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Publications Archives

Schwall, C.T., Greenwood, V.L., and Alder, N.N. (2012) The stability and activity of respiratory Complex II is cardiolipin-dependent. Biochimica et Biophysica Acta – Bioenergetics. doi:10.1016/j.bbabio.2012.04.015
Wosczyna, M. N., Biswas, A., Cogswell, C., and Goldhamer, D. J. (2012). Multipotent progenitors resident in the skeletal muscle interstitium exhibit robust BMP-dependent osteogenic activity and mediate heterotopic ossification. J. Bone Miner. Res. 27, 1004-1017
Nelson, M. and J. Graf. 2012. Bacterial Symbioses of Hirudo verbana. Gut Microbes 3:1-10
B. R. Menzies, M. B. Renfree, T. Heider, F. Mayer, T. B. Hildebrandt and A. J. Pask. 2012. Limited genetic diversity preceded extinction of the Tasmanian Tiger. PlosOne 7(4): e35433. doi:10.1371/journal.pone.0035433
Laufer H, Baclaski B, Koehn U (2012) Alkylphenols affect lobster (Homarus americanus) larval survival, molting and metamorphosis. Invertebrate Reproduction & Development, March 2012
Papke RT, Gogarten JP (2012) How Bacterial Lineages Emerge. Science 336: 45-46 10.1126/science.1219241
Fournier GP, Andam CP, Alm EJ, Gogarten JP Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life. Origins of Life and Evolution of Biospheres [Epub ahead of print]
Rice, J.M., Stern, L.J., Guignon, E.F., Lawrence, D.A., and Lynes, M.A. (2012) T cell phenotyping microarrays using Grating Coupled Surface Plasmon Resonance Imaging and Surface Plasmon Coupled Emission. Biosensors and Bioelectronics, 31(1) 264-269.
Kuratnik A, Senapati VE, Verma R, Mellone BG, Vella AT, Giardina C. 2012. Acute sensitization of colon cancer cells to inflammatory cytokines by prophase arrest. Biochem Pharmacol. 2012 Jan 25. [Epub ahead of print]
Rohit Ghai, Lejla Pašić, Ana Beatriz Fernández, Ana-Belen Martin-Cuadrado, Carolina Megumi Mizuno , Katherine D. McMahon, R. Thane Papke, Ramunas Stepanauskas, Beltran Rodriguez-Brito, Forest Rohwer, Cristina Sánchez-Porro, Antonio Ventosa, & Francisco Rodríguez-Valera (2011) New Abundant Microbial Groups in Aquatic Hypersaline Environments. Scientific Reports. 1:135
Marusov, G. P., A J Sweatt, K Pietrosimone, D R Benson, S J Geary, L K Silbart, S Challa, J Lagoy, D A Lawrence, and M Lynes. 2011. A Microarray Biosensor for Multiplexed Detection of Microbes Using Grating-Coupled Surface Plasmon Resonance Imaging. Environmental Science and Technology DOI: 10.1021/es201239f
Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP and Gogarten JP (2011) A Rooted Net of Life Biology Direct 6:45 doi:10.1186/1745-6150-6-45 (HIGHLY ACCESSED)
Schleicher TS, Nyholm SV (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) e25649
Andam CP, Gogarten JP (2011) Biased gene transfer and its implications for the concept of lineage. (Research) Biology Direct 6:47 doi:10.1186/1745-6150-6-47
Eric Anderson, Willythssa S. Pierre-Louis, C. Jason Wong, Jeffrey W. Lary and James L. Cole (2011) Heparin Activates PKR by Inducing Dimerization J. Mol. Biol., doi:0.1016/j.jmb.2011.09.025
Deshmukh L, Meller N, Alder NN, Byzova T, and Vinogradova O (2011) Tyrosine Phosphorylation as a Conformational Switch: A Case Study of Integrin Beta3 Cytoplasmic Tail. J. Biol. Chem. doi:10.1074/jbc.M111.231951
Ranaghan MJ, Schwall CT, Alder NN and Birge RR (2011) Green Proteorhodopsin Reconstituted into Nanoscale Phospholipid Bilayers (Nanodiscs) as Photoactive Monomers. J. Am. Chem. Soc. DOI: 10.1021/ja2070957
Swithers KS, Dipippo JL, Bruce DC, Detter C, Tapia R, Han S, Goodwin LA, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Mikhailova N, Land ML, Nesbø CL, Gogarten JP, Noll KM (2011) Genome Sequence of Kosmotoga olearia Strain TBF 19.5.1, a Thermophilic Bacterium with a Wide Growth Temperature Range, Isolated from the Troll B Oil Platform in the North Sea. J Bacteriol 193(19):5566-7 pubmed
Bansal MS, Banay G, Gogarten JP, Shamir R (2011) Detecting highways of horizontal gene transfer. J Comput Biol 18(9): 1087-1114. pubmed
Sarion R Bowers and Barbara G Mellone: Starting from scratch: de novo kinetochore assembly in vertebrates. The EMBO Journal 6 September 2011; doi:10.1038/emboj.2011.329
Swithers KS, Fournier GP, Green AG, Gogarten JP, Lapierre P: Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria. PLoS One. 2011;6(8):e23774. doi:10.1371/journal.pone.0023774
Derek M. Bickhart and David R. Benson. 2011. Transcriptomes of Frankia sp. strain CcI3 in growth transitions. BMC Microbiology 11:192 [doi:10.1186/1471-2180-11-192]
Papke, R.T. and Chimileski, S. (2011) Gene Transfer Mechanisms, Population Genetics/Genomics and the Evolution of Haloarchaea, in Advances in Understanding the Biology of Halophilc Bacteria and Archaea (Vreeland, R., ed). Springer (in press)
Ying Huang and D. R. Benson. 2011. Growth and development of Frankia sp. strain CcI3 at the single-hypha level in liquid culture. Archives of Microbiology DOI: 10.1007/s00203-011-0734-5
Rafael Ruiz de la Haba, M. del Carmen Marquez, R. Thane Papke and Antonio Ventosa (2011) Multilocus sequence analysis (MLSA) of the family Halomonadaceae. International Journal of Systematic and Evolutionary Microbiology.
