.A., Yew, J.Y. and Ruby, E.G., 2019. Acidic pH promotes lipopolysaccharide modification and alters colonization in a bacteria–animal mutualism. Molecular microbiology, 112(4), pp.1326-1338.
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Septer, A.N., 2019. The vibrio-squid symbiosis as a model for studying Interbacterial competition. MSystems, 4(3), pp.e00108-19.
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Soto, W., Travisano, M., Tolleson, A.R. and Nishiguchi, M.K., 2019. Symbiont evolution during the free-living phase can improve host colonization. Microbiology, 165(2), pp.174-187.
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Speare, L. and Septer, A.N., 2019. Coincubation assay for quantifying competitive interactions between Vibrio fischeri isolates. JoVE (Journal of Visualized Experiments), (149), p.e59759.
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Stabb, E.V., 2019. Should they stay or should they go? Nitric oxide and the clash of regulators governing Vibrio fischeri biofilm formation. Molecular microbiology, 111(1), pp.1-5.
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Stoudenmire, J.L., Black, M., Fidopiastis, P.M. and Stabb, E.V., 2019. Mutagenesis of Vibrio fischeri and Other Marine Bacteria Using Hyperactive Mini-Tn5 Derivatives. In Microbial Transposon Mutagenesis (pp. 87-104).
Humana, New York, NY.
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Thompson, C.M., Tischler, A.H., Tarnowski, D.A., Mandel, M.J. and Visick, K.L., 2019. Nitric oxide inhibits biofilm formation by Vibrio fischeri via the nitric oxide sensor HnoX. Molecular microbiology, 111(1), pp.187-203.
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Tischler, A.H., Hodge‐Hanson, K.M. and Visick, K.L., 2019. Vibrio fischeri–Squid Symbiosis. eLS, pp.1-9.
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Wasilko, N.P., Larios‐Valencia, J., Steingard, C.H., Nunez, B.M., Verma, S.C. and Miyashiro, T., 2019. Sulfur availability for Vibrio fischeri growth during symbiosis establishment depends on biogeography within the squid light organ. Molecular microbiology, 111(3), pp.621-636.
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2018

Coryell, R.L., Turnham, K.E., de Jesus Ayson, E.G., Lavilla‐Pltogo, C., Alcala, A.C., Sotto, F., Gonzales, B. and Nishiguchi, M.K., 2018. Phylogeographic patterns in the Philippine archipelago influence symbiont diversity in the bobtail squid–vibrio mutualism. Ecology and evolution, 8(15), pp.7421-7435.
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Dunn, A.K., 2018. Alternative oxidase activity reduces stress in Vibrio fischeri cells exposed to nitric oxide. Journal of bacteriology, 200(15), pp.e00797-17.
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Duscher, A.A., Conesa, A., Bishop, M., Vroom, M.M., Zubizarreta, S.D. and Foster, J.S., 2018. Transcriptional profiling of the mutualistic bacterium Vibrio fischeri and an hfq mutant under modeled microgravity. npj Microgravity, 4(1), p.25.
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Guo, H., Fauci, L., Shelley, M. and Kanso, E., 2018. Bistability in the synchronization of actuated microfilaments. Journal of Fluid Mechanics, 836, pp.304-323.
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Jones, R.M., Popham, D.L., Schmidt, A.L., Neidle, E.L. and Stabb, E.V., 2018. Vibrio fischeri DarR directs responses to d-aspartate and represents a group of similar LysR-type transcriptional regulators. Journal of Bacteriology, 200(15), pp.e00773-17.
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Kerwin, A.H. and Nyholm, S.V., 2018. Reproductive System Symbiotic Bacteria Are Conserved between Two Distinct Populations of Euprymna scolopes from Oahu, Hawaii. mSphere, 3(2), pp.e00531-17.
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Koch, E.J. and McFall-Ngai, M., 2018. Model systems for the study of how symbiotic associations between animals and extracellular bacterial partners are established and maintained. Drug Discovery Today: Disease Models, 28, pp.3-12.
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Kremer, N., Koch, E.J., El Filali, A., Zhou, L., Heath-Heckman, E.A., Ruby, E.G. and McFall-Ngai, M.J., 2018. Persistent interactions with bacterial symbionts direct mature-host cell morphology and gene expression in the squid-vibrio symbiosis. MSystems, 3(5), pp.e00165-18.
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Mandel, M.J., 2018. D-Fining DarR, a LysR-type transcriptional regulator that responds to D-aspartate. Journal of Bacteriology 200(15), pp, e00121-18
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Patelunas, A.J. and Nishiguchi, M.K., 2018. Vascular architecture in the bacteriogenic light organ of Euprymna tasmanica (Cephalopoda: Sepiolidae). Invertebrate biology, 137(3), pp.240-249.
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Peyer, S.M., Kremer, N. and McFall‐Ngai, M.J., 2018. Involvement of a host cathepsin L in symbiont‐induced cell death. MicrobiologyOpen, 7(5), p.e00632.
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Speare, L., Cecere, A.G., Guckes, K.R., Smith, S., Wollenberg, M.S., Mandel, M.J., Miyashiro, T. and Septer, A.N., 2018. Bacterial symbionts use a type VI secretion system to eliminate competitors in their natural host. Proceedings of the National Academy of Sciences, 115(36), pp.E8528-E8537.
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Stabb, E.V., 2018. Could positive feedback enable bacterial pheromone signaling to coordinate behaviors in response to heterogeneous environmental cues?. MBio, 9(3), pp.e00098-18.
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Stoudenmire, J.L., Essock-Burns, T., Weathers, E.N., Solaimanpour, S., Mrázek, J. and Stabb, E.V., 2018. An iterative, synthetic approach to engineer a high-performance PhoB-specific reporter. Appl. Environ. Microbiol., 84(14), pp.e00603-18.
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Thompson, C.M., Marsden, A.E., Tischler, A.H., Koo, J. and Visick, K.L., 2018. Vibrio fischeri biofilm formation prevented by a trio of regulators. Applied and environmental microbiology, 84(19), pp.e01257-18.
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Tischler, A.H., Lie, L., Thompson, C.M. and Visick, K.L., 2018. Discovery of calcium as a biofilm-promoting signal for Vibrio fischeri reveals new phenotypes and underlying regulatory complexity. Journal of bacteriology, 200(15), pp.e00016-18.
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Truong, T.V., Holland, D.B., Madaan, S., Andreev, A., Troll, J.V., Koo, D.E., Keomanee-Dizon, K., McFall-Ngai, M. and Fraser, S.E., 2018. Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast. bioRxiv, p.403303.
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Visick, K.L., Hodge-Hanson, K.M., Tischler, A.H., Bennett, A.K. and Mastrodomenico, V., 2018. Tools for rapid genetic engineering of Vibrio fischeri. Appl. Environ. Microbiol., 84(14), pp.e00850-18.
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2017

Casaburi, G., Goncharenko-Foster, I., Duscher, A.A. and Foster, J.S., 2017. Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions. Scientific reports, 7, p.46318.
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Chen, F., Krasity, B.C., Peyer, S.M., Koehler, S., Ruby, E.G., Zhang, X. and McFall-Ngai, M.J., 2017. Bactericidal permeability-increasing proteins shape host-microbe interactions. MBio, 8(2), pp.e00040-17.
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Guo, H. and Kanso, E., 2017. A computational study of mucociliary transport in healthy and diseased environments. European Journal of Computational Mechanics, 26(1-2), pp.4-30.
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Kerwin, A.H. and Nyholm, S.V., 2017. Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs. Environmental microbiology, 19(4), pp.1463-1475.
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Kimbrough, J.H. and Stabb, E.V., 2017. Comparative analysis reveals regulatory motifs at the ainS/ainR pheromone-signaling locus of Vibrio fischeri. Scientific reports, 7(1), p.11734.
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Lyell, N.L., Septer, A.N., Dunn, A.K., Duckett, D., Stoudenmire, J.L. and Stabb, E.V., 2017. An expanded transposon mutant library reveals that Vibrio fischeri δ-aminolevulinate auxotrophs can colonize Euprymna scolopes. Appl. Environ. Microbiol., 83(5), pp.e02470-16.
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Marsden, A.E., Grudzinski, K., Ondrey, J.M., DeLoney-Marino, C.R. and Visick, K.L., 2017. Impact of salt and nutrient content on biofilm formation by Vibrio fischeri. PloS one, 12(1), p.e0169521.
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McAnulty, S.J. and Nyholm, S.V., 2017. The role of hemocytes in the Hawaiian bobtail squid, Euprymna scolopes: a model organism for studying beneficial host–microbe interactions. Frontiers in microbiology, 7, p.2013.
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Nawroth, J.C., Guo, H., Koch, E., Heath-Heckman, E.A., Hermanson, J.C., Ruby, E.G., Dabiri, J.O., Kanso, E. and McFall-Ngai, M., 2017. Motile cilia create fluid-mechanical microhabitats for the active recruitment of the host microbiome. Proceedings of the National Academy of Sciences, 114(36), pp.9510-9516.
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Pan, S., Nikolakakis, K., Adamczyk, P.A., Pan, M., Ruby, E.G. and Reed, J.L., 2017. Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacterium Vibrio fischeri. Journal of Biological Chemistry, 292(24), pp.10250-10261.
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Pankey, M.S., Foxall, R.L., Ster, I.M., Perry, L.A., Schuster, B.M., Donner, R.A., Coyle, M., Cooper, V.S. and Whistler, C.A., 2017. Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria. Elife, 6, p.e24414.
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Peyer, S.M., Heath-Heckman, E.A., and McFall-Ngai, M.J., 2017. Characterization of the cell polarity gene crumbs during the early development and maintenance of the squid–vibrio light organ symbiosis. Development genes and evolution, 227(6), pp.375-387.
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Thompson, L.R., Nikolakakis, K., Pan, S., Reed, J., Knight, R. and Ruby, E.G., 2017. Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes. Environmental microbiology, 19(5), pp.1845-1856.
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von Byern, J., Cyran, N., Klepal, W., Nödl, M.T. and Klinger, L., 2017. Characterization of the adhesive dermal secretion of Euprymna scolopes Berry, 1913 (Cephalopoda). Zoology, 120, pp.73-82.
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2016

