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About Us2002 Faculty PublicationsValbuzzi, A., P. Gollnick, P. Babitzke, and C. Yanofsky. The anti-TRAP protein AT recognizes the tryptophan-activated RNA binding domain of the TRAP regulatory protein. J. Biol. Chem. 277:10608-10613. Baker, C.S., I. Morozov, K. Suzuki, T. Romeo, and P. Babitzke. CsrA regulates glycogen biosynthesis by preventing translation of glgC in Escherichia coli. Mol. Microbiol. 44:1599-1610. Yakhnin, A.V., and P. Babitzke. NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism in vitro. Proc. Natl. Acad. Sci. USA 99:11067-11072. Suzuki, K., X. Wang, T. Weilbacher, A.-K. Pernestig, Ö. Melefors, D. Georgellis, P. Babitzke, and T. Romeo. Regulatory circuitry of the CsrA/CsrB and BarA/UvrY systems of Escherichia coli. J. Bacteriol. 184:5130-5140. Gollnick, P., and P. Babitzke. Transcription attenuation. Biochim. Biophys. Acta. 1577:240-250. Gollnick, P., P. Babitzke, E. Merino, and C. Yanofsky. Aromatic amino acid metabolism in Bacillus subtilis. In: Bacillus subtilis and Its Close Relatives: From Genes to Cells. (A. Sonenshein, ed.), pp. 233-244, American Society for Microbiology, Washington, D.C. Yun, D., C. Krebs, G.P. Gupta, D.F. Iwig, B.H. Huynh, and J.M. Bollinger, Jr. Facile electron transfer during formation of cluster X and kinetic competence of X for tyrosyl radical production in protein R2 of ribonucleotide reductase from mouse. Biochemistry. 41:981-990. Krebs, C., J.M. Bollinger, Jr., E.C. Thiel, and B.H. Huynh. Exchange coupling constant J of peroxodiferric reaction intermediates determined by Mössbauer spectroscopy. J. Biol. Inorg. Chem. 7:863-869. Vassilieva, E.V., J.G. Ormerod, and D.A. Bryant. Biosynthesis of chlorosome proteins is not inhibited in acetylene-treated cultures of Chlorobium vibrioforme. Photosynth. Res. 71:69-81. Antonkine, M.L., G. Liu, D. Bentrop, I. Bertini, C. Luchinat, D. A. Bryant, J.H. Golbeck, and D. Stehlik. Solution structure of the unbound, oxidized photosystem I subunit PsaC, containing [4Fe-4S] clusters FA and FB. Conformational change upon binding to Photosystem I. J. Biol. Inorg. Chem. 7:461-472. Sakuragi, Y., B. Zybailov, G. Shen, A.D. Jones, P.R. Chitnis, A. van der Est, R. Bittl, S. Zech, D. Stehlik, J.H. Golbeck, and D.A. Bryant. Insertional inactivation of the menG Gene, encoding 2-phytyl-1,4-naphthoquinone methyltransferase of Synechocystis sp. PCC 6803, results in the incorporation of 2-phytyl-1,4-naphthoquinone into the A1 site and alteration of the equilibrium constant between A1 and FX in Photosystem I. Biochemistry. 41:394-405. Eisen, J.A., K.E. Nelson, I.T. Paulsen, J.F. Heidelberg, M. Wu, R.J. Dodson, R. Deboy, M.L. Gwinn, W.C. Nelson, D.H. Haft, E.K. Hickey, J.D. Peterson, A.S. Durkin, J.L. Kolonay, F. Yang, I. Holt, L.A. Umayam, T. Mason, M. Brenner, T.P. Shea, D. Parksey, T.V. Feldblyum, C.L. Hansen, M.B. Craven, D. Radune, H. Khouri, C.Y. Fujii, O. White, J.C. Venter, N. Volfovsky, T.M. Gruber, K.A. Ketchum, H. Tettelin, D.A. Bryant, and C.M. Fraser. The complete genome sequence of the green sulfur bacterium Chlorobium tepidum. Proc. Natl. Acad. Sci. USA. 99:9509-9514. Vassilieva, E.V., V.L. Stirewalt, C.U. Jakobs, N.