Cole, J.L, Correia, J.J. and Stafford, W.F. (2011) The use of analytical sedimentation velocity to extract thermodynamic linkage Biophys. Chem., in press: doi:10.1016/j.bpc.2011.05.014
Andam CP, Gogarten JP (2011) Biased gene transfer in microbial evolution. Nature Reviews Microbiology, Advanced Online Publication 13 June, doi:10.1038/nrmicro2593
Collins, AJ and Nyholm, SV (2011) Genome announcement: Draft genome of Phaeobacter gallaeciensis ANG1; a dominant member of the accessory nidamental gland of Euprymna scolopes. J. Bacteriol. (in press)
R. Bryk, K. Wu, B.C. Raimundo, P.E. Boardman, P. Chao, G.L. Conn, E. Anderson, J.L. Cole, N.P. Duffy, C.Nathan and J.H. Griffin (2011) Identification of new inhibitors of protein kinase R guided by statistical modeling. Biorganic and Medicinal Chemistry Letters in press: doi:10.1016/j.bmcl.2011.04.149
Mellone BG, Grive KJ, Shteyn V, Bowers SR, Oderberg I, et al. (2011) Assembly of Drosophila Centromeric Chromatin Proteins during Mitosis. PLoS Genet 7(5): e1002068. doi:10.1371/journal.pgen.1002068
Naor, A., Lazary, R., Barzel, A., Papke, R.T., Gopha, U. (2011) In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii. PLoS One. 6:1 e15833
Jha, S., Patil, S.M., Gibson, J., Nelson, C.E., Alder, N.N. & Alexandrescu, A.T. (2011) Mechanism of amylin fibrillization enhancement by heparin J. Biol. Chem., in press doi:10.1074/jbc.M110.215814
Andam CP, Fournier GP, Gogarten JP (2011) Multi-level populations and the evolution of antibiotic resistance through horizontal gene transfer. FEMS Microbiol Rev. 2011 Apr 27. doi: 10.1111/j.1574-6976.2011.00274
Starkey, J. D., Yamamoto, M., Yamamoto S., and Goldhamer, D. J. (2011). Skeletal muscle satellite cells are committed to myogenesis and do not spontaneously adopt non-myogenic fates. J. Histochem. Cytochem. 59, 33-46.
Bomar, L., M. Maltz, S. Colston and J. Graf. 2011. Directed culturing of microorganisms using metatranscriptomics. mBio. 2(2):e00012-11. doi:10.1128/mBio.00012-11
Bahl, J., M. C. Y. Lau, G. J. D. Smith, D. Vijaykrishna, S. C. Cary, D. C. Lacap, C. K. Lee, R. T. Papke, K. A. Warren-Rhodes, F. K. Y. Wong, et al. Ancient origins determine global biogeography of hot and cold desert Cyanobacteria. Nature Communications 2, 163 (25 January 2011) doi:10.1038/ncomms1167
Croke, R.L., Patil, S.M., Quevreaux, J., Kendall, D.A. & Alexandrescu, A.T. (2011) “NMR determination of pKa values in a-synuclein” Protein Science 20, 256-269
Patil, S.M., Mehta, A., Jha, S., & Alexandrescu, A.T. (2011) “Heterogeneous amylin fibril growth mechanisms imaged by total internal reflection fluorescence microscopy” Biochemistry, in press: doi/10.1021/bi101908m
Silver A.C., D. Williams, J. Faucher, A.J. Horneman, J.P. Gogarten and J. Graf. (2011) Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data. PlosOne 6(2): e16751. doi:10.1371/journal.pone.0016751
Andy J. Wowor, Dongmei Yu, Debra A. Kendall and James L. Cole (2011) Energetics of SecA dimerization. J. Mol. Biol., in press: doi:10.1016/j.jmb.2011.02.006
Papke RT, White E, Reddy P, Weigel G, Kamekura M, Minegishi H, Usami R, Ventosa A. 2011. A Multilocus Sequence Analysis (MLSA) Approach to Halobacteriales Phylogeny and Taxonomy. Int J Syst Evol Microbiol. 2011 Feb 4.
