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Category:TAMU CPT journal club

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 TAMU CPT Journal Club

Content of New Literature Pages

A Wiki writer will be designated for each paper. The Wiki writer will prepare a template page with "first draft" comments before the class discussion and notify the class members by email, linking to the Wiki page. The content of the Wiki page is meant to BRIEFLY summarize the question, the approach, the major findings, the major conclusions, and also problems associated with all of these. The initial Wiki will be graded but Wikis being Wikis, other members of the group and indeed from the outside world can and will edit the Wiki.

Creating New Literature Pages

To create a new Literature page:

  • You must be logged in. If you don't have an account, any JClub member with an account can create one for you.
  • Obtain the PMID number of the paper. Once you have that, simply enter PMID:### into the box below, where ### is the PMID number.
  • Once you've created the PMID page, add the new page to both Categories for the journal club. Go to the newly created page, edit the page, and add the following texts somewhere on the newly created page (the very end of the page is fine):
[[Category:TAMU CPT journal club]]

[[Category:TAMU CPT journal club Spring 2013]]
[[Category:TAMU CPT journal club Fall 2013]]
The first line above adds the new page to this one, and the second one adds a category tag for what semester the paper is being done.

Papers Done by the CPT Journal Club

  • Auzat, I, Dröge, A, Weise, F, Lurz, R, Tavares, P (2008) Origin and function of the two major tail proteins of bacteriophage SPP1. Mol. Microbiol. 70 557-69 PMID:18786146
  • Avrani, S, Wurtzel, O, Sharon, I, Sorek, R, Lindell, D (2011) Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature 474 604-8 PMID:21720364
  • Bae, B, Davis, E, Brown, D, Campbell, EA, Wigneshweraraj, S, Darst, SA (2013) Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of σ70 domain 1.1. Proc. Natl. Acad. Sci. U.S.A. 110 19772-7 PMID:24218560
  • Barr, JJ, Auro, R, Furlan, M, Whiteson, KL, Erb, ML, Pogliano, J, Stotland, A, Wolkowicz, R, Cutting, AS, Doran, KS, Salamon, P, Youle, M, Rohwer, F (2013) Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc. Natl. Acad. Sci. U.S.A. 110 10771-6 PMID:23690590
  • Basler, M, Pilhofer, M, Henderson, GP, Jensen, GJ, Mekalanos, JJ (2012) Type VI secretion requires a dynamic contractile phage tail-like structure. Nature 483 182-6 PMID:22367545
  • Berry, TM, Christie, PJ (2011) Caught in the act: the dialogue between bacteriophage R17 and the type IV secretion machine of plasmid R1. Mol. Microbiol. 82 1039-43 PMID:22023392
  • Bonnet, J, Subsoontorn, P, Endy, D (2012) Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc. Natl. Acad. Sci. U.S.A. 109 8884-9 PMID:22615351
  • Broussard, GW, Oldfield, LM, Villanueva, VM, Lunt, BL, Shine, EE, Hatfull, GF (2013) Integration-dependent bacteriophage immunity provides insights into the evolution of genetic switches. Mol. Cell 49 237-48 PMID:23246436
  • Burton, BM, Marquis, KA, Sullivan, NL, Rapoport, TA, Rudner, DZ (2007) The ATPase SpoIIIE transports DNA across fused septal membranes during sporulation in Bacillus subtilis. Cell 131 1301-12 PMID:18160039
  • Commichau, FM, Stülke, J (2012) A mystery unraveled: essentiality of RNase III in Bacillus subtilis is caused by resident prophages. PLoS Genet. 8 e1003199 PMID:23300472
  • Dupaigne, P, Tonthat, NK, Espéli, O, Whitfill, T, Boccard, F, Schumacher, MA (2012) Molecular basis for a protein-mediated DNA-bridging mechanism that functions in condensation of the E. coli chromosome. Mol. Cell 48 560-71 PMID:23084832
  • Durand, S, Gilet, L, Condon, C (2012) The essential function of B. subtilis RNase III is to silence foreign toxin genes. PLoS Genet. 8 e1003181 PMID:23300471
  • Espéli, O, Borne, R, Dupaigne, P, Thiel, A, Gigant, E, Mercier, R, Boccard, F (2012) A MatP-divisome interaction coordinates chromosome segregation with cell division in E. coli. EMBO J. 31 3198-211 PMID:22580828
