Biochemistry and Molecular Biology
Penn State Science
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2015

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PUBLICATIONS
Biochemistry and Molecular Biology Faculty
2015

 

  • El-Mowafi, S. A., E. Sineva, J. N. Alumasa, H. Nicoloff, J. W. Tomsho, S.E. Ades, K. C. Keiler.  Identification of inhibitors of a bacterial sigma factor using a new highthroughput screening assay. Antimicrob Agents Chemother. 59:193-205.
  • Liermann, L. J, I. Albert, H. L. Buss, M. Minyard, S. L. Brantley.  Relating microbial community structure and geochemistry in deep regolith developed on volcaniclastic rock in the Luquillo Mountains, Puerto Rico. Geomicrobiology Journal. 32:21:10:18.
  • Zou, D., C. McSweeney, A. Sebastian, D. J. Reynolds, F. Dong, Y. Zhou, D. Deng, Y. Wang, L. Liu, J. S. Zhu, Y. Shi, I. Albert, Y. Mao.  A critical role of RBM8a in proliferation and differentiation of embryonic neural progenitors.  Neural Dev. 10:18:3064-015-0045-7.
  • de Bekker, C., R.A. Ohm, R. G. Loreto, A. Sebastian, I. Albert, M. Merrow, A. Brachmann, D. P. Hughes.  Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation.  BMC Genomics. 6:620.
  • Tang, Y., H. Lu, A. Sebastian, Y. T. Yeh, C. A. Praul, I. Albert, S. Y. Zheng.  Genomic characterization of a turkey reovirus field strain by next-generation sequencing.  Infec Genet Evol. 32:313-21
  • Wan, Y., D. W. Renner, I. Albert, M. L. Szpara.  VirAmp: a galaxy-based viral genome assembly pipeline.  GigaScience. 4:19.
  • Cote, R., R. Katani, M. R. Moreau, I. T. Kudva, T. M. Aruthur, C. Debroy, M. M. Mwangi, I. Albert, A. R. Garay, L. Li, M. T. Brandl, M. Q. Carter, V. Kapur.  Comparative analysis of super-shedder strains of Escherichia Coli O157:H7 reveals distinctive genomic features and a strongly aggregative adherent phenotype on bovine rectoanal junction squamous epithelial cells. PLos One.  10:2:e0116743.
  • Jiang, C., C. Xie, F. Li, L. Zhang, R. G. Nichols, C. K. Krausz, J. Cai, Y. Qi, Z. Fang, S. Takahashi, N. Tanaka, D. Desai, S. G. Amin, I. Albert, A. D. Patterson, F. Gonzalez.  Intestinal farnesoid X receptor signaling promotes nonalcoholic fatty liver disease.  J. Clin Invest. 125:1:386-402.
  • Vakulskas, C. A., A. H, Potts, P. Babitzke, B. M. Ahmer, T. Romeo.  Regulation of bacterial virulence by Csr (Rsm) systems. Microbiol. Mol. Biol. Rev. 79:193-224.
  • Abbott, Z. D., H. Yakhnin, P. Babitzke, M. S. Swanson.  csrR, a paralog and direct target of CsrA, promotes Legionella pneumophila resilience in water. MBio. 6:e00595.
  • Yakhnin, H., P. Babitzke.  Ribosomal protein L10(L12)4 autoregulates expression of the Bacillus subtilis rplJL operon by a transcription attenuation mechanism. Nucl. Acids Res. 43:7032-7043.
  • Park, H., H. Yakhnin, M. Connolly, T. Romeo, P. Babitzke.  CsrA participates in a PNPase autoregulatory mechanism by selectively repressing translation of pnp transcripts that have been previously processed by RNase III and PNPase. J. Bacteriol. 197:3751-3759.
  • Yan C., D. Y. Zhang, J. A. Garay, M. M. Mwang, L. Bai.  Decoupling of divergent gene regulation by sequence-specific DNA binding factors. Nucleic Acid Research, 43:7292-305.
  • Zhang, S., A. Ganguly, P. Goyal, J. L. Bingaman, P. C. Bevilacqua, S. Hammes-Schiffer.  Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations.  J. Am. Chem. Soc. 137:784-798.
  • Kwok, C. K., Y. Ding, S. Shahid, S. M. Assmann, P. C. Bevilacqua.  A stable RNA G-quadruplex within the 5’-UTR of Arabidopsis thaliana ATR mRNA inhibits translation.  Biochem. J. 467:91-102.
  • Bevilacqua, P. C. The Wonder of RNA: A Personal Reflection of the Last 20 Years.  RNA 21:515-516.
  • Kwok, C.K., Y. Tang, S. M. Assmann, P. C. Bevilacqua.  The RNA structurome: transcriptome-wide structure probing with next-gen sequencing.  Trends in Biochem. Sci. 40:221-232.
  • Thaplyal, P., A. Ganguly, S. Hammes-Schiffer, P. C. Bevilacqua.  Inverse thio effects in the HDV ribozyme reveal that the reaction pathway is controlled by metal ion charge density.  Biochemistry. 54:2160-2175.
  • Ding. Y., C. K. Kwok, Y. Tang, P. C. Bevilacqua, S. M. Assmann.  Structure-seq: genome-wide profiling of in vivo RNA structure at single nucleotide resolution.  Nat. Protoc. 10:1050-1066.
  • Tang, Y., E. Bouvier, Y. Ding, A. Nekrutenko, P. C. Bevilacqua, S. M. Assmann.  StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.  Bioinformatics 31:2668-2675.