-U. Frigaard, M.A. Baker, A. Sotak, and D.A. Bryant. Cellular localization of chlorosome proteins in Chlorobium tepidum. Cloning and characterization of genes encoding CsmH, CsmF, and three additional chlorosome-associated polypeptides. Biochemistry. 41:4358-4370. Safarov, N., S. Miletti, S. Ciurli, S.K. Christensen, K. Kornetzky, D.A. Bryant, I. Vendenberghe, B. Devreese, H. Remaut, and J. V. Van Beeumen. Molecular characterization of Bacillus pasteurii UreE, a metal-binding chaperone for assembly of the urease active site. J. Biol. Inorg. Chem. 7:623-631. Frigaard, N.-U., G.D. Voigt, and D.A. Bryant. A bacteriochlorophyll c-less mutant of Chlorobium tepidum made by inactivation of the bchK gene encoding bacteriochlorophyll c synthase. J. Bacteriol. 184:3368-3376. Scott, N.L., C.J. Falzone, D.A. Vuletich, J. Zhao, D.A. Bryant, and J.T.J. Lecomte. Truncated hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002. Evidence for hexacoordination and covalent adduct formation in the ferric recombinant protein. Biochemistry. 41:6902-6910. Shen, G., J. Zhao, S.K. Reimer, M.L. Antonkine, Q. Cai, S.M. Weiland, J.H. Golbeck, and D. A. Bryant. Assembly of [4Fe-4S] clusters in Photosystem I. I. Inactivation of the rubA gene encoding a membrane-associated rubredoxin in the cyanobacterium Synechococcus sp. PCC 7002 causes a loss of photosystem I activity. J. Biol. Chem. 277:20343-20354. Shen, G., M.L. Antonkine, A. van der Est, I.R. Vassiliev, K. Brettel, R. Bittl, S.G. Zech, J. Zhao, D. Stehlik, D. A. Bryant, and J.H. Golbeck. Assembly of [4Fe-4S] clusters in Photosystem I. II. Rubredoxin is required for the in vivo assembly of FX in Synechococcus Sp. PCC 7002 as shown by optical and EPR spectroscopy. J. Biol. Chem. 277:20355-20366. Sakamoto, T., and D. A. Bryant. Synergistic effect of high-light and low temperature on cell growth of the Δ12 fatty acid desaturase mutant in Synechococcus sp. PCC 7002. Photosynth. Res. 42:231-242. Camarero, J.A., A. Shekhtman, E.A. Campbell, M. Chlenov, T.M. Gruber, D. A. Bryant, S.A. Darst, D. Cowburn, and T.W. Muir. Autoregulation of a bacterial sigma factor explored by using segmental isotopic labeling and NMR. Proc. Natl. Acad. Sci. USA. 99:8536-8541. Bryant, D.A., N.-U. Frigaard, E.V. Vassilieva, and H. Li. Selective protein extraction from chlorosomes of Chlorobium tepidum using detergents: evidence that CsmA forms multimers and binds bacteriochlorophyll a. Biochemistry. 41:14403-14411. Schluchter, W.M., and D.A. Bryant. Analysis and reconstitution of phycobiliproteins: methods for the characterization of bilin attachment reactions. In: Analytical Methods for Chlorophyll, Heme, and Related Molecules. (M. Witty and A. Smith, eds.), pp. 311-334, Humana Press, Totowa, NJ. Frigaard, N.