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2006 Faculty Publications

Costanzo, A. and S. E. Ades.  Growth phase dependent regulation of the extracytoplasmic stress factor, σE, by guanosine 3’5’ bisphosphate, ppGpp.  J. Bacteriol. 188:4627-4634.

Ades, S. E.  AAA+ Molecular Machines:  Firing on all cylinders.  Curr. Biol. 16:R46-48.

Yakhnin, H., A. V. Yakhnin, and P. Babitzke.  The trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis regulates translation initiation of ycbK, a gene encoding a putative efflux protein, by blocking ribosome binding.  Mol. Microbiol. 61:1252-1266.

Suzuki, K., P. Babitzke, S. R. Kushner, and T. Romeo.  Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E.  Genes Dev. 20:2605-2617.

Mercante, J., K. Suzuki, X. Cheng, P. Babitzke, and T. Romeo.  Comprehensive alanine-scanning mutagenesis of Escherichia coli CsrA defines two subdomains of critical functional importance.  J. Biol. Chem. 281:31832-31842.

Yakhnin, A. V., H. Yakhnin, and P. Babitzke.  RNA polymerase pausing participates in the Bacillus subtilis trpE translation control mechanism by providing additional time for TRAP to bind to the nascent trp leader transcript.  Mol. Cell 24:547-557.

Hoffart, L. M., E. W. Barr, R. B. Guyer, J. M. Bollinger, Jr., and C. Krebs.  Direct spectroscopic detection of a C-H-cleaving high-spin Fe(IV) complex in a Prolyl-4-hydroxylase.  Proc. Natl. Acad. Sci. USA 103:14738-14743.

Saleh, L. and J. M. Bollinger, Jr.  Cation mediation of radical transfer between Trp48 and Tyr356 during O2 activation by protein R2 of Escherichia coli ribonucleotide reductase: relevance to R1-R2 radical transfer in nucleotide reduction?  Biochemistry 45:8823-8830.

Kim, S. H., G. Xing, J. M. Bollinger, Jr., C. Krebs, and B. M. Hoffman.  Demonstration by 2H ENDOR spectroscopy that myo-inositol binds via an alkoxide bridge to the mixed-valent diiron center of myo-inositol oxygenase.  J. Am. Chem. Soc. 128:10374-10375.

Yeh, E., L. J. Cole, E. W. Barr, J. M. Bollinger, Jr., D. B. Ballou, and C. T. Walsh.  Flavin redox chemistry precedes substrate chlorination during reaction of the flavin-dependent halogenase RebH.  Biochemistry 45:7904-7912.

Xing, G., Y. Diao, L. M. Hoffart, S. Prabhu, R. J. Arner, C. C. Reddy, C. Krebs, and J. M. Bollinger, Jr.  Novel mechanisms of oxygen activation and C-H cleavage by a dinuclear iron cluster in myo-inositol oxygenase.  Proc. Natl. Acad. Sci. USA 103:6130-6135.

Xing, G., L. M. Hoffart, Y. Diao, S. Prabhu, R. J. Arner, C. C. Reddy, C. Krebs, and J. M. Bollinger, Jr.  Oxygen activation by a mixed-valent, diiron(II/III) cluster in the glycol-cleavage reaction catalyzed by myo-inositol oxygenase.  Biochemistry 45:5402-5412.

Xing, G., L. M. Hoffart, Y. Diao, S. Prabhu, R. J. Arner, C. C. Reddy, C. Krebs, and J. M. Bollinger, Jr.  Spectroscopic evidence for a coupled dinuclear iron cluster that coordinates the substrate in myo-inositol oxygenase.  Biochemistry 45:5393-5401.

Bollinger, J. M., Jr. and C. Krebs.  Stalking intermediates in oxygen activation by iron enzymes:  Motivation and method.  J. Inorg. Biochem. 100:586-605.

Biddle, J., J. S. Lipp, M. Lever, K. Lloyd, K. Soerensen, R. Anderson, H. F. Fredricks, M. Elvert, T. J. Kelly, D. P. Schrag, M. L. Sogin, J. E. Brenchley, A. Teske, C. H. House, and K-U. Hinrichs.  Novel heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc. Natl. Acad. Sci. USA 103:3846-3851.

