Biochemistry and Molecular Biology
Penn State Science
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2014

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Publications
Biochemistry and Molecular Biology Faculty
2014

 

  • El-Mowafi, S.A., J. N. Alumasa, S. E. Ades, and K. C. Keiler.  A cell-based assay to identify inhibitors of the Hfq-sRNA regulatory pathway.  Antimicrob. Agents Chemother. 58:5500-5509.
  • Gopalkrishnan, S., H. Nicoloff, and S. E. Ades.  Coordinated regulation of the extracytoplasmic stress factor, sigmaE, with other Escherichia coli sigma factors by (p)ppGpp and DksA may be achieved by specific regulation of individual holoenzymes.  Mol. Microbiol. 93:479-493.
  • Pena-Francesch, A., S. Florez, H. Jung, A. Sebastian, I. Albert, W. Curtis, and M. C. Demirel.  Materials fabrication from native and recombinant thermoplastic squid proteins.  Adv. Funct. Mater. 24:7401-7409.
  • Maalouf, S. W., W.-S. Liu, I. Albert, and J. L. Pate.  Regulating life or death: Potential role of microRNA in rescue of the corpus luteum.  Mol. Cell. Endocrinol. 398:78-88.
  • Ooi, J. H, A. Waddell, Y.-D. Lin, I. Albert, L. T. Rust, V. Holden, and M. T. Cantorna.  Dominant effects of the diet on the microbiome and the local and systemic immune response in mice.  Plos One 9:e86366.
  • Liermann, L. J., I. Albert, H. L. Buss, M. Minyard, and S. L. Brantley.  Relating microbial community structure and geochemistry in deep regolith developed on volcaniclastic rock in the Luquillo Mountains, Puerto Rico.  Geomicrobiology J. DOI:10.1080/01490451.2014.964885.
  • Yakhnin, A. V. and P. Babitzke.  NusG/Spt5:  are there universal functions of this ubiquitously conserved transcription elongation factor?  Curr. Opin. Microbiol. 16:68-71.
  • Vakulskas, C. A., A. Pannuri, D. Cortés-Selva, P. Babitzke, and T. Romeo.  Global effects of the DEAD-box RNA helicase DeaD (CsdA) on gene expression over a broad range of temperatures.  Mol. Microbiol. 92:945-958.
  • Parnell, E. J., Y. Yu, R. Lucena, Y. Yoon, L. Bai, D. R. Kellogg, and D. J. Stillman.  The Rts1 regulatory subunit of PP2A phosphatase controls expression of the HO endonuclease via localization of the Ace2 transcription factor.  J. Biol. Chem. 289:35431-35437.
  • Silakov, A., T. L. Grove, M. I. Radle, M. R. Bauerle, M. T. Green, A. C. Rosenzweig, A. K. Boal, and S. J. Booker.  Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN.  J. Am. Chem. Soc. 136:8221-8228.
  • Chang, W.-c., Y. Guo, C. Wang, S. E. Butch, A. C. Rosenzweig, A. K. Boal, C. Krebs, J. M. Bollinger, Jr.  Mechanism of the C5 stereoinversion reaction in the biosynthesis of carbapenem antibiotics.  Science 343:1140-1144.
  • Makhlynets, O., A. K. Boal, D. Rhodes, T. Kitten, A. C. Rosenzweig, and J. Stubbe.   Streptococcus sanguinis class Ib ribonucleotide reductase: high activity with both iron and manganese cofactors and structural insights.  J. Biol. Chem. 289:6259-6272.
  • Chang, W.-c., Y. Guo, C. Wang, S. E. Butch, A. C. Rosenzweig, A. K. Boal, C. Krebs, J. M. Bollinger, Jr. Mechanism of the C5 stereoinversion reaction in the biosynthesis of carbapenem antibiotics.  Science 343:1140-1144.
  • Matthews, M. L., W.-c. Chang, A. P. Layne, L. A. Miles, C. Krebs, and J. M. Bollinger, Jr. Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase.  Nat. Chem. Biol. 10:209-215.
  • Silakov, A., T. L. Grove, M. I. Radle, M. R. Bauerle, M. T. Green, A. C. Rosenzweig, A. K. Boal, and S. J. Booker.  Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN.  J. Am. Chem. Soc. 136:8221-8228.
