Graduate Student Publications and Awards

Graduate Students names are shown in bold



Brum, J. R., J. C. Ignacio-Espinoza, E. H. Kim, G. Trubl, R. M. Jones, S. Roux, N. C. VerBerkmoes, V. I. Rich and M. B. Sullivan (2016). "Illuminating structural proteins in viral "dark matter" with metaproteomics." Proc Natl Acad Sci U S A 113(9): 2436-2441.

Douglass, J.F., M. Radosevich, and O.H. Tuovinen (2016). “Atrazine biomineralization and molecular analysis of atrazine-degrading bacteria and catabolic genes in a former pesticide mixing site and a machinery washing area.” J Soils Sedim 16(9): 2263–2274.

Fleming, I. M., Z. Paris, K. W. Gaston, R. Balakrishnan, K. Fredrick, M. A. Rubio and J. D. Alfonzo (2016). "A tRNA methyltransferase paralog is important for ribosome stability and cell division in Trypanosoma brucei." Sci Rep 6: 21438.

Garfoot, A. L. and C. A. Rappleye (2016). "Histoplasma capsulatum surmounts obstacles to intracellular pathogenesis." FEBS J 283(4): 619-633.

Garfoot, A. L., Q. Shen, M. Wuthrich, B. S. Klein and C. A. Rappleye (2016). "The Eng1 beta-Glucanase Enhances Histoplasma Virulence by Reducing beta-Glucan Exposure." MBio 7(2): e01388-01315.

Katz, A., S. Elgamal, A. Rajkovic and M. Ibba (2016). "Non-canonical roles of tRNAs and tRNA mimics in bacterial cell biology." Mol Microbiol 101(4): 545-558.

Lopes, R. R., O. Silveira Gde, R. Eitler, R. S. Vidal, A. Kessler, S. Hinger, Z. Paris, J. D. Alfonzo and C. Polycarpo (2016). "The essential function of the Trypanosoma brucei Trl1 homolog in procyclic cells is maturation of the intron-containing tRNATyr." RNA 22(8): 1190-1199.

Natarajan, G., S. Oghumu, C. Terrazas, S. Varikuti, J. C. Byrd and A. R. Satoskar (2016). "A Tec kinase BTK inhibitor ibrutinib promotes maturation and activation of dendritic cells." Oncoimmunology 5(6): e1151592.

Natarajan, G., C. Terrazas, S. Oghumu, S. Varikuti, J. A. Dubovsky, J. C. Byrd and A. R. Satoskar (2016). "Ibrutinib enhances IL-17 response by modulating the function of bone marrow derived dendritic cells." Oncoimmunology 5(1): e1057385.

Solden, L., K. Lloyd and K. Wrighton (2016). "The bright side of microbial dark matter: lessons learned from the uncultivated majority." Curr Opin Microbiol 31: 217-226.

Trubl, G., N. Solonenko, L. Chittick, S. A. Solonenko, V. I. Rich and M. B. Sullivan (2016). "Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient." PeerJ 4: e1999.

Walker, M. A., K. P. Mohler, K. W. Hopkins, D. H. Oakley, D. A. Sweetser, M. Ibba, M. P. Frosch and R. L. Thibert (2016). "Novel Compound Heterozygous Mutations Expand the Recognized Phenotypes of FARS2-Linked Disease." J Child Neurol 31(9): 1127-1137.

Ying, L. and K. Fredrick (2016). "Epistasis analysis of 16S rRNA ram mutations helps define the conformational dynamics of the ribosome that influence decoding." RNA 22(4): 499-505.



Douglass, J.F., M. Radosevich, and O.H. Tuovinen (2015). “Molecular analysis of atrazine-degrading bacteria and catabolic genes in the water column and sediment of a constructed wetland in an agricultural watershed.” Ecol Eng 83: 405-412.

Carver, S.M., M.C. Nelson, Z. Yu, and O.H. Tuovinen (2015). “Fermentative metabolism of an anaerobic, thermophilic consortium on mono- and disaccharides, plant polymers, and commercial paper samples.” Biomass Bioenergy 75: 11-22. 

Simpson, B.W., May, J.M., Sherman, D.J., Kahne, D., Ruiz, N. (2015). Lipopolysaccharide transport to the cell surface: biosynthesis and extraction from the inner membrane. Phil Trans R Soc B 370:20150029.