Biddle, J., C. House, and J. Brenchley.  Microbial stratification of deeply buried marine sediment reflects changes in sulfate/methane profiles.  Geobiology 3:287-295.

Coker, J. and J. Brenchley.  Protein engineering of a cold-active b-galactosidase from Arthrobacter sp. SB to increase lactose hydrolysis reveals new sites affecting low temperature activity.  Extremophiles 10:515-524.

Shipkowski, S. and J. Brenchley.  Bioinformatic, genetic, and biochemical evidence that some glucoside hydrolase family 42 ß-galactosidases are arabinogalactan type I oligomer hydrolases. Appl. Environ. Microbiol. 72:7730-7738.

Nomura, C. T., S. Persson, G. Shen, K. Inoue-Sakamoto, and D. A. Bryant.  Characterization of two cytochrome oxidase operons in the marine cyanobacterium Synechococcus sp. PCC 7002. Inactivation of ctaDI affects the PS I:PS II ratio.  Photosynthesis Res. 87:215-228.

Balasubramanian, R., G. Shen, D. A. Bryant, and J. H. Golbeck.  Regulatory roles for IscA and SufA in iron homeostasis and redox stress responses in the cyanobacterium Synechococcus sp. strain PCC 7002.  J. Bacteriol. 188:3182-3191.

Sakuragi, Y., H. Maeda, D. DellaPenna, and D. A. Bryant. a-Tocopherol plays a role in photosynthesis and macronutrient homeostasis that is independent of its antioxidant function in the cyanobacterium Synechocystis sp. PCC 6803.  Plant Physiol. 141:508-521.

Ley, R. E., J. K. Harris, J. Wilcon, J. R. Spear, S. R. Miller, B. M. Bebout, J. A. Maresca, D. A.  Bryant, and N. R. Pace.  Unexpected diversity and complexity from the Guerrero Negro hypersaline microbial mat.  Appl. Environ. Microbiol. 72:3685-3695.

Nomura, C. T., T. Sakamoto, and D. A. Bryant.  Roles for heme-copper oxidases in extreme high light and oxidative stress response in the cyanobacterium Synechococcus sp. PCC 7002. Arch. Microbiol. 185:471-479.

Shen, G., N. A. Saunée, S. R. Williams, E. F. Gallo, W. M. Schluchter, and D. A. Bryant. Identification and characterization of a new class of bilin lyase: the cpcT gene encodes a bilin lyase responsible for attachment of phycocyanobilin to Cys-153 on the b-subunit of phycocyanin in Synechococcus sp. PCC 7002.  J. Biol. Chem. 281:17768-17778.

Li, H., N.-U. Frigaard, and D. A. Bryant.  Molecular contacts for chlorosome envelope proteins revealed by cross-linking studies with chlorosomes from Chlorobium tepidum.  Biochemistry 45: 9095-9103.

Bryant, D. A. and N.-U. Frigaard.  Prokaryotic photosynthesis and phototrophy illuminated. Trends Microbiol. 14:488-496.

Maresca, J. A. and D. A. Bryant.  Identification of two genes encoding new carotenoid-modifying enzymes in the green sulfur bacterium Chlorobium tepidum.  J. Bacteriol. 188:6217-6223.

Sakuragi, Y. and D. A. Bryant.  Genetic manipulation of quinone biosynthesis in cyanobacteria. In:  Advances in Photosynthesis and Respiration, Photosystem I: The light-driven plastocyanin:ferredoxin oxidoreductase in photosynthesis.  (J. H. Golbeck, ed.), vol. 24, pp. 205-222, Springer, Dordrecht, The Netherlands.

Shively, J. B., G. C. Cannon, D. A. Bryant, S. DasSarma, D. Bazylinski, J. Preiss, A.  Steinbüchel, and R. Docampo.  Bacterial Inclusions.  In:  Encyclopedia of Life Sciences, Nature Publishing Group, Macmillan Reference Ltd., London, United Kingdom. http://www.els.net/.