  • Lanz, N. D., M. E. Pandelia, E. S. Kakar, K.-H. Lee, C. Krebs, and S. J. Booker.  Evidence for a catalytically and kinetically competent enzyme-substrate cross-linked intermediate in catalysis by lipoyl synthase.  Biochemistry 53:4557-4572.
  • Lanz, N. D. and S. J. Booker.  The role of iron-sulfur clusters in the biosynthesis of the lipoyl cofactor.  In: Iron-Sulfur Clusters in Chemistry and Biology.  (T. Rouault, ed.), pp. 211-238, Walter De Gruyter Inc.
  • Niedzwiedzki, D. M., G. S. Orf, M. Tank, K. Vogl, D. A. Bryant, and R. E. Blankenship.  Photophysical properties of the excited states of bacteriochlorophyll f in solvents and in chlorosomes.  J. Phys. Chem. B 118:2295-2305.
  • Stolyar, S., Z. Liu, V. Thiel, L. P. Tomsho, N. Pinel, W. Nelson, S. Lindemann, M. Romine, S. Haruta, S. C. Schuster, D. A. Bryant, and J. K. Frederickson.  Genome sequence of the thermophilic cyanobacterium Thermosynechococcus sp. strain NK55a.  genomeA 2:e01060-13.
  • Miloslavina, Y., K. B. S. Sankar Gupta, M. Tank, D. A. Bryant, and H. J. M. de Groot. wPMLG-5 spectroscopy of self-aggregated BChl e in natural chlorosomes of Chlorobaculum limnaeum.  Israel J. Chem. 54:147-153.
  • Beliaev, A. S., M. Serres, B. E. Linggi, L. M. Markille, N. G. Isern, W. B. Chrisler, L. A. Kucek, E. A. Hill, G. E. Pinchuk, D. A. Bryant, H. S. Wiley, M. F. Romine, J. K. Frederickson, and A. Konopka.  Interactions between cyanobacteria and heterotrophs under different trophic conditions.  ISME J. 8:2243-2255.
  • Hartzler, D., D. M. Niedzwiedzki, D. A. Bryant, R. E. Blankenship, Y. Pushkar, and S. Savikhin.  Triplet excited state energies and phosphorescence spectra of (bacterio)chlorophylls.  J. Phys. Chem. Part B 118:7221-7232.
  • Hamilton, T. L., R. J. Bovee, V. Thiel, S. R. Sattin, W. Mohr, I. Schaperdoth, W. P. Gillhooly, 3rd, T. W. Lyons, L. P. Tomsho, S. C. Schuster, J. Overmann, D. A. Bryant, A. Pearson, and J. L. Macalady.  Coupled reductive and oxidative sulfur cycling in the phototrophic plate of a meromictic lake.  Geobiology 12:451-468.
  • Zhang, S., Z. Li, G. Shen, J. H. Golbeck, and D. A. Bryant.  Vipp1 in Synechococcus sp. PCC 7002 is not essential but is required for photosystem I assembly.  J. Biol. Chem. 289:15904-15910.
  • Ludwig, M., M.-E. Pandelia, C. Y. Chew, B. Zhang, J. H. Golbeck, C. Krebs, and D. A. Bryant.  ChlR protein of Synechococcus sp. PCC 7002 is a transcription activator that uses an oxygen-sensitive [4Fe-4S] cluster to control genes involved in pigment biosynthesis.  J. Biol. Chem. 289:16624-16639.
  • Sinninghe Damsté, J., W. I. C. Rijpstra, E. C. Hopmans, B. U. Foesel, P. K. Wüst, J. Overmann, M. Tank, D. A. Bryant, P. F. Dunfield, and M. B. Stott.  Ether- and ester-bound iso-diabolic acid and other lipids in Acidobacterium of subdivision 4.  Appl. Environ. Microbiol. 80:5207-5218.
  • Konopka, A., H. C. Bernstein, M. R. Melnicki, E. A. Hill, L. A. Kucek, G. Shen, D. A. Bryant, S. Zhang, G. Shen, and A. S. Beliaev.  Effect of mono- and dichromatic light quality on growth rates and photosynthetic performance of Synechococcus sp. PCC 7002.  Front. Microbio. 5:488.