-U., E.V. Vassilieva, H. Li, K.J. Milks, J. Zhao, and D. A. Bryant. The remarkable chlorosome. In: PS2001 Proceedings, 12th International Congress on Photosynthesis, Brisbane, Australia. Article S1-003. CSIRO Publishing, Canberra, Australia. Morris, P.D., A.K. Byrd, A.J. Tackett, C.E. Cameron, and K.D. Raney. NS3 helicase displaces streptavidin from 5’-biotinylated oligonucleotides but not from 3’-biotinylated oligonucleotides: Evidence for a directional bias in translocation on single-stranded DNA. Biochemistry. 41:2372-2378. Harki, D.A., J.D. Graci, V.S. Korneeva, S.K.B. Ghosh, Z. Hong, C. E. Cameron, and B.R. Peterson. Synthesis and antiviral evaluation of a mutagenic and non-hydrogen bonding ribonucleoside analogue: 1-β-D-ribofuranosyl-3-nitropyrrole. Biochemistry. 41:9026-9033. Green, K.Y., A. Mory, M.H. Fogg, A. Weisberg, G. Belliot, M. Wagner, T. Mitra, E. Ehrenfeld, C.E. Cameron, and S.V. Sosnovtsev. Isolation of enzymatically-active replication complexes from feline calicivirus-infected cells. J. Virol. 76:8582-8595. Pathak, H.P., S.K.B. Ghosh, A.W. Roberts, S.D. Sharma, J.D. Yoder, J.J. Arnold, D.W. Gohara, D.J. Barton, A.V. Paul, and C.E. Cameron. Structure-function relationships of the RNA-dependent RNA polymerase from poliovirus (3Dpol): A surface of the primary oligomerization domain functions in capsid precursor processing and VPg uridylylation. J. Biol. Chem. 277:31551-31562. Gorbalenya, A.E., F.M. Pringle, J.-L. Zeddam, B.T. Luke, C.E. Cameron, J. Kalmakoff, T. Hanzlik, K. Gordon, and V.K. Ward. 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Atnoor, A. Brown, N. Allen, J. Naylor, N. Stange-Thomann, K. DeArellano, R. Johnson, L. Linton, P. McEwan, K. McKernan, J. Talamas, A. Tirrell, W. Ye, A. Zimmer, R.D. Barber, I. Cann, D.E. Graham, D.A. Grahame, A. Guss, R. Hedderich, C. Ingram-Smith, H.C. Kuettner, J.A. Krzycki, J.A. Leigh, W. Li, J. Liu, B. Mukhopadhyay, J.N. Reeve, K. Smith, T. Springer, L.A. Umayam, O. White, R.H. White, E. Conway de Macario, J.G. Ferry, K.F. Jarrell, H. Jing, A.J.L. Macario, I. Paulsen, M. Pritchett, K.R. Sowers, R.V. Swanson, S.H. Zinder, E. Lander, W.W. Metcalf, and B. Birren. The genome of Methanosarcina acetivorans reveals unprecedented metabolic and physiological diversity. Genome Res. 12:532-542. Miles, R.D., A. Gorrell, and J.G. Ferry. Evidence for a transition state analog, MgADP-aluminum fluoride-acetate, in acetate kinase from Methanosarcina thermophila. J. Biol. Chem. 277:22547-22552. Smith, K.S., C. Ingram-Smith, and J.G. Ferry. 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Cell. Biochem. 84:625-635. Shiels, M.S., A.M. Mastro, and C.V. Gay. The effect of donor age on the sensitivity of osteoblasts to the proliferative effects of TGFβ and 1,25 (OH)2 vitamin D3. Life Sci. 70:2967-2975. Wang, X., G.J. Fosmire, C.V. Gay, and R.M. Leach. Short-term zinc deficiency inhibits chondrocyte proliferation and induces cell apoptosis in the epiphyseal growth plate of young chickens. J. Nutr. 132:665-673. Leibovitch, B.A., Q. Lu, L.R. Benjamin, Y. Liu, D.S. Gilmour, and S.C. Elgin. GAGA factor and the TFIID complex collaborate in generating an open chromatin structure at the Drosophila melanogaster hsp26 promoter. Mol. Cell. Biol. 22:6148-6157. Sakuragi, Y., B. Zybailov, G. Shen, A.D. Jones, P.R. Chitnis, A. van der Est, R. Bittl, S. Zech, D. Stehlik, J.H. Golbeck, and D.A. Bryant. Insertional inactivation of the menG Gene, encoding 2-phytyl-1,4-naphthoquinone methyltransferase of Synechocystis sp. PCC 6803, results in the incorporation of 2-phytyl-1,4-naphthoquinone into the A1 site and alteration of the equilibrium constant between A1 and FX in Photosystem I. Biochemistry. 