  • Hull, C. M., P. C. Bevilacqua.  Mechanistic analysis of activation of the innate immune sensor PKR by bacterial RNA.  J. Mol. Biol. 427:3501-3515.
  • Crenshaw, E., B. P. Leung, C. K. Kwok, K. Olson, N. P. Sebastian, S. Ansaloni, R. Schweitzer-Stenner, M. R. Akins, P. C. Bevilacqua, A. J. Saunders.  Amyloid precursor protein translation is regulated by a 3’UTR guanine quadruplex.  PLoS One. 10:e0143160:1-18.
  • Boal, A. K., J. M. Bollinger, W. –c Chang.  Assembly of the unusual oxacycles in the orthomycin antibiotics. Proc. Natl. Acad. Sci. USA 112:11989-11990.
  • Boal, A. K., A. C. Rosenzweig.  Response to ‘Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.  Acta Crystallogr. 71:1984-1986.
  • Rajakovich, L. J., H. Nørgaard, H., N. Li, D. M. Warui, S. J. Booker, C. Krebs, J. M., Bollinger, Jr., M.-E. Pandelia.  Rapid reduction of the diferric-peroxyhemiacetal intermediate in aldehyde-deformylating oxygenase by a cyanobacterial ferredoxin: evidence for a free-radical mechanism.  J. Am. Chem. Soc. 137:11695-11709.
  • Livada, J., R. Martinie, L. M. Dassama, C. Krebs, J. M. Bollinger, Jr., A. Silakov, A.  Direct measurement of the radical translocation distance in the class I ribonucleotide reductase from chlamydia trachomatis.  J. Phys. Chem. B. 119:13777-13784.
  • Martinie, R. J., J. Livada, J., W-c Chang, M. T. Green, C. Krebs, J. M. Bollinger, Jr., A. Silakov. Experimental correlation of substrate position with reaction outcome in the aliphatic halogenase, SyrB2.  J. Am. Chem. Soc. 137:6912-6919.
  • Warui, D. M., M. E. Pandelia, L. J. Rajakovich, C. Krebs, J. M. Bollinger, Jr., S. J. Booker. Efficient delivery of long-chain fatty aldehydes from the Nostoc punctiforme acyl–acyl carrier protein reductase to its cognate aldehyde deformylating oxygenase. Biochemistry. 54:1006–10015.
  • Bauerle, M. R., E. L. Schwalm, S. J. Booker. Mechanistic diversity of radical SAM-dependent methylation. J. Biol. Chem. 290:3995–4002.
  • Lanz, N. D., S. J. Booker. Auxiliary iron-sulfur cofactors in radical SAM enzymes. Biochim. Biophys. Acta.  1853:1316–1334.
  • Pandelia, M. E., N. D. Lanz, S. J. Booker, C. Krebs, C. Mössbauer spectroscopy of Fe/S proteins. Biochim. Biophys. Acta. 1853:1395–1405.
  • Maiocco, S. J., T. L. Grove, S. J. Booker, S. J. Elliott.  Electrochemical resolution of the [4Fe–4S] centers of the AdoMet radical enzyme BtrN: evidence of proton–coupling and an unusual, low-potential auxiliary cluster. J. Am. Chem. Soc. 137:8664–8667.
  • Marous, D. R., E. P. Lloyd, A. R. Buller, K. A. Mopshos, T. L. Grove, A. J. Blaszczyk, S. J. Booker, C. A. Townsend.  Consecutive radical S-adenosylmethionine methylations form the ethyl side chain in thienamycin biosynthesis. Proc. Natl. Acad. Sci. USA, 112:10354–10358.
  • Rajakovich, L. J., H. Nørgaard, D. M. Warui, W. –C Chang, N. Li, S. J. Booker, C. Krebs, J. M. Bollinger, Jr., M. E. Pandelia.  Rapid reduction of the differic-peroxyhemiacetal intermediate in aldehyde-deformylating oxygenase by a cyanobacterial ferredoxin: Evidence for a free-radical mechanism. J. Am. Chem. Soc. 137:11695–11709.
  • McCarthy, E. L, S. J. Booker.  Bridging a gap in iron–sulfur cluster assembly. Elife, doi: 10.7554/eLife.10479.
  • Lanz, N. D., J. Rectenwald, B. Wang, E. Kakar, T. Laremore, S. J. Booker, A. Silakov. Characterization of a radical intermediate in lipoyl cofactor biosynthesis. J. Am. Chem. Soc., 137:13216­–13219.
  • Rockwell, N. C., S. S. Martin, F. Gan, D. A. Bryant, J. C. Lagarias.  NpR3784 is the prototype for a distinctive group of red/green cyanobacteriochromes using alternative Phe residues for photoproduct tuning. Photochem. Photobiol. Sci. 14:258-269.
  • Yang, M., Y. Yang, Z. Chen, J. Zhang, Lin, Y., Yan, Y. Wang, Q. Xiong, T. Li, F. Ge, D. A. Bryant, J. Zhao.  Proteogenomic analysis and global discovery of post-translational modifications in prokaryotes. Proc. Natl. Acad. Sci. USA 111:E5633-42.
  • Gan, F., G. Shen, D. A. Bryant.  Widespread distribution of far-red light photoacclimation (FaRLiP) among cyanobacteria. Life 5:4-24.