  • Gan, F., S. Zhang, N. C. Rockwell, S. S. Martin, J. C. Lagarias, and D. A. Bryant.  Extensive remodeling of a cyanobacterial photosynthetic apparatus in far-red light.  Science 345:1312-1317.
  • Therien, J. B., O. Zadvornyy, M. C. Posewitz, D. A. Bryant, and J. W. Peters.  Growth of Chlamydomonas reinhardtii in acetate-free medium when co-cultured with alginate-encapsulated strains of Synechococcus sp. PCC 7002.  Biotech. Biofuels. 7:154.
  • Zhang, S. and D. A. Bryant.  Learning new tricks from an old cycle: the TCA cycle of cyanobacteria, algae and plants.  Perspect. Phycol. 1:73-86.
  • Thiel, V., L. P. Tomsho, R. Burhans, S. E. Gay, R. F. Ramaley, S. C. Schuster, L. Steinke, and D. A. Bryant.  Draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone) (Bacteroidetes).  genomeA 2:e00860-14.
  • Thiel, V., L. P. Tomsho, R. Burhans, S. C. Schuster, and D. A. Bryant.  Draft genome of a sulfide-oxidizing, autotrophic Chloroflexus sp. strain MS-G (Yellowstone National Park, WY). genomeA 2:e00872-14.
  • Bryant, D. A. A brief history of cyanobacterial research: past, present and future prospects…   In:  The Cell Biology of Cyanobacteria, (A. Herrero and E. Flores, eds.), pp. 1-5, Caister Academic Press, Norfolk, UK.
  • Alphonse, S., J. J. Arnold, S. Bhattacharya, H. Wang, B. Kloss, C. E. Cameron, and R. Ghose.  Cystoviral polymerase complex protein P7 uses its acidic C-terminal tail to regulate the RNA-directed RNA polymerase P2.  J. Mol. Biol. 426:2580-2593.
  • Liu, Y. C., R. L. Kuo, J. Y. Lin, P. N. Huang, H. Liu, J. J. Arnold, S. J. Chen, R. Y. Wang, C. E.  Cameron, and S. R. Shih.  Cytoplasmic viral RNA-dependent RNA polymerase disrupts the intracellular splicing machinery by entering the nucleus and interfering with Prp8.  PLoS Pathog. 10:e1004199.
  • Cordek, D. G., T. J. Croom-Perez, J. Hwang, M. R. S. Hargittai, C. V. Subba-Reddy, Q. Han, M. F. Lodeiro, G. Ning, T. S. McCrory, J. J. Arnold, H. Koc, B. D. Lindenbach, S. A. Showalter,  and C. E. Cameron.  PKA phosphorylation near a polyproline-II motif in HCV NS5A induces and SH3-binding conformation important for viral replication.  J. Biol. Chem. 289:24397-24416.
  • Korboukh, V. K., C. A. Lee, M. Vignuzzi, J. J. Arnold, S. Hemperly, J. D. Graci, A. August, R. Andino, and C. E. Cameron.  RNA population diversity: An optimum for maximal fitness and virulence.  J. Biol. Chem. 289:29531-29544.
  • Li, S., F. Guo, Y. Chen, X. Ding, P. Li, C. E. Cameron, and T. J. Huang.  Standing surface acoustic wave (SSAW)-based cell co-culture.  Anal. Chem. 86:9853-9859.
  • Zafar, M. K., A. Ketkar, M. F. Lodeiro, C. E. Cameron, and R. L. Eoff.  Kinetic analysis of human PrimPol DNA polymerase activity reveals generally error-prone enzyme capable of accurately bypassing 7,8-dihydro-8-oxo-2'-deoxyguanosine.  Biochemistry 53:6584-6594.
  • Moustafa, I. M., V. K. Korboukh, J. J. Arnold, E. D. Smidansky, L. L. Marcotte, D. W. Gohara, X. Yang, M. A. Sanchez-Farran, D. Filman, J. K. Maranas, D. D. Boehr, J. M. Hogle, C. M. Colina, and C. E. Cameron.  Structural dynamics as a contributor to error-prone replication by a RNA-dependent RNA polymerase.  J. Biol. Chem. 289:36229-36248.
