Recent Publications

H. Guo, R. Benndorf, D. Leichnitz, J. L. Klassen, J. Vollmers, H. Görls, M. Steinacker, C. Weigel, H.-M. Dahse, A.-K. Kaster, Z. W. de Beer, M. Poulsen, C. Beemelmanns. (2017) Isolation, Biosynthesis and Chemical Modifications of Rubterolones A–F: Rare Tropolone Alkaloids from Actinomadura sp. 5-2, Chem. Eur. J. DOI: 10.1002/chem.201701005.

Boyd, K.K., Alder, N.N., May, E.R. (2017) Buckling Under Pressure: Curvature Based Lipid Segregation and Stability Modulation in Cardiolipin Containing Bilayers. Langmuir, DOI: 10.1021/acs.langmuir.7b01185

Mayo, C.B. and Cole, J.L. (2017) Interaction of PKR with single-stranded RNA. Sci. Rep.7, 3335.

Anne R Kaplan, Katherine Kaus, Swastik De, Rich Olson & Andrei T Alexandrescu (2017) “NMR structure of the Bacillus cereus hemolysin II C-terminal domain reveals a novel fold.” Scientific Reports 7: 3277, DOI: www.nature.com/articles/s41598-017-02917-4.

Christine Beemelmanns, Timothy R. Ramadhar, Ki Hyun Kim, Jonathan L. Klassen, Shugeng Cao, Thomas P. Wyche, Yanpeng Hou, Michael Poulsen, Tim S. Bugni, Cameron R. Currie, and Jon Clardy (2017) Macrotermycins A–D, Glycosylated Macrolactams from a Termite-Associated Amycolatopsis sp. M39. Organic Letters, DOI: 10.1021/acs.orglett.6b03831.

Wyche TP, Ruzzini AC, Beemelmanns C, Kim KH, Klassen JL, Cao S, Poulsen M, Bugni TS, Currie CR, Clardy J (2017) Linear Peptides Are the Major Products of a Biosynthetic Pathway That Encodes for Cyclic Depsipeptides. Organic Letters, DOI:10.1021/acs.orglett.7b00545

Kerwin AH, Nyholm SV. (2017) Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs. Environ Microbiol. doi: 10.1111/1462-2920.13665.

McAnulty SJ, Nyholm SV. (2017) The Role of Hemocytes in the Hawaiian Bobtail Squid, Euprymna scolopes: A Model Organism for Studying Beneficial Host-Microbe Interactions. Front Microbiol. doi: 10.3389/fmicb.2016.02013.

Nangia, S., May, E.R. (2017) Influence of membrane composition on the binding and folding of a membrane lytic peptide from the non-enveloped flock house virus. BBA-Biomembranes (in press).

Javier Periz, Jamie Whitelaw, Clare Harding, Simon Gras, Mario Igor Del Rosario Minina, Fernanda Latorre-Barragan, Leandro Lemgruber, Madita, Alice Reimer, Robert Insall, Aoife Heaslip, Markus Meissner (2017) Toxoplasma gondii F-actin forms an extensive filamentous network required for material exchange and parasite maturation. eLife 2017;10.7554/eLife.24119

Malhotra, K. and Alder, N.N. (2017) Reconstitution of mitochondrial proteins into nanodiscs by cell-free expression. Methods Mol. Biol. 1567: 155-178.

Anne R Kaplan, Megan R Brady, Mark W Maciejewski, Richard A Kammerer & Andrei T Alexandrescu (2017) “NMR Structures of GCN4p are Largely Conserved when Ion Pairs are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix.” Biochemistry, in press, DOI: 10.1021/acs.biochem.6b00634 [Epub ahead of print]

Fischer C, Trautman E, Crawford J, Stabb E, Handelsman Jo, Broderick N. (2017) Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior. eLife 6:e18855.

Benoit J, Vigneron A, Broderick N, Wu Y, Sun J, Carlson J, Aksoy S, Weiss B. (2017) Symbiont-induced odorant binding proteins mediate insect host hematopoiesis. eLife 6: e19535.

Ward, M.D., Nangia, S., May, E.R.(2017) Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides. J. Comput. Chem., DOI: 10.1002/jcc.24694 .

Rosin, L. and Mellone, B.G. (2017)  Centromeres Drive a Hard Bargain. Review. Trends in Genetics (in press). doi:10.1016/j.tig.2016.12.001.

Mellone, B.G. Winged Migration. (2017) Review. Mol Biol Cell. 2016 Nov 1;27(21):3189-3191.

Dick AA, Harlow TJ, Gogarten JP (2017) Short branches lead to systematic artifacts when BLAST searches are used as surrogate for phylogenetic reconstruction. Mol Phylogenet 107:338-344. doi: 10.1016/j.ympev.2016.11.016. [Epub ahead of print]

Omer S, Harlow TJ, GogartenJP (2017) Does Sequence Conservation Provide Evidence for Biological Function? Trends in Microbiology 25(1):11-18, doi: 10.1016/j.tim.2016.09.010

Gogarten JP , Deamer D (2016) Is LUCA a thermophilic progenote? Nature Microbiology 1, 16229; doi: 10.1038/nmicrobiol.2016.229

Albert A, Alexander D, Boesze-Battaglia K (2016). Cholesterol in the rod outer segment: A complex role in a “simple” system. Chem Phys Lipids 2016 Sep;199:94-105. doi: 10.1016/j.chemphyslip.2016.04.008.

Kopac SM and Klassen JL (2016) Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche. Front. Microbiol. 7:1647. doi: 10.3389/fmicb.2016.01647.

Samantha M. Gromek, Anne A. Sung, Jonathan L. Klassen, Marcy J. Balunas (2016). Draft Genome Sequence of Streptomyces sp. Strain PTY087I2, Isolated from Styela canopus, a Panamanian Tunicate. Genome Announc. September/October 2016 vol. 4 no. 5 e00856-16. doi: 10.1128/genomeA.00856-16.

Gromek SM, Suria AM, Fullmer MS, Garcia JL, Gogarten JP, Nyholm SV and Balunas MJ (2016) Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios. Front. Microbiol. 7:1342. doi: 10.3389/fmicb.2016.01342.

Raja Dey,Yan Xia, Mu-Ping Nieh, and Peter Burkhard. (2016) Molecular Design of a Minimal Peptide Nanoparticle. ACS Biomaterials Science & Engineering DOI:10.1021/acsbiomaterials.6b00243.