Aschtgen, M.S., Lynch, J.B., Koch, E., Schwartzman, J., McFall-Ngai, M. and Ruby, E., 2016. Rotation of Vibrio fischeri flagella produces outer membrane vesicles that induce host development. Journal of bacteriology, 198(16), pp.2156-2165.
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Aschtgen, M.S., Wetzel, K., Goldman, W., McFall‐Ngai, M. and Ruby, E., 2016. Vibrio fischeri‐derived outer membrane vesicles trigger host development. Cellular microbiology, 18(4), pp.488-499.
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Beeby, M., Ribardo, D.A., Brennan, C.A., Ruby, E.G., Jensen, G.J. and Hendrixson, D.R., 2016. Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold. Proceedings of the National Academy of Sciences, 113(13), pp.E1917-E1926.
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Bongrand, C., Koch, E.J., Moriano-Gutierrez, S., Cordero, O.X., McFall-Ngai, M., Polz, M.F. and Ruby, E.G., 2016. A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior. The ISME journal, 10(12), p.2907.
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Brooks, J.F. and Mandel, M.J., 2016. The histidine kinase BinK is a negative regulator of biofilm formation and squid colonization. Journal of bacteriology, 198(19), pp.2596-2607.
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Chavez-Dozal, A. and Nishiguchi, M.K., 2016. Impact of Metabolomics in Symbiosis Research. Metabolomics: Fundamentals and Applications, p.139.
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Chavez-Dozal, A.A., Nourabadi, N., Erken, M., McDougald, D. and Nishiguchi, M.K., 2016. Comparative analysis of quantitative methodologies for Vibrionaceae biofilms. Folia microbiologica, 61(6), pp.449-453.
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Gromek, S.M., Suria, A.M., Fullmer, M.S., Garcia, J.L., Gogarten, J.P., Nyholm, S.V. and Balunas, M.J., 2016. Leisingera sp. JC1, a bacterial isolate from Hawaiian bobtail squid eggs, produces indigoidine and differentially inhibits vibrios. Frontiers in microbiology, 7, p.1342.
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Guo, H. and Kanso, E., 2016. Evaluating efficiency and robustness in cilia design. Physical Review E, 93(3), p.033119.
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Heath‐Heckman, E.A., Foster, J., Apicella, M.A., Goldman, W.E. and McFall‐Ngai, M., 2016. Environmental cues and symbiont microbe‐associated molecular patterns function in concert to drive the daily remodelling of the crypt‐cell brush border of the Euprymna scolopes light organ. Cellular microbiology, 18(11), pp.1642-1652.
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Kimbrough, J.H. and Stabb, E.V., 2016. Antisocial luxO mutants provide a stationary-phase survival advantage in Vibrio fischeri ES114. Journal of bacteriology, 198(4), pp.673-687.
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Mandel, M.J. and Dunn, A.K., 2016. Impact and influence of the natural vibrio-squid symbiosis in understanding bacterial–animal interactions. Frontiers in microbiology, 7, p.1982.
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Nyholm, S.V., 2016. Fiat Lux: the Squid–Vibrio association as a model for understanding host–microbe associations. In The Mechanistic Benefits of Microbial Symbionts (pp. 295-315). Springer, Cham.
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Schwartzman, J.A. and Ruby, E.G., 2016. Stress as a normal cue in the symbiotic environment. Trends in microbiology, 24(5), pp.414-424.
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Schwartzman, J.A. and Ruby, E.G., 2016. A conserved chemical dialog of mutualism: lessons from squid and vibrio. Microbes and infection, 18(1), pp.1-10.
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Sun, Y., LaSota, E.D., Cecere, A.G., LaPenna, K.B., Larios-Valencia, J., Wollenberg, M.S. and Miyashiro, T., 2016. Intraspecific competition impacts Vibrio fischeri strain diversity during initial colonization of the squid light organ. Appl. Environ. Microbiol., 82(10), pp.3082-3091.
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Verma, S.C. and Miyashiro, T., 2016. Niche-specific impact of a symbiotic function on the persistence of microbial symbionts within a natural host. Appl. Environ. Microbiol., 82(19), pp.5990-5996.
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Vincent, L. and Kanso, E., 2017. Under the microscope cover slip: spontaneous flows and bacterial behavior. In Chaos, Complexity and Transport: Proceedings of the CCT’15 Conference on Chaos, Complexity and Transport 2015 (pp. 83-103).
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Wollenberg, M.S. and Ruby, E.G., 2012. Phylogeny and fitness of Vibrio fischeri from the light organs of Euprymna scolopes in two Oahu, Hawaii populations. The ISME journal, 6(2), p.352.
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2015

Alivisatos, A.P., Blaser, M.J., Brodie, E.L., Chun, M., Dangl, J.L., Donohue, T.J., Dorrestein, P.C., Gilbert, J.A., Green, J.L., Jansson, J.K. and Knight, R., 2015. A unified initiative to harness Earth’s microbiomes. Science, 350(6260), pp.507-508.
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Biteen, J.S., Blainey, P.C., Cardon, Z.G., Chun, M., Church, G.M., Dorrestein, P.C., Fraser, S.E., Gilbert, J.A., Jansson, J.K., Knight, R. and Miller, J.F., 2015. Tools for the microbiome: nano and beyond. : 6-37
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Brooks, J.F., Gyllborg, M.C., Kocher, A.A., Markey, L.E. and Mandel, M.J., 2015. TfoX-based genetic mapping identifies Vibrio fischeri strain-level differences and reveals a common lineage of laboratory strains. Journal of bacteriology, 197(6), pp.1065-1074.
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Chavez-Dozal, A., Gorman, C. and Nishiguchi, M.K., 2015. Proteomic and metabolomic profiles demonstrate variation among free-living and symbiotic Vibrio fischeri biofilms. BMC microbiology, 15(1), p.226.
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Collins, A.J., Fullmer, M.S., Gogarten, J.P. and Nyholm, S.V., 2015. Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes. Frontiers in microbiology, 6, p.123.
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Colton, D.M. and Stabb, E.V., 2016. Rethinking the roles of CRP, cAMP, and sugar-mediated global regulation in the Vibrionaceae. Current genetics, 62(1), pp.39-45.
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Colton, D.M., Stoudenmire, J.L. and Stabb, E.V., 2015. Growth on glucose decreases cAMP‐CRP activity while paradoxically increasing intracellular cAMP in the light‐organ symbiont Vibrio fischeri. Molecular microbiology, 97(6), pp.1114-1127.
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Colton, D.M., Stabb, E.V. and Hagen, S.J., 2015. Modeling analysis of signal sensitivity and specificity by Vibrio fischeri LuxR variants. PloS one, 10(5), p.e0126474.
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Ding, Y. and Kanso, E., 2015. Selective particle capture by asynchronously beating cilia. Physics of Fluids, 27(12), p.121902.
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Dunn, A.K., Rader, B.A., Stabb, E.V. and Mandel, M.J., 2015. Regulation of bioluminescence in Photobacterium leiognathi strain KNH6. Journal of bacteriology, 197(23), pp.3676-3685.
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Foxall, R.L., Ballok, A.E., Avitabile, A. and Whistler, C.A., 2015. Spontaneous phenotypic suppression of GacA-defective Vibrio fischeri is achieved via mutation of csrA and ihfA. BMC microbiology, 15(1), p.180.
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Howard, J.H., Williams, B.L., Breen, M. and Nishiguchi, M.K., 2015. Genomics of an environmentally-transmitted symbiosis: newly sequenced Vibrio fischeri genomes from different host squids and geographic locations. Vie et Milieu-Life and Environment, 65(4), pp.187-200.
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Krasity, B.C., Troll, J.V., Lehnert, E.M., Hackett, K.T., Dillard, J.P., Apicella, M.A., Goldman, W.E., Weiss, J.P. and McFall-Ngai, M.J., 2015. Structural and functional features of a developmentally regulated lipopolysaccharide-binding protein. MBio, 6(5), pp.e01193-15.
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McFall-Ngai, M.J., 2015. Giving microbes their due–animal life in a microbially dominant world. Journal of Experimental Biology, 218(12), pp.1968-1973.
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Nikolakakis, K., Lehnert, E., McFall-Ngai, M.J. and Ruby, E.G., 2015. Use of hybridization chain reaction-fluorescent in situ hybridization to track gene expression by both partners during initiation of symbiosis. Appl. Environ. Microbiol., 81(14), pp.4728-4735.
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Nikolakakis, K., Monfils, K., Moriano-Gutierrez, S., Brennan, C.A. and Ruby, E.G., 2016. Characterization of the Vibrio fischeri fatty acid chemoreceptors, VfcB and VfcB2. Appl. Environ. Microbiol., 82(2), pp.696-704.
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Norsworthy, A.N. and Visick, K.L., 2015. Signaling between two interacting sensor kinases promotes biofilms and colonization by a bacterial symbiont. Molecular microbiology, 96(2), pp.233-248.
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Pan, M., Schwartzman, J.A., Dunn, A.K., Lu, Z. and Ruby, E.G., 2015. A single host-derived glycan impacts key regulatory nodes of symbiont metabolism in a coevolved mutualism. MBio, 6(4), pp.e00811-15.
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Ray, V.A., Driks, A. and Visick, K.L., 2015. Identification of a novel matrix protein that promotes biofilm maturation in Vibrio fischeri. Journal of bacteriology, 197(3), pp.518-528.
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Septer, A.N., Bose, J.L., Lipzen, A., Martin, J., Whistler, C. and Stabb, E.V., 2015. Bright luminescence of Vibrio fischeri aconitase mutants reveals a connection between citrate and the Gac/Csr regulatory system. Molecular microbiology, 95(2), pp.283-296.
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Singh, P., Brooks, J.F., Ray, V.A., Mandel, M.J. and Visick, K.L., 2015. CysK plays a role in biofilm formation and colonization by Vibrio fischeri. Appl. Environ. Microbiol., 81(15), pp.5223-5234.
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Schwartzman, J.A. (2015) Physiological and chemical negotiations of the squid-vibrio symbiosis. The University of Wisconsin-Madison.
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Sun, Y., Verma, S.C., Bogale, H. and Miyashiro, T., 2015. NagC represses N-acetyl-glucosamine utilization genes in Vibrio fischeri within the light organ of Euprymna scolopes. Frontiers in microbiology, 6, p.741.
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Thompson, C.M. and Visick, K.L., 2015. Assessing the function of STAS domain protein SypA in Vibrio fischeri using a comparative analysis. Frontiers in microbiology, 6, p.760.
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2014