  • Zhao, C., Z. Li, T. Li, Y. Zhang, D. A. Bryant, J. Zhao.  High-yield production of extracellular type-I cellulose by the cyanobacterium Synechococcus sp. PCC 7002. Cell Discovery 1:15004.
  • Tank, M., D. A. Bryant.  Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium. Int. J. Syst. Evol. Microbiol. 65:1426-1430.
  • Tank, M., D. A. Bryant. Nutrient requirements and growth physiology of the photoheterotrophic Acidobacterium, Chloracidobacterium thermophilum. Front. Microbiol. 6:226.
  • Kim, Y.-M., S., Olsen, M. T., E. D. Becraft, V. Thiel, D. A. Bryant, J. K. Fredrickson, D. M. Ward, T. O. Metz.  Diel Metabolomics analysis of a Yellowstone National Park hot spring chlorophototrophic microbial community reveals in situ metabolisms of predominant mat inhabitants. Front. Microbiol. 6:209.
  • Becraft, E. D., J. M. Wood, D. B. Rusch, M. Kühl, S. I. Jensen, D. A. Bryant, D. W. Roberts, F. M. Cohan, D. M. Ward.  The molecular dimension of microbial species. 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park, Front. Microbiol. 6:590.
  • Nowack, S., M. T. Olsen, G. Schaible, E. D. Becraft, G. Shen, D. A. Bryant, I. Klapper, I., D. M. Ward. The molecular dimension of microbial species. 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light. Front. Microbiol. 6:626.
  • Olsen, M. T., S. Nowack, J. M. Wood, E. D. Becraft, K. LaButti, A. Lipzen, J. Martin, W. S. Schackwitz, D. B. Rusch, F. M. Cohan, D. A. Bryant, D. M. Ward.  The molecular dimension of microbial species. 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat. Front. Microbiol. 6:604.
  • Schieferdecker, S., N. Domin, C. Hoffmeier, D. A. Bryant, M. Roth, M., M. Nett.  Structure and absolute configuration of auriculamide, a natural product from the predatory bacterium Herpetosiphon aurantiacus. Eur. J. Org. Chem. 2015:3057-3062.
  • Jackson, S. A., J. J. Eaton-Rye, D. A. Bryant, M.C. Posewitz, F. K. Davies. Absence of global nitrogen deprivation responses in the Synechococcus sp. PCC 7002 glycogen-deficient ΔglgC mutant. Appl. Environ. Microbiol. 81:6210-6222.
  • Thiel, V., L. P. Tomsho, R. Burhans, S. C. Schuster, D. A. Bryant.  Draft genome sequence of Meiothermus ruber strain A (Deinococcus-Thermus). Genome Announc. 3:e00202-15.
  • Zhang, S., D. A. Bryant.  Biochemical validation of the glyoxylate cycle in the cyanobacterium Chlorogloeopsis fritschii strain PCC 9212. J. Biol. Chem. 290:14019-14030.
  • Gan, F., D. A. Bryant.  Adaptive and acclimative responses of the photosynthetic apparatus in cyanobacteria to far-red light. Environ. Microbiol. 17:3450-3465.
  • Zhang, S., Y. Liu, D. A. Bryant.  Metabolic engineering of Synechococcus sp. PCC 7002 to produce poly-3-hydroxybutyrate and poly-3-hydroxybutyrate-co-4-hydroxybutryate. Metab. Eng., 32:174-183.
  • Gorka, M., A. Peréz, C. S. Baker, B. Ferlez, A. van der Est, D. A. Bryant, J. H. Golbeck.  Electron transfer from the A1A and A1B sites to a tethered Pt nanoparticle requires FeS cluster for suppression of the recombination channel. J. Photochem. Photobiol. B: Biology 152:325-334.
  • Melendrez, M. C., E. Becraft, J. M. Wood, M. T. Olsen, D. A. Bryant, J. F. Heidelberg, D. Rusch, F. M. Cohan, D. M. Ward.  Recombination does not hinder formation or detection of ecological species of Synechococcus inhabiting a hot spring cyanobacterial mat. Front. Microbiol. 6:1540.
  • Ludwig, M., T. T. Chua, C. Y. Chew, D. A. Bryant.  Fur-type transcription repressors and metal homeostasis in the cyanobacterium Synechococcus sp. PCC 7002. Front. Microbiol. 6:1217.
  • Zhao, C., F. Gan, G. Shen, D. A. Bryant.  RfpA, RfpB, and RfpC are the master control elements for far-red light photoacclimation (FaRLiP). Front. Microbiol. 6:1303.
  • Kolli, S., X. Meng, X. Wu, D. Shengjuler, C. E. Cameron, Y. Xiang, J. Deng.  Structure-function analysis of vaccinia virus H7 protein reveals a novel phosphoinositide binding fold essential for poxvirus replication. Journal of Virology 89:2209-2219.
  • Li, S., X. Ding, Z. Mao, Y. Chen, N. Nama, F. Guo, P. Li, L. Wang, C. E. Cameron, T. J. Huang.  Standing surface acoustic wave (SSAW)-based cell washing. Lab on a chip 15:331-338.
  • Liu, X., D. M. Musser, C. A. Lee, X. Yang, J. J. Arnold, C. E. Cameron, D. D. Boehr.  Nucleobase but not Sugar Fidelity is Maintained in the Sabin I RNA-Dependent RNA Polymerase. Viruses 7:5571-5586.