Ram-Mohan, N., Oren, A., and Papke, R.T. (2016) Analysis of the bacteriorhodopsin-producing haloarchaea reveals a core community that is stable over time in the salt crystallizer pond in Eilat, Israel. Extremophiles DOI: 10.1007/s00792-016-0864-4.

Benjamino J, Graf J. 2016. Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes. Front Microbiol 7:171 (PMC4756164).

Crapser J, Ritzel R, Verma R, Venna VR, Liu F, Chauhan A, Koellhoffer E, Patel A, Ricker A, Maas K, Graf J, McCullough LD. 2016. Ischemic stroke induces gut permeability and enhances bacterial translocation leading to sepsis in aged mice. Aging (Albany NY) 8(5):1049-63 (PMC4931853)

Cong X, Xu W, Janton S, Henderson WA, Matson A, McGrath JM, Maas K, Graf J. 2016. Gut Microbiome Developmental Patterns in Early Life of Preterm Infants: Impacts of Feeding and Gender. PLoS ONE 11(4):e0152751 (PMC4844123).

Adit Naor, Neta Altman-Price, Shannon M. Soucy, Anna G. Green (UConn undergrad), Yulia Mitiagin, Israela Turgeman-Grott, Noam Davidovich, Johann Peter Gogarten*, Uri Gophna*  (2016). Impact of a homing intein on recombination frequency and organismal fitness. PNAS 2016; published ahead of print July 26, 2016, doi:10.1073/pnas.1606416113.

Andersson, R., Chen, Y., Core, L., Lis, J.T., Sandelin, A. & Jensen, T.H. 2015, “Human Gene Promoters Are Intrinsically Bidirectional”, Molecular cell, vol. 60, no. 3, pp. 346-347.

Mahat, D.B., Kwak, H., Booth, G.T., Jonkers, I.H., Danko, C.G., Patel, R.K., Waters, C.T., Munson, K., Core, L.J. & Lis, J.T. 2016, “Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)”, Nature protocols, vol. 11, no. 8, pp. 1455-1476.

Stulberg E, GL Lozano, JB Morin, H Park, EG Baraban, C Mlot, C Heffelfinger, GM Phillips, JS Rush, AJ Phillips, NA Broderick, MG Thomas, EV Stabb, J. Handelsman. 2016. Genomic and secondary metabolite analyses of Streptomyces sp. 2AW provide insight into the evolution of the cycloheximide pathway. Front Microbiol 7:573

Broderick, NA 2016. Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila–microbe interactions. Phil Trans R Soc. B 371:20150295

Palladino, J, Mellone, B.G. (2016) The KAT’s out of the bag: histone acetylation promotes centromere assembly. Developmental Cell (Preview). doi: 10.1016/j.devcel.2016.05.019

Chen, CC, Mellone, B.G. (2016) Chromatin assembly: Journey to the CENter of the chromosome. J Cell Biol. (Review). doi: 10.1083/jcb.201605005 .

Rice, J.M., Zweifach, A., and Lynes, M.A. (2016) Metallothionein Regulates Intracellular Zinc Signaling during CD4+ T cell Activation. BMC Immunology; DOI: 10.1186/s12865-016-0151-2.

Dennis, K.K., Marder, M.E., Balshaw, D.M., Cui, Y., Lynes, M.A., Patti, G.J, Rappaport, S.M., Shaughnessy, D., Sosnoff, C., Vrijheid, M., Barr, D.B. (2016) Biomonitoring in the Era of the Exposome. Environmental Health Perspectives; DOI:10.1289/EHP474.

Emeny RE, Kasten-Jolly J,  Mondal T, Lynes MA, Lawrence DA (2015) Metallothionein differentially affects the host response to Listeria infection both with and without an additional stress from cold-restraint. Cell Stress and Chaperones. 20(6):1013-22 PMID: 26267326

Mayo, C.B., Wong, C.J., Lopez P.E., Lary, J.W., Cole, J.L. (2016) Activation of PKR by short stem-loop RNAs containing single-stranded arms. RNA, DOI:10.1261/rna.053348.115.

Karch, Christopher P., Burkhard, Peter. (2016) Vaccine technologies: From whole organisms to rationally designed protein assemblies. Biochemical Pharmacology doi:10.1016/j.bcp.2016.05.001.

Rosin, L., Mellone, B. (2016) Co-evolving CENP-A and CAL1 Domains Mediate Centromeric CENP-A Deposition across Drosophila Species. Developmental Cell doi:10.1016/j.devcel.2016.03.021.

Theis KR, Dheilly NM, Klassen JL, Brucker RM, Baines JF, Bosch TCG, Cryan JF, Gilbert SF, Goodnight CJ, Lloyd EA, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein SR. 2016. Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes. mSystems 1(2):e00028-16. doi:10.1128/mSystems.00028-16.

Rischer M, Klassen JL, Wolf T, Guo H, Shelest E, Clardy J, Beemelmanns C. 2016. Draft genome sequence of Shewanella sp. strain P1-14-1, a bacterial inducer of settlement and morphogenesis in larvae of the marine hydroid Hydractinia echinata. Genome Announc 4(1):e00003-16. doi:10.1128/genomeA.00003-16.

Sathappa, M., and Alder, N.N. (2016) “The ionization properties of cardiolipin and its variants in model bilayers” BBA-Biomembranes [Epub ahead of print].

J.G. Pattis, E.R. May (2016). Influence of RNA Binding on the Structure and Dynamics of the Lassa Virus Nucleoprotein, Biophys. J., 110(6):1246-1254.

Christina Harprecht, Oghenfejiro Okifo, Kevin J. Robbins, Tina Motwani, Andrei T. Alexandrescu & Carolyn M. Teschke (2016) “Contextual role of a salt-bridge in the phage P22 coat protein I-domain.” J. Biol. Chem, in press.

Russo AJ, Mathiowetz AJ, Hong S, Welch MD, and Campellone KG (2016).  Rab1 recruits the actin nucleation machinery but limits filament assembly during membrane remodeling.  Mol Biol Cell. 27(6):967-978. (Cover)

A. Aggarwal, E.R. May, C.L. Brooks III, W.S. Klug (2016) Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature, Phys. Rev. E 92, 012417.

Nelson, M.C., T. Welch and J. Graf. 2015. Complete genome sequence of Yersinia ruckeri str. CSF007-82, etiologic agent of red mouth disease in salmonid fish. Genome Announcements. doi: 10.1128/genomeA.01491-14

Ott, B., L. Beka, J. Graf, and R.V.M. Rio. 2015. Draft genome sequence of Pedobacter sp. strain Hv1, an isolate from medicinal leech mucosal castings. Genome Announc. 3:e01469-15.