May, J.M., Sherman, D.J., Simpson, B.W., Ruiz, N., Kahne, D. (2015). Lipopolysaccharide transport to the cell surface periplasmic transport and assembly into the outer membrane. Phil Trans R Soc B 370:20150027.

Bayer, A., E. Delorme-Axford, C. Sleigher, T. K. Frey, D. W. Trobaugh, W. B. Klimstra, L. A. Emert-Sedlak, T. E. Smithgall, P. R. Kinchington, S. Vadia, S. Seveau, J. P. Boyle, C. B. Coyne and Y. Sadovsky (2015). "Human trophoblasts confer resistance to viruses implicated in perinatal infection." Am J Obstet Gynecol 212(1): 71 e71-78.

Bhattacharya, M., D. J. Wozniak, P. Stoodley and L. Hall-Stoodley (2015). "Prevention and treatment of Staphylococcus aureus biofilms." Expert Rev Anti Infect Ther 13(12): 1499-1516.

Brum, J. R., J. C. Ignacio-Espinoza, S. Roux, G. Doulcier, S. G. Acinas, A. Alberti, S. Chaffron, C. Cruaud, C. de Vargas, J. M. Gasol, G. Gorsky, A. C. Gregory, L. Guidi, P. Hingamp, D. Iudicone, F. Not, H. Ogata, S. Pesant, B. T. Poulos, S. M. Schwenck, S. Speich, C. Dimier, S. Kandels-Lewis, M. Picheral, S. Searson, C. Tara Oceans, P. Bork, C. Bowler, S. Sunagawa, P. Wincker, E. Karsenti and M. B. Sullivan (2015). "Ocean plankton. Patterns and ecological drivers of ocean viral communities." Science 348(6237): 1261498.

Carter, M. S. and B. E. Alber (2015). "Transcriptional Regulation by the Short-Chain Fatty Acyl Coenzyme A Regulator (ScfR) PccR Controls Propionyl Coenzyme A Assimilation by Rhodobacter sphaeroides." J Bacteriol 197(19): 3048-3056.

Caserta, E., L. C. Liu, F. J. Grundy and T. M. Henkin (2015). "Codon-Anticodon Recognition in the Bacillus subtilis glyQS T Box Riboswitch: RNA-DEPENDENT CODON SELECTION OUTSIDE THE RIBOSOME." J Biol Chem 290(38): 23336-23347.

Furman, R., E. M. Danhart, M. NandyMazumdar, C. Yuan, M. P. Foster and I. Artsimovitch (2015). "pH dependence of the stress regulator DksA." PLoS One 10(3): e0120746.

Gerst, M. M., E. Huang, L. Zhang and A. E. Yousef (2015). "Development of a New Paenibacillin-Producing Strain and Testing its Usability in Improving Food Safety." J Food Sci 80(7): M1538-1543.

Goughenour, K. D., J. M. Balada-Llasat and C. A. Rappleye (2015). "Quantitative Microplate-Based Growth Assay for Determination of Antifungal Susceptibility of Histoplasma capsulatum Yeasts." J Clin Microbiol 53(10): 3286-3295.

Liu, L. C., F. J. Grundy and T. M. Henkin (2015). "Non-Conserved Residues in Clostridium acetobutylicum tRNA(Ala) Contribute to tRNA Tuning for Efficient Antitermination of the alaS T Box Riboswitch." Life (Basel) 5(4): 1567-1582.

Liu, Z. and I. Artsimovitch (2015). "Mapping the Escherichia coli transcription elongation complex with exonuclease III." Methods Mol Biol 1276: 1-12.

Lopes, R. R., A. C. Kessler, C. Polycarpo and J. D. Alfonzo (2015). "Cutting, dicing, healing and sealing: the molecular surgery of tRNA." Wiley Interdiscip Rev RNA 6(3): 337-349.

NandyMazumdar, M. and I. Artsimovitch (2015). "Ubiquitous transcription factors display structural plasticity and diverse functions: NusG proteins - Shifting shapes and paradigms." Bioessays 37(3): 324-334.