  • Moustafa, I. M., D. W. Gohara, A. Uchida, N. Yennawar, C. E. Cameron. Conformational Ensemble of the Poliovirus 3CD Precursor Observed by MD Simulations and Confirmed by SAXS: A Strategy to Expand the Viral Proteome? Viruses 7:5962-5986.
  • Moustafa, I. M., A. Uchida, Y. Wang, N. Yennawar, C. E. Cameron. Structural models of mammalian mitochondrial transcription factor B2. Biochimica et biophysica acta 1849:987-1002.
  • Murugesapillai, D., M. F. Lodeiro, J. L. Maher, 3rd, C. E. Cameron, M. C. Williams.  26 Sequence-specific DNA looping by mitochondrial transcription factor A (TFAM). J. Biomol. Struct. Dyn. 33 Suppl 1:15-16.
  • Reynolds, K. A., C. E. Cameron, K. D. Raney.  Melting of Duplex DNA in the Absence of ATP by the NS3 Helicase Domain through Specific Interaction with a Single-Strand/Double-Strand Junction. Biochemistry 54:4248-4258.
  • van der Linden, L., L. Vives-Adrian, B. Selisko, C. Ferrer-Orta, X. Liu, K. Lanke, R. Ulferts, A. M. De Palma, F. Tanchis, N. Goris, D. Lefebvre, K. De Clercq, P. Leyssen, C. Lacroix, G. Purstinger, B. Coutard, B. Canard, D. D. Boehr, J. J. Arnold, C. E. Cameron, N. Verdaguer, J. Neyts, F. J. van Kuppeveld. The RNA template channel of the RNA-dependent RNA polymerase as a target for development of antiviral therapy of multiple genera within a virus family. PLoS Pathog. 11:e1004733.
  • Van Slyke, G. A., J. J. Arnold, A. J. Lugo, S. B. Griesemer, I. M. Moustafa, L. D. Kramer, C. E. Cameron, A. T. Ciota.  Sequence-Specific Fidelity Alterations Associated with West Nile Virus Attenuation in Mosquitoes. PLoS Pathog. 11:e1005009.
  • Chunming L., D. Huang, Y. Tinglu, P. S. Cremer.  The simultaneous detection of multiple proteins that bind to the identical ligand on supported lipid bilayers.  Anal. Chem. 87:7163-7170.
  • Cong, X., M. F. Poyton, A. J. Baxter, S. Pullanchery, P. S. Cremer. Unquenchable surface potential dramatically enhances Cu2+ binding to phosphatidylserine lipids.  J. Am. Chem. Soc. 137:7785-7792.
  • Rembert, K. B., H. I. Okur, C. Hilty, P.S. Cremer.  An NH moiety is not required for anion binding to amides in aqueous solution.  Langmuir. 31:3459-3464.
  • Prebihalo, S., A. Brockman, J. Cochran, F. L. Dorman. Determination of emerging contaminants in wastewater utilizing comprehensive two-dimensional gas-chromatography coupled with time-of-flight mass spectrometry. J. Chromatogr. A. 1419:109-115.
  • Organtini, K. L., A. L. Myers, K. J. Jobst, E. J. Reiner, B. Ross, A. Ladak, L. Mullin, D. Stevens, F. L. Dorman. Quantitative analysis of mixed halogen dioxins and furans in fire debris utilizing atmospheric pressure ionization gas chromatography-triple quadrupole mass spectrometry.  Anal. Chem. 87:10368-10377.
  • Boswell, H., F. L. Dorman. Uncertainty of blood alcohol concentration (BAC) results as related to instrumental conditions: optimization and robustness of BAC analysis parameters. Chromatography. 2: 691-708.
  • Organtini, K. L., L. Haimovici, K. J. Jobst, E. J. Reiner, A. Ladak, D. Stevens, J. W. Cochran, F. L. Dorman. Comparison of atmospheric pressure ionization gas chromatography-triple quadrupole mass spectrometry to traditional high-resolution mass spectrometry for the identification and quantification of halogenated dioxins and rurans. Anal. Chem. 87:7902–7908.
  • Llewellyn, G. T., F. L. Dorman, J. L. Westland, D. Yoxtheimer, P. Grieve, T. Sowers, E. Humston-Fulmer, S. L. Brantley. Evaluating a groundwater supply contamination incident attributed to Marcellus Shale gas development. Proc. Natl. Acad. Sci. USA. 112:6325–6330.
  • Parette, R., R. McCrindle, K.  S. McMahon, M. Pena-Abaurrea, E. Reiner, B. Chittim, N. Riddell, G. Voss, F. L. Dorman,W. N. Pearson. Halogenated Indigo Dyes: The Likely Source of 1,3,6,8-Tetrabromocarbazole and Other Halogenated Carbazoles Found in the Environment. Chemosphere. 127:18-26.
  • Mueller, T. J., M. J. Grisewood, H. Nazem-Bokaee, S. Gopalakrishnan, J. G. Ferry, T. K. Wood and C. D. Maranas. Methane oxidation by anaerobic archaea for conversion to liquid fuels. J. Ind. Microbiol. Biotechnol. 42:391-401.
  • Kumar, A. K., R. S. Kumar, N. H. Yennawar, H. P. Yennawar, J. G. Ferry. Structural and biochemical characterization of a ferredoxin:thioredoxin reductase-like enzyme from Methanosarcina acetivorans. Biochemistry. 54:3122-3128.
  • Ferry, J. G. Acetate metabolism in anaerobes from the domain Archaea. Life. 5:1454-1471.