  • Yang, S., D. Slotcavage, J. D., Mai, F. Guo, S. Li, Y. Zhao, Y. Lei, C. E. Cameron, and T. J. Huang.  Electrochemically created highly surface roughened Ag nanoplate arrays for SERS biosensing applications.  J. Mater. Chem. C 2:8350-8356.
  • Boehr, D. D., J. J. Arnold, I. M. Moustafa, and C. E. Cameron.  Structure, dynamics and fidelity of RNA-dependent RNA polymerases.  In: Nucleic Acid Polymerases. (K. S. Murakami and M. A. Trakselis, eds.), pp. 309-333, Springer, Heidelberg, Germany.
  • Dey, K. K., S. Das, M. F. Poyton, S. Sengupta, P. Butler, P. S. Cremer, and A. Sen.  Chemotactic separation of enzymes.  ACS Nano 8:11841-11949.
  • Jungwirth, P. and P. S. Cremer.  Beyond Hofmester.  Nature Chem. 6:261-263.
  • Suharti, S., M. Wang, S. de Vries, and J. G. Ferry.  Characterization of the RnfB and RnfG subunits of the Rnf complex from the archaeon Methanosarcina acetivorans.  PLoS One 9:e97966.
  • Ayayee, P, C. Rosa, J. G. Ferry, G. Felton, M. Saunders, and K. Hoover.  Gut microbes contribute to nitrogen provisioning in a wood-feeding cerambycid. Environ. Entomol. 43:903-912.
  • Guan, Y, D. Ngugi, J. Blom, S. Ali, J. Ferry, and U. Stingl.  Draft genome sequence of an obligately methylotrophic methanogen, Methanococcoides methylutens, isolated from marine sediment. Genome Announc. 2:6.
  • Kumar, R. S. S. and J. G. Ferry.  Prokaryotic carbonic anhydrases of earth’s environment.  In: Carbonic Anhydrase: Mechanism, Regulation, Links to Disease, and Industrial Applications, Vol. Subcellular Biochemistry 75.  (S. C. Frost and R. McKenna, eds.), pp. 77-87, Springer Science Business Media, Dordrecht, The Netherlands.
  • Achary, B. G., K. M. Campbell, I. S. Co, and D. S. Gilmour.  RNAi screen in Drosophila larvae identifies histone deacetylase 3 as a positive regulator of the hsp70 heat shock gene expression during heat shock.  Biochim. Biophys. Acta. 5:355-363.
  • Jones, M. A., S. Amr, A. Ferebee, P. Huynh, J. A. Rosenfeld, M. F. Miles, A. G. Davies, C. A. Korey, J. M. Warrick, R. Shiang, S. H. Elsea, S. Girirajan, and M. Grotewiel.  Genetic studies in Drosophila and humans support a model for the concerted function of CISD2, PPT1 and CLN3 in disease.  Biol. Open 3:342-352.
  • McMichael, G., S. Girirajan, A. Moreno-De-Luca, J. Gecz, C. Shard, L. S. Nguyen, J. Nicholl, C. Gibson, E. Haan, E. E. Eichler, C. L. Martin, and A. MacLennan.  Rare copy number variation in cerebral palsy.  Eur. J. Hum. Genet. 22:40-45.
  • Ghosh, D. and S. Girirajan.  Statistical considerations in the analysis of rare variants.  In:  Statistical Analysis of Next Generation Sequencing Data.  (S. Datta and D. Nettleton, eds.), pp. 405-422, Springer, Heidelberg, Germany.
  • Pirbadian, S., S. E. Barchinger, K. M. Leung, H. S. Byun, Y. Jangir, R. A. Bouhenni, S. B. Reed,  M. F. Romine, D. A. Saffarini, L. Shi, Y. A. Gorby, J. H. Golbeck, and M. Y. El-Naggar. Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components.  Proc. Natl. Acad. Sci. USA 111:12883-12888.
  • Gorka, M., J. Schartner, A. van der Est, M. Rogner, and J. H. Golbeck.   Light-mediated hydrogen generation in Photosystem I: attachment of a naphthoquinone-molecular wire-Pt nanoparticle to the A1A and A1B sites.  Biochemistry 53:2295-2306.