Li, Y.F, J. Shi, M. C. Nelson, P.H. Chen, J. Graf, Y. Li, Z. Yu. 2016. Impact of different ratios of feedstock to liquid anaerobic digestion effluent on the performance and microbiome of solid-state anaerobic digesters digesting corn stover. Bioresource Technol. 200, 744-752.

Mosser, T., E. Talagrand-Reboul, S. M. Colston, J. Graf, MJ Figueras, E. Jumas-Bilak, B. Lamy. 2015. Co-infections with multiple Aeromonas spp. enhance their virulence in the Caenorhabditis elegans model. Frontiers in Microbiol. DOI: 10.3389/fmicb.2015.01218

Li,Y.F., C. Abraham, M.C. Nelson, P.H. Chen, J. Graf, Z. Yu. 2015. Effect of organic loading on the microbiota in a temperature-phased anaerobic digestion (TPAD) system co-digesting dairy manure and waste whey. Appl. Microbiol. Biotechnol. 99: 8777-8792.

Brooks, J. M. and D. R. Benson.  2016.  Comparative metabolomics of root nodules infected with Frankia sp. strains and uninfected roots from Alnus glutinosa and Casuarina cunninghamiana reflects physiological integration.  Symbiosis doi: 10.1007/s13199-016-0379-x.

Jonathan L Klassen, Maja Rischer, Thomas Wolf, Huijuan Guo, Ekaterina Shelest, Jon Clardy, Christine Beemelmanns  Genome Sequences of Three Pseudoalteromonas Strains (P1-8, P1-11, and P1-30), Isolated from the Marine Hydroid Hydractinia echinata (2015) Genome Announcements 3(6): e01380-15

Jonathan L Klassen, Thomas Wolf, Maja Rischer, Huijuan Guo, Ekaterina Shelest, Jon Clardy, Christine Beemelmanns Draft genome sequences of six Pseudoalteromonas strains, P1-7a, P1-9, P1-13-1a, P1-16-1b, P1-25, and P1-26, which induce larval settlement and metamorphosis in Hydractinia echinata (2015) Genome Announcements 3(6): e01477-15

Husain, B., Mayo, C. and Cole, J.L. (2015) Role of the interdomain linker in PKR activation. Biochemistry, in press, DOI:10.1021/acs.biochem.5b01171.

Newcomer, R.L., Fraser, L.C.R., Teschke, C.M. & Alexandrescu, A.T. (2015) “Mechanism of protein denaturation: partial unfolding of the P22 coat protein I-domain by urea binding.”, Biophysical J. 109, 2666-2677. doi: 10.1016/j.bpj.2015.11.010

Paulina Corral, Rafael R. de la Haba, Cristina Sanchez-Porro, Mohammad Ali Amoozegar, R. Thand Papke, and Antonio Ventosa. (2015) Halorubrum halodurans sp. nov., an extremely halophilic archaeon isolated from a hypersaline lake.  IJSEM, doi: 10.1099/ijsem.0.000738

Alexandrescu, A.T. (2016) “Quenched Hydrogen Exchange NMR of Amyloid Fibrils.” Methods in Mol. Biol. 1345, 211-222. doi: 10.1007/978-1-4939-2978-8_14

Tripler, T.N., Maciejewski, M.W., Teschke, C.M. & Alexandrescu, A.T. (2015) “NMR assignments for the insertion domain of bacteriophage CUS-3 coat protein.” Biomolecular NMR Assignments 9, 333-336. doi: 10.1007/s12104-015-9604-4

Patil S.M., & Alexandrescu, A.T. (2015) “Charge-based inhibitors of amylin fibrillization and totoxicity.” J. Diabetes Res., Article ID 946037.

Murfin, K.E., Whooley, A.C., Klassen, J.L., Goodrich-Blair, H. Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions. 2015. BMC Genomics doi:10.1186/s12864-015-2000-8.

Burkhard P, Lanar DE. 2015. Malaria vaccine based on self-assembling protein nano particles. Expert Rev Vaccines. 2015 Oct 15:1-3.

Doll TA, Neef T, Duong N, Lanar DE, Ringler P, Müller SA, Burkhard P. 2015. Optimizing the design of protein nanoparticles as carriers for vaccine applications. Nanomedicine doi: 10.1016/j.nano.2015.05.003.

Husain, B., Hesler, S. and Cole, J.L. (2015) Regulation of PKR by RNA: Formation of active and inactive dimers. Biochemistry, in press, DOI:10.1021/acs.biochem.5b01046

Medema, M.H. et al. [150 authors, including Klassen, J.L.] 2015. Minimum Information about a Biosynthetic Gene cluster. Nature Chemical Biology. Nat Chem Biol 11:625-631

Maltz, M. B. LeVarge and J. Graf. 2015. Identification of Iron and Heme Utilization Genes in Aeromonas and their Role in the Colonization of the Leech Digestive Tract. Front. Microbiol. doi:10.3389/fmicb.2015.00763

Cong, X., W. Henderson, J. Graf, and J. McGrath. 2015. Brain-Gut-Microbiota Signaling System in Regulation of Early Life Experience. Adv. Neonatal Care. doi: 10.1097/ANC.0000000000000191.

Boyd, K.J., Bansal, P., Feng, J., May, E.R. (2015) Stability of Norwalk virus capsid protein interfaces evaluated by in-silico nanoindentation. Front. Bioeng. Biotechnol. 3:00103

Fullmer, M.S., Soucy, S.M., Gogarten, J.P. (2015) The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis. Front. Microbiol.

Soucy, S. M., Huang, J., Gogarten, J.P., (2015) Horizontal gene transfer: building the web of life. Nature Reviews Genetics doi:10.1038/nrg3962.

Murfin KE, Lee M, Klassen JL, McDonald BR, Larget B, Forst S, Stock SP, Currie CR, Goodrich-Blair H. (2015) Xenorhabdus bovienii strain diversity impacts coevolution and symbiotic maintenance with Steinernema spp. nematode hosts. mBio 6(3):e00076-15. doi:10.1128/mBio.00076-15.