Photochemical and Thermal Stability of Green and Blue Proteorhodopsins: Implications for Application in Protein-Based Devices. Ranaghan, M. J., Shima, S., Ramos, L., Poulin, D. S., Whited, G., Rajasekaran, S., Stuart, J. A., Albert, A. D., Birge, R. R. (2010) J. Phys. Chem. B 144 (44): 14064-70. (DOI: 10.1021/jp106633w)
Maltz, M. and J. Graf. 2011. The Type II Secretion System is Essential for Erythrocyte Lysis and Gut Colonization of the Leech Digestive-Tract Symbiont Aeromonas veronii. Appl. Environ. Microbiol. 77:597-603.
C. Jason Wong, Katherine Launer-Felty and James L. Cole (2011) Analysis of PKR-RNA interactions by sedimentation velocity. Methods in Enzymology 488, 59-79.
Fournier GP, Dick AA, Williams D and Gogarten JP. 2010. Evolution of the Archaea: Emerging views on origins and phylogeny. Res. Microbiol. (Epub ahead of print).
Kapinos, L. E., Schumacher, J., Mucke, N., Machaidze, G.kl Burkhard, P., Aebi, U., Strelkov, S. V., Herrmann, H. 2010. Characterization of the Head-to-Tail Overlap Complexes Formed by Human Lamin A, B1 and B2 "Half-minilamin" Dimers. J. Mol. Biol. 396:719-731.
Sheftic, S. R., Garcia, P. P., Robinison, V. L., Gage, D. J. and A. T. Alexandrescu (2010) NMR Assignments for the Sinorhizobium meliloti Response Regulator Sma0114. Biomolecular NMR Assignments Published online: DOI 10.1007/s12104-010-9266-1
Garcia, P. P. Bringhurst, R.M. and D. J. Gage (2010). Characterization of a two-component regulatory system which regulates succinate-mediated catabolite repression in Sinorhizobium meliloti. J. Bacteriol 192: 5725-5735
Marcus, PI, Ngunjiri, JM, Sekellick,MJ, Wang, L, and Le, C -W, 2010. In Vitro Analysis of Virus Particle Subpopulations in Candidate Live-Attenuated Influenza Vaccines Distinguishes Effective from Ineffective Vaccines. J. Virol. 84:10974-10981.
Katherine Launer-Felty, C. Jason Wong, Ahmed A. Wahid, Graeme L. Conn and James L. Cole (2010) Magnesium-Dependent Interaction of PKR with Adenovirus VAI.J. Mol. Biol. [Epup ahead of print]
Suhanovsky MM, Parent KN, Dunn SE, Baker TS, Teschke CM. (2010) Determinants of bacteriophage P22 polyhead formation: the role of coat protein flexibility in conformational switching. Mol Microbiol. In press
Molecular Phylogeny of Microorganisms (2010) Aharon Oren and R. Thane Papke (eds.). Caister Academic Press
Cheryl P. Andam, David Williams and J. Peter Gogarten (2010)Natural taxonomy in light of horizontal gene transfer. Biology & Philosophy, Published online: 14 May 2010, DOI: 10.1007/s10539-010-9212-8
Parent KN, Khayat R, Tu LH, Suhanovsky MM, Cortines JR, Teschke CM, Johnson JE, Baker TS. P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks. Structure. 2010 Mar 10;18(3):390-401
Cheryl P. Andam, David Williams, and J. Peter Gogarten (2010) Biased gene transfer mimics patterns created through shared ancestry. PNAS published ahead of print May 21, doi:10.1073/pnas.1001418107
Reviewed by Yuri Wolf as a 'Must Read' on Faculty of 1000.
Cole, James L. (2010) Analysis of PKR activation using analytical ultracentrifugation. Macromol. Biosci. DOI: 10.1002/mabi.201000069
Fournier GP, Gogarten JP (2010) Rooting the Ribosomal Tree of Life. Molecular Biology and Evolution [Epub ahead of print]
Poptsova MS, Gogarten JP. Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology. 2010 Apr 29;. [Epub ahead of print]
Teschke CM, Parent KN.'Let the phage do the work': Using the phage P22 coat protein structures as a framework to understand its folding and assembly mutants. Virology. 2010 Mar 15. [Epub ahead of print]
Parent KN, Khayat R, Tu LH, Suhanovsky MM, Cortines JR, Teschke CM, Johnson JE, Baker TS. P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks. Structure. 2010 Mar 10;18(3):390-401. On the Cover.