  • Friedman, DI, Mozola, CC, Beeri, K, Ko, CC, Reynolds, JL (2011) Activation of a prophage-encoded tyrosine kinase by a heterologous infecting phage results in a self-inflicted abortive infection. Mol. Microbiol. 82 567-77 PMID:21985444
  • Hensel, Z, Feng, H, Han, B, Hatem, C, Wang, J, Xiao, J (2012) Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysis. Nat. Struct. Mol. Biol. 19 797-802 PMID:22751020
  • Hill, NS, Kadoya, R, Chattoraj, DK, Levin, PA (2012) Cell size and the initiation of DNA replication in bacteria. PLoS Genet. 8 e1002549 PMID:22396664
  • Hu, B, Margolin, W, Molineux, IJ, Liu, J (2013) The bacteriophage t7 virion undergoes extensive structural remodeling during infection. Science 339 576-9 PMID:23306440
  • Jakutytė, L, Baptista, C, São-José, C, Daugelavičius, R, Carballido-López, R, Tavares, P (2011) Bacteriophage infection in rod-shaped gram-positive bacteria: evidence for a preferential polar route for phage SPP1 entry in Bacillus subtilis. J. Bacteriol. 193 4893-903 PMID:21705600
  • Kiro, R, Molshanski-Mor, S, Yosef, I, Milam, SL, Erickson, HP, Qimron, U (2013) Gene product 0.4 increases bacteriophage T7 competitiveness by inhibiting host cell division. Proc. Natl. Acad. Sci. U.S.A. 110 19549-54 PMID:24218612
  • Lang, S, Kirchberger, PC, Gruber, CJ, Redzej, A, Raffl, S, Zellnig, G, Zangger, K, Zechner, EL (2011) An activation domain of plasmid R1 TraI protein delineates stages of gene transfer initiation. Mol. Microbiol. 82 1071-85 PMID:22066957
  • Lemke, JJ, Durfee, T, Gourse, RL (2009) DksA and ppGpp directly regulate transcription of the Escherichia coli flagellar cascade. Mol. Microbiol. 74 1368-79 PMID:19889089
  • Lu, TK, Collins, JJ (2007) Dispersing biofilms with engineered enzymatic bacteriophage. Proc. Natl. Acad. Sci. U.S.A. 104 11197-202 PMID:17592147
  • Luo, Y, Helmann, JD (2012) Analysis of the role of Bacillus subtilis σ(M) in β-lactam resistance reveals an essential role for c-di-AMP in peptidoglycan homeostasis. Mol. Microbiol. 83 623-39 PMID:22211522
  • Marquis, KA, Burton, BM, Nollmann, M, Ptacin, JL, Bustamante, C, Ben-Yehuda, S, Rudner, DZ (2008) SpoIIIE strips proteins off the DNA during chromosome translocation. Genes Dev. 22 1786-95 PMID:18593879
  • Menard, KL, Grossman, AD (2013) Selective pressures to maintain attachment site specificity of integrative and conjugative elements. PLoS Genet. 9 e1003623 PMID:23874222
  • Mercier, R, Kawai, Y, Errington, J (2013) Excess membrane synthesis drives a primitive mode of cell proliferation. Cell 152 997-1007 PMID:23452849
  • Mercier, R, Petit, MA, Schbath, S, Robin, S, El Karoui, M, Boccard, F, Espéli, O (2008) The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain. Cell 135 475-85 PMID:18984159
  • Merrikh, H, Ferrazzoli, AE, Lovett, ST (2009) Growth phase and (p)ppGpp control of IraD, a regulator of RpoS stability, in Escherichia coli. J. Bacteriol. 191 7436-46 PMID:19820090
  • Myers, KS, Yan, H, Ong, IM, Chung, D, Liang, K, Tran, F, Keleş, S, Landick, R, Kiley, PJ (2013) Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet. 9 e1003565 PMID:23818864
  • Osmundson, J, Montero-Diez, C, Westblade, LF, Hochschild, A, Darst, SA (2012) Promoter-specific transcription inhibition in Staphylococcus aureus by a phage protein. Cell 151 1005-16 PMID:23178120
  • Parry, BR, Surovtsev, IV, Cabeen, MT, O'Hern, CS, Dufresne, ER, Jacobs-Wagner, C (2014) The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity. Cell 156 183-94 PMID:24361104
  • Pedrido, ME, de Oña, P, Ramirez, W, Leñini, C, Goñi, A, Grau, R (2013) Spo0A links de novo fatty acid synthesis to sporulation and biofilm development in Bacillus subtilis. Mol. Microbiol. 87 348-67 PMID:23170957
  • Plisson, C, White, HE, Auzat, I, Zafarani, A, São-José, C, Lhuillier, S, Tavares, P, Orlova, EV (2007) Structure of bacteriophage SPP1 tail reveals trigger for DNA ejection. EMBO J. 26 3720-8 PMID:17611601
  • Rabinovich, L, Sigal, N, Borovok, I, Nir-Paz, R, Herskovits, AA (2012) Prophage excision activates Listeria competence genes that promote phagosomal escape and virulence. Cell 150 792-802 PMID:22901809