Frigaard, N.-U. and D. A. Bryant.  Chlorosomes: antenna organelles in green photosynthetic bacteria.  In:  Complex Intracellular Structures in Prokaryotes, Microbiology Monographs.  (J. M. Shively, ed.), vol. 2, pp. 79-114, Springer, Berlin, Germany.

Frigaard, N.-U., A. Gomez Maqueo Chew, J. A. Maresca, and D. A. Bryant. Bacteriochlorophyll biosynthesis in green bacteria.  In:  Advances in Photosynthesis and Respiration.  Chlorophylls and Bacteriochlorophylls: Biochemistry, Biophysics, Functions and Applications.  (B. Grimm, R. Porra, W. Rüdiger, and H. Scheer, eds.), vol. 25, pp. 201-221, Springer, Dordrecht, The Netherlands.

Mackintosh, S. G., J. Z. Lu, J. B. Jordan, M. K. Harrison, B. Sikora, S. D. Sharma, C. E.  Cameron, K. D. Raney, and J. Sakon.  Structural and biological identification of residues on the surface of NS3 helicase required for optimal replication of the hepatitis C virus.  J. Biol. Chem. 281:3528-3535.

Arnold, J. J., A. Bernal, U. Uche, D. E. Sterner, T. R. Butt, C. E. Cameron, and M. R. Mattern. Small ubiquitin-like modifying protein isopeptidase assay based on poliovirus RNA polymerase activity.  Anal. Biochem. 350:214-221.

Vignuzzi, M., J. K. Stone, J. J. Arnold, C. E. Cameron, and R. Andino.  Genomic diversity in a viral population determines fitness, tissue tropism and pathogenesis.  Nature 439:344-348.

van Ooij, M. J. M., D. A. Vogt, A. Paul, C. Castro, J. Kuijpers, F. J. M. van Kuppeveld, C. E. Cameron, E. Wimmer, R. Andino, and W. J. G. Melchers.  Structural and functional characterization of the coxsackievirus B3 CRE(2C): Role of CRE(2C) in negative and positive strand RNA synthesis.  J. Gen. Virol. 87:103-113.

Takhampunya, R., S. Ubol, H.-S. Houng, C. E. Cameron, and R. Padmanabhan.  Inhibition of Dengue viral replication by mycophenolic acid and ribavirin.  J. Gen. Virol. 87:1947-1952.

Lanzi, G., J. R. de Miranda, M. B. Boniotti, C. E. Cameron, A. Lavazza, L. Capucci, S. M. Camazine, and C. Rossi.  Molecular and biological characterization of deformed wing virus of honeybees (Apis mellifera L.).  J. Virol. 80:4998-5009.

D’Abramo, C. M., J. Deval, C. E. Cameron, L. Cellai, and M. Gotte.  Control of template positioning during de novo initiation of RNA synthesis by bovine viral diarrhea virus NS5B polymerase.  J. Biol. Chem. 281:24991-24998.

Harki, D. A., J. D. Graci, J. E. Galarrage, W. J. Chain, C. E. Cameron, and B. R. Peterson. Synthesis and antiviral activity of 5-substituted cytidine analogues: Identification of a potent inhibitor of viral RNA-dependent RNA polymerases.  J. Med. Chem. 49:6166-6169.

Graci, J. D. and C. E. Cameron.  Mechanisms of action of ribavirin against distinct viruses.  Rev. Med. Virol. 16:37-48.

Li, Q., L. Li, T. Rejtar, D. J. Lessner, B. L. Karger, and J. G. Ferry.  Electron transport in the pathway of acetate conversion to methane in the marine archaeon Methanosarcina acetivorans.  J. Bacteriol. 188:702-710.

Lawrence, S. H., K. B. Luther, H. Schindelin, and J. G. Ferry.  Structural and functional studies suggest a catalytic mechanism for the phosphotransacetylase from Methanosarcina thermophila.  J. Bacteriol. 188:1143-1154.

Lawrence, S. H. and J. G. Ferry.  Steady-state kinetic analysis of phosphotransacetylase from Methanosarcina thermophila.  J. Bacteriol. 188:1155-1158.

Cruz, F. and J. G. Ferry.  Interaction of iron-sulfur flavoprotein with oxygen and hydrogen peroxide.  Biochim. Biophys. Acta. 1760:858-864.