Brennan, C.A., Hunt, J.R., Kremer, N., Krasity, B.C., Apicella, M.A., McFall-Ngai, M.J. and Ruby, E.G., 2014. A model symbiosis reveals a role for sheathed-flagellum rotation in the release of immunogenic lipopolysaccharide. Elife, 3, p.e01579.
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Brooks, J.F., Gyllborg, M.C., Cronin, D.C., Quillin, S.J., Mallama, C.A., Foxall, R., Whistler, C., Goodman, A.L. and Mandel, M.J., 2014. Global discovery of colonization determinants in the squid symbiont Vibrio fischeri. Proceedings of the National Academy of Sciences, 111(48), pp.17284-17289.
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Chavez-Dozal, A.A., Gorman, C., Lostroh, C.P. and Nishiguchi, M.K., 2014. Gene-swapping mediates host specificity among symbiotic bacteria in a beneficial symbiosis. PloS one, 9(7), p.e101691.
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Ding, Y., Nawroth, J.C., McFall-Ngai, M.J. and Kanso, E., 2014. Mixing and transport by ciliary carpets: a numerical study. Journal of Fluid Mechanics, 743, pp.124-140.
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Foster, J.S., Wheeler, R.M. and Pamphile, R., 2014. Host-microbe interactions in microgravity: assessment and implications. Life, 4(2), pp.250-266.
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Guo, H., Nawroth, J., Ding, Y. and Kanso, E., 2014. Cilia beating patterns are not hydrodynamically optimal. Physics of Fluids, 26(9), p.091901.
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Heath‐Heckman, E.A., Gillette, A.A., Augustin, R., Gillette, M.X., Goldman, W.E. and McFall‐Ngai, M.J., 2014. Shaping the microenvironment: evidence for the influence of a host galaxin on symbiont acquisition and maintenance in the squid‐vibrio symbiosis. Environmental microbiology, 16(12), pp.3669-3682.
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Koropatnick T, Goodson MS, Heath-Heckman EA, McFall-Ngai M. Identifying the cellular mechanisms of symbiont-induced epithelial morphogenesis in the squid-vibrio association. The Biological Bulletin. 2014 Feb;226(1):56-68.
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Kremer, N., Schwartzman, J., Augustin, R., Zhou, L., Ruby, E.G., Hourdez, S. and McFall-Ngai, M.J., 2014. The dual nature of haemocyanin in the establishment and persistence of the squid–vibrio symbiosis. Proceedings of the Royal Society B: Biological Sciences, 281(1785), p.20140504.
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McFall-Ngai, M.J., 2014. The importance of microbes in animal development: lessons from the squid-vibrio symbiosis. Annual Review of Microbiology, 68, pp.177-194.
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McFall-Ngai, M., 2014. Divining the essence of symbiosis: insights from the squid-vibrio model. PLoS Biology, 12(2), p.e1001783.
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Miyashiro, T., Oehlert, D., Ray, V.A., Visick, K.L. and Ruby, E.G., 2014. The putative oligosaccharide translocase SypK connects biofilm formation with quorum signaling in Vibrio fischeri. Microbiologyopen, 3(6), pp.836-848.
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Nabhitabhata, J. and Nishiguchi, M.K., 2014. Euprymna hyllebergi and Euprymna tasmanica. In Cephalopod Culture (pp. 253-269). Springer, Dordrecht.
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Nishiguchi, M.K., Nabhitabhata, J., Moltschaniwskyj, N.A. and Boletzky, S.V., 2014. A review of the pygmy squid idiosepius: perspectives emerging from an “inconspicuous” cephalopod. Vie et Milieu – Life and Environment, 64, pp.23-34.
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Ondrey, J.M. and Visick, K.L., 2014. Engineering Vibrio fischeri for inducible gene expression. The open microbiology journal, 8, p.122.
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Pankey, M.S., Minin, V.N., Imholte, G.C., Suchard, M.A. and Oakley, T.H., 2014. Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid. Proceedings of the National Academy of Sciences, 111(44), pp.E4736-E4742.
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Schleicher, T.R., VerBerkmoes, N.C., Shah, M. and Nyholm, S.V., 2014. Colonization state influences the hemocyte proteome in a beneficial squid–vibrio symbiosis. Molecular & Cellular Proteomics, 13(10), pp.2673-2686.
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Schwartzman, J.A., Koch, E., Heath-Heckman, E.A., Zhou, L., Kremer, N., McFall-Ngai, M.J. and Ruby, E.G., 2015. The chemistry of negotiation: rhythmic, glycan-driven acidification in a symbiotic conversation. Proceedings of the National Academy of Sciences, 112(2), pp.566-571.
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Soto, W. and Nishiguchi, M.K., 2014. Microbial experimental evolution as a novel research approach in the Vibrionaceae and squid-vibrio symbiosis. Frontiers in microbiology, 5, p.593.
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Soto, W., Rivera, F.M. and Nishiguchi, M.K., 2014. Ecological diversification of Vibrio fischeri serially passaged for 500 generations in novel squid host Euprymna tasmanica. Microbial ecology, 67(3), pp.700-721.
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2013

Abucayon, E., Ke, N., Cornut, R., Patelunas, A., Miller, D., Nishiguchi, M.K. and Zoski, C.G., 2013. Investigating catalase activity through hydrogen peroxide decomposition by bacteria biofilms in real time using scanning electrochemical microscopy. Analytical chemistry, 86(1), pp.498-505.
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Altura, M.A., Heath‐Heckman, E.A., Gillette, A., Kremer, N., Krachler, A.M., Brennan, C., Ruby, E.G., Orth, K. and McFall‐Ngai, M.J., 2013. The first engagement of partners in the Euprymna scolopes–Vibrio fischeri symbiosis is a two‐step process initiated by a few environmental symbiont cells. Environmental microbiology, 15(11), pp.2937-2950.
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Brennan, C.A., DeLoney-Marino, C.R. and Mandel, M.J., 2013. Chemoreceptor VfcA mediates amino acid chemotaxis in Vibrio fischeri. Appl. Environ. Microbiol., 79(6), pp.1889-1896.
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Brennan, C.A., Mandel, M.J., Gyllborg, M.C., Thomasgard, K.A. and Ruby, E.G., 2013. Genetic determinants of swimming motility in the squid light‐organ symbiont Vibrio fischeri. MicrobiologyOpen, 2(4), pp.576-594.
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Chavez-Dozal, A., Gorman, C., Erken, M., Steinberg, P.D., McDougald, D. and Nishiguchi, M.K., 2013. Predation response of Vibrio fischeri biofilms to bacterivorus protists. Appl. Environ. Microbiol., 79(2), pp.553-558.
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DeLoney-Marino, C.R., 2013. Observing chemotaxis in Vibrio fischeri using soft agar assays in an undergraduate microbiology laboratory. Journal of Microbiology & Biology Education: JMBE, 14(2), p.271.
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Foster, J.S., Khodadad, C.L., Ahrendt, S.R. and Parrish, M.L., 2013. Impact of simulated microgravity on the normal developmental timeline of an animal-bacteria symbiosis. Scientific reports, 3, p.1340.
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Guerrero-Ferreira, R., Gorman, C., Chavez, A.A., Willie, S. and Nishiguchi, M.K., 2013. Characterization of the bacterial diversity in Indo-West Pacific loliginid and sepiolid squid light organs. Microbial ecology, 65(1), pp.214-226.
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Heath-Heckman, E.A., Peyer, S.M., Whistler, C.A., Apicella, M.A., Goldman, W.E. and McFall-Ngai, M.J., 2013. Bacterial bioluminescence regulates expression of a host cryptochrome gene in the squid-Vibrio symbiosis. MBio, 4(2), pp.e00167-13.
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Kimbrough, J.H. and Stabb, E.V., 2013. Substrate specificity and function of the pheromone receptor AinR in Vibrio fischeri ES114. Journal of bacteriology, 195(22), pp.5223-5232.
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Koch, E.J., Miyashiro, T., McFall‐Ngai, M.J. and Ruby, E.G., 2014. Features governing symbiont persistence in the squid–vibrio association. Molecular ecology, 23(6), pp.1624-1634.
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Kremer, N., Philipp, E.E., Carpentier, M.C., Brennan, C.A., Kraemer, L., Altura, M.A., Augustin, R., Häsler, R., Heath-Heckman, E.A., Peyer, S.M. and Schwartzman, J., 2013. Initial symbiont contact orchestrates host-organ-wide transcriptional changes that prime tissue colonization. Cell host & microbe, 14(2), pp.183-194.
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Lyell, N.L. and Stabb, E.V., 2013. Symbiotic characterization of Vibrio fischeri ES114 mutants that display enhanced luminescence in culture. Appl. Environ. Microbiol., 79(7), pp.2480-2483.
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Lyell, N.L., Colton, D.M., Bose, J.L., Tumen-Velasquez, M.P., Kimbrough, J.H. and Stabb, E.V., 2013. Cyclic AMP receptor protein regulates pheromone-mediated bioluminescence at multiple levels in Vibrio fischeri ES114. Journal of bacteriology, 195(22), pp.5051-5063.
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McFall-Ngai, M., Hadfield, M.G., Bosch, T.C., Carey, H.V., Domazet-Lošo, T., Douglas, A.E., Dubilier, N., Eberl, G., Fukami, T., Gilbert, S.F. and Hentschel, U., 2013. Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences, 110(9), pp.3229-3236.
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Morris, A.R. and Visick, K.L., 2013. Inhibition of SypG-induced biofilms and host colonization by the negative regulator SypE in Vibrio fischeri. PLoS One, 8(3), p.e60076.
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Norsworthy, A.N. and Visick, K.L., 2013. Gimme shelter: how Vibrio fischeri successfully navigates an animal’s multiple environments. Frontiers in microbiology, 4, p.356.
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Peyer, S.M., Pankey, M.S., Oakley, T.H. and McFall-Ngai, M.J., 2014. Eye-specification genes in the bacterial light organ of the bobtail squid Euprymna scolopes, and their expression in response to symbiont cues. Mechanisms of development, 131, pp.111-126.
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Ray, V.A., Eddy, J.L., Hussa, E.A., Misale, M. and Visick, K.L., 2013. The syp enhancer sequence plays a key role in transcriptional activation by the σ54-dependent response regulator SypG and in biofilm formation and host colonization by Vibrio fischeri. Journal of bacteriology, 195(23), pp.5402-5412.
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Septer, A.N., Lyell, N.L. and Stabb, E.V., 2013. The iron-dependent regulator Fur controls pheromone signaling systems and luminescence in the squid symbiont Vibrio fischeri ES114. Appl. Environ. Microbiol., 79(6), pp.1826-1834.
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Stabb, E.V. and Flores-Cruz, Z., 2013. Who turned on the lights?: What the regulation of bacterial bioluminescence tells us about this and other bacterial group behaviours. The Biochemist, 35(5), pp.18-23.
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Stabb, E.V. and Visick, K.L., 2013. Vibrio fischeri: a bioluminescent light-organ symbiont of the bobtail squid Euprymna scolopes, p 497–532. The prokaryotes, 4th ed. Springer-Verlag, Berlin, Germany.
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Studer, S.V., Schwartzman, J.A., Ho, J.S., Geske, G.D., Blackwell, H.E. and Ruby, E.G., 2014. Non‐native acylated homoserine lactones reveal that LuxIR quorum sensing promotes symbiont stability. Environmental microbiology, 16(8), pp.2623-2634.
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Sun, Y., Bernardy, E.E., Hammer, B.K. and Miyashiro, T., 2013. Competence and natural transformation in vibrios. Molecular microbiology, 89(4), pp.583-595.
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Verma, S.C. and Miyashiro, T., 2013. Quorum sensing in the squid-Vibrio symbiosis. International journal of molecular sciences, 14(8), pp.16386-16401.
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Visick, K.L., Quirke, K.P. and McEwen, S.M., 2013. Arabinose induces pellicle formation by Vibrio fischeri. Appl. Environ. Microbiol., 79(6), pp.2069-2080.
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Yim, S., Clark, C.M., Peters, T., Prodanov, V. and Fidopiastis, P., 2013, September. ROV-based tracking of a shallow water nocturnal squid. In 2013 OCEANS-San Diego (pp. 1-8). IEEE.
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2012

