2006 Publications

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Sogin, M.L., Morrison, H.G., Huber, J.A., Mark Welch, D., Huse, S.M., Neal, P.R., Arrieta, J.M., and G.J. Herndl.  2006.  Microbial diversity in the deep sea and the  under-explored “rare biosphere.”  Proc. Natl. Acad. Sci. USA.  103:12115-12120.

Aguilera, A., Amaral Zettler, L. A., Souza-Egipsy, V., Zettler, E., and Amils, R. Eukaryotic community structure from Rio Tinto (SW, Spain), a highly acidic river In. (ed. Seckbach, J.), Extremophilic algae, cyanobacteria and non-photosynthetic protists: From Prokaryotes to Astrobiology. 2006. In press.

Amaral-Zettler, L. A., Cole, J., Laatsch, A. D., Nerad, T. A., Anderson, O. R. & Reysenbach, A-L., 2006. Vannella epipetala n. sp. Isolated from the Leaf Surface of Spondias mombin (Anacardiaceae) Growing in the Dry Forest of Costa Rica. Journal of Eukaryotic Microbiology. 53(6):522-530.

Arkhipova, I.R. (2006) Distribution and Phylogeny of Penelope-like elements in Eukaryotes. Syst. Biol., 55(6): 875-885.

Bach, W., K.J. Edwards, J.M. Hayes, J.A. Huber, S.M. Sievert and M.L. Sogin. Energy in the Dark: Fuel for Life in the Deep Ocean and Beyond. Eos 87(7): 73, 78 (2006).

Baldo, L., S.R. Bordenstein, J.J. Wernegreen and J.H. Werren. (2006) Widespread recombination throughout Wolbachia genomes. Molecular Biology and  Evolution 23: 437-449.

Baldo, L., Dunning-Hotopp, J., Bordenstein, S.R., Biber, S.A., Jollie, K., Tettelin, H., Maiden M., Hayashi, C., and J.H. Werren. (2006) A Multilocus Sequence Typing system for the endosymbiont Wolbachia. Applied and Environmental Microbiology 72(11): 7098-7110.

Biddle, J.F., J.S. Lipp, M.A. Lever, K.G. Lloyd, K.B. Sørensen, R. Anderson, H.F. Fredricks, M. Elvert, T.J. Kelly, D.P. Schrag, M.L. Sogin, J.E. Brenchley, A. Teske, C.H. House and K.-U. Hinrichs. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc. Natl. Acad. Sci. USA 103(10): 3846-3851 (2006).

Bordenstein, S.R., M.L. Marshall, A.J. Fry, U. Kim, and J.J Wernegreen. (2006) The tripartite associations of bacteriophage, Wolbachia, and arthropods PLoS Pathogens 2 (5): 384-393.

Clelland, E., Kohli, G., Campbell, R.K., Sharma, S., Shimasaki, S. and Peng, C. Bone morphogenetic protein 15 in the zebrafish ovary: cDNA cloning, genomic organization, tissue distribution and role in oocyte maturation. Endocrinology 147:201-209. (2006)

D’Andrea, W. J., Lage, M., Martiny, J. B. H,. Laatsch, A.D., Amaral-Zettler, L. A., Sogin, M.L., and Y. Huang. 2006. Alkenone producers inferred from well-preserved 18S rDNA in Greenland lake sediments. J. Geophys. Res. 111, G03013, doi:10.1029/2005JG000121.

Davids, B.J., D.S. Reiner, S.R. Birkeland, S.P. Preheim, M.J. Cipriano, A.G. McArthur, & F.D. Gillin. 2006. A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein. PLoS ONE, 1, e44.

Dyhrman, S.T., S.T. Haley, S.R. Birkeland, L.L. Wurch, M.J. Cipriano, & A.G. McArthur. 2006. Long-SAGE (serial analysis of gene expression) for gene discovery and transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi. Applied and Environmental Microbiology, 72, 252-260.

Faulkner, S.D., M.W. Oli, R. Kieft, L. Cotlin, J. Widener, A. Shiflett, M.J. Cipriano, S.E. Pacocha, S.R. Birkeland, S.L. Hajduk & A.G. McArthur. 2006. In vitro generation of human HDL resistant Trypanosoma brucei brucei. Eukaryotic Cell, 5, 1276-1286.

Golden D.E. and Hajduk, S.L.  (2006) The importance of RNA structure in RNA editing and a potential proofreading mechanism for correct guide RNA:pre-mRNA binary complex formation. J. Molec. Biol. 359, 585-596.

Goldstone, H.M. & J.J. Stegeman. 2006. A revised evolutionary history of the CYP1A subfamily: gene duplication, gene conversion, and positive selection. 2006. Journal of Molecular Evolution, 62, 708-717.

