Graduate Student Publication and Award Archive

Past Publications


2010

Carver SM, Lepistö R, & Tuovinen OH (2010) Hydrolysis and metabolism of cellulose by an anaerobic, thermophilic consortium. In: Proceedings of the Third Conference on Energy from Biomass and Waste. International Waste Working Group, CISA – Environmental Sanitary Engineering Centre, Padova, Italy, Paper 436, 9 p

Gonalez-Escobedo G, Marshall JM & Gunn GS. (2010) Chronic and acute infection of the gallbladder by Salmonella Typhi: understanding the carrier state. Nat Rev Microbiol. PMID: 21113180.

Godinic-Mikulcic V, Jaric J, Hausmann CD, Ibba M & Weygand-Durasevic I. (2010) An archaeal tRNA-synthetase complex that enhances aminoacylation under extreme conditions. J. Biol. Chem. In Press.

Reynolds NM, Lazazzera BA & Ibba M. (2010) Cellular mechanisms that control mistranslation. Nat Rev Microbiol 8849-856.

Katz A, Banerjee R, de Armas M, Ibba M & Orellana O. (2010) Redox status affects the catalytic activity of glutamyl-tRNA synthetase. Biochem Biophys Res Comm 398, 51-55.

Goltermann L, Larsen MSY, Banerjee R, Joerger AC, Ibba M & Bentin T. (2010) Protein evolution via amino acid and codon elimination. PLoSOne 5, e10104.

Sevostyanova A & Artsimovitch I (2010) Functional analysis of Thermus thermophilus transcription factor NusG. Nucleic Acids Res. 38, 7432-7445. PMID: 20639538.

Crawford RW, Gonzalez-Escobedo G & Gunn JS (2010) Salmonella Biofilms: From Food to Human Disease, In Salmonella enterica: From Genome to Function, Horizon Scientific Press, S. Porwollik, ed. (in press)

Rajaram MV, Brooks MN, Morris JD, Torrelles JB, Azad AK & Schlesinger LS (2010) Mycobacterium tuberculosis Activates Human Macrophage Peroxisome Proliferator-Activated Receptor {gamma} Linking Mannose Receptor Recognition to Regulation of Immune Responses. J. Immunol. [Epub ahead of print] PMID: 20554962.

Laguna R, Joshi GS, Dangel AW, Luther AK & Tabita FR (2010) Integrative control of carbon, nitrogen, hydrogen, and sulfur metabolism: the central role of the calvin-benson-bassham cycle. Adv. Exp. Med. Biol. 675, 265-271. PMID:20532746.

Pupov D, Miropolskaya N, Sevostyanova A, Bass I, Artsimovitch I, Kulbachinskiy A (2010) Multiple roles of the RNA polymerase β' SW2 region in transcription initiation, promoter escape, and RNA elongation. Nucleic Acids Res38, 5784-5796. PMID: 20457751.

Cummings HE, Tuladhar R, Satoskar AR. (2010) Cytokines and their STATs in cutaneous and visceral leishmaniasis. J. Biomed. Biotechnol. [Epub Mar 15]. PMID: 20300429.

Witte B, John D, Wawrik B, Paul JH, Dayan D & Tabita FR (2010) Functional prokaryotic RubisCO from an oceanic metagenomic library. Appl. Environ. Microbiol. 76, 2997-3003. PMID: 20228113.

Oghumu S, Lezama-Dávila CM, Isaac-Márquez AP, Satoskar AR (2010) Role of chemokines in regulation of immunity against leishmaniasis. Exp. Parasitol. [Epub ahead of print] PMID: 20206625.

Reynolds NM, Ling J, Roy H, Banerjee R, Repasky SE, Hamel P & Ibba M.(2010) Cell-specific differences in the requirements for translation quality control. Proc. Natl. Acad. Sc.i USA 107, 4063-4068. PMID: 20160120.