41:394-405. Antonkine, M.L., D. Bentrop, I. Bertini, C. Luchinat, G. Shen, D.A. Bryant, J.H. Golbeck, and D. Stehlik. NMR solution structure of the unbound, oxidized Photosystem I subunit PsaC containing [4Fe-4S] clusters FA and FB. A conformational change occurs upon binding to Photosystem I. J. Biol. Inorg. Chem. 7:461-472. Shen, G., J. Zhao, S.K. Reimer, M.L. Antonkine, Q. Cai, S.M. Weiland, J.H. Golbeck, and D.A. Bryant. Assembly of [4Fe-4S] clusters in Photosystem I. I. Inactivation of the rubA gene encoding a membrane-associated rubredoxin in the cyanobacterium Synechococcus sp. PCC 7002 causes a loss of photosystem I activity. J. Biol. Chem. 277:20343-20354. Shen, G., M.L Antonkine, A. van der Est, I.R. Vassiliev, K. Brettel, R. Bittl, S.G. Zech, J. Zhao, D. Stehlik, D.A. Bryant, and J.H. Golbeck. Assembly of [4Fe-4S] clusters in Photosystem I. II. Rubredoxin is required for the in vivo assembly of FX in Synechococcus Sp. PCC 7002 as shown by optical and EPR spectroscopy. J. Biol. Chem. 277:20355-20366. Shinkarev, V.P., B. Zybailov, I.R. Vassiliev, and J.H. Golbeck. Mathematical modeling of the P700+ charge recombination kinetics with phylloquinone and plastoquinone-9 in the A1 site of Photosystem I. Biophys. J. 83:2885-2897. Hanna-Rose, W., and M. Han. The Caenorhabditis elegans EGL-26 protein mediates vulval cell morphogenesis. Dev. Biol. 241:247-258. Hardison, R.C., D.H.K. Chui, B. Giardine, C. Riemer, G.P. Patrinos, N. Anagnou, W. Miller and H. Wajcman. HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server. Hum. Mutat. 19:225-233. Molete, J.M., H. Petrykowska, M. Sigg, W. Miller, and R. C. Hardison. Functional and binding studies of HS3.2 of the beta-globin locus control region. Gene. 283:185-197. Elnitski, L., C. Riemer, H. Petrykowska, S. Schwartz, L. Florea, W. Miller, and R.C. Hardison. PipTools: A computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics. 80:681-690. Waterston, R.H., K. Lindblad-Toh, E. Birney, J. Rogers, J.F. Abril, P. Agarwal, R. Agarwala, R. Ainscough, M. Alexandersson, P. An, S.E. Antonarakis, J. Attwood, R. Baertsch, J. Bailey, K. Barlow, S. Beck, E. Berry, B. Birren, T. Bloom, P. Bork, M. Botcherby, N. Bray, M.R. Brent, D.G. Brown, S.D. Brown, C. Bult, J. Burton, J. Butler, R.D. Campbell, P. Carninci, S. Cawley, F. Chiaromonte, A.T. Chinwalla, D.M. Church, M. Clamp, C. Clee, F.S. Collins, L.L. Cook, R.R. Copley, A. Coulson, O. Couronne, J. Cuff, V. Curwen, T. Cutts, M. Daly, R. David, J. Davies, K.D. Delehaunty, J. Deri, E.T. Dermitzakis, C. Dewey, N.J. Dickens, M. Diekhans, S. Dodge, I. Dubchak, D.M. Dunn, S.R. Eddy, L. Elnitski, R.D. Emes, P. Eswara, E. Eyras, A. Felsenfeld, G.A. Fewell, P. Flicek, K. Foley, W.N. 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