Fournier GP, Neumann JE, Gogarten JP (2010) Inferring the Ancient History of the Translation Machinery and Genetic Code via Recapitulation of Ribosomal Subunit Assembly Orders. PLoS ONE 5(3): e9437. doi:10.1371/journal.pone.0009437
Messina G, Biressi S, Monteverde S, Magli A, Pistocchi A, Gargioli C, Campbell CE, Tagliafico E, Grossi M, Cotelli F, Goldhamer DJ, Gronostajski RM, Cossu G (2010). NFIX regulates fetal specific transcription in developing skeletal muscle. Cell 140, 554-566.
Williams D, Gogarten JP, Lapierre P (2010) Filling the gaps in the genomic landscape. Genome Biology 11:103
McFall-Ngai, MJ, Nyholm SV, Castillo MG (2009) The role of the immune system in the initiation and persistence of the Euprymna scolopes-Vibrio fischeri symbiosis. Semin. Immunol. (in press) published online Dec. 2009
Wier AM, Nyholm SV, Mandel MJ, Massengo-Tiassé RP, Schaefer AL, Koroleva I, Splinter-Bondurant S, Brown B, Manzella L, Snir E, Almabrazi H, Scheetz TE, Bonaldo Mde F, Casavant TL, Soares MB, Cronan JE, Reed JL, Ruby EG, McFall-Ngai MJ. (2010) Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis. Proc. Nat. Acad. Sci., USA, 107, 2259-64
Collins AJ, Nyholm SV (2010). Obtaining Hemocytes from the Hawaiian Bobtail Squid Euprymna scolopes and Observing their Adherence to Symbiotic and Non-Symbiotic Bacteria. JoVE. 36.
Sheftic, S.R., Croke, R.L., LaRochelle, J.R., & Alexandrescu, A.T. (2009) “Electrostatic contributions to the stabilities of native proteins and amyloid complexes.” Methods in Enzymology 466, 233-258.
Anderson, E., Quartararo, C., Brown, R.S., Shi, Y., Yao, X. and Cole, J.L (2010) Analysis of monomeric and dimeric phosphorylated forms of protein kinase R. Biochemistry 10.1021/bi901873p
P. M. Herron, D. J. Gage, and Z. G. Cardon (2010) Microscale water potential gradients visualized in soil around plant root tips using microbiosensors. Plant, Cell and Environment 33:199-210
Auclair SM, Moses JP, Musial-Siwek M, Kendall DA, Oliver DB, Mukerji I. Mapping of the Signal Peptide-Binding Domain of Escherichia coli SecA Using Forster Resonance Energy Transfer. Biochemistry. 2010 Jan 8. [Epub ahead of print] PubMed PMID: 20025247
Gage, D. J. (2009) Architecture of infection thread networks in nitrogen-fixing root nodules. In Plant Cell Monographs Volume 12, Root Hairs, A. M. C. Emons and T. Ketelaar (ed.), Springer, Heidelberg, Germany
Gage, D. J. (2009) Legume Nodule Formation. In D. W. Emerich and H. B. Krishnan (ed.), Nitrogen Fixation in Crop Production. American Society of Agronomy, Madison, WI, USA
Arango-Pinedo and D. J. Gage. (2009) Plasmids that insert into the rhamnose utilization locus, rha: a versatile tool for genetic studies in Sinorhizobium meliloti. Journal of Molecular Biology and Biotechnology 17:201-210
Alekseev, A. E, Reyes, S., Yamada. S., Hodgson-Zingman, D. M., Sattiraju, S., Zhu, Z., Sierra, A., Gerbin, M., Coetzee, W. A., Goldhamer, D. J., Terzic, A., and Zingman, L. V. (2010). Sarcolemmal ATP-sensitive K+ channels control energy expenditure determining body weight. Cell Metabolism 11, 58-69
Kaba SA, Brando C, Guo Q, Mittelholzer C, Raman SK, Tropel D, Aebi U, Burkhard P, Lanar DE. (2009). A non-adjuvanted polypeptide nanoparticle vaccine confers long-lasting protection against rodent malaria. J Immunol. 183(11):7268-77
Rio, R.V.M., M. Maltz, B. McCormick, A. Reiss and J. Graf. 2009. Symbiont Succession during the Embryonic Development of the European Medicinal Leech, Hirudo verbana. Appl. Environ. Microbiol. 75:6890-6895
Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP (2009) Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus. Genome Biology and Evolution 2009: doi:10.1093/gbe/evp032
Swithers KS, Senejani AG, Fournier GP, Gogarten JP (2009) Conservation of intron and intein insertion sites: Implications for life histories of parasitic genetic elements. BMC Evolutionary Biology 2009, 9:303 doi:10.1186/1471-2148-9-303
Mastronunzio, J. E & D. R. Benson. 2010. Wild nodules can be broken: proteomics of Frankia in field-collected root nodules. Symbiosis 49:10.1007/s13199-009-0030-1.