Belogurov GA, Sevostyanova A, Svetlov V & Artsimovitch I (2010) Functional regions of the N-terminal domain of the antiterminator RfaH. Mol. Microbiol. 76, 286-301. PMID: 20132437.

Dyszel JL,Soares JA, Swearingen MC, Lindsay A, Smith JN & Ahmer BM (2010) E. coli K-12 and EHEC Genes Regulated by SdiA. PLoS ONE 5, e8946. PMID: 20126629.

Smith AM, Fuchs RT & Henkin TM (2010) Riboswitch RNAs: Regulation of gene expression by direct monitoring of a physiological signal. RNA Biol. 7, 104-110.PMID: 20061810.

Singh J & Tabita FR (2010) Roles of RubisCO and the RubisCO-like protein in 5-methylthioadenosine metabolism in the Nonsulfur purple bacterium Rhodospirillum rubrum. J. Bacteriol. 192, 1324-1331. PMID: 20038587. 

Shoji S, Janssen BD, Hayes CS & Fredrick K (2010) Translation factor LepA contributes to tellurite resistance in Escherichia coli but plays no apparent role in the fidelity of protein synthesis. Biochimie 92, 157-163.PMID: 19925844.

Banerjee R, Chen S, Dare K, Gilreath M, Praetorius-Ibba M, Raina M, Reynolds NM, Rogers T, Roy H, Yadavalli SS, Ibba M (2010) tRNAs: cellular barcodes for aminoacids. FEBS Lett. 584, 387-395. PMID:19903480.

Green NR, Grundy FJ & Henkin TM (2010) The T box mechanism: tRNA as a regulatory molecule. FEBS Lett. 584, 318-324.

Dyszel JL, Smith JN, Lucas DE, Soares JA, Swearingen MC, Vross MA, Yong GM & Ahmer BM (2010) Salmonella enterica serovar Typhimurium can detect acyl homoserine lactone production by Yersinia enterocolitica in mice. J. Bacteriol. 192, 29-37.PMID: 19820103.


2009

Yadavalli SS, Klipcan L, Zozulya A, Banerjee R, Svergun D, Safro M, Ibba M (2009) Large-scale movement of functional domains facilitates aminoacylation by human mitochondrial phenylalanyl-tRNA synthetase. FEBS Lett. 583, 3204-3208. PMID: 19737557.

Ataide SF, Rogers TE, Ibba M (2009) The CCA anticodon specifies separate functions inside and outside translation in Bacillus cereus. RNA Biol. 6, 479-487. PMID: 19667754.

Barbi J, Snider, HM, Bhardwaj N, Durbin J & Satoskar AR (2009) STAT1 in CD4+ T cells plays an indispensable role in host resistance against cutaneous leishmaniasis caused by L. major by mediating recruitment of Th1 cells to site of infection. FASEB J. 23, 3990-3999. PMID: 19641143. 

Garza-Sánchez F, Shoji S, Fredrick K, & Hayes CS (2009) RNase II is important forA-site mRNA cleavage during ribosome pausing. Mol. Microbiol. 73, 882-97. PMID: 19627501.

Wohlgamuth-Benedum JM, Rubio MA, Paris Z, Long S, Poliak P, Lukes J & Alfonzo JD (2009) Thiolation controls cytoplasmic tRNA stability and acts as a negative determinant for tRNA editing in mitochondria. J. Biol. Chem. 284, 23947-23953.PMID: 19574216.

Ling J, Reynolds NM, Ibba M (2009) Aminoacyl-tRNA synthesis and translational quality control. Annu. Rev. Microbiol. 63, 61-78. PMID: 19379069.

Shoji S, Abdi NM, Bundschuh R & Fredrick K (2009) Contribution of ribosomal residues to P-site tRNA binding. Nucleic Acids Res. 37, 4033-4042.PMID: 19417061.