Patridge, E. V. and J. G. Ferry.  WrbA from Escherichia coli and Archaeoglobus fulgidus is an NAD(P)H:quinone oxidoreductase.  J. Bacteriol. 188:3498-3506.

Ferry, J. G. and C. H. House.  The stepwise evolution of early life driven by energy conservation.  Mol. Biol. Evol. 23:1286-1292.

Zimmerman, S. A. and J. G. Ferry.  Proposal for a hydrogen bond network in the active site of the prototypic gamma-class carbonic anhydrase.  Biochemistry 45:5149-5157.

Andreev, V. P., L. Li, T. Rejtar, Q. Li, J. G. Ferry, and B. L. Karger.  A new algorithm for 15N/14N quantitation with LC-ESI-MS using LTQ-FT mass spectrometry.  J. Proteome Res. 5:2039-2045.

Lessner, D. J., L. Li, Q. Li, T. Rejtar, V. P. Andreev, M. Reichlen, K. Hill, J. J. Moran, B. L. Karger, and J. G. Ferry.  An unconventional pathway for reduction of CO2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics.  Proc. Natl. Acad. Sci. USA 103:17921-17926.

Verma, S., K. Ziegler, P. Ananthula, J. K. G. Co, R. J. Frisque, R. Yanagihara, and V. R. Nerurkar.  JC virus induces altered patterns of cellular gene expression: Interferon inducible genes as major transcriptional targets.  Virology 345:457-467.

Tyagarajan, S. K. and R. J. Frisque.  The stability and function of JC virus large T antigen and T' proteins are altered by mutation of their phosphorylated threonine 125 residue.  J. Virol. 80: 2083-2091.

Bollag, B., L. H. Kilpatrick, S. K. Tyagarajan, M. J. Tevethia, and R. J. Frisque.  JC virus proteins T'135, T'136 and T'165 interact with cellular regulatory factors and influence viral transformation potential.  J. Neurovirol. 12:428-442.

Frisque, R. J., C. Hofstetter, and S. Tyagarajan.  Transforming activities of JC virus early proteins.  In:  Polyomaviruses and Human Diseases, Advances in Experimental Medicine and Biology.  (N. Ahsan, ed.), vol. 577, pp. 288-309, Eurekah.com and Springer Science+Business Media, New York, NY.

Zhang, A. and D. S. Gilmour.  Pcf11 is a transcription termination factor in Drosophila that dismantles the elongation complex by bridging the CTD of RNA polymerase II to the nascent transcript.  Mol. Cell 21:65-74.

Ishikita, H., D. Stehlik, J. H. Golbeck, and E-W. Knapp.  Electrostatic influence of PsaC protein binding to the PsaA/PsaB heterodimer in Photosystem I.  Biophys. J.  90:1081-1089.

Balasubramanian, R., G. Shen, D. A. Bryant, and J. H. Golbeck.  Regulatory roles for IscA and SufA in iron homeostasis and redox stress responses in the cyanobacterium Synechococcus sp. strain PCC 7002.  J. Bacteriol. 188:3182-3191.

Heinnickel, M., R. Agalarov, N. Svensen, C. Krebs, and J. H. Golbeck.  Identification of FX in the heliobacterial reaction center as a [4Fe-4S] cluster with an S = 3/2 ground spin state. Biochemistry 45:6756-6764.

Karyagina, I., J. H. Golbeck, N. Srinivasan, D. Stehlik, and H. Zimmerman.  Single-sided hydrogen bonding to the quinone cofactor in Photosystem I probed by selective 13C-labeled naphthoquinones and transient EPR.  Appl. Magn. Reson. 30:287-310.

Photosystem I: The Light-Driven Plastocyanin:Ferredoxin Oxidoreductase.  (J. H. Golbeck, ed.), Springer, Dordrecht, The Netherlands.

Antonkine, M. and J. H. Golbeck.  Molecular interactions of the stromal subunit PsaC with the PsaA/PsaB heterodimer.  In:  Photosystem I: The Light-Driven Plastocyanin:Ferredoxin Oxidoreductase (J. H. Golbeck, ed.), pp. 79-98, Springer, Dordrecht, The Netherlands.