Albertin, C.B., Bonnaud, L., Brown, C.T., Crookes-Goodson, W.J., da Fonseca, R.R., Di Cristo, C., Dilkes, B.P., Edsinger-Gonzales, E., Freeman, R.M., Hanlon, R.T. and Koenig, K.M., 2012. Cephalopod genomics: a plan of strategies and organization. Standards in genomic sciences, 7(1), p.175.
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Cao, X., Studer, S.V., Wassarman, K., Zhang, Y., Ruby, E.G. and Miyashiro, T., 2012. The novel sigma factor-like regulator RpoQ controls luminescence, chitinase activity, and motility in Vibrio fischeri. MBio, 3(1), pp.e00285-11.
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Chavez-Dozal, A., Hogan, D., Gorman, C., Quintanal-Villalonga, A. and Nishiguchi, M.K., 2012. Multiple Vibrio fischeri genes are involved in biofilm formation and host colonization. FEMS microbiology ecology, 81(3), pp.562-573.
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Collins, A.J., LaBarre, B.A., Won, B.S.W., Shah, M.V., Heng, S., Choudhury, M.H., Haydar, S.A., Santiago, J. and Nyholm, S.V., 2012. Diversity and partitioning of bacterial populations within the accessory nidamental gland of the squid Euprymna scolopes. Appl. Environ. Microbiol., 78(12), pp.4200-4208.
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Collins, A.J., Schleicher, T.R., Rader, B.A. and Nyholm, S.V., 2012. Understanding the role of host hemocytes in a squid/vibrio symbiosis using transcriptomics and proteomics. Frontiers in immunology, 3, p.91.
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DeLoney-Marino, C.R. and Visick, K.L., 2012. Role for cheR of Vibrio fischeri in the Vibrio–squid symbiosis. Canadian journal of microbiology, 58(1), pp.29-38.
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Fidopiastis, P.M., Rader, B.A., Gerling, D.G., Gutierrez, N.A., Watkins, K.H., Frey, M.W., Nyholm, S.V. and Whistler, C.A., 2012. Characterization of a Vibrio fischeri aminopeptidase and evidence for its influence on an early stage of squid colonization. Journal of bacteriology, 194(15), pp.3995-4002.
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Gyllborg, M.C., Sahl, J.W., Cronin, D.C., Rasko, D.A. and Mandel, M.J., 2012. Draft genome sequence of Vibrio fischeri SR5, a strain isolated from the light organ of the Mediterranean squid Sepiola robusta. 1639
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Mandel, M.J., Schaefer, A.L., Brennan, C.A., Heath-Heckman, E.A., DeLoney-Marino, C.R., McFall-Ngai, M.J. and Ruby, E.G., 2012. Squid-derived chitin oligosaccharides are a chemotactic signal during colonization by Vibrio fischeri. Appl. Environ. Microbiol., 78(13), pp.4620-4626.
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McFall-Ngai, M., Heath-Heckman, E.A., Gillette, A.A., Peyer, S.M. and Harvie, E.A., 2012, February. The secret languages of coevolved symbioses: insights from the Euprymna scolopes–Vibrio fischeri symbiosis. In Seminars in immunology (Vol. 24, No. 1, pp. 3-8). Academic Press.
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Miyashiro, T. and Ruby, E.G., 2012. Shedding light on bioluminescence regulation in Vibrio fischeri. Molecular microbiology, 84(5), pp.795-806.
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Naughton, L.M. and Mandel, M.J., 2012. Colonization of Euprymna scolopes squid by Vibrio fischeri. JoVE (Journal of Visualized Experiments), (61), p.e3758.
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Nyholm, S.V. and Graf, J., 2012. Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses. Nature Reviews Microbiology, 10(12), p.815.
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Post, D.M., Yu, L., Krasity, B.C., Choudhury, B., Mandel, M.J., Brennan, C.A., Ruby, E.G., McFall-Ngai, M.J., Gibson, B.W. and Apicella, M.A., 2012. O-antigen and core carbohydrate of Vibrio fischeri lipopolysaccharide composition and analysis of their role in Euprymna scolopes light organ colonization. Journal of Biological Chemistry, 287(11), pp.8515-8530.
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Rader, B.A. and Nyholm, S.V., 2012. Host/microbe interactions revealed through “omics” in the symbiosis between the Hawaiian bobtail squid Euprymna scolopes and the bioluminescent bacterium Vibrio fischeri. The Biological Bulletin, 223(1), pp.103-111.
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Rader, B.A., Kremer, N., Apicella, M.A., Goldman, W.E. and McFall-Ngai, M.J., 2012. Modulation of symbiont lipid A signaling by host alkaline phosphatases in the squid-vibrio symbiosis. MBio, 3(3), pp.e00093-12.
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Ray, V.A. and Visick, K.L., 2012. Two-component regulators in the Vibrio fischeri-Euprymna scolopes symbiosis, p 371–404. Two-component systems in bacteria. Caister Academic Press, Norfolk, United Kingdom.
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Ray, V.A. and Visick, K.L., 2012. LuxU connects quorum sensing to biofilm formation in Vibrio fischeri. Molecular microbiology, 86(4), p.954.
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Ray, V.A., Morris, A.R. and Visick, K.L., 2012. A semi-quantitative approach to assess biofilm formation using wrinkled colony development. JoVE (Journal of Visualized Experiments), (64), p.e4035.
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Septer, A.N. and Stabb, E.V., 2012. Coordination of the arc regulatory system and pheromone-mediated positive feedback in controlling the Vibrio fischeri lux operon. PLoS One, 7(11), p.e49590.
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Shibata, S., Yip, E.S., Quirke, K.P., Ondrey, J.M. and Visick, K.L., 2012. Roles of the structural symbiosis polysaccharide (syp) genes in host colonization, biofilm formation, and polysaccharide biosynthesis in Vibrio fischeri. Journal of bacteriology, 194(24), pp.6736-6747.
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Soto, W., Punke, E.B. and Nishiguchi, M.K., 2012. Evolutionary perspectives in a mutualism of sepiolid squid and bioluminescent bacteria: combined usage of microbial experimental evolution and temporal population genetics. Evolution: International Journal of Organic Evolution, 66(5), pp.1308-1321.
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Wollenberg, M.S., Preheim, S.P., Polz, M.F. and Ruby, E.G., 2012. Polyphyly of non‐bioluminescent Vibrio fischeri sharing a lux‐locus deletion. Environmental microbiology, 14(3), pp.655-668.
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Wollesen, T., Nishiguchi, M.K., Seixas, P., Degnan, B.M. and Wanninger, A., 2012. The VD 1/RPD 2 α1-neuropeptide is highly expressed in the brain of cephalopod mollusks. Cell and tissue research, 348(3), pp.439-452.
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2011