J. E. Mastronunzio, Y. Huang, and D. R. Benson. 2009. Diminished Exoproteome of Frankia spp. in Culture and Symbiosis. Appl. Environ. Microbiol. 75: 6721-6728.
Williamson A*, Wickliffe KE*, Mellone BG, Song L, Karpen GH, Rape M. Identification of a physiological E2 module for the human anaphase-promoting complex. PNAS epub ahead of print.
Kikuchi, Y. L. Bomar and J. Graf. (2009) Stratified bacterial community in the bladder of the medicinal leech, Hirudo verbana. Environ. Microbiol. 11:2758-2770. Cover article
Pores-Fernando AT, Zweifach A. Calcium influx and signaling in cytotoxic T-lymphocyte lytic granule exocytosis. Immunol Rev. 2009 Sep;231(1):160-73. PMID: 19592494
Pores-Fernando AT, Ranaghan MY, Zweifach A. No specific subcellular localization of protein kinase C is required for cytotoxic T cell granule exocytosis. J Biol Chem. 2009 Sep 11;284(37):25107-15. Epub 2009 Jul 10. PMID: 19754896
Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR (2009) Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia. BMC Genomics. 2009 Oct 12;10(1):468
Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupre J, Dagan T, Boucher Y, Martin W (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct. 2009 Sep 29;4:34.
Olendzenski L, Gogarten JP (2009) Evolution of Genes and Organisms: The Tree/Web of Life in Light of Horizontal Gene Transfer. Annals of the New York Academy of Sciences 1178: 137-145 doi: 10.1111/j.1749-6632.2009.04998.x
Pores-Fernando, A. T., S. Gaur, M. J. Grybko, and A Zweifach. 2008. ERK activation is only one role of PKC in TCR-independent cytotoxic T cell granule exocytosis. Biochem Biophys Res Commun. 371: 630–634.
Tang, L., J. Franca-Koh, Y. Xiong, M. Y. Chen, Y. Long, R. M. Bickford, D. A. Knecht, P. A. Iglesias and P. N. Devreotes. 2008. tsunami, the Dictyostelium homolog of the Fused kinase, is required for polarization and chemotaxis. Genes Dev. 22:2278-2290.
Musial-Siwek, M., P. Y. Yeagle and D. A. Kendall. 2008. A small set of signal peptidase residues are perturbe by signal peptide binding. Chem. Biol. Drug Des. 72:140-146
Sallum, U. W., W. Ulysses and T. Chen. 2008. Inducible resistance of fish bacterial pathogens to the antimicrobial peptide cecropin B. Antimicrobial Agents Chemotherapy 53:3006-3012
Pimentel, T.A., Z. Yan, S. A. Jeffers, K. V. Holmes, R. S. Hodges, P. Burkhard. 2009. Peptide nanoparticles as novel immunogens: design and analysis of a prototypic severe acute respiratory syndrome vaccine. Chem. Biol. Drug Des. 73:53-61.
Longo, M.S., Carone, D.M., Marzelli, M., M.J. O’Neill, E. Green, NISC Sequencing Consortium, R.J. O’Neill. 2009. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty. BMC Genomics 10:334.
Brown J.D. and R.J. O’Neill. 2009. The Mysteries of Chromosome Evolution in Gibbons: Methylation Is a Prime Suspect. PLoS Genet 5(6): e1000501. doi:10.1371/journal.pgen.1000501.
O’Neill, R.J. and D.M. Carone. 2009. Chapter 4: The role of ncRNA in centromeres: lessons from marsupials. in: Centromere: structure and evolution ed: D. Ugarkovic, Springer Press. Pp77-101.
Gage, D. J., Herron, P. M., Arango-Pinedo, C., and Z. G. Cardon (2008). Live reports from the soil grain--the promise and challenge of microbiosensors. Functional Ecology 22:983.
C. Arango-Pinedo and D. J. Gage (2009) HPrK regulates succinate- mediated catabolite repression in the Gram negative symbiont Sinorhizobium meliloti. J. Bacteriol. 191:298-309
Zhang, N., Wang, Q. Ehlinger, A., Randles, L., Lary, J. W., Kang, Y., Haririnia, A., Storaska, A. J., Cole, J. L., Fushman, D., Walters, K. J. (2009) Structure of the S5a:K48-Linked Diubiquitin Complex and Its Interactions with Rpn13. Mol. Cell 35, 280-290.