  • Ludwig, M., M.-E. Pandelia, C. Y. Chew, B. Zhang, J. H. Golbeck, C. Krebs, and D. A. Bryant.  ChlR protein of Synechococcus sp. PCC 7002 is a transcription activator that uses an oxygen-sensitive [4fe-4s] cluster to control genes involved in pigment biosynthesis.  J. Biol. Chem. 289:16624-16639.
  • Milanovsky, G. E., V. V. Ptushenko, J. H. Golbeck, A. Y. Semenov, and D. A. Cherepanov.  Molecular dynamics study of the primary charge separation reactions in Photosystem I: Effect of the replacement of the axial ligands to the electron acceptor A0.  Biochim. Biophys. Acta 1837:1472-1483.
  • Saboe, P. O., C. E. Lubner, N. S. McCool, N. M. Vargas-Barbosa, H. Yan, S. Chan, B. Ferlez, G. C. Bazan, J. H. Golbeck, and M. Kumar.  Two-Dimensional protein crystals for solar energy conversion.  Adv. Mater. 26:7064-7069.
  • Sun, J., S. Hao, M. Radle, W. Xu, I. Shelaev, V. Nadtochenko, V. Shuvalov, A. Semenov, H. Gordon, A. van der Est, and J. H. Golbeck.  Evidence that histidine forms a coordination bond to the A0A and A0B chlorophylls and a second H-bond to the A1A and A1B phylloquinones in M688HPsaA and M668HPsaB variants of Synechocystis sp. PCC 6803.  Biochim. Biophys. Acta 1837:1362-1375.
  • Zhang, S., G. Shen, Z. Li, J. H. Golbeck, and D. A. Bryant.  Vipp1 is essential for the biogenesis of Photosystem I but not thylakoid membranes in Synechococcus sp. PCC 7002.  J. Biol. Chem. 289:15904-15914.
  • Applegate, A. M., C. E. Lubner, P. Knorzer, T. Happe, and J. H. Golbeck.  Quantum yield measurements of light-induced H generation in a Photosystem I-[FeFe]-H2ase nanoconstruct.  Photosynth Res. DOI: 10.1007/s11120-014-0064-y
  • Golbeck, J. and A. van der Est (eds.).  The Biophysics of Photosynthesis, Springer, New York, ISBN 978-1-4939-1147-9.
  • Brabham, C.*, L. Lei*, J. Stork, M. Barrett, Y. Gu, and S. Debol.   Indaziflam herbicidal action: a potent cellulose biosynthesis inhibitor. *Joint first authors.  Plant Physiol. 166:1177-1185.
  • Lei, L., T. Zhang, R. Strasser, C. M. Lee, M. Gonneau, L. Mach, S. Vernhettes, S. H. Kim, D. Cosgrove, S. Li, and Y. Gu.  The jiaoyao1 mutant is an allele of korrigan that abolishes endoglucanase activity and affects the organization of both cellulose microfibrils and microtubules in Arabidopsis.  Plant Cell 26:2601-2616.
  • Ye, X., L. Lei, C. Brabham, J. Stork, J. Strickland, A. Ladak, Y. Gu, I. Wallace, and S. Debolt. Acetobixan, an inhibitor of cellulose synthesis identified by microbial bioprospecting.  PLoS ONE 9:e95245.
  • Lei, L., S. Li, L. Bashline, and Y. Gu.  Dissecting the molecular mechanism underlying intimate relationship between cellulose microfibrils and cortical microtubules.  Front. Plant Sci. 5:90.
  • Bashline, L, S. Li, and Y. Gu.  Trafficking of the cellulose synthase complex in higher plants.  Ann. Bot. 114:1059-1067.
  • Bashline, L, L. Lei, S. Li, and Y. Gu.  Cell wall, cytoskeleton, and cell expansion in higher plants.  Mol. Plant 7:586-600.
  • Li, S, L. Bashline, L. Lei, and Y. Gu.  Cellulose biosynthesis and its regulation. The Arabidopsis Book 11:e0169. doi:10.1199/tab.0169.