Chen C-C., Bowers, S., Lipinszki, Z., Palladino, J., Trusiak, S., Bettini, E., Rosin, L., Przewloka, M.R., Glover, D.M., O’Neill, R. J., Mellone, B.G. (2015) Establishment of Centromeric Chromatin by the CENP-A Assembly Factor CAL1 Requires FACT-Mediated Transcription. Developmental Cell doi:10.1016/j.devcel.2015.05.012

Ventosa, A., De la Haba, R.R., Sánchez-Porro, C. and Papke, R.T. (2015) Microbial diversity of hypersaline environments: a metagenomic approach. Current Opinions in Microbiology.25:80-87

Papke, R.T., Corral, P., Ram-Mohan, N., de la Haba, R.R., Sánchez-Porro, C., Makkay, A. and Ventosa, A. (2015) Horizontal gene transfer, dispersal and haloarchaeal speciation. Life 5:1405-1426.

Nogueira, J. M., Hawrot, K., Sharpe, C., Noble, A., Wood, W. M., Jorge, E. C., Goldhamer, D. J., Kardon, G., and Dietrich, S.  (2015). The emergence of Pax7-expressing muscle stem cells during vertebrate head muscle development.  Front. Aging Neurosci.

Chimileski S and Papke RT (2015) Getting a hold on archaeal type IV pili: an expanding repertoire of cellular appendages implicates complex regulation and diverse functions. Front. Microbiol. 6:362. doi: 10.3389/fmicb.2015.00362

Fournier G, Andam CP, Gogarten JP (2015) Ancient horizontal gene transfer and the last common ancestors. BMC Evolutionary Biology 15 (1) p. 70 doi: 10.1186/s12862-015-0350-0.

Suhanovsky, M., Teschke, C. (2015) Nature׳s favorite building block: Deciphering folding and capsid assembly of proteins with the HK97-fold. Virology doi:10.1016/j.virol.2015.02.055.

Ouellette, M., Jackson, L., Chimileski, S. and Papke, R.T. (2015) Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006.  Frontiers in Microbiology  doi: 10.3389/fmicb.2015.00251.

Nelson, M. C. and J. Graf. 2015. Complete genome sequence of the novel leech symbiont Mucinivorans hirudinis M3T. Genome Announcements. doi: 10.1128/genomeA.01530-14.

Nelson, M. C., L. Bomar, M. Maltz and J. Graf. 2015. Mucinivorans hirudinis gen. nov., sp. nov., an anaerobic, mucin-degrading bacterium isolated from the digestive tract of the Hungarian medicinal leech, Hirudo verbana. Int. J. Syst. Evol. Microbiol. 65:990-5. doi: 10.1099/ijs.0.000052.

Corral, P., de la Haba, R.R., Sánchez-Porro, C., Amoozegar, M.A., Papke, R.T., and Ventosa, A. (2015) Halorubrum persicum sp. nov., an extremely halophilc archeaon isolated from sediment of a hypersaline lake.  IJSEM doi:10.1099/ijs.0.000175.

Launer-Felty, K., Wong, J.C. and Cole, J.L. (2014) Structural analysis of Adenovirus VAI RNA defines the mechanism of inhibition of PKR. Biophysical Journal 108,748-757.

Lee, K.K., Imaizumi, N., Chamberland, S.R., Alder, N.N., and Boelsterli, U.A. (2014). Targeting mitochondria with methylene blue protects mice against acetaminophen-induced liver injury. Hepatology. doi: 10.1022/hep.27385.

Colston#, S., M. Fullmer#, L. Beka, B. Lamy, J. P. Gogarten*, J. Graf*. 2014. Evaluation of Bioinformatic Genome Comparisons for Taxonomic and Phylogenic Assignments using Aeromonas as a Test Case. #Co-first authors, *Co-corresponding authors. mBio doi:10.1128/mBio.02136-14

Li, Y.-F., M.C. Nelson, P.-H. Chen, J. Graf, Y. Li, and Z. Yu. 2014. Comparison of the microbial communities in solid-state anaerobic digesters (SS-ADs) operated at mesophilic and thermophilic temperatures. Appl. Microbiol. Biotechnol. DOI 10.1007/s00253-014-6036-5.

Core, L.J., Martins, A.L., Danko, C.G., Waters, C.T., Siepel, A., and Lis, J.T. (2014) Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat. Genet.  doi:10.1038/ng.3142

Luk, A.W.S., Williams, T.J., Erdman, S., Papke, R.T., and Cavicchioli, R. (2014) Viruses of Haloarchaea. Life. doi:10.3390/life4040681
http://www.mdpi.com/2075-1729/4/4/681

Dharia, AP, Obla A, Gajdosik MD, Simon A, Nelson CE (2014) Tempo and Mode of Gene Duplication in Mammalian Ribosomal Protein Evolution. PLOS One DOI: 10.1371/journal.pone.0111721.

Chimileski S, Franklin MJ and Papke RT (2014) Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer. BMC Biology 12:65. doi:10.1186/s12915-014-0065-5.

Andrew J. Muinonen-Martin, Olivia Susanto, Qifeng Zhang, Elizabeth Smethurst, William J. Faller, Douwe M. Veltman, Gabriela Kalna, Colin Lindsay, Dorothy C. Bennett, Owen J. Sansom, Robert Herd, Robert Jones, Laura M. Machesky, Michael J. O. Wakelam, David A. Knecht, Robert H. Insall (2014) Melanoma Cells Break Down LPA to Establish Local Gradients That Drive Chemotactic Dispersal. PLoS Biology. DOI: 10.1371/journal.pbio.1001966

Klassen, JL (2014) Microbial secondary metabolites and their impacts on insect symbioses. Current Opinion in Insect Science. DOI: 10.1016/j.cois.2014.08.004 [Epub ahead of print].

Schleicher TR, VerBerkmoes NC, Shah M, Nyholm SV. (2014). Colonization state influences the hemocyte proteome in a beneficial squid-vibrio symbiosis. Mol Cell Proteomics. 2014 Jul 18. pii: mcp.M113.037259. [Epub ahead of print]

Shannon M. Soucy, Matthew S. Fullmer, R. Thane Papke and Johann Peter Gogarten: Inteins as indicators of gene flow in the halobacteria. Frontiers in  Microbiol ogy  5: 299, 25 June 2014 | doi:10.3389/fmicb.2014.00299

Hwang, M.S., Schwall C.T., Pazarentzos, E., Datler, C., Alder, N.N., and Grimm, S. (2014). Mitochondrial Ca2+ influx targets cardiolipin to disintegrate respiratory chain complex II for cell death induction. Cell Death Differ. doi: 10.1038/cdd.2014.84 [Epub ahead of print].