Silver, A.C. and J. Graf. 2009. Prevalence of genes encoding type three secretion system and the effectors AexT and AexU in the Aeromonas veronii group. DNA Cell Biol. 28:383-388.
Swithers KS, Gogarten JP, Fournier GP (2009) Trees in the Web of Life, Journal of Biology 2009, 8:54 doi:10.1186/jbiol160
Fournier GP, Huang JL, Gogarten JP (2009) Horizontal gene transfer from extinct and extant lineages: Biological innovation and the coral of life. Philos Trans R Soc Lond B Biol Sci. 364 (1527):2229-39.
Kanisicak, O., Mendez, J. J., Yamamoto, S., Yamamoto, M., and Goldhamer, D. J. (2009). Progenitors of skeletal muscle satellite cells express the muscle determination gene, MyoD. Dev. Biol. 332, 131 141.
R.T. Emeny, G. Marusov, D.A. Lawrence, J. Pederson-Lane, X. Yin, M.A. Lynes, Manipulations of metallothionein gene dose accelerate the response to Listeria monocytogenes, Chemico-Biological Interactions (2009), doi:10.1016/j.cbi.2009.06.018
Marcus P.I., Ngunjiri J.M. and M.J. Sekellick. 2009. Dynamics of Biologically Active Subpopulations of Influenza Virus: Plaque-Forming, Noninfectious Cell-Killing, and Defective-Interfering Particles. J. Virol. doi:10.1128/JVI.02680-08
Guardino, K.M., Sheftic, S.R., Slattery, R.E., & Alexandrescu, A.T. (2009) “Hallmarks of conserved and non-conserved structures in the OB-fold superfamily”. Int. J. Mol. Sci. 10, 2412-2430
Patil, S.M., Xu, S., Sheftic, S.R., & Alexandrescu, A.T. (2009) “Dynamic alpha-helix structure of micelle-bound human amylin”, J Biol Chem, 284, 11982-11991
Heinicke, L.A., Wong, C.J., Lary, J., Nallagatla, S.R., Deigelman-Parente, A., Zheng, X., Cole, J.L. and Bevilacqua, P.C. (2009) RNA Dimerization promotes PKR dimerization and activation. J. Mol. Biol. doi:10.1016/j.jmb.2009.05.005
Whitaker, I. S., C. Kamya, E. A. Azzopardi, J. Graf, M. Kon, W. C. Lineaweaver. 2009. Preventing infective complications following leech therapy: is practice keeping pace with current research? Microsurgery in press.
Papke RT (2009) A critique of prokaryotic species concepts. Methods Mol Biol 532:379-95.
Noll KM, Thirangoon K (2009) Interdomain transfers of sugar transporters overcome barriers to gene expression. Methods Mol Biol 532:309-22.
Huang J, Gogarten JP (2009) Ancient gene transfer as a tool in phylogenetic reconstruction. Methods Mol Biol. 2009; 532:127-39.
Olendzenski L, Gogarten JP (2009) Gene transfer: who benefits? Methods Mol Biol. 2009;532:3-9.
Poptsova M (Gogarten Lab)(2009) Testing phylogenetic methods to identify horizontal gene transfer. Methods Mol Biol. 2009;532:227-40.
Fournier G (Gogarten Lab) (2009) Horizontal gene transfer and the evolution of methanogenic pathways. Methods Mol Biol. 2009;532:163-79.
Gogarten, M.B., Gogarten, J.P., Olendzenski, L.C. (editors), (2009) Horizontal Gene Transfer: Genomes in Flux. Humana Press - Springer ISBN-13: 978-1603278522
Alexandrescu, A. T. & Croke, R.L. (2008) “NMR of Amyloidogenic proteins”, in Protein Misfolding ISBN 978-1-60456-881-3
Croke, R.L., Sallum, C.O., Watson, E., Watt, E.D. & Alexandrescu, A. T. (2008) “Hydrogen exchange of monomeric a-synuclein shows unfolded structure persists at physiological temperature and is independent of molecular crowding in Escherichia coli”. Protein Science 17, 1434-1445.
Lounev, V. Y., Ramachandran, R., Wosczyna, M. N., Yamamoto, M., Maidment, A. D. A., Shore, E. M., Glaser, D. L., Goldhamer, D. J., and Kaplan, F. S. (2009). Identification of progenitor cells that contribute to heterotopic skeletogenesis. J Bone Joint Surg 91:652-663.
Mellone, B.G. (2009). Structural and temporal regulation of centromeric chromatin. Biochem Cell Biol. 87(1):255-64.
Yamamoto, M., Shook, N. A., Kanisicak, O., Yamamoto, S., Wosczyna, M. N., Camp, J. R., and Goldhamer, D. J. (2009). A multifunctional reporter mouse line for Cre- and FLP-dependent lineage analysis. Genesis 47, 107-114.