  • Ram, G, Chen, J, Kumar, K, Ross, HF, Ubeda, C, Damle, PK, Lane, KD, Penadés, JR, Christie, GE, Novick, RP (2012) Staphylococcal pathogenicity island interference with helper phage reproduction is a paradigm of molecular parasitism. Proc. Natl. Acad. Sci. U.S.A. 109 16300-5 PMID:22991467
  • Rotman, E, Bratcher, P, Kuzminov, A (2009) Reduced lipopolysaccharide phosphorylation in Escherichia coli lowers the elevated ori/ter ratio in seqA mutants. Mol. Microbiol. 72 1273-92 PMID:19432803
  • Savage, DF, Afonso, B, Chen, AH, Silver, PA (2010) Spatially ordered dynamics of the bacterial carbon fixation machinery. Science 327 1258-61 PMID:20203050
  • Schwarzer, D, Buettner, FF, Browning, C, Nazarov, S, Rabsch, W, Bethe, A, Oberbeck, A, Bowman, VD, Stummeyer, K, Mühlenhoff, M, Leiman, PG, Gerardy-Schahn, R (2012) A multivalent adsorption apparatus explains the broad host range of phage phi92: a comprehensive genomic and structural analysis. J. Virol. 86 10384-98 PMID:22787233
  • Seed, KD, Lazinski, DW, Calderwood, SB, Camilli, A (2013) A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature 494 489-91 PMID:23446421
  • Sun, F, Ding, Y, Ji, Q, Liang, Z, Deng, X, Wong, CC, Yi, C, Zhang, L, Xie, S, Alvarez, S, Hicks, LM, Luo, C, Jiang, H, Lan, L, He, C (2012) Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance. Proc. Natl. Acad. Sci. U.S.A. 109 15461-6 PMID:22927394
  • São-José, C, Lhuillier, S, Lurz, R, Melki, R, Lepault, J, Santos, MA, Tavares, P (2006) The ectodomain of the viral receptor YueB forms a fiber that triggers ejection of bacteriophage SPP1 DNA. J. Biol. Chem. 281 11464-70 PMID:16481324
  • Tao, P, Mahalingam, M, Marasa, BS, Zhang, Z, Chopra, AK, Rao, VB (2013) In vitro and in vivo delivery of genes and proteins using the bacteriophage T4 DNA packaging machine. Proc. Natl. Acad. Sci. U.S.A. 110 5846-51 PMID:23530211
  • Taylor, PL, Rossi, L, De Pascale, G, Wright, GD (2012) A forward chemical screen identifies antibiotic adjuvants in Escherichia coli. ACS Chem. Biol. 7 1547-55 PMID:22698393
  • Toprak, E, Veres, A, Michel, JB, Chait, R, Hartl, DL, Kishony, R (2012) Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat. Genet. 44 101-5 PMID:22179135
  • Traxler, MF, Zacharia, VM, Marquardt, S, Summers, SM, Nguyen, HT, Stark, SE, Conway, T (2011) Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the 'feast to famine' gradient in Escherichia coli. Mol. Microbiol. 79 830-45 PMID:21299642
  • Xiao, Y, Gerth, K, Müller, R, Wall, D (2012) Myxobacterium-produced antibiotic TA (myxovirescin) inhibits type II signal peptidase. Antimicrob. Agents Chemother. 56 2014-21 PMID:22232277
  • Xiao, Y, Wall, D (2014) Genetic redundancy, proximity, and functionality of lspA, the target of antibiotic TA, in the Myxococcus xanthus producer strain. J. Bacteriol. 196 1174-83 PMID:24391051
  • Xu, J, Hendrix, RW, Duda, RL (2014) Chaperone-protein interactions that mediate assembly of the bacteriophage lambda tail to the correct length. J. Mol. Biol. 426 1004-18 PMID:23911548
  • Yamaichi, Y, Bruckner, R, Ringgaard, S, Möll, A, Cameron, DE, Briegel, A, Jensen, GJ, Davis, BM, Waldor, MK (2012) A multidomain hub anchors the chromosome segregation and chemotactic machinery to the bacterial pole. Genes Dev. 26 2348-60 PMID:23070816
  • Yang, G, Dowling, AJ, Gerike, U, ffrench-Constant, RH, Waterfield, NR (2006) Photorhabdus virulence cassettes confer injectable insecticidal activity against the wax moth. J. Bacteriol. 188 2254-61 PMID:16513755
  • Yao, Z, Davis, RM, Kishony, R, Kahne, D, Ruiz, N (2012) Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 109 E2561-8 PMID:22908292
  • Yardimci, H, Wang, X, Loveland, AB, Tappin, I, Rudner, DZ, Hurwitz, J, van Oijen, AM, Walter, JC (2012) Bypass of a protein barrier by a replicative DNA helicase. Nature 492 205-9 PMID:23201686
  • Zhang, Y, Xiang, Y, Van Etten, JL, Rossmann, MG (2007) Structure and function of a chlorella virus-encoded glycosyltransferase. Structure 15 1031-9 PMID:17850743

Subcategories

This category has the following 4 subcategories, out of 4 total.

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