Joshi GS, Romagnoli S, VerBerkmoes NC, Hettich RL, Pelletier D & Tabita FR (2009) Differential accumulation of form I RubisCO in Rhodopseudomonas palustris CGA010 under photoheterotrophic growth conditions with reduced carbon sources. J. Bacteriol. 191, 4243-4250. PMID: 19376869.

Ling J, So BR, Yadavalli SS, Roy H, Shoji S, Fredrick K, Musier-Forsyth K, Ibba M (2009) Resampling and editing of mischarged tRNA prior to translation elongation. Mol. Cell. 33, 654-660. PMID: 19285947.

Blum JS, Han S, Lanoil B, Saltikov C, Witte B, Tabita FR, Langley S, Beveridge TJ, Jahnke L & Oremland RS (2009) Ecophysiology of Halarsenatibacter silvermanii strain SLAS-1T, gen. nov., sp. nov., a facultative chemo- autotrophic arsenate-respirer of the Halanaerobiales isolated from salt-saturated Searles Lake, California. Appl. Env. Microbiol. 75, 1950-1960. PMID: 19218420. 

Shoji S, Walker SE & Fredrick K (2009) Ribosomal Translocation: One Step Closer to the Molecular Mechanism. ACS Chem. Biol. 4, 93-107.PMID: 19173642. 

Qin D & Fredrick K (2009) Control of translation initiation involves a factor-induced rearrangement of helix 44 of 16S ribosomal RNA. Mol. Microbiol. 71, 1239-1249.PMID: 19154330.

Devaraj A, Shoji S, Holbrook ED & Fredrick K (2009) A role for the 30S subunit E site in maintenance of the translational reading frame. RNA 15, 255-265. PMID: 19095617.

Li WT, Mahapatra A, Longstaff DG, Bechtel J, Zhao G, Kang, PT, Chan MK & Krzycki JA (2009) Specificity of pyrrolysyl-tRNA synthetase for pyrrolysine and pyrrolysine analogs. J. Mol. Biol. 385, 1156-1164. PMID: 19063902.

Roy H, Dare K and Ibba M (2009) Adaptation of the bacterial membrane to changing environments using aminoacylated phospholipids. Mol. Microbiol. 71, 547-550. PMID: 19054327.

Ferguson T, Soares JA, Lienard T, Gottschalk G & Krzycki JA (2009) RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea. J. Biol. Chem. 284, 2285-95.PMID: 19043046

Roth, KM, Gunn JS, Lafuse, W & Satoskar AR (2009) Francisella inhibits STAT1-mediated signaling in macrophages and prevents activation of antigen-specific T cells. Int. Immunol. 21, 19. PMID: 19001470.

Martin J, Duncan FJ, Keiser T, Shin S, Kusewitt D, Oberyszyn T, Satoskar AR & VanBuskirk AM (2009) Macrophage migration inhibitory factor (MIF) plays a critical role in pathogenesis of ultraviolet-B (UVB) induced non-melanoma skin cancer (NMSC). FASEB J. 23, 720-730. PMID: 18952710.

Belogurov GA, Vassylyeva MN, Sevostyanova A, Appleman JR, Xiang AX, Lira R, Webber SE, Klyuyev S, Nudler E, Artsimovitch I& Vassylyev DG (2009) Transcription inactivation through local refolding of the RNA polymerase structure. Nature 457, 332-335. PMID: 18946472.


Past Awards

Sean McClory, an OSBP post-doctoral student in the Kurt Fredrick lab, won an RNA Biology Institute Graduate Fellowship (2011). We congratulate Sean on becoming an RNA fellow and Kurt Fredrick, Ph. D on mentoring an excellent student. We are sure that Sean will help us to understand the ribosome much better in the near future. Good luck!

Sarah Carver was invited to attend a course/workshop on biofuels called The Advanced Course on Biochemistry of Biofuels in Ubatuba, São Paulo (Brazil). It was a worldwide application process that is jointly sponsored by the American, International and Brazilian Societies for Biochemistry and Molecular Biology (ASBMB, IUBMB and SBBq). Contratulations, Sarah!

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