Bose, J.L., Wollenberg, M.S., Colton, D.M., Mandel, M.J., Septer, A.N., Dunn, A.K. and Stabb, E.V., 2011. Contribution of rapid evolution of the luxR-luxI intergenic region to the diverse bioluminescence outputs of Vibrio fischeri strains isolated from different environments. Appl. Environ. Microbiol., 77(7), pp.2445-2457.
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Chavez‐Dozal, A. and Nishiguchi, M.K., 2011. Variation in biofilm formation among symbiotic and free‐living strains of Vibrio fischeri. Journal of basic microbiology, 51(5), pp.452-458.
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Collins, A.J. and Nyholm, S.V., 2011. Draft genome of Phaeobacter gallaeciensis ANG1, a dominant member of the accessory nidamental gland of Euprymna scolopes.
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Foster, J.S., Kerney, K.R., Parrish, M.L., Khodadad, C.L. and Ahrendt, S.R., 2011. Potential of the Euprymna/Vibrio symbiosis as a model to assess the impact of microgravity on bacteria-induced animal development. Gravitational and Space Research, 25(1).
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Guerrero-Ferreira, R.C. and Nishiguchi, M.K., 2011. Bacterial biodiversity in natural environments. The Importance of Biological Interactions in the Study of Biodiversity, p.1.
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Heath-Heckman, E.A. and McFall-Ngai, M.J., 2011. The occurrence of chitin in the hemocytes of invertebrates. Zoology, 114(4), pp.191-198.
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Miyashiro, T., Klein, W., Oehlert, D., Cao, X., Schwartzman, J. and Ruby, E.G., 2011. The N‐acetyl‐d‐glucosamine repressor NagC of Vibrio fischeri facilitates colonization of Euprymna scolopes. Molecular microbiology, 82(4), pp.894-903.
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Morris, A.R., Darnell, C.L. and Visick, K.L., 2011. Inactivation of a novel response regulator is necessary for biofilm formation and host colonization by Vibrio fischeri. Molecular microbiology, 82(1), pp.114-130.
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Schleicher, T.R. and Nyholm, S.V., 2011. Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri. PLoS One, 6(10).
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Septer, A.N., Wang, Y., Ruby, E.G., Stabb, E.V. and Dunn, A.K., 2011. The haem‐uptake gene cluster in Vibrio fischeri is regulated by Fur and contributes to symbiotic colonization. Environmental microbiology, 13(11), pp.2855-2864.
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Shibata, S. and Visick, K.L., 2012. Sensor kinase RscS induces the production of antigenically distinct outer membrane vesicles that depend on the symbiosis polysaccharide locus in Vibrio fischeri. Journal of bacteriology, 194(1), pp.185-194.
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Wang, Y. and Ruby, E.G., 2011. The roles of NO in microbial symbioses. Cellular microbiology, 13(4), pp.518-526.
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Zamborsky, D.J. and Nishiguchi, M.K., 2011. Phylogeographical patterns among Mediterranean sepiolid squids and their Vibrio symbionts: environment drives specificity among sympatric species. Appl. Environ. Microbiol., 77(2), pp.642-649.
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2010

Bassis, C.M. and Visick, K.L., 2010. The cyclic-di-GMP phosphodiesterase BinA negatively regulates cellulose-containing biofilms in Vibrio fischeri. Journal of bacteriology, 192(5), pp.1269-1278.
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Collins, A.J. and Nyholm, S.V., 2010. Obtaining hemocytes from the Hawaiian bobtail squid Euprymna scolopes and observing their adherence to symbiotic and non-symbiotic bacteria. JoVE (Journal of Visualized Experiments), (36), p.e1714.
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Guerrero‐Ferreira, R.C. and Nishiguchi, M.K., 2010. Differential gene expression in bacterial symbionts from loliginid squids demonstrates variation between mutualistic and environmental niches. Environmental microbiology reports, 2(4), pp.514-523.
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Lyell, N.L., Dunn, A.K., Bose, J.L. and Stabb, E.V., 2010. Bright mutants of Vibrio fischeri ES114 reveal conditions and regulators that control bioluminescence and expression of the lux operon. Journal of bacteriology, 192(19), pp.5103-5114.
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Mandel, M.J., 2010. Models and approaches to dissect host–symbiont specificity. Trends in microbiology, 18(11), pp.504-511.
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McFall-Ngai, M., Nyholm, S.V. and Castillo, M.G., 2010, February. The role of the immune system in the initiation and persistence of the Euprymna scolopes–Vibrio fischeri symbiosis. In Seminars in immunology (Vol. 22, No. 1, pp. 48-53). Academic Press.
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Miyashiro, T., Wollenberg, M.S., Cao, X., Oehlert, D. and Ruby, E.G., 2010. A single qrr gene is necessary and sufficient for LuxO‐mediated regulation in Vibrio fischeri. Molecular microbiology, 77(6), pp.1556-1567.
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Morris, A.R. and Visick, K.L., 2010. Control of biofilm formation and colonization in Vibrio fischeri: a role for partner switching?. Environmental microbiology, 12(8), pp.2051-2059.
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Nair, V. and Nishiguchi, M.K., 2009. Biological properties (in vitro) exhibited by free-living and symbiotic Vibrio isolates. Vie et milieu (Paris, France: 1980), 59(3-4), p.277.
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Pollack‐Berti, A., Wollenberg, M.S. and Ruby, E.G., 2010. Natural transformation of Vibrio fischeri requires tfoX and tfoY. Environmental microbiology, 12(8), pp.2302-2311.
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Schuster, B.M., Perry, L.A., Cooper, V.S. and Whistler, C.A., 2010. Breaking the language barrier: experimental evolution of non-native Vibrio fischeri in squid tailors luminescence to the host. Symbiosis, 51(1), pp.85-96.
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Septer, A.N., Bose, J.L., Dunn, A.K. and Stabb, E.V., 2010. FNR-mediated regulation of bioluminescence and anaerobic respiration in the light-organ symbiont Vibrio fischeri. FEMS microbiology letters, 306(1), pp.72-81.
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Soto, W., Lostroh, C.P. and Nishiguchi, M.K., 2010. Physiological responses to stress in the Vibrionaceae. In Symbioses and Stress (pp. 407-426). Springer, Dordrecht.
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Wang, Y., Dunn, A.K., Wilneff, J., McFall‐Ngai, M.J., Spiro, S. and Ruby, E.G., 2010. Vibrio fischeri flavohaemoglobin protects against nitric oxide during initiation of the squid–Vibrio symbiosis. Molecular microbiology, 78(4), pp.903-915.
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Wang, Y., Dufour, Y.S., Carlson, H.K., Donohue, T.J., Marletta, M.A. and Ruby, E.G., 2010. H-NOX–mediated nitric oxide sensing modulates symbiotic colonization by Vibrio fischeri. Proceedings of the National Academy of Sciences, 107(18), pp.8375-8380.
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Wier, A.M., Nyholm, S.V., Mandel, M.J., Massengo-Tiassé, R.P., Schaefer, A.L., Koroleva, I., Splinter-BonDurant, S., Brown, B., Manzella, L., Snir, E. and Almabrazi, H., 2010. Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis. Proceedings of the National Academy of Sciences, 107(5), pp.2259-2264.
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Wolfe, A.J. and Visick, K.L., 2010. Roles of diguanylate cyclases and phosphodiesterases in motility and biofilm formation in Vibrio fischeri. The Second Messenger Cyclic Di-GMP.
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2009

Adin, D.M., Engle, J.T., Goldman, W.E., McFall-Ngai, M.J. and Stabb, E.V., 2009. Mutations in ampG and lytic transglycosylase genes affect the net release of peptidoglycan monomers from Vibrio fischeri. Journal of bacteriology, 191(7), pp.2012-2022.
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Ariyakumar, D.S. and Nishiguchi, M.K., 2009. Characterization of two host-specific genes, mannose-sensitive hemagglutinin (mshA) and uridyl phosphate dehydrogenase (UDPDH) that are involved in the Vibrio fischeri–Euprymna tasmanica mutualism. FEMS microbiology letters, 299(1), pp.65-73.
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Geszvain, K. and Visick, K.L., 2008. The hybrid sensor kinase RscS integrates positive and negative signals to modulate biofilm formation in Vibrio fischeri. Journal of bacteriology, 190(13), pp.4437-4446.
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Guerrero-Ferreira, R.C. and Nishiguchi, M.K., 2009. Ultrastructure of light organs of loliginid squids and their bacterial symbionts: A novel model system for the study of marine symbioses. Vie et milieu (Paris, France: 1980), 59(3-4), p.307.
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Lee, P.N., Callaerts, P. and de Couet, H.G., 2009. The embryonic development of the Hawaiian bobtail squid (Euprymna scolopes). Cold Spring Harbor Protocols, 2009(11), pp.pdb-ip77.
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Mandel, M.J., Wollenberg, M.S., Stabb, E.V., Visick, K.L. and Ruby, E.G., 2009. A single regulatory gene is sufficient to alter bacterial host range. Nature, 458(7235), pp.215-218.
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Nyholm, S.V., Stewart, J.J., Ruby, E.G. and McFall‐Ngai, M.J., 2009. Recognition between symbiotic Vibrio fischeri and the haemocytes of Euprymna scolopes. Environmental microbiology, 11(2), pp.483-493.
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Nyholm, S.V., 2009. Peptidoglycan monomer release and Vibrio fischeri. Journal of bacteriology, 191(7), pp.1997-1999.
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Soto, W., Gutierrez, J., Remmenga, M.D. and Nishiguchi, M.K., 2009. Salinity and temperature effects on physiological responses of Vibrio fischeri from diverse ecological niches. Microbial ecology, 57(1), pp.140-150.
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Stabb, E.V. and Millikan, D.S., 2009. Is the Vibrio fischeri–Euprymna scolopes symbiosis a defensive mutualism?. In Defensive mutualism in microbial symbiosis (pp. 103-116). CRC Press.
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Tong, D., Rozas, N.S., Oakley, T.H., Mitchell, J., Colley, N.J. and McFall-Ngai, M.J., 2009. Evidence for light perception in a bioluminescent organ. Proceedings of the National Academy of Sciences, 106(24), pp.9836-9841.
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Troll, J.V., Adin, D.M., Wier, A.M., Paquette, N., Silverman, N., Goldman, W.E., Stadermann, F.J., Stabb, E.V. and McFall‐Ngai, M.J., 2009. Peptidoglycan induces loss of a nuclear peptidoglycan recognition protein during host tissue development in a beneficial animal‐bacterial symbiosis. Cellular microbiology, 11(7), pp.1114-1127.
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Troll, J.V., Bent, E.H., Pacquette, N., Wier, A.M., Goldman, W.E., Silverman, N. and McFall‐Ngai, M.J., 2010. Taming the symbiont for coexistence: a host PGRP neutralizes a bacterial symbiont toxin. Environmental microbiology, 12(8), pp.2190-2203.
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Wollenberg, M.S. and Ruby, E.G., 2009. Population structure of Vibrio fischeri within the light organs of Euprymna scolopes squid from two Oahu (Hawaii) populations. Appl. Environ. Microbiol., 75(1), pp.193-202.
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2008