  • Wei, Y., B. Li, D. Prakash, J. G. Ferry, S. J. Elliott, J. Stubbe. A ferredoxin disulfide reductase delivers electrons to the Methanosarcina barkeri class III ribonucleotide reductase. Biochemistry. 54:7019-7028.
  • Yenugudhati, D., D. Prakash, A. K. Kumar, R. S. Kumar, N. H. Yennawar, H. P. Yennawar, J. G. Ferry. Structural and biochemical characterization of methanoredoxin from Methanosarcina acetivorans, a glutaredoxin-like enzyme with coenzyme M-dependent protein disulfide reductase activity. Biochemistry. 55:313-321.
  • Li, J., D.S. Gilmour. Reconstitution of factor-dependent, promoter proximal pausing in Drosophila nuclear extracts. Methods Mol. Biol. 1276:133-152.
  • Schröder J., S. Girirajan, A.T. Papenfuss, P. Medvedev. Improving the Power of Structural Variation Detection by Augmenting the Reference. PLoS One. 10(8):e0136771.
  • Polyak A., J.A. Rosenfeld, S. Girirajan. An assessment of sex bias in neurodevelopmental disorders. Genome Med. 7(1):94.
  • Polyak A., R. Kubina, S. Girirajan. Comorbidity of intellectual disability confounds ascertainment of autism: Implications for genetic diagnosis. Am. J. Med. Genet B Neuropsychiatr Genet. 168(7):600-608.
  • Korvatska O., J. B. Leverenz, S. Jayadev, P. McMillan, I. Kurtz, X. Guo, M. Rumbaugh, M. Matsushita, S. Girirajan, M. O. Dorschner, K. Kiianitsa, C. E. Yu, Z. Brkanac, G. A. Garden, W. H. Raskind, T. D. Bird, R47H Variant of TREM2 Associated with Alzheimer Disease in a Large Late-Onset Family: Clinical, Genetic, and Neuropathological Study. JAMA Neurol. 72(8):920-927.
  • Mazina V., J. Gerdts, S. Trinh, K. Ankenman, T. Ward, M. Y. Dennis, S. Girirajan, E. E. Eichler, R. Bernier. Epigenetics of autism-related impairment: copy number variation and maternal infection. J. Dev. Behav. Pediatr. 36(2):61-67.
  • McConnell, M.D., J. Sun, R. Siavashi, A. Webber, K.E. Redding, J. H. Golbeck, and A. van der Est. “Species-dependent alteration of electron transfer in the early stages of charge stabilization in Photosystem I, Biochem. Biophys. Acta 1847:429-440.
  • Applegate, A., C. Lubner, P. Knorzer, T. Happe and J. H. Golbeck. "Quantum yield measurements of light-induced H2 generation in a photosystem I-[FeFei-H2ase nanoconstruct." Photosynth Res 127(1) 5-11.
  • Ferlez, B., W. Dong, R. Siavashi, K. Redding, H. J. Hou, J. H. Golbeck and A. van der Est. "The effect of bacteriochlorophyll g oxidation on energy and electron transfer in reaction Centers from Heliobacterium modesticaldum." JPhys Chem B 119(43):13714-13725.
  • Sun, J. and J. H. Golbeck. "The presence of the IsiA-PSI supercomplex leads to enhanced Photosystem I Electron throughput in iron-starved cells of Synechococcus sp. PCC 7002." JPhys Chem B 119(43): 13549-13559.
  • Gorka, M., A. Perez, C. S. Baker, B. Ferlez, A. van der Est, D. A. Bryant, and J. H. Golbeck. "Electron transfer from the ALA and Am sites to a tethered Pt nanoparticle requires the FeS clusters for suppression of the recombination channel." J Photochem Photobiol B 152(B): 325-334.
  • Ishara Silva, K., B. Jagannathan, J. H. Golbeck, and K. V. Lakshmi, “Elucidating the design principles of photosynthetic electron-transfer proteins by site-directed spin labeling EPR spectroscopy, Biochim Biophys Acta 2015 DOI: 10.1016/j .bbabio.2015.08.009
  • Lei L., A. Singh, L. Bashline, S. Li, Y. G. Yingling, Y. Gu. The Arabidopsis cellulose synthase interactive 1 is required for a fast recycling of cellulose synthase complex to the plasma membrane. Plant Cell. (10):2926-2940.
  • Li S., L. Lei, Y. G. Yingling, Y. Gu. Microtubules and cellulose biosynthesis: the emergence of new players. Curr. Opin. Plant Biol. 28:76-82.
  • Bashline L., S. Li, X. Zhu, Y. Gu. The TWD40-2 protein and the AP2 complex cooperate in the clathrin-mediated endocytosis of cellulose synthase to regulate cellulose biosynthesis. Proc. Natl. Acad. Sci. USA 112(41):12870-12875.
  • Wang S., X. A. Chen, J. Hu, J. K. Jiang, Y. Li, K. Y. Chan-Salis, Y. Gu, G. Chen, C. Thomas, B. F. Pugh, Y. Wang. ATF4 gene network mediate cellular response to the anticancer PAD4 inhibitor YW3-56. Mol. Cancer Ther. 14:877-888.
  • Bashline L., Y. Gu. Using the Split-Ubiquitin yeast two-hybrid systems to test protein-protein interactions of transmembrane proteins. Method. Mol. Biol. 1242:143-158
  • Wang W., M. R. McReynolds, J. F. Goncalves, M. Shu, I. Dhondt, B. P. Braeckman, S. E. Lange, K. Kho, A. C. Detwiler, M. J. Pacella, W. Hanna-Rose. Comparative metabolomic profiling reveals that dysregulated glycolysis stemming from lack of salvage NAD+ biosynthesis impairs reproductive development in Caenorhabditis elegans. J Biol Chem. 290(43):26163-26179.