  • Crook, M., M. R. McReynolds, W. Wang, and W. Hanna-Rose.  An NAD+ biosynthetic pathway enzyme functions cell non-autonomously in C.elegans development.  Dev. Dynam. 243:955-976.
  • Giardine, B., J. Borg, E. Viennas, C. Pavlidis, K. Moradkhani, P. Joly, M. Bartsakoulia, C. Riemer, W. Miller, G. Tzimas, H. Wajcman, R. C. Hardison, and G. P. Patrinos.  Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.  Nucleic Acids Res. 42:D1063-D1069.
  • Lee, Y., D. Ghosh, R. Hardison, and Y. Zhang.  MRHMMs: Multivariate regression hidden Markov models and variants.  Bioinformatics 30:1755-1756.
  • Kellis, M., B. Wold, M. P. Snyder, B. E. Bernstein, A. Kundaje, G. K. Marinov, L. D. Ward, E. Birney, G. E. Crawford, L. Dekker, I. Dunham, L. L. Elnitski, P. J. Farnham, E. A. Feingold, M. Gerstein, M. C. Giddings, D. M. Gilbert, T. R. Gingeras, E. D. Green, R. Guigo, T. Hubbard, J. Kent, J. D. Lieb, R. M. Myers, M. J. Pazin, B. Ren, J. A. Stamatoyannopoulos, Z. Weng, K. P. White, and R. C. Hardison.  Defining functional DNA elements in the human genome.  Proc. Natl. Acad. Sci. USA 111:6131-6138.
  • Chang, G. S., X. A. Chen, B. Park, H. S. Rhee, P. Li, K. H. Han, T. Mishra, K. Y. Chan-Salis, Y. Li, R. C. Hardison, Y. Wang, and B. F. Pugh.  A comprehensive and high resolution genome-wide response of p53 to stress.  Cell Rep. 8:514-527.
  • Paralkar, V. R., T. Mishra, J. Luan, Y. Yao, A.V. Kossenkov, S. M. Anderson, M. Dunagin, M. Pimkin, M. Gore, D. Sun, N. Konuthula, A. Raj, X. An, N. Mohandas, D. M. Bodine, R. C. Hardison, and M. J. Weiss.  Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development.  Blood 123:1927-1937.
  • Pimkin, M., A. V. Kossenkov, T. Mishra, C. S. Morrissey, W. Wu, C. A. Keller, G. A. Blobel, D. Lee, M. A. Beer, R. C. Hardison, and M. J. Weiss.  Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis. Genome Res. 24:1932-1944.
  • Wu, W., C. S. Morrissey, C. A. Keller, T. Mishra, M. Pimkin, G. A. Blobel, M. J. Weiss, and R. C. Hardison.  Dynamic shifts in occupancy by TAL are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis. Genome Res. 24:1945-1962.
  • The Mouse ENCODE Consortium, including W. Wu (co-first author with 10 others), C. A. Keller, C. S. Morrissey, T. Mishra, D. Jain, N. Dogan, R. S. Harris, G. A. Blobel, M. J. Weiss, J. Taylor, R. C. Hardison (co-corresponding author with 7 others) last author Bing Ren.  A comparative encyclopedia of DNA elements in the mouse genome.  Nature 515:355-364.
  • Cheng, Y., Z. Ma, B.-H. Kim, W. Wu, P. Cayting, A. P. Boyle, V. Sundaram, X. Xing, N. Dogan, J. Li, G. Euskirchen, S. Lin, Y. Lin, A. Visel, T. Kawli, X. Yang, D. Patacsil, C. A. Keller, B. Giardine, The Mouse ENCODE Consortium, A. Kundaje, T. Wang, L. A. Pennacchio, Z. Weng, R. C. Hardison, and M. P. Snyder.  Principles of regulatory information conservation between mouse and human. Nature 515:371-375.
  • Pope, B. D., T. Ryba, V. Dileep, F. Yue, W. Wu, O. Denas, D. L. Vera, Y. Wang, R. S. Hansen, T. K. Canfield, R. E. Thurman, Y. Cheng, G. Gülsoy, J. H. Dennis, M. P. Snyder, J. A. Stamatoyannopoulos, J. Taylor, R. C. Hardison, T. Kahveci, B. Ren, and D. M. Gilbert.  Topologically-associating domains are stable units of replication-timing regulation. Nature 515:402-405.