Goldstone, H.M. & J.J. Stegeman. 2006. Molecular mechanisms of 2,3,7,8-tetrachlorodibenzo-p-dioxin cardiovascular embryotoxicity. 2006. Drug Metabolism Reviews, 38, 261-289.

Greenberg, R.M. (2006) Praziquantel: Mechanism of action. In: “Parasitic Flatworms: Molecular Biology, Biochemistry, Immunology and Physiology” (A. Maule, Marks, N.J., eds.)., pp. 269-281, CABI, Oxfordshire, UK.

Hutchison, L. Mustard, J., Gendrin, A., Fernández-Remolar, D., Amils, R., and Amaral-Zettler, L. 2006. Finding Mineralogically Interesting Targets for Exploration from Spatially Coarse Visible and Near IR Spectra. Earth and Planetary Science Letters. 252: 201-214.

Jeziorski, M.C. and Greenberg, R.M. (2006) Voltage-gated Ca2+ channel subunits from schistosomes and other platyhelminths: potential role in praziquantel action. (2006) Int. J. Parasitol. 36, 625-632.

Kohn, A.B., Lea, J., Moroz, L.L, and Greenberg, R.M. (2006) Schistosoma mansoni: Use of a fluorescent indicator to detect nitric oxide and related species in living parasites. Experimental Parasitology 113, 130-133.

Ley, R.E., J.K. Harris, J. Wilcox, J.R. Spear, S.R. Miller, B.M. Bebout, J.A. Maresca, D.A. Bryant, M.L. Sogin, and N.R. Pace. Unexpected diversity and complexity from the Guerrero Negro hypersaline microbial mat. Applied and Environmental Microbiology 72: 3685-3695 (2006).

Messerli, S.M., Birkeland, S.R., Bernier, J., Cipriano, M.J., Morgan, W., McArthur, A.G., and Greenberg, R.M. Nitric oxide-dependent changes in Schistosoma mansoni gene expression. Mol. Biochem. Parasitol., in press.

Messerli, S.M., W. Morgan, S.R. Birkeland, J. Bernier, M.J. Cipriano, A.G. McArthur & R.M. Greenberg. 2006. Nitric oxide-dependent changes in Schistosoma mansoni gene expression. Molecular and Biochemical Parasitology, 150, 367-370.

Mukherjee, M., M.T. Brown, A.G. McArthur & P.J. Johnson. 2006. Proteins of the glycine decarboxylase complex in the hydrogenosome of Trichomonas vaginalis. Eukaryotic Cell, 5, 2062-2071.

Murray, S.,  Hoppenrath, M.,  Preisfeld, A., Larsen, J., Yoshimatsu, S., Topriumi, S., and Patterson, D. J. 2006. Phylogenetics of Rhinodinium broomeense gen. et sp. nov., a peridinioid, sand-dwelling dinoflagellate (Dinophyceae). J. Phycol. 42, 934–942

Paraskevopoulos, C., S.R. Bordenstein, J.J. Wernegreen, J.H. Werren, and K. Bourtzis. (2006) Towards a Wolbachia multilocus sequence typing system: Discrimination of Wolbachia strains present in Drosophila species. Current Microbiology 53(5): 388-395.

Patterson. D. J., Remsen, D., Norton, C., Marino, W. 2006. Taxonomic Indexing—extending the role of Taxonomy. Systematic Biology, 55: 367-373.

Remsen, D. P., Norton, C.,  and Patterson, D. J. 2006. Taxonomic informatics tools for the electronic Nomenclator Zoologicus. Biol. Bull. 210: 18-24.

Schoen, I., and Arkhipova, I.R. (2006). Two families of non-LTR retrotransposons, Syrinx and Daphne, from the Darwinulid ostracod, Darwinula stevensoni. Gene, 371(2): 296-30

Serres MH, Riley M. Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments. J Bacteriol. 2006 Jul;188(13):4601-9.

Simpson, A. G. B. and Patterson, D. J. 2006.  Current perspectives on high-level groupings of protists. In Katz, L and Bhattacharya. D., Genomics and Evolution of Microbial Eukaryotes, Oxford University press, pp 7-30.

Wegener-Parfrey, L., Barbero, E., Lasser, B., Dunthorn, M., Bhattacharya, D., Patterson, D. J., Katz, L. A. 2006. Evaluating support for the current classification of eukaryotic diversity.  PLOS Genetics, 2: 2062-2073.

Williams, D.L., A.A. Sayed, D. Ray, & A.G. McArthur. 2006. Schistosoma mansoni albumin, a major defense against oxidative damage, was acquired by lateral gene transfer from a mammalian host. 2006. Molecular and Biochemical Parasitology, 150, 359-363.
Toxicological Sciences, 92, 394-407.

Prabhu A, Morrison HG, Martinez CR 3rd, Adam RD. 2006. “Characterisation of the subtelomeric regions of Giardia lamblia genome isolate WBC6”. Int J Parasitol. 37(5):503-13.