  • Hsiung, C. C., C. S. Morrissey, M. Udugama, C. L. Frank, C. A. Keller, S. Baek, B. Giardine, G. E. Crawford, M.H. Sung, R. C. Hardison, G. A. Blobel. Genome accessibility is widely preserved and locally modulated during mitosis. Genome Res. 25:213-225.
  • Olgert D., R. Sandstrom, Y. Cheng, K. Beal, J. Herrero, R. C. Hardison, J. Taylor. Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution. BMC Genomics. 16:87.
  • Byrska-Bishop, M., D.  VanDorn, A. E. Campbell, M. Betensky, P. R. Arca, Y. Yao, P. Gadue, F. F. Cost, R. L. Nemiroff, G. A. Blobel, D. L. French, R. C. Hardison, M. J. Weiss, S. T. Chou. Pluripotent stem cells reveal novel erythroid activities of the GATA1 N-terminus. J Clin Invest. 125:993-1005.
  • Stonestrom, A. J., S. C. Hsu, K. S. Jahn, P. Huang, S. Kadauke, A. E. Campbell, C. A. Keller, B. Giardine, R. C. Hardison, G. A. Blobel. Function of BET proteins in GATA1-mediated transcriptional activation. Blood. 125(18):2825-34.
  • Deepti J., M. Tejaswini, B. M. Giardine, C. A. Keller, C. S. Morrissey, S. Magargee, C. M. Dorman, M.  Long, M. J. Weiss, R. C. Hardison. Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system. Genomics Data. 4:1-7.
  • Makova, K. D., R. C. Hardison. The Effects of Chromatin Organization on Variation in Mutation Rates in the Genome. Nat Rev Genet. 16:213-223.
  • Nergiz D., W. Wu, C. S. Morrissey, K. B. Chen, A. Stonestrom, M. Long, C. A. Keller, Y. Cheng, D. Jain, A. Visel, L. A. Pennacchio, M. J. Weiss, G. A. Blobel, R. C. Hardison. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics and Chromatin. 8:16.
  • Han, G. C., V. Vinayachandran, A. R. Bataille, B. Park, K. Y. Chan-Salis, C. A. Keller, M. Long, S. Mahony, R. C. Hardison, B. F. Pugh. Genome-wide organization of GATA1 and TAL1 determined at high resolution. Mol. Cell. Biol. 36:157-172.
  • Holland, M., J. McElhoe. A Custom Software Solution for Forensic mtDNA Analysis of MiSeq Data. Forensic Science International: Genetics. (Supplemental Series), 5:e614-e16.
  • Basic, Z., A. R. Fox, I. Anteric, I. Jerkovic, O. Polasek, S. Andelinovic, M. Holland, D. Primorac.  Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast. Croat Med J. 56:230-238.
  • Holland, M., F. Wendt. Evaluation of the RapidHIT™ 200, an automated human identification system for STR analysis of single source samples. Forensic Science International: Genetics. 14:76-85.
  • Deng Y., N. Nagachar, L. Fang, X. Luan, J. M. Catchmark, M. Tien, T-h. Kao. Identification and characterization of two cellulose morphology mutants of Gluconacetobacter hansenii ATCC23769 producing cellulose with lower crystallinity. PLoS ONE. 10:(3):e0119504.
  • Williams, J. S., L. Wu, S. Li, P. Sun, T-h. Kao. Insight into S-RNase-based self-incompatibility in Petunia: recent findings and future directions. Front Plant Sci. oi:10.3389/fpls.2015.00041.
  • Sun, P., S. Li, D. Lu, J. S. Williams, T-h. Kao. Pollen S-locus F-box proteins of Petunia involved in S-RNase-based self-incompatibility are themselves subject to ubiquitin-mediated degradation. Plant J. 83:213-223.
  • McManus, J.B., Y. Deng, N. Nagachar, T-h. Kao, M. Tien. AcsA-AcsB: The core of the cellulose synthase complex from Glucoacetobacter hansenii ATCC23769. Enzyme Microb Technol. doi: 10.1016/j.enzmictec.2015.08.015.
  • El-Mowafi, S. A, E. Sineva, J. N. Alumasa, H. Nicoloff, J. W. Tomsho, S. E. Ades, K. C. Keiler. Identification of inhibitors of a bacterial sigma factor using a new high-throughput screening assay. Antimicrob Agents and Chemother. 59: 193-205.
  • Fagerlund, R. D., A. Perederina, I. Berezin, A. S. Krasilnikov. Footprinting analysis of interactions between the largest eukaryotic RNase P/MRP protein Pop1 and RNase P/MRP RNA components. RNA 21:1591-1605
  • Warui, D. M., M.-E Pandelia, L. J. Rajakovich, C. Krebs, J. M. Bollinger, Jr., S. J. Booker. Efficient delivery of long-chain fatty aldehydes from the nostoc punctiforme Acyl Acyl carrier protein reductase to its cognate aldehyde-deformylating oxygenase. Biochemistry. 54:1006-1015.