Shen, G. and J. H. Golbeck.  Assembly of the bound iron-sulfur clusters in Photosystem I.  In: Photosystem I: The Light-Driven Plastocyanin Ferredoxin Oxidoreductase.  (J. H. Golbeck, ed.), pp. 529-547, Springer, Dordrecht, The Netherlands

Nelms, B. and W. Hanna-Rose.  C. elegans HIM-8 has a meiosis-independent function in antagonizing the activity of the EGL-13 Sox protein.  Dev. Biol. 293:392-402.

Huang, L. and W. Hanna-Rose.  EGF signaling overcomes a uterine cell death associated with temporal mis-coordination of organogenesis within the C. elegans egg-laying apparatus.  Dev. Biol. 300:599-611.

Wang, H., Y. Zhang, Y. Cheng, Y. Zhou, D. C. King, J. Taylor, F. Chiaromonte, J. Kasturi, H. Petrykowska, B. Gibb, C. Dorman, W. Miller, L. C. Dore, J. Welch, M. J. Weiss, and R. C. Hardison.  Experimental validation of predicted mammalian erythroid cis-regulatory modules.  Genome Res. 16:1480-1492.

Taylor, J., S. Tyekucheva, D. C. King, R. C. Hardison, W. Miller, and F. Chiaromonte.  ESPERR:  Learning strong and weak signals in genomic sequence alignments to identify functional elements.  Genome Res. 16:1585-1595.

Elnitski, L., D. C. King, and R. C. Hardison.  Computational prediction of cis-regulatory modules from multispecies alignments using galaxy, table browser and GALA.  In:  Gene Mapping, Discovery and Expression, in series Methods in Molecular Biology.  (M. Bina, ed.), pp. 91-103, Humana Press Inc., Totowa, NJ. 

Holland, M., D. Sykes, and R. Shaler.  Forensic Science Education:  Designing an effective curriculum.  In:  Forensic Magazine.  June/July issue, pp. 29-37, Vicon Publishing, Amherst, NH.

Skirpan, A. L., P. E. Dowd, P. Sijacic, C. J. Jaworski, S. Gilroy, and T-h. Kao.  Isolation and characterization of PiORP1, a Petunia oxysterol-binding-protein related protein involved in receptor-kinase mediated signaling in pollen, and analysis of the ORP gene family in Arabidopsis.  Plant Mol. Biol. 61:553-565.

Dowd, P. E., S. Coursol, A. L. Skirpan, T-h. Kao, and S. Gilroy.  Petunia phospholipase C1 is involved in pollen tube growth.  Plant Cell 18:1438-1453.

Kokubun, H., M. Nakano, T. Tsukamoto, H. Watanabe, G. Hashimoto, E. Marchesi, L. Bullrich, I. L. Basualdo, T-h. Kao, and T. Ando.  Distribution of self-compatible and self-incompatible populations of Petunia axillaris (Solanaceae) outside Uruguay.  J. Plant Res. 119:419-430.

Hua, Z. and T-h. Kao.  Identification and characterization of components of a putative PiSLF-containing E3 ligase complex involved in S-RNase-based self-incompatibility.  Plant Cell 18: 2531-2553.

Moura, A. A., D. A. Chapman, H. Koc, and G. J. Killian.  Proteins of the cauda epididymal fluid associated with fertility of mature dairy bulls.  J. Androl. 27:534-541.

Moura, A. A., H. Koc, D. A Chapman, and G. J. Killian.  Identification of proteins in the accessory sex gland fluid associated with fertility indexes of dairy bulls:  a proteomic approach.  J. Androl. 27:201-211.

Baird, N. J., N. Srividya, A. S. Krasilnikov, A. Mondragon, T. R. Sosnick, and T. Pan.  Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium.  RNA 12:598-606.

Hoffart, L. M., E. W. Barr, R. B. Guyer, J. M. Bollinger, Jr., and C. Krebs.  Direct spectroscopic detection of a C-H-cleaving high-spin Fe(IV) complex in a Prolyl-4-hydroxylase.  Proc. Natl. Acad. Sci. USA 103:14738-14743.