VanOudenhove, J., Anderson, E., Krueger, S. and Cole, J.L. (2009) Analysis of PKR structure by small angle scattering. J. Mol. Biol. doi:10.1016/j.jmb.2009.02.019
Lapierre P, Gogarten JP (2009) Estimating the size of the bacterial pan-genome Trends in Genetics, doi:10.1016/j.tig.2008.12.004
Carone DM, Longo MS, Ferreri GC, Hall L, Harris M, Shook N, Bulazel KV, Carone BR, Obergfell C, O'Neill MJ, O'Neill RJ. 2008. A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres. Chromosoma. 2008 Oct 7. [Epub ahead of print]
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Nukaga, M., C. R. Bethel, J. M. Thomson, A. M. Hujer, A. Distler, V. E. Anderson, J. R. Knox and R. A. Bonomo. 2008. Inhibition of class A ß-lactamases by carbapenems: Crystallographic observation of two conformations of meropenem in SHV-1. J. Am. Chem. Soc. 130: 12656–12662.
Laufer, A., M. Siddall and J. Graf. 2008. Characterization of the Digestive-Tract Microbiota of Hirudo orientalis, a European Medicinal Leech. Appl. Environ. Microbiol. 74:6151-6154.
Edrington TC, Bennett MP, Albert AD. 2008. Calorimetric Studies of Bovine Rod Outer Segment Disk Membranes Support a Monomeric Unit for Both Rhodopsin and Opsin. Biophys J. Jun 27. Epub ahead of print.
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Jinling Huang and J. Peter Gogarten (2008) Concerted gene recruitment in early plant evolution Genome Biology 9(7): R109
Lemaire, P.A., Anderson, E., Lary, J. and Cole, J.L. (2008) Mechanism of PKR activation by dsRNA. J. Mol. Biol. 381, 351-360.
Hou JM, D'Lima NG, Rigel NW, Gibbons HS, McCann JR, Braunstein M, Teschke CM. (2008) ATPase activity of Mycobacterium tuberculosis SecA1 and SecA2 proteins and its importance for SecA2 function in macrophages. J Bacteriol. 190:4880-7.
Hamel, L., Nahar, N., Poptsova, M.S., Zhaxybayeva, O. and Gogarten, J.P. 2008. Unsupervised Learning in Detection of Gene Transfer.Journal of Biomedicine and Biotechnology [Epub ahead of print] doi: 10.1155/2008/472719.
Santos CL, Vieira J, Tavares F, Benson DR, Tisa LS, Berry AM, Moradas-Ferreira P, Normand P. 2008. On the nature of fur evolution: a phylogenetic approach in Actinobacteria. BMC Evol Biol. 25:8:185. [Epub ahead of print];PMID: 18578876.
Sudi J, Zhang S, Intrieri G, Hao X, Zhang P. Coincidence of p-insertion sites and breakpoints of deletions induced by activating p elements in Drosophila. Genetics. 2008. 179:227-35.
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Arango-Pinedo, C., Bringhurst, R.M. and D. J. Gage (2008). Sinorhizobium meliloti mutants lacking phosphotransferase system enzyme HPr or EIIA are altered in diverse processes, including carbon metabolism, cobalt requirements, and succinoglycan production. J. Bacteriol. 190:2947
Noll KM, Lapierre P, Gogarten JP and Nanavati DM (2008) Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales
BMC Evolutionary Biology 2008, 8:7
Metcalfe, C.J., K.V. Bulazel, G. C. Ferreri, W. Rens, E. Schroeder-Reiter, G. Wanner, M. D. B. Eldridge, and R. J. O'Neill. 2007. Genomic instability within centromeres of interspecific marsupial hybrids. Genetics 177: 2507-2517.
Brown, J.D., D. Golden, R.J.O’Neill. 2008. Methylation perturbations in retroelements within the genome of a Mus interspecific hybrid correlate with double minute chromosome formation. Genomics 91: 267-273.
Sen, A., S. Sur, A. K. Bothra, D. R. Benson, P. Normand and L. S. Tisa. 2008. The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia genomes. Antonie van Leeuwenhoek Published on-line, Feb.
Robertson, P.D., Warren, E.M., Zhang, H., Friedman, D.B., Lary, J.W., Cole, J.L., Tutter, A.V., Walter, J.C., Fanning, E., Eichman, B.F. (2008) Domain architecture and biochemical characterization of vertebrate MCM10. J. Biol. Chem. 83, 3338-3348.