  • Bollinger, J. M., Jr., W-c. Chang, M. L. Matthews, R. J. Martinie, A. K. Boal, C. Krebs. “Mechanisms of 2-oxoglutarate-dependent oxygenases: The hydroxylation paradigm and beyond” in “2-oxoglutarate-dependent oxygenases.” Hausinger, R. P. and Schofield, C. J.; The Royal Society of Chemistry, London, 95-122.
  • Pandelia, M.-E., N. D. Lanz, S. J. Booker, C. Krebs. Mössbauer Spectroscopy of Fe/S Proteins. Biochem. Biophys. Acta. 1853:1395-1405.
  • Martinie, R. J., J. Livada, W-c. Chang, M. T. Green, C. Krebs, J. M. Bollinger, Jr., A. Silakov. Experimental correlation of substrate position with reaction outcome in the aliphatic halogenase, SyrB2. J. Am. Chem. Soc. 137: 6912-6919.
  • Livada, J., R. J. Martinie, L. M. Dassama, C. Krebs, J. M. Bollinger, Jr., A. Silakov. Direct measurement of the radical translocation distance in the class I ribonucleotide reductase from chlamydia trachomatis. J. Phys. Chem B. 119:13777-13784.
  • Rajakovich, L. J., H. Nørgaard, D. M. Warui, W-c. Chang, S. J. Booker, C. Krebs, J. M. Bollinger, Jr., M.-E Pandelia. “Rapid Reduction of the Diferric-Peroxyhemiacetal Intermediate in Aldehyde-Deformylating Oxygenase by a Cyanobacterial Ferredoxin: Evidence for a Free-Radical Mechanism.” J. Am. Chem. Soc.  137: 11695-11709.
  • Nakashige, T. G.; B. Zhang, C. Krebs, E. M. Nolan. “Human Calprotectin is an Iron-Sequestering Host-Defense Protein” Nature Chem. Biol. 11:765-771.
  • Li, Q. and Z.-C Lai. Recent progress in studies of factors that elicit -cell expansion. Protein & Cell. 6: 81-87.
  • Yu, T., Bachman, J., and Z.-C Lai. “Mutation analysis of large tumor suppressor genes LATS1 and LATS2 supports a tumor suppressor role in human cancer.” Protein & Cell. 6: 6-11.
  • Reddy, B.P.N., S. Shrestha, K. J. Hart, X. Liang, K. Kemirembe, L. Cui, S. E. Lindner. “A bioinformatic survey of RNA-binding proteins in Plasmodium.” BMC Genomics 16:890.
  • Mikolajczak, S.A., A. V. Vaughan, N. Kangwanrangsan, N. Yimamnuaychok, N. Rezakhani, M. Fishbauger, V. Lakshmanan, N. Singh, A. Kaushansky, M. Baldwin, S. E. Lindner, J. H. Adams, J. Prachumsri, and S. H. Kappe. “Plasmodium vivax liver stage development and hypnozoite persistence in human liver chimeric mice.” Cell Host Microbe. 17(4): 526-35.
  • Cobbold S.A., M. Llinás, K. Kirk. “Sequestration and metabolism of host cell arginine by the intraerythrocytic malaria parasite Plasmodium falciparum.” Cellular Microbiology. Dec 3;doi: 10.1111/cmi.12552.
  • Adjalley SH, D. Scanfeld, M. Muhle, E. Kozlowski, M. Llinás, D.A. Fidock. “Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum
  • transporters and drug resistance determinants PfCRT and PfMDR1.” BMC Genomics. 16(1):1090.
  • Ochoa A, J. D. Storey, M. Llinás, M. Singh. “Beyond the E-value: stratified statistics for protein domain prediction.” PLoS Computational Biology. 11(11):e1004509.
  • Pulcini S, H. M. Staines, A. H. Lee, S. H. Shafik, G. Bouyer, C. M. Moore, D. A. Daley, M. J. Hoke, L. M. Altenhofen, H. J. Painter, J. Mu, M. Llinás, D.J.P. Ferguson, R.E. Martin, D.A. Fidock, R. A. Cooper, S. Krishna. “Mutations in PfCRT enlarge the malaria parasite’s food vacuole and alter drug sensitivities.” Scientific Reports. 5:14552: doi:10.1038/srep14552.
  • Ke H, I. A. Lewis, J. M. Morrisey, K. J. McLean, S. M. Ganesan, H. J. Painter, M. W. Mather, M. Jacobs-Lorena, M. Llinás, A. B. Vaidya. “Genetic Investigation of Tricarboxylic Acid Metabolism during the Plasmodium falciparum Life Cycle.” Cell Reports. pii: S2211-1247(15)00264-8. doi: 10.1016/j.celrep.2015.03.011.
  • Eshar S, L. Altenhofen, A. Rabner, P. Ross, Y. Fastman, Y. Mandel-Gutfreund, R. Karni R, M. Llinás,  R. Dzikowski. “PfSR1 controls alternative splicing and steady state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs.” Molecular Microbiology. doi: 10.1111/mmi.13007.
  • Ren Z, N. Sahir, S. Murakami, B.A. Luellen, J. C. Earnheart, R. Lal, J. Y. Kim, H. Song, B. Luscher. “Defects in dendrite and spine maturation and synaptogenesis associated with an anxious-depressive-like phenotype of GABAA receptor-deficient mice.” Neuropharmacology. 89:171-179.
  • Luscher B, T. Fuchs. “GABAergic control of depression-related brain states, In Diversity and function of GABA receptors: A tribute to Hanns Möhler, Part B.” Advances in Pharmacology. 73:97-144.