Kim, S. H., G. Xing, J. M. Bollinger, Jr., C. Krebs, and B. M. Hoffman.  Demonstration by 2H ENDOR spectroscopy that myo-inositol binds via an alkoxide bridge to the mixed-valent diiron center of myo-inositol oxygenase.  J. Am. Chem. Soc. 128:10374-10375.

Xing, G., Y. Diao, L. M. Hoffart, S. Prabhu, R. J. Arner, C. C. Reddy, C. Krebs, and J. M. Bollinger, Jr.  Novel mechanisms of oxygen activation and C-H cleavage by a dinuclear iron cluster in myo-inositol oxygenase.  Proc. Natl. Acad. Sci. USA 103:6130-6135.

Xing, G., L. M. Hoffart, Y. Diao, S. Prabhu, R. J. Arner, C. C. Reddy, C. Krebs, and J. M. Bollinger, Jr.  Oxygen activation by a mixed-valent, diiron(II/III) cluster in the glycol-cleavage reaction catalyzed by myo-inositol oxygenase.  Biochemistry 45:5402-5412.

Xing, G., L. M. Hoffart, Y. Diao, S. Prabhu, R. J. Arner, C. C. Reddy, C. Krebs, and J. M. Bollinger, Jr.  Spectroscopic evidence for a coupled dinuclear iron cluster that coordinates the substrate in myo-inositol oxygenase.  Biochemistry 45:5393-5401.

Bollinger, J. M., Jr. and C. Krebs.  Stalking intermediates in oxygen activation by iron enzymes:  Motivation and method.  J. Inorg. Biochem. 100:586-605.

Behan, R. K., K. L. Stone, L. M. Hoffart, C. Krebs, and M. T. Green.  Evidence for protonated ferryls in compound II of cytochromes P450.  J. Am. Chem. Soc. 128:11471-11474.

Stone, K. L., L. M. Hoffart, R. K. Behan, C. Krebs, and M. T. Green.  Evidence for two ferryl species in chloroperoxidase compound II.  J. Am. Chem. Soc. 128:6147-6153.

Heinnickel, M., R. Agalarov, N. Svensen, C. Krebs, and J. H. Golbeck.  Identification of FX in the heliobacterial reaction center as a [4Fe-4S] cluster with an S = 3/2 ground spin state. Biochemistry 45:6756-6764.

Yuan, Y., Z.-Y. Zhu, Z.-C. Lai, and W.-X. Zhang.  Progress on breast cancer metastasis suppressor 1 (BRMS1).  Hereditas 28:1-8.

Zanuy, D., K. Gunasekaran, A. M. Lesk, and R. Nussinov.  Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices.  J. Mol. Biol. 358:330-345.

Konagurthu, A. S., P. J. Stuckey, J. C. Whisstock, and A. M. Lesk.  MUSTANG:  A MUltiple STructural AligNment AlGorithm.  Proteins 64:559-574.

Lezon, T., J. R. Banavar, A. M. Lesk, and A. Maritan.  What determines the spectrum of protein native state structures?  Proteins 63:273-277.

Qi, J., J. Yao, C. Fang, B. Lüscher, and G. Chen.  Downregulation of tonic GABA currents following epileptogenic stimulation of rat hippocampal cultures.  J. Physiol. 577:579-590.

Fang, C., L. Deng, C. A. Keller, M. Fukata, Y. Fukata, G. Chen, and B. Lüscher.  GODZ-mediated palmitoylation of GABA(A) receptors is required for normal assembly and function of GABAergic inhibitory synapses.  J. Neurosci. 26:12758-12768.

Phadke, P. A., R. R. Mercer, J. F. Harms, Y. Jia, J. C. Kappes, A. R. Frost, J. L. Jewell, K. M. Bussard, S. Nelson, C. Moore, C. V. Gay, A. M. Mastro, and D. R. Welch.  Kinetics of metastatic breast cancer cell trafficking in bone.  Clin. Cancer Res. 12:1431-1440.

Bush, J. S., A. M. Mastro, and W. J. Kraemer.  Proenkephalin peptide F immunoreactivity in different circulatory biocompartments.  Peptides 27:1498-1506.