Adin, D.M., Visick, K.L. and Stabb, E.V., 2008. Identification of a cellobiose utilization gene cluster with cryptic β-galactosidase activity in Vibrio fischeri. Appl. Environ. Microbiol., 74(13), pp.4059-4069.
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Adin, D.M., Phillips, N.J., Gibson, B.W., Apicella, M.A., Ruby, E.G., McFall-Ngai, M.J., Hall, D.B. and Stabb, E.V., 2008. Characterization of htrB and msbB mutants of the light organ symbiont Vibrio fischeri. Appl. Environ. Microbiol., 74(3), pp.633-644.
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Bose, J.L., Rosenberg, C.S. and Stabb, E.V., 2008. Effects of luxCDABEG induction in Vibrio fischeri: enhancement of symbiotic colonization and conditional attenuation of growth in culture. Archives of microbiology, 190(2), p.169.
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Browne-Silva, J. and Nishiguchi, M.K., 2008. Gene sequences of the pil operon reveal relationships between symbiotic strains of Vibrio fischeri. International journal of systematic and evolutionary microbiology, 58(Pt 6), p.1292.
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Castillo, M.G., Goodson, M.S. and McFall-Ngai, M., 2009. Identification and molecular characterization of a complement C3 molecule in a lophotrochozoan, the Hawaiian bobtail squid Euprymna scolopes. Developmental & Comparative Immunology, 33(1), pp.69-76.
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Chun, C.K., Troll, J.V., Koroleva, I., Brown, B., Manzella, L., Snir, E., Almabrazi, H., Scheetz, T.E., de Fatima Bonaldo, M., Casavant, T.L. and Soares, M.B., 2008. Effects of colonization, luminescence, and autoinducer on host transcription during development of the squid-vibrio association. Proceedings of the National Academy of Sciences, 105(32), pp.11323-11328.
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Darnell, C.L., Hussa, E.A. and Visick, K.L., 2008. The putative hybrid sensor kinase SypF coordinates biofilm formation in Vibrio fischeri by acting upstream of two response regulators, SypG and VpsR. Journal of bacteriology, 190(14), pp.4941-4950.
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Hussa, E.A., Darnell, C.L. and Visick, K.L., 2008. RscS functions upstream of SypG to control the syp locus and biofilm formation in Vibrio fischeri. Journal of Bacteriology, 190(13), pp.4576-4583.
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Lyell, N.L., Dunn, A.K., Bose, J.L., Vescovi, S.L. and Stabb, E.V., 2008. Effective mutagenesis of Vibrio fischeri by using hyperactive mini-Tn5 derivatives. Appl. Environ. Microbiol., 74(22), pp.7059-7063.
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Mandel, M.J., Stabb, E.V. and Ruby, E.G., 2008. Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: focus on point miscalls and artefactual expansions. BMC genomics, 9(1), p.138.
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McFall-Ngai, M., 2008. Host-microbe symbiosis: the squid-Vibrio association—a naturally occurring, experimental model of animal/bacterial partnerships. In Gi Microbiota and Regulation of the Immune System (pp. 102-112). Springer, New York, NY.
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McFall-Ngai, M., 2008. Are biologists in ‘future shock’? Symbiosis integrates biology across domains. Nature Reviews Microbiology, 6(10), pp.789-792.
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Nishiguchi, M.K., and Mapes, R.H., 2008. Cephalopoda. Phylogeny and evolution of the Mollusca, pp.163-199.
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Nishiguchi, M.K., Hirsch, A.M., Devinney, R., Vedantam, G., Riley, M.A. and Mansky, L.M., 2008. Deciphering evolutionary mechanisms between mutualistic and pathogenic symbioses. Vie et Milieu (Paris, France: 1980), 58(2), p.87.
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Nyholm, S.V. and Nishiguchi, M.K., 2008. The evolutionary ecology of a sepiolid squid-Vibrio association: from cell to environment. Vie et milieu (Paris, France: 1980), 58(2), p.175.
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Ruby, E.G., 2008. Symbiotic conversations are revealed under genetic interrogation. Nature reviews microbiology, 6(10), pp.752-762.
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Stabb, E.V., Schaefer, A., Bose, J.L. and Ruby, E.G., 2008. Quorum signaling and symbiosis in the marine luminous bacterium Vibrio fischeri. In Chemical Communication among Bacteria (pp. 233-250). American Society of Microbiology.
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Studer, S.V., Mandel, M.J. and Ruby, E.G., 2008. AinS quorum sensing regulates the Vibrio fischeri acetate switch. Journal of bacteriology, 190(17), pp.5915-5923.
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Yildiz, F.H. and Visick, K.L., 2009. Vibrio biofilms: so much the same yet so different. Trends in microbiology, 17(3), pp.109-118.
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2007

Bose, J.L., Kim, U., Bartkowski, W., Gunsalus, R.P., Overley, A.M., Lyell, N.L., Visick, K.L. and Stabb, E.V., 2007. Bioluminescence in Vibrio fischeri is controlled by the redox‐responsive regulator ArcA. Molecular microbiology, 65(2), pp.538-553.
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Dethlefsen, L., McFall-Ngai, M. and Relman, D.A., 2007. An ecological and evolutionary perspective on human–microbe mutualism and disease. Nature, 449(7164), pp.811-818.
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Dunn, A.K. and Stabb, E.V., 2007. Beyond quorum sensing: the complexities of prokaryotic parliamentary procedures. Analytical and bioanalytical chemistry, 387(2), p.391.
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Guerrero‐Ferreira, R.C. and Nishiguchi, M.K., 2007. Biodiversity among luminescent symbionts from squid of the genera Uroteuthis, Loliolus and Euprymna (Mollusca: Cephalopoda). Cladistics, 23(5), pp.497-506.
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Jones, B.W., Maruyama, A., Ouverney, C.C. and Nishiguchi, M.K., 2007. Spatial and temporal distribution of the Vibrionaceae in coastal waters of Hawaii, Australia, and France. Microbial ecology, 54(2), pp.314-323.
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Koropatnick, T.A., Kimbell, J.R. and McFall-Ngai, M.J., 2007. Responses of host hemocytes during the initiation of the squid-Vibrio symbiosis. The Biological Bulletin, 212(1), pp.29-39.
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McFall-Ngai, M., 2007. Care for the community. Nature, 445(7124), pp.153-153.
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Moltschaniwskyj, N.A., Hall, K., Lipinski, M.R., Marian, J.E., Nishiguchi, M., Sakai, M., Shulman, D.J., Sinclair, B., Sinn, D.L., Staudinger, M. and Van Gelderen, R., 2007. Ethical and welfare considerations when using cephalopods as experimental animals. Reviews in Fish Biology and Fisheries, 17(2-3), pp.455-476.
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Nelson, E.J., Tunsjø, H.S., Fidopiastis, P.M., Sørum, H. and Ruby, E.G., 2007. A novel lux operon in the cryptically bioluminescent fish pathogen Vibrio salmonicida is associated with virulence. Appl. Environ. Microbiol., 73(6), pp.1825-1833.
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Strugnell, J. and Nishiguchi, M.K., 2007. Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) inferred from three mitochondrial and six nuclear loci: a comparison of alignment, implied alignment and analysis methods. Journal of Molluscan Studies, 73(4), pp.399-410.
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2006

Chun, C.K., Scheetz, T.E., de Fatima Bonaldo, M., Brown, B., Clemens, A., Crookes-Goodson, W.J., Crouch, K., DeMartini, T., Eyestone, M., Goodson, M.S. and Janssens, B., 2006. An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeri. BMC genomics, 7(1), p.154.
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Dunn, A.K., Millikan, D.S., Adin, D.M., Bose, J.L. and Stabb, E.V., 2006. New rfp-and pES213-derived tools for analyzing symbiotic Vibrio fischeri reveal patterns of infection and lux expression in situ. Appl. Environ. Microbiol., 72(1), pp.802-810.
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Giribet, G., Okusu, A., Lindgren, A.R., Huff, S.W., Schrödl, M. and Nishiguchi, M.K., 2006. Evidence for a clade composed of molluscs with serially repeated structures: monoplacophorans are related to chitons. Proceedings of the National Academy of Sciences, 103(20), pp.7723-7728.
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Goodson, M.S., Crookes-Goodson, W.J., Kimbell, J.R. and McFall-Ngai, M.J., 2006. Characterization and role of p53 family members in the symbiont-induced morphogenesis of the Euprymna scolopes light organ. The Biological Bulletin, 211(1), pp.7-17.
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Jones, B.W. and Nishiguchi, M.K., 2006. Differentially expressed genes reveal adaptations between free-living and symbiotic niches of Vibrio fischeri in a fully established mutualism. Canadian journal of microbiology, 52(12), pp.1218-1227.
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Jones, B.W., Lopez, J.E., Huttenburg, J. and Nishiguchi, M.K., 2006. Population structure between environmentally transmitted vibrios and bobtail squids using nested clade analysis. Molecular Ecology, 15(14), pp.4317-4329.
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Kimbell, J.R., Koropatnick, T.A. and McFall-Ngai, M.J., 2006. Evidence for the participation of the proteasome in symbiont-induced tissue morphogenesis. The Biological Bulletin, 211(1), pp.1-6.
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Stabb, E.V., 2006. The Vibrio fischeri–Euprymna scolopes light organ symbiosis. In The Biology of Vibrios (pp. 204-218). American Society of Microbiology.
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Sycuro, L.K., Ruby, E.G. and McFall‐Ngai, M., 2006. Confocal microscopy of the light organ crypts in juvenile Euprymna scolopes reveals their morphological complexity and dynamic function in symbiosis. Journal of Morphology, 267(5), pp.555-568.
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Visick, K.L. and Ruby, E.G., 2006. Vibrio fischeri and its host: it takes two to tango. Current opinion in microbiology, 9(6), pp.632-638.
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Walker, E.L., Bose, J.L. and Stabb, E.V., 2006. Photolyase confers resistance to UV light but does not contribute to the symbiotic benefit of bioluminescence in Vibrio fischeri ES114. Appl. Environ. Microbiol., 72(10), pp.6600-6606.
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Whistler, C.A., Koropatnick, T.A., Pollack, A., McFall‐Ngai, M.J. and Ruby, E.G., 2007. The GacA global regulator of Vibrio fischeri is required for normal host tissue responses that limit subsequent bacterial colonization. Cellular microbiology, 9(3), pp.766-778.
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Yip, E.S., Geszvain, K., DeLoney‐Marino, C.R. and Visick, K.L., 2006. The symbiosis regulator RscS controls the I gene locus, biofilm formation and symbiotic aggregation by Vibrio fischeri. Molecular microbiology, 62(6), pp.1586-1600.
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2005