Fournier, Gregory P., and Gogarten, J. Peter (2008) Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia J. Bacteriol. 190(3): 1124-7 [Abstract] [online] [PDF]
Sharma, AK, Zhaxybayeva, O., Papke, RT, Doolittle, WF. 2008. Actinorhodopsins: proteorhodopsin-like gene sequence found predominantly in non-marine environments. Environmental Microbiology (OnlineEarly Articles). doi:10.1111/j.1462-2920.2007.01525.x
Juliana E Mastronunzio , L S Tisa , P. Normand and D R Benson. 2008. Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbiont. BMC Genomics 2008, 9:47
Ngunjiri, J. M., M. J. Sekellick and P. I. Marcus. 2008. Clonogenic Assay of Type A Influenza Viruses Reveals Noninfectious Cell-Killing (Apoptosis-Inducing) Particles. J. Virol. 0: JVI.02221-07 [published online ahead of print]
Spurling CC, Godman CA, Noonan EJ, Rasmussen TP, Rosenberg DW, Giardina C. 2007. HDAC3 overexpression and colon cancer cell proliferation and differentiation. Mol Carcinogenesis [EPub ahead of print, September].
J Peter Gogarten, Gregory Fournier and Olga Zhaxybayeva (2007) Gene transfer and the reconstruction of life's early history from the molecular record. Space Science Reviews [Epub ahead of print] DOI: 10.1007 /s11214-007-9253-8
Hadjout, N., X. Yin, D. A. Knecht, and M. A. Lynes. 2007. Automated real-time measurements of leukocyte chemotaxis. J Immunol Methods. 2007 320:70-80
Sun, C., S. L. Rusch, J. Kim and D. A. Kendall. 2007. Chloroplast SecA and Escherichia coli SecA have distinct lipid and signal peptide preferences. J. Bacteriol. 189:1171-1175.
M. Willian, Dagan, T., Koonin, E. B., Dipippo, J. L., Gogarten, J. P. and Lake, J. A. 2007. The Evolution of Eukaryotes, Letter on "Genomics and the irreducible nature of eukaryotic cells" Science 316:542-543
Huang, Jinling and J. Peter Gogarten (2007) Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biology 8(6): R99
Laufer, H., Demir, N., Capulong, C, Pan, X., Biggers, W.J. 2006. Hormonal Responses to Lobsters of Long Island Sound. Long Island Sound Research Conference Proceedings. 7:41-43.
Zhaxybayeva O, Gogarten JP, Doolittle WF (2007) A hyperconserved protein in Prochlorococcus and marine Synechococcus. FEMS Microbiol Lett. 274 (1): 30-4.
Silver, A.C., N. M. Rabinowitz, S. Küffer and J. Graf. 2007. Identification of Aeromonas veronii genes required for colonization of the medicinal leech, Hirudo verbana. J Bacteriol. 189:6763-72.
Fournier, G. P. and J. P. Gogarten. 2007. Signature of a primitive genetic code in ancient protein lineages. J. Mol. Evol. 65:425-36.
R.T. Papke, O. Zhaxybayeva, E. Feil, K. Sommerfeld, D. Muise and W.F. Doolittle. 2007. Searching for species in haloarchaea. PNAS 104:14092-14097.
Q. Yan., V.N. Malashkevich, A. Fedorov, E. Fedorov, E. Cao, J.W. Lary, J.L. Cole, S.G. Nathenson and S.C. Almo. 2007. Structure of CD84 provides insight into SLAM family function. PNAS 104: 10583-10588.
E. Watson, W.M. Matousek, E.L. Irimies, A.T. Alexandrescu 2007. Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins. Biochemistry 46:9484-9494.
Huang, Jinling and J. Peter Gogarten (2007) Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biology 8(6): R99
M. A. Lynes, J. Kang, S. L. Sensi, G. A. Perdrizet, and L. E. Hightower. 2007. Heavy metal ions in normal physiology, toxic stress and cytoprotection. Ann N Y Acad Sci. May 4 e-pub
A. C. Silver, Y. Kikuchi, A. A. Fadl, J. Sha, A. K. Chopra, and J. Graf. 2007. Interaction between innate immune cells and a bacterial type III secretion system in mutualistic and pathogenic associations. PNAS 104:9481-9486.
Normand, P., P. Lapierre, L. S. Tisa, J. P. Gogarten, N. Alloisio, E.Bagnarol, C.A. Bassi, A.M. Berry, D. M. Bickhart, N. Choisne,, A. Couloux, B. Cournoyer, S. Cruveiller, V. Daubin, N. Demange, M. P. Francino, E. Goltsman, Y. Huang, O.R. Kopp, L. Labarre, A. Lapidus, C. Lavire, J. Marechal, M. Martinez, J. E. Mastronunzio, B. C. Mullin, J. Niemann, P. Pujic, T. Rawnsley, Z. Rouy, C. Schenowitz, A. Sellstedt, F. Tavares, J. P. Tomkins, D.Vallenet, C. Valverde, L.G. Wall, Y.Wang, C. Medigue, & D. R. Benson. 2007. Genome sizes of facultatively symbiotic Frankia sp. strains reflect host plant biogeography. Genome Res. 17:7-15