Malhotra, K., and Alder, N.N. (2014) Advances in the use of nanoscale bilayers to study membrane protein structure and function. Biotechnol. Genet. Eng. Rev. 30:79-93. doi: 10.1080/02648725.2014.921502.

Maltz, M.A., L. Bomar, P. Lapierre, H.G. Morrison, E.A. McClure, M.L. Sogin and J. Graf. 2014. Metagenomic Analysis of the Medicinal Leech Gut Microbiota. Front. Microbiol. doi: 10.3389/fmicb.2014.00151

Yu, R. B. F. Smets, P. Gan, A. A. MacKay, and J. Graf. 2014. Seasonal and Spatial Variations in Microbial Activity at Various Phylogenetic Resolutions at a Groundwater Surface Water Interface: Critical Role of Flooding in Microbial Activity Determination. Can. J. Microbiol. 60(5): 277-286, 10.1139/cjm-2014-0048

Rizzo, A.A., Suhanovsky, M.M., Baker, M.L., Fraser, L.C.R., Jones, L.M., Rempel, D.L., Gross, M.L., Chiu, W., Alexandrescu, A.T. & Teschke, C.M. (2014) “Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and cryoEM modeling”. Structure 22, 830-841.

Zhou C, Mao F, Yin Y, Huang J, Gogarten JP, Xu Y (2014): AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees. PLos One 9(6):e98844. doi: 10.1371/journal.pone.0098844.

Cortines JR, Motwani T, Vyas AA, Teschke CMJ Virol. (2014) Highly specific salt bridges govern bacteriophage P22 icosahedral capsid assembly: identification of the site in coat protein responsible for interaction with scaffolding protein. May;88(10):5287-97. doi: 10.1128/JVI.00036-14. Epub 2014 Mar 5.

Kaus, K., Lary, J.W., Cole, J.L. and Olson, R. (2014) Glycan specificity of the Vibrio vulnificus hemolysin lectin outlines evolutionary history of membrane targeting by a toxin family. J. Mol. Biol., in press, DOI:10.1016/j.jmb.2014.05.021

Devisscher L, H.P., Lynes M, Waeytens A, Cuvelier C, De Vos F, Vanhove C, De Vos M, Laukens D.(2014) Role of metallothioneins as danger signals in the pathogenesis of colitis. J. Pathol 233:89-100 DOI: 10.1002/path.4330

Lynes, M.A., Hidalgo, J., Manso, Y., Devisscher, L., Laukens, D., and Lawrence, D.A. (2014) Metallothionein and stress combine to affect multiple organ systems. Cell Stress and Chaperones. In press. PMID: 24584987

Wowor, A.J., Yan, Y., Auclair, S.M., Yu, D., Zhang, J., May, E.R., Gross, M.L., Kendall, D.A. and Cole, J.L. (2014) Analysis of SecA Dimerization in Solution. Biochemistry, in press, DOI:10.1021/bi500348p

E.R. May (2014) Recent developments in molecular simulation approaches to study spherical virus
capsids, Molecular Simulation, DOI: 10.1080/08927022.2014.907899

Chung KM, Kolling IV F, Gajdosik M, Burger S, Russell A, Nelson C (2014) Single Cell Analysis Reveals the Stochastic Phase of Reprogramming to Pluripotency Is an Ordered Probabilistic Process. POLS One DOI: 10.1371/journal.pone.0095304

Zerulla K, Chimileski S, Näther D, Gophna U, Papke RT, et al. (2014) DNA as a Phosphate Storage Polymer and the Alternative Advantages of Polyploidy for Growth or Survival. PLoS ONE 9(4): e94819. doi:10.1371/journal.pone.0094819 

Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT:
Population and genomic analysis of the genus Halorubrum.
Frontiers in Microbiology 2014, 5: 140. doi: 10.3389/fmicb.2014.00140

Nelson, M.C.,, H.G. Morrison, J. Benjamino, S.L. Grim, J. Graf. 2014. Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys. PLOS One 9(4): e94249. doi:10.1371/journal.pone.0094249.

Whitaker, I., M. Maltz, M.E. Siddall, and J. Graf. 2014. Characterization of the digestive tract microbiota of Hirudo orientalis (medicinal leech) and antibiotic resistance profile. Plast. Recon. Surgery 133, p 408e–418e. DOI: 10.1097/01.prs.0000438461.06217.bb

Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP and Papke RT (2014) Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations. Front. Microbiol. 5:143. doi: 10.3389/fmicb.2014.00143

Amanda K. Dupuy, Marika S. David, Lu Li, Thomas N. Heider, Jason D. Peterson, Elizabeth A. Montano, Anna Dongari-Bagtzoglou, Patricia I. Diaz, Linda D. Strausbaugh (2014) Redefining the Human Oral Mycobiome with Improved Practices in Amplicon-based Taxonomy: Discovery of Malassezia as a Prominent Commensal. PLoS ONE, DOI: 10.1371/journal.pone.0090899

Chimileski S, Dolas K, Naor A, Gophna U and Papke RT (2014) Extracellular DNA metabolism in Haloferax volcanii. Frontiers in Microbiology 5:57. doi:10.3389/fmicb.2014.00057

Veltman DM, Lemieux MG, Knecht DA, Insall RH (2014) PIP(3)-dependent macropinocytosis is incompatible with chemotaxis. J Cell Biol 204: 497-505.

E.R. May, K. Arora, C.L. Brooks, III (2014) pH Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway. J. Am. Chem. Soc.

Chopra AS, Anderson A, Giardina C (2014). “Novel piperazine-based compounds inhibit microtubule dynamics and sensitize colon cancer cells to Tumor Necrosis Factor-induced apoptosis.” J. Biol. Chem. doi: 10.1074/jbc.M113.499317

David R. Benson and Roger K. Kjelgren. 2014. Tacit diplomacy in the life sciences. A foundation for science diplomacy. Science and Diplomacy (AAAS). 3(1):Jan. 13

Chin-Chi Chen, Mekonnen Lemma Dechassa, Emily Bettini, Mary B. Ledoux, Christian Belisario, Patrick Heun, Karolin Luger, and Barbara G. Mellone. 2014. CAL1 is the Drosophila CENP-A assembly factor. J. Cell Biol. 10.1083/jcb.201305036, highlighted in JCB

Jha, S., Snell, J.M., Sheftic, S.R., Patil S.M., Daniels, S.B., Kolling, F.W., & Alexandrescu, A.T. (2014) “pH dependence of amylin fibrillization”. [Epub ahead of print ]

Sheftic, S.R., White, E., Gage, D.J. & Alexandrescu, A.T. (2014) “NMR structure of the HWE kinase associated response regulator Sma0114 in its activated state”. [Epub ahead of print]

Katherine Launer-Felty and James L. Cole (2014) Domain interactions in Adenovirus VAI RNA mediate high affinity PKR binding J. Mol. Biol., DOI: 10.1016/j.jmb.2013.12.019

Butzin NC, Lapierre P, Green AG, Swithers KS, Gogarten JP, Noll KM (2013). Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants. PLoS One 8(12):e84300. doi: 10.1371/journal.pone.0084300.