Dunn, A.K., Martin, M.O. and Stabb, E.V., 2005. Characterization of pES213, a small mobilizable plasmid from Vibrio fischeri. Plasmid, 54(2), pp.114-134.
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Geszvain, K. and Visick, K.L., 2005. Roles of bacterial regulators in the symbiosis between Vibrio fischeri and Euprymna scolopes. In Molecular Basis of Symbiosis (pp. 277-290). Springer, Berlin, Heidelberg.
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Goodson, M.S., Kojadinovic, M., Troll, J.V., Scheetz, T.E., Casavant, T.L., Soares, M.B. and McFall-Ngai, M.J., 2005. Identifying components of the NF-κB pathway in the beneficial Euprymna scolopes-Vibrio fischeri light organ symbiosis. Appl. Environ. Microbiol., 71(11), pp.6934-6946.
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Lindgren, A.R., Katugin, O.N., Amezquita, E. and Nishiguchi, M.K., 2005. Evolutionary relationships among squids of the family Gonatidae (Mollusca: Cephalopoda) inferred from three mitochondrial loci. Molecular Phylogenetics and Evolution, 36(1), pp.101-111.
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Lupp, C. and Ruby, E.G., 2005. Vibrio fischeri uses two quorum-sensing systems for the regulation of early and late colonization factors. Journal of bacteriology, 187(11), pp.3620-3629.
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Ruby, E.G., Urbanowski, M., Campbell, J., Dunn, A., Faini, M., Gunsalus, R., Lostroh, P., Lupp, C., McCann, J., Millikan, D. and Schaefer, A., 2005. Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners. Proceedings of the National Academy of Sciences, 102(8), pp.3004-3009.
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Stabb, E.V., 2005. Shedding light on the bioluminescence “paradox”, ASM News, 71(5), pp. 223-229.
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von Boletsky, S., Nishiguchi, M., Nabhitabhata, J., Nugranad, J., 2005. Idiosepius: ecology, biology and biogeography of a mini-maximalist. Phuket Mar. Biol. Cent. Res. Bull., 66, pp.11-22.
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Yip, E.S., Grublesky, B.T., Hussa, E.A. and Visick, K.L., 2005. A novel, conserved cluster of genes promotes symbiotic colonization and σ54‐dependent biofilm formation by Vibrio fischeri. Molecular microbiology, 57(5), pp.1485-1498.
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2004

Crookes, W.J., Ding, L.L., Huang, Q.L., Kimbell, J.R., Horwitz, J. and McFall-Ngai, M.J., 2004. Reflectins: the unusual proteins of squid reflective tissues. Science, 303(5655), pp.235-238.
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Davidson, S.K., Koropatnick, T.A., Kossmehl, R., Sycuro, L. and McFall‐Ngai, M.J., 2004. NO means ‘yes’ in the squid‐vibrio symbiosis: Nitric oxide (NO) during the initial stages of a beneficial association. Cellular microbiology, 6(12), pp.1139-1151.
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Jones, B.W. and Nishiguchi, M.K., 2004. Counterillumination in the hawaiian bobtail squid, Euprymna scolopes Berry (Mollusca: Cephalopoda). Marine Biology, 144(6), pp.1151-1155.
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Kimbell, J.R. and McFall-Ngai, M.J., 2004. Symbiont-induced changes in host actin during the onset of a beneficial animal-bacterial association. Appl. Environ. Microbiol., 70(3), pp.1434-1441.
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Koropatnick, T.A., Engle, J.T., Apicella, M.A., Stabb, E.V., Goldman, W.E. and McFall-Ngai, M.J., 2004. Microbial factor-mediated development in a host-bacterial mutualism. Science, 306(5699), pp.1186-1188.
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Lindgren, A.R., Giribet, G. and Nishiguchi, M.K., 2004. A combined approach to the phylogeny of Cephalopoda (Mollusca). Cladistics, 20(5), pp.454-486.
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Lupp, C. and Ruby, E.G., 2004. Vibrio fischeri LuxS and AinS: comparative study of two signal synthases. Journal of bacteriology, 186(12), pp.3873-3881.
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Millikan, D.S. and Ruby, E.G., 2004. Vibrio fischeri flagellin A is essential for normal motility and for symbiotic competence during initial squid light organ colonization. Journal of bacteriology, 186(13), pp.4315-4325.
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Nishiguchi, M.K. and Jones, B.W., 2004. Microbial biodiversity within the Vibrionaceae. In Origins (pp. 533-548). Springer, Dordrecht.
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Nishiguchi, M.K., Lopez, J.E. and Boletzky, S.V., 2004. Enlightenment of old ideas from new investigations: more questions regarding the evolution of bacteriogenic light organs in squids. Evolution & development, 6(1), pp.41-49.
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Nyholm, S.V. and McFall-Ngai, M., 2004. The winnowing: establishing the squid–Vibrio symbiosis. Nature Reviews Microbiology, 2(8), pp.632-642.
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Stabb, E.V., Butler, M.S. and Adin, D.M., 2004. Correlation between osmolarity and luminescence of symbiotic Vibrio fischeri strain ES114. Journal of bacteriology, 186(9), pp.2906-2908.
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Visick, K.L. and Ruby, E.G., 2003. TnluxAB insertion mutants of Vibrio fischeri with symbiosis-regulated phenotypes. Nova Acta Leopoldina, 333, pp.93-100.
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2003

DeLoney-Marino, C.R., Wolfe, A.J. and Visick, K.L., 2003. Chemoattraction of Vibrio fischeri to serine, nucleosides, and N-acetylneuraminic acid, a component of squid light-organ mucus. Appl. Environ. Microbiol., 69(12), pp.7527-7530.
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Kimbell, J.R. and McFall-Ngai, M.J., 2003. The squid-vibrio symbioses: from demes to genes. Integrative and comparative biology, 43(2), pp.254-260.
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Lupp, C., Urbanowski, M., Greenberg, E.P. and Ruby, E.G., 2003. The Vibrio fischeri quorum‐sensing systems ain and lux sequentially induce luminescence gene expression and are important for persistence in the squid host. Molecular microbiology, 50(1), pp.319-331.
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McCann, J., Stabb, E.V., Millikan, D.S. and Ruby, E.G., 2003. Population dynamics of Vibrio fischeri during infection of Euprymna scolopes. Appl. Environ. Microbiol., 69(10), pp.5928-5934.
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Millikan, D.S. and Ruby, E.G., 2003. FlrA, a σ54-dependent transcriptional activator in Vibrio fischeri, is required for motility and symbiotic light-organ colonization. Journal of bacteriology, 185(12), pp.3547-3557.
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Nishiguchi, M.K. and Nair, V.S., 2003. Evolution of symbiosis in the Vibrionaceae: a combined approach using molecules and physiology. International Journal of Systematic and Evolutionary Microbiology, 53(6), pp.2019-2026.
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Nyholm, S.V. and McFall-Ngai, M.J., 2003. Dominance of Vibrio fischeri in secreted mucus outside the light organ of Euprymna scolopes: the first site of symbiont specificity. Appl. Environ. Microbiol., 69(7), pp.3932-3937.
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Stabb, E.V. and Ruby, E.G., 2003. Contribution of pilA to competitive colonization of the squid Euprymna scolopes by Vibrio fischeri. Appl. Environ. Microbiol., 69(2), pp.820-826.
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Whistler, C.A. and Ruby, E.G., 2003. GacA regulates symbiotic colonization traits of Vibrio fischeri and facilitates a beneficial association with an animal host. Journal of bacteriology, 185(24), pp.7202-7212.
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2002

Fidopiastis, P.M., Miyamoto, C.M., Jobling, M.G., Meighen, E.A. and Ruby, E.G., 2002. LitR, a new transcriptional activator in Vibrio fischeri, regulates luminescence and symbiotic light organ colonization. Molecular microbiology, 45(1), pp.131-143.
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Foster, J.S., von Boletzky, S. and McFall-Ngai, M.J., 2002. A comparison of the light organ development of Sepiola robusta Naef and Euprymna scolopes Berry (Cephalopoda: Sepiolidae). Bulletin of marine science, 70(1), pp.141-153.
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Lupp, C., Hancock, R.E. and Ruby, E.G., 2002. The Vibrio fischeri sapABCDF locus is required for normal growth, both in culture and in symbiosis. Archives of microbiology, 179(1), pp.57-65.
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Millikan, D.S. and Ruby, E.G., 2002. Alterations in Vibrio fischeri motility correlate with a delay in symbiosis initiation and are associated with additional symbiotic colonization defects. Appl. Environ. Microbiol., 68(5), pp.2519-2528.
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Nishiguchi, M.K., 2002. Host-symbiont recognition in the environmentally transmitted sepiolid squid-Vibrio mutualism. Microbial ecology, 44(1), pp.10-18.
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Nishiguchi, M.K., 2002. The use of physiological data to corroborate cospeciation events in symbiosis. In Molecular Systematics and Evolution: Theory and Practice (pp. 237-245). Birkhäuser, Basel.
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Nyholm, S.V., Deplancke, B., Gaskins, H.R., Apicella, M.A. and McFall-Ngai, M.J., 2002. Roles of Vibrio fischeri and nonsymbiotic bacteria in the dynamics of mucus secretion during symbiont colonization of the Euprymna scolopes light organ. Appl. Environ. Microbiol., 68(10), pp.5113-5122.
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Stabb EV, Ruby EG. RP4-based plasmids for conjugation between Escherichia coli and members of the Vibrionaceae. In Methods in enzymology 2002 Jan 1 (Vol. 358, pp. 413-426). Academic Press.
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2001

Aeckersberg, F., Lupp, C., Feliciano, B. and Ruby, E.G., 2001. Vibrio fischeri outer membrane protein OmpU plays a role in normal symbiotic colonization. Journal of bacteriology, 183(22), pp.6590-6597.
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Nishiguchi, M.K. 2001. Co-evolution of symbionts and hosts: The sepiolid-Vibrio model. In: J. Seckbach (ed.), Symbiosis: Mechanisms and Model Systems, Cole-Kluwer Academic Publishers, Dordrecht, The Netherlands, pp. 757-774.
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Stabb, E.V., Reich, K.A. and Ruby, E.G., 2001. Vibrio fischeri Genes hvnA and hvnB Encode Secreted NAD+-Glycohydrolases. Journal of Bacteriology, 183(1), pp.309-317.
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Visick, K.L. and Skoufos, L.M., 2001. Two-component sensor required for normal symbiotic colonization of Euprymna scolopes by Vibrio fischeri. Journal of Bacteriology, 183(3), pp.835-842.
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2000