Cantarel BL, Morrison HG, Pearson W. 2006. “Exploring the relationship between sequence similarity and accurate phylogenetic trees”. Mol Biol Evol. 23(11):2090-100.

Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL. 2006. “Escherichia coli K-12: a cooperatively developed annotation snapshot–2005”. Nucleic Acids Res. 34(1):1-9.

Oli MW, Cotlin LF, Shiflett AM, Hajduk, SL. (2006) Serum resistance-associated protein blocks lysosomal targeting of trypanosome lytic factor in Trypanosoma brucei.  Eukaryot Cell. 5,132-9.

Hajduk, S.L. (2006) Perspective:  Timing sexual development of parasites. Science 313, 626-627.

Ochsenreiter, T. and Hajduk, S.L. (2006) Alternative editing of mRNA generates protein diversity.  EMBO Reports 7, 1128-1133.

Shiflett, A.M. Faulkner, S.D., Cotlin, L.F., Widener, J., Stephens, N., and Hajduk, S.L. (2006) African Trypanosomes: Intracellular Trafficking of Host Defense Molecules. Eukaryot. Microb. 54,18-21.

Ochsenreiter, T. Cipriano, M. and Hajduk, S.L. (2007) KISS: The Kinetoplastid Editing Sequence Search Tool.  RNA 13, 1-4.

Gladyshev, E.G., Meselson, M., Arkhipova, I.R. (2006) A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers. Gene; doi 10.1016 j. gene.2006.09.025

Serres MH, Riley M. Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments. J Bacteriol., 2006 Jul;188(13):4601-9.

Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL. Escherichia coli K-12: a cooperatively developed annotation snapshot–2005. Nucleic Acids Res., 2006 Jan 5;34(1):1-9. Print 2006.

Inagaki, F., T. Nunoura, S. Nakagawa, A. Teske, M. Lever, A. Lauer, M. Suzuki, K. Takai, M. Delwiche, F.S. Colwell, K.H. Nealson, K. Horikoshi, S.L. D’Hondt, and B.B. Jørgensen. 2006. Biogeographical distribution and diversity of microbes in methane-hydrate bearing deep marine sediments on the Pacific Ocean Margin. Proc. Natl. Acad. Sci. USA. 103(8):2815-2820.

Biddle, J.F., J. S. Lipp, M. Lever, K. Lloyd, K. Sørensen, R. Anderson, H. F. Fredricks, M. Elvert, T. J. Kelly, D. P. Schrag, M. L. Sogin, J. E. Brenchley, A.Teske, C.H. House, K.-U. Hinrichs. 2006. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc. Natl. Acad. Sci 103(10):3846-3851.

Kubota A, Iwata H, Goldstone HM, Kim EY, Stegeman JJ, Tanabe S. 2006. “Cytochrome P450 1A4 and 1A5 in common cormorant (Phalacrocorax carbo): evolutionary relationships and functional implications associated with dioxin and related compounds”. Toxicol Sci. 92(2):394-408.

Gribble, K.E. and D.M. Anderson.  2006.  Molecular phylogeny of the heterotrophic dinoflagellates, Protoperidinium, Diplopsalis, and Preperidinium (Dinophyceae), inferred from LSU rDNA. Journal of Phycology 42, 1081-1095.

Bach, W., Edward, K.J, Hayes, J.M., Huber, J.A., Sievert, S.M., and M.L. Sogin.  2006. Energy in the dark: Fuel for life in the deep ocean and beyond.  Eos, Trans. AGU.  87:73-  78.

Huber, J.A., Butterfield, D.A., Johnson, H.P., and J.A. Baross.  2006.  Microbial life in ridge flank crustal fluids.  Environmental Microbiology.  88:88-99.

Huber, J.A., Butterfield, D.A, and Baross, J.A.  2006.  Diversity and distribution of   subseafloor Thermococcales populations in diffuse hydrothermal vents at an active deep-sea volcano in the northeast Pacific Ocean.  J. Geophys. Res. 111:G04016,   doi:10.1029/2005JG000097.

Messerli, S. M., Prabhakar, S., Tang, Y., Maymood, U., Giovannini, M., Weissleder, R., Bronson, R., Martuza, R., Rabkin, S., & Breakefield, X. O. (2006).  Treatment of schwannomas  with an oncolytic HSV recombinant virus in murine models of neurofibromatosis type 2. Human Gene Therapy, 17: 1-11.

Messerli, S. M. and Greenberg, R. M. (2006). Cnidarian toxins and voltage-gated ion channels. Marine Drugs, 4:70-81.

Messerli, S. M., Morgan, W, Birkeland, S. R., McArthur, A. G., & Greenberg, R. M. (2006).  NO-dependent changes in Schistosoma mansoni gene expression identified by SAGE. Molecular and Biochemical Parasitology, 150: 367-70.

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