Dhurjati R., X. Liu, C. V. Gay, A. M. Mastro, and E. A. Vogler.  Extended-term culture of bone cells in a compartmentalized bioreactor.  Tissue Eng. 12:3045-3054.

Kraemer, W. J., B. C. Nindl, J. O. Marx, L. A. Gotshalk, J. A. Bush, J. R. Welsch, J. S. Volek,  B. A. Spoering, C. M. Maresh, A. M. Mastro, and W. C. Hymer.  Chronic resistance in women potentiates growth hormone in vivo bioactivity: characterization of molecular mass variants.  Am. J. Physiol.-Endoc. M. 291:E1177-1187.

Imashimizu, M., M. Hanaoka, A. Seki, K. S. Murakami, and K. Tanaka.  The cyanobacterial principal sigma factor region 1.1 is involved in DNA-binding in the free form and in transcription activity as holoenzyme.  FEBS Lett. 580:3439-3444.

Nekrutenko, A. and J. He.  Functionality of unspliced XBP1 is required to explain the evolution of overlapping reading frames.  Trends Genet. 22:645-648.

Wilson, C. and A. Nekrutenko.  mNSC1 shows no evidence of protein-coding capacity.  Gene 29:83-85. 

Chung, W.-Y., R. Albert, I. Albert, A. Nekrutenko, and K. Makova.  Role of duplicate gene in the evolution and robustness of human gene co-expression network.  BMC Bioinformatics 27:46-60.

De Carlo, S., B. Chen, T. R. Hoover, E. Kondrashkina, E. Nogales, and B. T. Nixon.  The structural basis for assembly and function of the transcriptional activator NtrC.  Genes & Dev. 20:1485-1495.

Irvin, J. D. and B. F. Pugh.  Genome-wide transcriptional dependence on TAF1 functional domains.  J. Biol. Chem. 281:6404-6412.

Durant, M. and B. F. Pugh.  Genome-wide relationships between TAF1 and histone acetyltransferases in Saccharomyces cerevisiae.  Mol. Cell. Biol. 26:2791-2802.

Zanton, S. J. and B. F. Pugh.  Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock.  Genes Dev. 20:2250-2265.

Ioshikhes, I., I. Albert, S. J. Zanton, and B. F. Pugh.  Nucleosome positions predicted through comparative genomics.  Nat. Genet. 38:1210-1215.

Pugh, B. F.  HATs off to PIC assembly.  Mol. Cell 23:776-777.

Zhang, Z., B. Li, and J. C. Reese.  Isolation of yeast nuclei and micrococcal nuclease mapping of nucleosome positioning.  Methods Mol. Biol. 313:245-256.

Shmuel, M., L. C. Santy, S. Frank, D. Avrahami, J. E. Casanova, and Y. Altschuler.  ARNO through its coiled-coil domain regulates endocytosis at the apical surface of polarized epithelial cells.  J. Biol. Chem. 281:13300-13308.

Clarke, M., M.-A. Ewart, L. C. Santy, R. Prekeris, and G. W. Gould.  ACRP30 is secreted from 3T3-L1 adipocytes via a Rab11-dependent pathway.  Biochem. Biophys. Res. Commun. 342:1361-1367.

Paterson, J., K. Renkema, L. Burden, M. Halleck, R. A. Schlegel, P. Williamson, and D. L. Daleke.  Lipid specific activation of the murine P4-ATPase Atp8a1 (ATPase II).  Biochemistry 45:5367-5376.

Gekonge, B. N., G. Schiralli, R. A. Schlegel, and A. J. Henderson.  Signal transduction induced by apoptotic cells inhibits HIV transcription in monocytes/macrophages.  J. Leukoc. Biol. 80:953-960.

Gilbert, M. T., J. Binladen, W. Miller, C. Wiuf, E. Willerslev, H. Poinar, J. E. Carlson, J. H. Leebens-Mack, and S. C. Schuster.  Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis.  Nucleic Acids Res. 35:1-10.

Eppinger, M., C. Baar, B. Linz, G. Raddatz, C. Lanz, H. Keller, G. Morelli, H. Gressmann, M. Achtman, and S. C. Schuster.  Who ate whom?  Adaptive Helicobacter genomic changes that accompanied a host jump from primates to large felines.  PLoS Genet. 2:120.