  • Chen, K. B., R. C. Hardison, and Y. Zhang.  dCaP: detecting differential binding events in multiple conditions and proteins.  BMC Genomics 15 (Suppl 9):S12.
  • Williams, J. S., C. A. Natale, N. Wang, S. Li, T. R. Brubaker, P. Sun, and T-h. Kao.  Four previously identified Petunia inflata S-locus-F-box genes are involved in pollen specificity in self-incompatibility.  Mol. Plant 7:567-569.
  • Li, S., P. Sun, J. S. Williams, and T-h. Kao.  Identification of the self-incompatibility locus F-box protein-containing complex in Petunia inflata.  Plant Reprod. 27:31-45.
  • Williams, J. S., J. P. Der, C. W. dePamphilis, and T-h. Kao.  Transcriptome analysis reveals the same 17 S-locus F-box genes in two haplotypes of the self-incompatibility locus of Petunia inflata.  Plant Cell 26:2873-2888.
  • Sun, P, J. S. Williams, S. Li, and T-h. Kao.  S-RNase-based self-incompatibility in Petunia: a complex non-self recognition system between pollen and pistil.  In: Sexual Reproduction in Animals and Plants.  (H. Sawada, N. Inoue, and M. Iwano, eds.), pp. 289-303, Springer Tokyo Heidelberg New York Dordrecht London.
  • Feaga, H. A., P. H. Viollier, and K. C. Keiler.  Release of non-stop ribosomes is essential.  mBio 5:e01916-14.
  • El-Mowafi, S. A., J. N. Alumasa, S. E. Ades, and K. C. Keiler.  A cell-based assay to identify inhibitors of the Hfq-sRNA regulatory pathway.  Antimicrob. Agents Chemother. 58:5500-5509.
  • Keiler, K. C. and H. A. Feaga.  Releasing nonstop translation complexes is a matter of life and death.  J. Bacteriol. 196:2123-2130.
  • Krasilnikov, A. S. Applying UV-crosslinking to study RNA-protein interactions in multicomponent ribonucleoprotein complexes.  Methods Mol. Biol. 1086:193-207.
  • Lanz, N. D., M. E. Pandelia, E. S. Kakar, K.-H. Lee, C. Krebs, and S. J. Booker.  Evidence for a catalytically and kinetically competent enzyme-substrate cross-linked intermediate in catalysis by lipoyl synthase.  Biochemistry 53:4557-4572.
  • Ludwig, M., M.-E. Pandelia, C. Y. Chew, B. Zhang, J. H. Golbeck, C. Krebs, and D. A. Bryant.  ChlR protein of Synechococcus sp. PCC 7002 is a transcription activator that uses an oxygen-sensitive [4fe-4s] cluster to control genes involved in pigment biosynthesis.  J. Biol. Chem. 289:16624-16639.
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  • Savchenko, A. S., J. I. Borissoff, K. Martinod, S. F. De Meyer, M. Gallant, L. Erpenbeck, A. Brill, Y. Wang, and D. Wagner.  VWF-mediated leukocyte recruitment with chromatin decondensation by PAD4 increases myocardial ischemia/reperfusion injury in mice.  Blood 23:141-148.
  • McAnulty, M. J. and T. K. Wood.  YeeO from Escherichia coli exports flavins.  Bioengineered 5:386-392.
  • Lord, D. M., A. U. Baran, V. W. C. Soo, T. K. Wood, W. Peti, and R. Page.  McbR/YncC: implications for the mechanism of ligand and DNA binding by a bacterial GntR transcriptional regulator involved in biofilm formation.  Biochemistry 53:7223-7231.
  • Lord, D. M., A. Uzgoren Baran, T. K. Wood, W. Peti, and R. Page.  BdcA, a protein important for Escherichia coli biofilm dispersal, is a short-chain dehydrogenase/reductase that binds specifically to NADPH.  PLoS ONE 9:e105751.