Oghumu, S., J. C. Stock, S. Varikuti, R. Dong, C. Terrazas, J. A. Edwards, C. A. Rappleye, A. Holovatyk, A. Sharpe and A. R. Satoskar (2015). "Transgenic expression of CXCR3 on T cells enhances susceptibility to cutaneous Leishmania major infection by inhibiting monocyte maturation and promoting a Th2 response." Infect Immun 83(1): 67-76.

Oghumu, S., C. A. Terrazas, S. Varikuti, J. Kimble, S. Vadia, L. Yu, S. Seveau and A. R. Satoskar (2015). "CXCR3 expression defines a novel subset of innate CD8+ T cells that enhance immunity against bacterial infection and cancer upon stimulation with IL-15." FASEB J 29(3): 1019-1028.

Sample, P. J., K. W. Gaston, J. D. Alfonzo and P. A. Limbach (2015). "RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids." Nucleic Acids Res 43(10): e64.

Sample, P. J., L. Koreny, Z. Paris, K. W. Gaston, M. A. Rubio, I. M. Fleming, S. Hinger, E. Horakova, P. A. Limbach, J. Lukes and J. D. Alfonzo (2015). "A common tRNA modification at an unusual location: the discovery of wyosine biosynthesis in mitochondria." Nucleic Acids Res 43(8): 4262-4273.

Terrazas, C., S. Oghumu, S. Varikuti, D. Martinez-Saucedo, S. M. Beverley and A. R. Satoskar (2015). "Uncovering Leishmania-macrophage interplay using imaging flow cytometry." J Immunol Methods 423: 93-98.

Tuladhar, R., S. Oghumu, R. Dong, A. Peterson, A. H. Sharpe and A. R. Satoskar (2015). "Ox40L-Ox40 pathway plays distinct roles in regulating Th2 responses but does not determine outcome of cutaneous leishmaniasis caused by Leishmania mexicana and Leishmania major." Exp Parasitol 148: 49-55.

Turan, E., Y. Yesilova, H. A. Surucu, N. Ardic, N. Doni, M. Aksoy, A. Yesilova, S. Oghumu, S. Varikuti and A. R. Satoskar (2015). "A Comparison of Demographic and Clinical Characteristics of Syrian and Turkish Patients with Cutaneous Leishmaniasis." Am J Trop Med Hyg 93(3): 559-563.

Williams-Wagner, R. N., F. J. Grundy, M. Raina, M. Ibba and T. M. Henkin (2015). "The Bacillus subtilis tyrZ gene encodes a highly selective tyrosyl-tRNA synthetase and is regulated by a MarR regulator and T box riboswitch." J Bacteriol 197(9): 1624-1631.



Douglass, J.F., M. Radosevich, and O.H. Tuovinen (2014). “Mineralization of atrazine in the river water intake and sediments of a constructed flow-through wetland.” Ecol Eng 72: 35-39. 

Arnett, E., S. Vadia, C. C. Nackerman, S. Oghumu, A. R. Satoskar, K. R. McLeish, S. M. Uriarte and S. Seveau (2014). "The pore-forming toxin listeriolysin O is degraded by neutrophil metalloproteinase-8 and fails to mediate Listeria monocytogenes intracellular survival in neutrophils." J Immunol 192(1): 234-244.

Balakrishnan, R., K. Oman, S. Shoji, R. Bundschuh and K. Fredrick (2014). "The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli." Nucleic Acids Res 42(21): 13370-13383.

Bullwinkle, T. J., N. M. Reynolds, M. Raina, A. Moghal, E. Matsa, A. Rajkovic, H. Kayadibi, F. Fazlollahi, C. Ryan, N. Howitz, K. F. Faull, B. A. Lazazzera and M. Ibba (2014). "Oxidation of cellular amino acid pools leads to cytotoxic mistranslation of the genetic code." Elife 3.

Dare, K., J. Shepherd, H. Roy, S. Seveau and M. Ibba (2014). "LysPGS formation in Listeria monocytogenes has broad roles in maintaining membrane integrity beyond antimicrobial peptide resistance." Virulence 5(4): 534-546.

Deng, L., J. C. Ignacio-Espinoza, A. C. Gregory, B. T. Poulos, J. S. Weitz, P. Hugenholtz and M. B. Sullivan (2014). "Viral tagging reveals discrete populations in Synechococcus viral genome sequence space." Nature 513(7517): 242-245.