Leininger, S., T. Urich, M. Schloter, L. Schwart, J. Qi, G. W. Nicol, J. I. Prosser, S. C. Schuster, and C. Schleper.  Archaea predominate among ammonia-oxidizing prokaryotes in soils.  Nature 442:806-809.

Velicer, G. J., G. Raddatz, S. Deiss, C. Lanz, H. Keller, S. Kadam, and S. C. Schuster.  Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor.  Proc. Natl. Acad. Sci. USA 103:8107-8112.

Lambert, C., K. J. Evans, R. Till, L. Hobley, S. Rendulic, S. C. Schuster, S. I. Aizawa, and R. E. Sockett.  Characterising the flagellar filament and the role of motility in bacterial prey-penetration by Bdellovibrio bacteriovorus.  Mol. Microbiol. 60:274-286.

Poinar, H. N., C. Schwarz, J. Qi, B. Shapiro, R. D. E. MacPhee, B. Buigues, A. Tikhonov, D. H. Huson, L. P. Tomsho, A. Auch, M. Rampp, W. Miller, and S. C. Schuster.  Metagenomics to paleogenomics: Large scale sequencing of Mammoth DNA.  Science 311:392-394.

Doyon, Y., C. Cayrou, M. Ullah, A. J. Landry, V. Cote, W. Selleck, W. S. Lane, S. Tan, X. J. Yang, and J. Cote.  ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation.  Mol. Cell 21:51-64.

Sermwittaaywong, D. and S. Tan.  SAGA binds TBP via its Spt8 subunit in competition with DNA:  implications for TBP recruitment.  EMBO J. 25:3791-3800.

Romero, H. M., E. J. Pell, and M. Tien.  Expression profile analysis and biochemical properties of the peptide methionine sulfoxide reductase A (PMSRA) gene family in Arabidopsis.  Plant Sci. 170:705-714.

Ruebush, S. S., S. L. Brantley, and M. Tien.  Reduction of soluble and insoluble iron forms by membrane fractions of Shewanella oneidensis grown under aerobic and anaerobic conditions.  Appl. Environ. Microb. 72:2925-2935.

Ruebush, S. S., G. A. Icopini, S. L. Brantley, and M. Tien.  In vitro enzymatic reduction kinetics of mineral oxides by membrane fractions from Shewanella oneidensis MR-1.  Geochim. Cosmochim. Acta 70:56-70.

Brantley, S. L., S. Ruebush, J-H Jang, and M. Tien.  Analysis of (bio)geochemical kinetics of Fe(III) oxides.  In:  Methods of Investigating Microbial-Mineral Interactions, CMS Workshop Lectures.  (J. P. A. Maurice and L. A. Warren, eds.), vol. 14, pp. 79-116, The Clay Mineral Society, Chantilly, VA.

Wang, Y.  Methylation and demethylation of histone Lys and Arg residues in chromatin structure and function.  In:  Enzymes Protein Methyltransferases.  (S. G. Clarke and F. Tamanoi, eds.), pp. 123-153, Academic Press, New York, NY.

Vaughan, D. E. W., H. P. Yennawar, and A. J. Perrotta.  Synthesis and structure of large optically clear crystals of gallogermanate sodalite.  Cryst. Growth Des. 6:2072-2075.

Zhang, W., S. Wu, Z. Zhang, H. P. Yennawar, and X. Zhang.  Practical synthesis of chiral 9,9’-spirobixanthene-1,1’-diol.  Org. Biomol. Chem. 4:4474-4477.

Vaughan, D. E. W., H. P. Yennawar, and A. J. Perrotta.  Synthesis and structure of an aluminophosphate built from 3-rings.  Chem. Mater. 18:3611-3615.

Funk, J. K., H. P. Yennawar, and A. Sen.  Cobalt-catalyzed carbonylation of N-alkylbenzaldimines to ‘N-alkylphtalimidines’(=2,3-dihydro-1H-isoindol-1-ones) via tandem C-H activation and cyclocarbonylation.  Helv. Chim. Acta 89:1687-1695.