  • Hidalgo-Romano, B., J. D. Gollihar, S. A. Brown, M. Whiteley, E. Valenzuela, H. B. Kaplan, T. K. Wood, and R. J. C. McLean.  Indole inhibition of AHL-mediated quorum signaling is widespread in gram-negative bacteria.  Microbiology 160:2464-2473.
  • Osbourne, D. O., V. W. C. Soo, I. Konieczny, and T. K. Wood.  Polyphosphate, cyclic AMP, guanosine tetraphosphate, and c-di-GMP reduce in vitro Lon activity.  Bioengineered 5:1-5.
  • Hu, Y., B. W. Kwan, D. O. Osbourne1, M. J. Benedik, and T. K. Wood.  Toxin YafQ increases persister cell formation by reducing indole signaling.   Environ. Microbiol. doi:10.1111/1462-2920.12567.
  • Soo, V. W. C., H.-Y. Cheng, B. W. Kwan, and T. K. Wood.  de novo synthesis of a bacterial toxin/antitoxin system.  Scientific Reports 4:4807.
  • Guo, Y., C. Quiroga, Q. Chen, M. J. McAnulty, M. J. Benedik, T. K. Wood, and X. Wang.  RalR (a DNase) and RalA (a small RNA) form a type I toxin–antitoxin system in Escherichia coli.  Nucl. Acids Res. 42:6448-6462.
  • Tran, K. T., T. Maeda, and T. K. Wood.  Metabolic engineering of Escherichia coli to enhance hydrogenproduction from glycerol.  Appl. Microbiol.  Biotechnol. 98:4757-4770.
  • Sönmez, B., K. C. Yanık-Yıldırım, T. K. Wood, and G. Vardar-Schara.  The role of substrate binding pocket residues phenylalanine 176 and phenylalanine 196 on Pseudomonas sp. OX1 toluene o-xylene monooxygenase activity and regiospecificity.   Biotechnol. Bioeng. 111:1506-1512.
  • Cheng, H.-Y., V. W. C. Soo, S. Islam, M. J. McAnulty, M. J. Benedik, and T. K. Wood.  Toxin GhoT of the GhoT/GhoS TA system damages the cell membrane to reduce ATP and to reduce growth under stress.   Environ. Microbiol. 16:1741–1754.
  • Zhao, W., S. M. McCarthy, T. Y. Lai, H. P. Yennawar, and A. T. Radosevich.  Reversible intermolecular e-h oxidative addition to a geometrically deformed and structurally dynamic phosphorous triamide.  J. Am. Chem. Soc. 136:17634-17644.
  • Yennawar, H. P., J. Tierney, and L. J. Silverberg.  2,3-Diphenyl-1,3-thia-zolidin-4-one.  Acta Crystallogr. Sect. E Struct. Rep. 70(Pt 8):o847.
  • Yennawar, H. P., H. Singh, and L. J. Silververg.  2,3-Diphenyl-2,3-di-hydro-4H-pyrido[3,2-e][1,3]thia-zin-4-one.  Acta Crystallogr. Sect. E Struct. Rep. 70(Pt 6):o638.
  • Yennawar, H. P., R. V. Bendinsky, D. J. Coyle, A. S. Cali, and L. J. Silverberg.  2,3-Diphenyl-2,3-di-hydro-4H-1,3-benzo-thia-zin-4-one.  Acta Crystallogr Sect. E Struct. Rep. 70(Pt 4):o465.
  • Yennawar, H. P. and L. J. Silverberg.  2,3-Diphenyl-2,3,5,6-tetra-hydro-4H-1,3-thia-zin-4-one.  Acta Crystallogr. Sect. E Struct. Rep. 70(Pt 2):o133.
  • McCarthy, S. M., Y. C. Lin, D. Devarajan, J. W. Chang, H. P. Yennawar, R. M. Rioux, D. H. Ess, and A. T. Radosevich.  Intermolecular N-H oxidative addition of ammonia, alkylamines, and arylamines to a planar s(3)-phosphorus compound via an entropy-controlled electrophilic mechanism.  J. Am. Chem. Soc. 136:4640-4650.


Archive of publications by year.

2013, 2012, 2011,2010, 2009, 2008,2007,2006,2005,2004,2003,2002,2001
2000,1999,1998,1997,1996, 1995