Marcellino, N. and D. R. Benson. 2013. The good, the bad and the ugly: Tales of mold-ripened cheese. Microbiology Spectrum ASM 1:doi:10.1128/microbiolspec.CM-0005-2012.

Anne R. Kaplan, Mark W. Maciejewski, Rich Olson, Andrei T. Alexandrescu (2013). NMR assignments for the cis and trans forms of the hemolysin II C-terminal domain. Biomol NMR Assign [Epub ahead of print] . doi: 10.1007/s12104-013-9530-2

Marcellino, N. and D. R. Benson. 2013. The good, the bad and the ugly: Tales of mold-ripened cheese. Microbiology Spectrum ASM 1:doi:10.1128/microbiolspec.CM-0005-2012.

Matthew Ouellette, Andrea M. Makkay, and R. Thane Papke (2013) Dihydroxyacetone metabolism in Haloferax volcanii. Front. Microbiol. doi: 10.3389/fmicb.2013.00376

J. S. Yuk, E. F. Guignon, M. A. Lynes (2013) Sensitivity enhancement of a grating-based surface plasmon-coupled emission (SPCE) biosensor chip by optimizing gold thickness Chemical Physics Letters [Advance Access. Author’s preprint version]

Baile MG, Sathappa M, Lu YW, Pryce E, Whited K, McCaffery JM, Han X, Alder NN, Claypool SM. (2013) Unremodeled and remodeled cardiolipin are functionally indistinguishable in yeast. J. Biol. Chem. doi:10.1074/jbc.M113.525733

Wanczyk, H., Barker, T., Rood, D., Zapata, D.I., Howell, A.R., Richardson, S.K., J., Marusov, G.P., Lynes, M.A., Silbart, L.K. (2013) Cloning and Characterization of a Hybridoma Secreting a 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK)-Specific Monoclonal Antibody and Recombinant F(ab).Toxins 5(3):568-89. DOI:10.3390/toxins5030568.

Kristen S. Swithers, Shannon M. Soucy, Erica Lasek-Nesselquist, Pascal Lapierre and Johann Peter Gogarten (2013) Distribution and Evolution of the Mobile vma-1b Intein Molecular Biology and Evolution Advance Access doi: 10.1093/molbev/mst164, authors’ preprint version

Lemieux MG, Janzen D, Hwang R, Roldan J, Jarchum I et al. (2013) Visualization of the actin cytoskeleton: Different F-actin-binding probes tell different stories. Cytoskeleton (Hoboken)

Joshi GN, Knecht DA (2013) Silica phagocytosis causes apoptosis and necrosis by different temporal and molecular pathways in alveolar macrophages. Apoptosis 18: 271-285.

Wood, W. M., Etemad, S., Yamamoto, M., and Goldhamer, D. J. (2013). MyoD-expressing progenitors are essential for skeletal myogenesis and satellite cell development. Dev. Biol. 384, 114-127.

Butzin N, Secinaro M, Swithers KS, Gogarten JP, and Noll K (2013) Thermotoga lettingae can salvage cobinamide to synthesize vitamin B12 Applied and Environmental Microbiology Published ahead of print 6 September 2013,  doi: 10.1128/AEM.01800-13

Lee, K.K., Fujimoto, K., Zhang, C., Schwall, C.T., Alder, N.N. , Pinkert, C.A., Krueger, W., Rasmussen, T., and Boelsterli, U.A. (2013). Isoniazid-induced cell death is precipitated by underlying mitochondrial complex I dysfunction in mouse hepatocytes. [Epub ahead of print]

Anna G. Green, Kristen S. Swithers, Jan F. Gogarten and J. Peter Gogarten (2013) Reconstruction of Ancestral 16S rRNA Reveals Mutation Bias in the Evolution of Optimal Growth Temperature in the Thermotogae Phylum. Molecular Biology and Evolution Advance Access doi:10.1093/molbev/mst145, authors’ pre-print version

de al Haba, R.R., Sánchez-Porro, C., León, M.J., Papke, R.T., . and Ventosa, A. (2013) Draft genome of the moderately halophilic bacterium Pseudoalteromonas ruthenica strain CP76. Genome Announcements. 1:e00268-13

Papke, R.T., de al Haba, R.R., Infante, C., Perez, D., Sánchez-Porro, C., Lapierre, P, and Ventosa, A. (2013) Draft genome of the moderately halophilic bacterium Marinobacter lipolyticus strain SM19. Genome Announcements 1:e00379-13.

Malhotra, K., Sathappa, M., Landin, J.S., Johnson, A.E. and Alder, N.N. (2013) Structural changes in the mitochondrial Tim23 channel are coupled to the proton-motive force. Nat. Struct. Mol. Biol. Epub ahead of print

Malhotra, K., Sathappa, M., Landin, J.S., Johnson, A.E. and Alder, N.N. (2013) Structural changes in the mitochondrial Tim23 channel are coupled to the proton-motive force. Nat. Struct. Mol. Biol. Epub

Long, A.R., OBrien, C.C., Malhotra, K., Schwall, C.T., Albert, A.D., Watts, A., and Alder, N.N. (2013) A detergent-free strategy for the reconstitution of active enzyme complexes from native biological membranes into nanoscale discs. BMC Biotechnol. May 11; 13:41.

Ross, B.D., Rosin, L., Thomae A.W., Hiatt, M.A., Vermaak, D., de la Cruz A.F., Imhof A., Mellone, B.G., Malik, H.S. Stepwise evolution of essential centromere function in a Drosophila neogene. Science, 2013 Vol. 340 no. 6137 pp. 1211-1214.