Elgamal, S., A. Katz, S. J. Hersch, D. Newsom, P. White, W. W. Navarre and M. Ibba (2014). "EF-P dependent pauses integrate proximal and distal signals during translation." PLoS Genet 10(8): e1004553.

Garfoot, A. L., O. Zemska and C. A. Rappleye (2014). "Histoplasma capsulatum depends on de novo vitamin biosynthesis for intraphagosomal proliferation." Infect Immun 82(1): 393-404.

Hersch, S. J., S. Elgamal, A. Katz, M. Ibba and W. W. Navarre (2014). "Translation initiation rate determines the impact of ribosome stalling on bacterial protein synthesis." J Biol Chem 289(41): 28160-28171.

Katz, A., L. Solden, S. B. Zou, W. W. Navarre and M. Ibba (2014). "Molecular evolution of protein-RNA mimicry as a mechanism for translational control." Nucleic Acids Res 42(5): 3261-3271.

Malinen, A. M., M. Nandymazumdar, M. Turtola, H. Malmi, T. Grocholski, I. Artsimovitch and G. A. Belogurov (2014). "CBR antimicrobials alter coupling between the bridge helix and the beta subunit in RNA polymerase." Nat Commun 5: 3408.

Moghal, A., K. Mohler and M. Ibba (2014). "Mistranslation of the genetic code." FEBS Lett 588(23): 4305-4310.

Oghumu, S., A. Bracewell, U. Nori, K. H. Maclean, J. M. Balada-Lasat, S. Brodsky, R. Pelletier, M. Henry, A. R. Satoskar, T. Nadasdy and A. A. Satoskar (2014). "Acute pyelonephritis in renal allografts: a new role for microRNAs?" Transplantation 97(5): 559-568.

Oghumu, S., G. Gupta, H. M. Snider, S. Varikuti, C. A. Terrazas, T. L. Papenfuss, M. H. Kaplan and A. R. Satoskar (2014). "STAT4 is critical for immunity but not for antileishmanial activity of antimonials in experimental visceral leishmaniasis." Eur J Immunol 44(2): 450-459.

Oghumu, S., S. Varikuti, C. Terrazas, D. Kotov, M. W. Nasser, C. A. Powell, R. K. Ganju and A. R. Satoskar (2014). "CXCR3 deficiency enhances tumor progression by promoting macrophage M2 polarization in a murine breast cancer model." Immunology 143(1): 109-119.

Rajaram, M. V., B. Ni, C. E. Dodd and L. S. Schlesinger (2014). "Macrophage immunoregulatory pathways in tuberculosis." Semin Immunol 26(6): 471-485.

Ticak, T., D. J. Kountz, K. E. Girosky, J. A. Krzycki and D. J. Ferguson, Jr. (2014). "A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase." Proc Natl Acad Sci U S A 111(43): E4668-4676.

Vadia, S. and S. Seveau (2014). "Fluxes of Ca2+ and K+ are required for the listeriolysin O-dependent internalization pathway of Listeria monocytogenes." Infect Immun 82(3): 1084-1091.

Awards and Fellowships

Garrett Smith, graduate student with Dr. Wrighton's lab, received an NSF Graduate Fellowship for the 2016-2017 academic year.

Gabriel Silveira d'Almeida, graduate student with Dr. Alfonzo's lab, received the 2016-2017 academic year RNA Fellowship Award from the Center for RNA Biology.

Andrew Garfoot, graduate student with Dr. Rappleye's lab, received NSF Fellowship for the 2015-2016 academic year.

Jenna Antonucci, graduate student with Dr. Li Wu's lab, received an HHMI Fellowship for the 2014-2015 academic year.

Claire Dodd, graduate student with Dr. Larry Schlesinger's lab, received an HHMI Fellowship for the 2014-2015 academic year.

Kyle Mohler, graduate student with Dr. Mike Ibba's lab, received the 2014-2015 academic year RNA Fellowship Award from the Center for RNA Biology.

Mike Allen, graudate student with Dr. Tina Henkin's lab, received the 2013-2014 academic year RNA Fellowship Award from the Center for RNA Biology.