Foster, J.S., Apicella, M.A. and McFall-Ngai, M.J., 2000. Vibrio fischeri lipopolysaccharide induces developmental apoptosis, but not complete morphogenesis, of the Euprymna scolopes symbiotic light organ. Developmental biology, 226(2), pp.242-254.
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Graf, J. and Ruby, E.G., 2000. Novel effects of a transposon insertion in the Vibrio fischeri glnD gene: defects in iron uptake and symbiotic persistence in addition to nitrogen utilization. Molecular microbiology, 37(1), pp.168-179.
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Lemus, J.D. and McFall-Ngai, M.J., 2000. Alterations in the proteome of the Euprymna scolopes light organ in response to symbiotic Vibrio fischeri. Appl. Environ. Microbiol., 66(9), pp.4091-4097.
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Nishiguchi, M.K., 2000. Temperature affects species distribution in symbiotic populations of Vibrio spp. Appl. Environ. Microbiol., 66(8), pp.3550-3555.
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Nyholm, S.V., Stabb, E.V., Ruby, E.G. and McFall-Ngai, M.J., 2000. Establishment of an animal–bacterial association: recruiting symbiotic vibrios from the environment. Proceedings of the National Academy of Sciences, 97(18), pp.10231-10235.
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Visick, K.L., Foster, J., Doino, J., McFall-Ngai, M. and Ruby, E.G., 2000. Vibrio fischeri lux genes play an important role in colonization and development of the host light organ. Journal of Bacteriology, 182(16), pp.4578-4586.
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Visick, K.L. and McFall-Ngai, M.J., 2000. An exclusive contract: specificity in the Vibrio fischeri-Euprymna scolopes partnership. Journal of Bacteriology, 182(7), pp.1779-1787.
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1999

Fidopiastis, P.M., Sørum, H. and Ruby, E.G., 1999. Cryptic luminescence in the cold-water fish pathogen Vibrio salmonicida. Archives of microbiology, 171(3), pp.205-209.
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McFall-Ngai, M.J. 1999. Consequences of evolving with bacterial symbionts: insights from the squid-vibrio associations. Annual Review of Ecology and Systematics, 30(1), pp.235-256.
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Ruby, E.G. and McFall-Ngai, M.J., 1999. Oxygen-utilizing reactions and symbiotic colonization of the squid light organ by Vibrio fischeri. Trends in microbiology, 7(10), pp.414-420.
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Small, A.L. and McFall‐Ngai, M.J., 1999. Halide peroxidase in tissues that interact with bacteria in the host squid Euprymna scolopes. Journal of cellular biochemistry, 72(4), pp.445-457.
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Visick, K.L. and Ruby, E.G., 1999. The emergent properties of quorum sensing: consequences to bacteria of autoinducer signaling in their natural environment. Cell-cell signaling in bacteria. ASM Press, Washington, DC, pp.333-352.
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1998

Fidopiastis, P.M., von Boletzky, S., Ruby, E.G., 1998. A new niche for Vibrio logei, the predominant light organ symbiont of squids in the genus Sepiola. Journal of Bacteriology, 180(1), pp.59 – 64.
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Foster, J.S. and McFall-Ngai, M.J., 1998. Induction of apoptosis by cooperative bacteria in the morphogenesis of host epithelial tissues. Development genes and evolution, 208(6), pp.295-303.
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Lamarcq, L.H. and McFall-Ngai, M.J., 1998. Induction of a gradual, reversible morphogenesis of its host’s epithelial brush border by Vibrio fischeri. Infection and immunity, 66(2), pp.777-785.
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McFall-Ngai, M.J. and Ruby, E.G., 1998. Sepiolids and vibrios: when first they meet. BioScience, 48(4), pp.257-265.
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McFall-Ngai, M., Brennan, C., Weis, V. and Lamarcq, L., 1998. Mannose sdhesin—glycan interactions in the Euprymna scolopes—Vibrio fischeri symbiosis. In New Developments in Marine Biotechnology (pp. 273-276). Springer, Boston, MA.
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Montgomery, M.K. and McFall-Ngai, M.J., 1998. Late postembryonic development of the symbiotic light organ of Euprymna scolopes (Cephalopoda: Sepiolidae). The Biological Bulletin, 195(3), pp.326-336.
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Nishiguchi, M.K., Ruby, E.G. and McFall-Ngai, M.J., 1998. Competitive dominance among strains of luminous bacteria provides an unusual form of evidence for parallel evolution in sepiolid squid-Vibrio symbioses. Appl. Environ. Microbiol., 64(9), pp.3209-3213.
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Nyholm, S.V. and McFall-Ngai, M.J., 1998. Sampling the light-organ microenvironment of Euprymna scolopes: description of a population of host cells in association with the bacterial symbiont Vibrio fischeri. The Biological Bulletin, 195(2), pp.89-97.
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Ruby, E.G. and Lee, K.H., 1998. The Vibrio fischeri-Euprymna scolopes light organ association: current ecological paradigms. Appl. Environ. Microbiol., 64(3), pp.805-812.
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1997

Aloha! In 1996 the Ruby and McFall-Ngai labs made the journey from the mainland to the University of Hawai’i for the first time, which resulted in no squid-vibrio papers in 1997.

1996

Boettcher, K.J., Ruby, E.G. and McFall-Ngai, M.J., 1996. Bioluminescence in the symbiotic squid Euprymna scolopes is controlled by a daily biological rhythm. Journal of Comparative Physiology A, 179(1), pp.65-73.
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Ruby, E.G., 1996. Lessons from a cooperative, bacterial-animal association: the Vibrio fischeri–Euprymna scolopes light organ symbiosis. Annual review of microbiology, 50(1), pp.591-624.
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Visick, K.G. and Ruby, E.G., 1996. Construction and symbiotic competence of a luxA-deletion mutant of Vibrio fischeri. Gene, 175(1-2), pp.89-94.
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Weis, V.M., Small, A.L. and McFall-Ngai, M.J., 1996. A peroxidase related to the mammalian antimicrobial protein myeloperoxidase in the Euprymna–Vibrio mutualism. Proceedings of the National Academy of Sciences, 93(24), pp.13683-13688.
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1995

Boettcher, K.J. and Ruby, E.G., 1995. Detection and quantification of Vibrio fischeri autoinducer from symbiotic squid light organs. Journal of bacteriology, 177(4), pp.1053-1058.
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Doino, J.A. and McFall-Ngai, M.J., 1995. A transient exposure to symbiosis-competent bacteria induces light organ morphogenesis in the host squid. The Biological Bulletin, 189(3), pp.347-355.
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Lee, K.H. and Ruby, E.G., 1995. Symbiotic role of the viable but nonculturable state of Vibrio fischeri in Hawaiian coastal seawater. Appl. Environ. Microbiol., 61(1), pp.278-283.
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1994

Boettcher, K.J. and Ruby, E.G., 1994. Occurrence of plasmid DNA in the sepiolid squid symbiont Vibrio fischeri. Current Microbiology, 29(5), pp.279-286.
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Graf, J., Dunlap, P.V. and Ruby, E.G., 1994. Effect of transposon-induced motility mutations on colonization of the host light organ by Vibrio fischeri. Journal of bacteriology, 176(22), pp.6986-6991.
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Lee, K.H. and Ruby, E.G., 1994. Effect of the squid host on the abundance and distribution of symbiotic Vibrio fischeri in nature. Appl. Environ. Microbiol., 60(5), pp.1565-1571.
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Lee, K.H. and Ruby, E.G., 1994. Competition between Vibrio fischeri strains during initiation and maintenance of a light organ symbiosis. Journal of bacteriology, 176(7), pp.1985-1991.
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Montgomery, M.K. and McFall-Ngai, M., 1994. Bacterial symbionts induce host organ morphogenesis during early postembryonic development of the squid Euprymna scolopes. Development, 120(7), pp.1719-1729.
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1993

Ruby, E.G. and Asato, L.M., 1993. Growth and flagellation of Vibrio fischeri during initiation of the sepiolid squid light organ symbiosis. Archives of Microbiology, 159(2), pp.160-167.
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Weis, V.M., Montgomery, M.K. and McFall-Ngai, M.J., 1993. Enhanced production of ALDH-like protein in the bacterial light organ of the sepiolid squid Euprymna scolopes. The Biological Bulletin, 184(3), pp.309-321.
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1992

Lee, K.H. and Ruby, E.G., 1992. Detection of the light organ symbiont, Vibrio fischeri, in Hawaiian seawater by using lux gene probes. Appl. Environ. Microbiol., 58(3), pp.942-947.
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Montgomery, M.K. and McFall-Ngai, M.J., 1992. The muscle-derived lens of a squid bioluminescent organ is biochemically convergent with the ocular lens. Evidence for recruitment of aldehyde dehydrogenase as a predominant structural protein. Journal of Biological Chemistry, 267(29), pp.20999-21003.
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1991

McFall-Ngai, M.J. and Ruby, E.G., 1991. Symbiont recognition and subsequent morphogenesis as early events in an animal-bacterial mutualism. Science, 254(5037), pp.1491-1494.
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1990

Boettcher, K.J. and Ruby, E.G., 1990. Depressed light emission by symbiotic Vibrio fischeri of the sepiolid squid Euprymna scolopes. Journal of Bacteriology, 172(7), pp.3701-3706.
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1977

Ruby, E.G. and Nealson, K.H., 1977. Pyruvate production and excretion by the luminous marine bacteria. Appl. Environ. Microbiol., 34(2), pp.164-169.
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1976

Ruby, E.G. and Nealson, K.H., 1976. Symbiotic association of Photobacterium fischeri with the marine luminous fish Monocentris japonica: a model of symbiosis based on bacterial studies. The Biological Bulletin, 151(3), pp.574-586.
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The Bobtail Squid Database