Lasek-Nesselquist E, Gogarten JP.:The effects of model choice and mitigating bias on the ribosomal tree of life. Mol Phylogenet Evol. 2013 May 22;. [Epub ahead of print]

Yu, D., Wowor, A.J., Cole, J.L. and Kendall, D.A. (2013). Defining the Escherichia coli SecA Dimer Interface Residues through in Vivo Site-specific Photo-crosslinking. J. Bacteriol., in press

Aaron Ehlinger, Soyeon Park, Amr Fahmy, Jeffrey W. Lary, James L. Cole, Daniel Finley, and Kylie J. Walters (2013) Conformational Dynamics of the Rpt6 ATPase in Proteasome Assembly and Rpn14 Binding Structure., in press

Brit Winnen, Eric Anderson, James L. Cole, Glenn F. King, and Susan L. Rowland (2013). Role of the PAS sensor domains in the Bacillus subtilis sporulation kinase KinA. J. Bacteriol., in press

Daniel F. Lyons, Jeffrey W. Lary, Bushra Husain, John J. Correia and James L. Cole (2013) Are fluorescence-detected sedimentation velocity data reliable? Analytical Biochemistry, in press

Carone, D.M. Ferreri, G.C., J.D. Brown, C. Obergfell, B.R. Carone, M.J. O’Neill, R.J. O’Neill. 2013. Hypermorphic expression of centromeric retroelement-encoded small RNAs impairs CENP-A loading. Chromosome Research DOI 10.1007/s10577-013-9337-0

McFall-Ngai M, MHadfield, T Bosch, H Carey, T Domazet-Loso, A Douglas, N Dubilier, G Eber, T Fukami, S Gilbert, U Hentschel, N King, S Kjelleberg, AH Knoll, N Kremer, S Mazmanian, J Metcalf, K Nealson, N Pierce, J Rawls, A Reid, E Ruby, M Rumpho, J Sanders, D Tautz and J Wernegreen (2013) Animals in a bacterial world: A new imperative for the life sciences. Proceedings of the National Academy of Sciences USA 110 (9): 3229-3236; doi:10.1073/pnas.1218525110

J Snijder, VS Reddy, ER May, WH Roos, GR Nemerow, GJL Wuite (2013) Integrin and Definsin Modulate the Mechanical Properties of Adenovirus. Journal of Virology 87 (5), 2756-2766 doi:10.1128/JVI.02516-12

Andrei T. Alexandrescu (2013) Amide proton protection in amylin fibrils probed by quenched hydrogen exchange NMR PLoS ONE, doi:10.1371/journal.pone.005646

Olga Zhaxybayeva, Ramunas Stepanauskas, Nikhil Ram Mohan, R. Thane Papke (2013) Cell Sorting Analysis of Geographically Separated Hypersaline Environments. Extremophiles, doi:10.1007/s00792-013-0514-z

Bansal MS, Banay, G, Harlow TJ, Gogarten JP, Shamir R
Systematic Inference of Highways of Horizontal Gene Transfer in Prokaryotes Bioinformatics First published online: January 17, 2013 doi:10.1093/bioinformatics/btt021

Christopher Wostenberg, Jeffrey W. Lary, Debashish Sahu, Roderico Acevedo, Kaycee A. Quarles, James L. Cole, Scott A. Showalter (2012) The Role of Human Dicer-dsRBD in Processing Small Regulatory RNAs PLoS ONE, doi:10.1371/journal.pone.0051829

Williams, D., Gogarten, J.P., and Papke, R.T. (2012) Quantifying homologous replacement of loci between haloarchaeal species. Genome Biology and Evolution 4:1223-1244

Nyholm SV, Graf J. (2012) Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses. Nature Reviews Microbiology

Yang and Burkhard: Encapsulation of gold nanoparticles into self-assembling protein nanoparticles. Journal of Nanobiotechnology 2012 10:42.

Ngunjiri JM, Mohni KN, Sekellick MJ, Schultz-Cherry S, Webster RG, Marcus PI. (2012). Lethal H5N1 influenza viruses are not resistant to interferon action in human, simian, porcine, or chicken cells. Nature Medicine 18:1456­1457 (2012) DOI:10.1038/nm.2879

Ashley R. Long, Catherine C. O¹Brien, and Nathan N. Alder (2012). The Cell-Free Integration of a Polytopic Mitochondrial Membrane Protein into Liposomes Occurs Cotranslationally and in a Lipid-Dependent Manner. PLoS ONE 7(9): e46332. doi:10.1371/journal.pone.0046332

Shen QT, Hsiue PP, Sindelar CV, Welch MD, Campellone KG, and Wang HW (2012). Structural insights into WHAMM-mediated cytoskeletal coordination during membrane remodeling. J Cell Biol. 199:111-124. Cover, Preview, Pape

Bushra Husain, Ishita Mukerji and James L. Cole (2012) Analysis of high affinity binding of PKR to dsRNA Biochemistry, DOI:10.1021/bi301226h

Long AR, O’Brien CC, Alder NN (2012) The Cell-Free Integration of a Polytopic Mitochondrial Membrane Protein into Liposomes Occurs Cotranslationally and in a Lipid-Dependent Manner. PLoS ONE 7(9): e46332. doi:10.1371/journal.pone.0046332

Nelson, M.C. and J. Graf. 2012. Bacterial symbioses of the medicinal leech Hirudo verbena. Gut Microbes 4(3):dx.doi.org/10.4161/gmic.20227

Bomar, L. and J. Graf. 2012. Investigation into the physiologies of Aeromonas veronii in vitro and inside the digestive tract of the medicinal leech using RNA-seq. Biol. Bull. 223:155-66

Rizzo, A.A., Fraser, L.C.R., Sheftic, S.R., Suhanovsky, M.S., Teschke, C.M., Alexandrescu, A.A. (2012) NMR assignments for the telokin-like domain of P22 coat protein. Biomol. NMR Assign.

Chin-Chi Chen, Elizabeth Greene, Sarion R. Bowers, Barbara G. Mellone. A Role for the CAL1-Partner Modulo in Centromere Integrity and Accurate Chromosome doi:10.1371/journal.pone.0045094PLoS ONE 7(9): e45094. Segregation in Drosophila. (2012).

Sheftic, S.R., Garcia, P.P., White, E., Robinson, V.L., Gage, D. & Alexandrescu, A.T. (2012) “NMR Structure and Dynamics of the Response Regulator Sma0114 from Sinorhizobium meliloti”. Biochemistry 51, 6932-6941.DOI: 10.1021/bi300922z

Sheftic, S.R., Snell, J. M., Jha, S. & Alexandrescu, A.T. (2012) “Inhibition of Semen-derived Enhancer of Virus Infection (SEVI) fibrillogenesis by physiological zinc and copper concentrations”, European Biophysics Journal, in press. DOI: 10.1007/s00249-012-0846-0

Lapierre P, Lasek-Nesselquist E, and Gogarten JP (2012)
The impact of HGT on phylogenomic reconstruction methods
Brief Bioinform [first published online August 20, 2012] doi:10.1093/bib/bbs050 [Fulltext]

Parent KN, Deedas CT, Egelman EH, Casjens SR, Baker TS, Teschke CM: Stepwise molecular display utilizing icosahedral and helical complexes of phage coat and decoration proteins in the development of robust nanoscale display vehicles. Biomaterials 33(22):5628-37, 2012; doi:j.biomaterials.2012.04.026

Padilla-Meier GP, Gilcrease EB, Weigele PR, Cortines JR, Siegel M, Leavitt JC, Teschke CM, Casjens SR. (2012) Unraveling the Role of the C-terminal Helix-Turn-Helix of the Coat-binding Domain of Bacteriophage P22 Scaffolding Protein. J Biol Chem. 2012 Aug 9. [Epub ahead of print] doi:10.1074/jbc.M112.393132

Campellone KG, Siripala AD, Leong JM, and Welch MD (2012). Membrane-deforming proteins play distinct roles in actin pedestal biogenesis by enterohemorrhagic Escherichia coli. J Biol Chem 287: 20613-20624

Bateman,JR, Larschan, E., D’Souza, R., Marshall,L.S, Dempsey, K.E., Johnson, J.E., Mellone, B.G. and Kuroda, M.I. Genome-Wide Screen Identifies Genes That Affect Somatic Homolog Pairing in Drosophila. G3: Genes, Genomes, Genetics. doi: 10.1534/g3.112.002840 G3 July 1, 2012 vol. 2 no. 7 731-740

Ragini Phansalkar, Pascal Lapierre and Barbara G. Mellone. Evolutionary insights into the role of the essential centromere protein CAL1 in Drosophila. Chromosome Research 2012, DOI: 10.1007/s10577-012-9299-

Swithers KS, Petrus AK, Secinaro MA, Nesbo; CL, Gogarten JP, Noll KM and Butzin NC (2012). Vitamin B12 synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales. Genome Biology and Evolution [Epub before print] doi:10.1093/gbe/evs057

Andam CP, Harlow TJ, Papke RT, Gogarten JP (2012) Ancient origin of the divergent forms of leucyl-tRNA synthetases in the halobacteriales Journal: BMC Evolutionary Biology 12:85 doi:10.1186/1471-2148-12-85

Swithers KS, Soucy SM, Gogarten JP (2012) The Role of Reticulate Evolution in Creating Innovation and Complexity. International Journal of Evolutionary Biology 2012, ID 418964, 10 pages, doi:10.1155/2012/418964

Mao F, Williams D, Zhaxybayeva O, Poptsova M, Lapierre P, Gogarten JP, Xu Y (2012) Quartet decomposition server: a platform for analyzing phylogenetic trees BMC Bioinformatics 13:123 doi:10.1186/1471-2105-13-123

Petrus AK, Swithers KS, Ranjit C, Wu S, Brewer HM, Gogarten JP, Pasa-Tolic L, Noll KM (2012) Genes for the Major Structural Components of Thermotogales Species’ Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs. PLoS One 7(6):e40236 doi:10.1371/journal.pone.0040236

Pietrosimone, K. M., Yin, X., Knecht, D. A., Lynes, M. A. Measurement of Cellular Chemotaxis with ECIS/Taxis. J. Vis. Exp. (62), e3840; DOI: 10.3791/3840

Yuk*, J., Gibson*, G., Rice, J., Guignon, E., and Lynes, M.A. (* co-first authors) (2012) Analysis of immunoarrays using a gold grating-based dual mode surface plasmon-coupled emission (SPCE) sensor chip, Analyst, 2012,137, 2574-2581; DOI: 10.1039/C2AN35143A.

Collins AJ*, Schleicher TR*, Rader BA, Nyholm SV. (2012) Understanding the role of host hemocytes in a squid/Vibrio symbiosis using transcriptomics and proteomics. Frontiers Immunol. 3: 91. *co-primary authors

Collins AJ, LaBarre BA, Wong Won BS, Shah MV, Heng S, Choudhury MH, Haydar SA, Santiago J, Nyholm SV (2012) Diversity and partitioning of bacterial populations within the accessory nidamental gland of the squid Euprymna scolopes. Appl. Environ. Microbiol. 78: 4200-4208

Fidopiastis P, Rader BA, Gerling D, Gutierrez N, Watkins K, Frey M, Nyholm SV, Whistler CA. (2012) Characterization of a Vibrio fischeri aminopeptidase and evidence for its influence on an early state of squid colonization. J. Bacteriol. (Epub ahead of print)

Ngunjiri, J. M., C-W Lee, A. Ali, and P.I. Marcus (2012). “Influenza virus interferon-inducing particle efficiency is reversed in avian and mammalian cells, and enhanced in cells co-infected with defective-interfering particles.” J. Interferon & Cytokine Res. 32(6):In press. (doi:10.1089/jir.2011.0102)

Malinoski, C.P., and P.I. Marcus (2012). “Influenza virus: A single noninfectious interferon-suppressing particle blocks expression of interferon-inducing particles.” J. Interferon & Cytokine Res. 32(3):121-126. (doi:10.1089/jir.2011.0078)

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/es201239

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

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. 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.20100006

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, German

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, US

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 17:201-21

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: 1975489

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.2009.06.01

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, 11982-1199

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]

Erhardt, S., Mellone B. G., Betts, C. M. et al. 2008. Genome-wide analysis reveals a cell cycle-dependent mechanism controlling centromere propagation. The Journal of Cell Biology. Vol. 183 No. 5: 805-818

Nyholm, S. V. et al. 2008. Recognition between symbiotic Vibrio fischeri and the haemocytes of Euprymna scolopes. Environ. Microbiol. 9:1462-2920.

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.

deLivron, M.A. and Robinson, V.L. (2008) Salmonella enterica sv. Typhimurium BipA Exhibits Two Distinct Ribosome Binding Modes J. Bacteriol. E-Publ. ahead of print.

Jinling Huang and J. Peter Gogarten (2008) Concerted gene recruitment in early plant evolution Genome Biology 9(7): R10

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.

Eric Anderson and James L. Cole 2008. Domain stabilities in PKR: evidence for weak interdomain interactions. Biochemistry 47: 4887-4897.

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.

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-pu

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