  • Ebersole, B., J. Petko, M. Woll, S. Murakami, K. Sokolina, V. Wong, I. Stagljar, B. Luscher, R. Levenson. “Effect of C-terminal S-palmitoylation on D2 dopamine receptor trafficking and stability.”  PLoS One. 10: e0140661.
  • Mahony, S., B.F. Pugh. “Protein-DNA binding in high resolution.” Critical Reviews in Biochemistry and Molecular Biology. 50(4):269-283.
  • Sosnoski, D.M., R. J. Norgard, C. D. Grove, S. F. Foster, A. M. Mastro. “Dormancy and growth of metastatic breast cancer cells in a bone-like microenvironment.” Clin Exp Metastasis. 32: 335-44.
  • Krishnan, V, E. A. Vogler, A. M. Mastro. “Three-Dimensional in vitro model to study osteobiology and osteopathology.” J Cell Biochem. 116: 2715-23.
  • Santiago, M., L. M. Matano, S. H. Moussa, M. S. Gilmore, S. Walker, T. C. Meredith. “A new platform for ultra-high-density Staphylococcus aureus transposon libraries.” BMC Genomics. 16:252. doi: 10.1186/s12864-015-1361-3.
  • Mamat, U., K. Wilke, D. Bramhill, A. B. Schrommc, B. Lindner, B., T. A. Kohle, J. L. Corcherof, A. Villaverde, L. Schafferi, S. R. Head, C. Souvignier, T. C. Meredith, and R. W. Woodard.  “Detoxifying Escherichia coli for endotoxin-free production of recombinant proteins.” Microb Cell Factories. 14(1):57. doi: 10.1186/s12934-015-0241-5.
  • Sun, Y., S. C. Verma, H. Bogale, H., & T. Miyashiro. “NagC represses N-acetyl-glucosamine utilization genes in Vibrio fischeri within the light organ of Euprymna scolopes.” Frontiers in microbiology. 6:741.
  • Miyashiro, T. “The curious meeting of two partners: the squid-vibrio symbiosis.” Microbiology Today Charlesworth Press. 43(3), 106-109.
  • Yang Y, V. C. Darbari, N. Zhang, D. Lu, R. Glyde, Y.P. Wang, J. T. Winkelman, R. L. Gourse, K. S.  Murakami, M. Buck, X. Zhang. “TRANSCRIPTION. Structures of the RNA polymerase-σ54 reveal new and conserved regulatory strategies.” Science. 349:882-885.
  • Murakami KS. “Structural biology of bacterial RNA polymerase.” Biomolecules. 5:848-864.
  • Hauryliuk V, G. C. Atkinson, K. S. Murakami, T. Tenson, K. Gerdes K. “Recent functional insights into the role of (p)ppGpp in bacterial physiology.” Nat Rev Microbiol. 13:298-309.
  • Molodtsov V, P. R. Fleming, C. J. Eyermann, A. D. Ferguson, M. A. Foulk, D. C. McKinney, C. E. Masse, E. T. Buurman, K. S. Murakami. “X-ray crystal structures of Escherichia coli RNA polymerase with switch region binding inhibitors enable rational design of squaramides with an improved fraction unbound to human plasma protein.” J MedChem. 58:3156-3171.
  • Tang, Y., E. Bouvier, C. K. Kwok, Y. Ding, A. Nekrutenko, P. C. Bevilacqua, & S. M. Assmann. “StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.” Bioinformatics. (Oxford, England). 31(16), 2668-75.
  • Blankenberg, D. J., J. C. Taylor, & A. Nekrutenko. “Online resources for genomic analysis using high-throughput sequencing.” Cold Spring Harbor protocols. (4), 324-35.
  • Vandavasi, V.G., D. K. Putnam, Q. Zhang, L. Petridis, W. T. Heller, B. T. Nixon, C. H. Haigler, U. Kalluri, L. Coates, P. Langan, J. C. Smith, J. Meiler, H. O'Neill. “A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers.” Plant Physiol. 170, 123-135. doi: 10.1104/pp.15.01356.
  • Cho, S.H., J. Du, I. Sines, V. G. Poosarla, V. Vepachedu, K. Kafle, Y. B. Park, S. H. Kim, M. Kumar, B. T. Nixon. “In vitro synthesis of cellulose microfibrils by a membrane protein from protoplasts of the non-vascular plant Physcomitrella patens.” Biochem J. 470, 195-205. doi: 10.1042/BJ20141391.
  • Erbakan, M., B. S. Curtis, B. T. Nixon, M. Kumar, W. R. Curtis. “Advancing Rhodobacter sphaeroides as a platform for expression of functional membrane proteins.” Protein Expr Purif. 115,109-117. doi: 10.1016/j.pep.2015.05.012.
  • Gresock, M.G., K. A. Kastead, and K. Postle.  “From Homodimer to Heterodimer and Back: Elucidating the TonB Energy Transduction Cycle.”  J. Bacteriol.  197:3433-3445.
  • Wang S., X. A. Chen, J. Hu, J. K. Jiang, Y. Li, K. Y. Chen-Salis, Y. Gu, G, Chen, C. Thomas, B. F. Pugh, Y. Wang. “ATF4 Gene Network Mediates Cellular Response to the Anticancer PAD Inhibitor YW3-56 in Triple Negative Breast Cancer Cells.” Mol Cancer Ther. 14, 877-888.
  • Mahony S, B. F. Pugh. Protein-DNA binding in high-resolution. Crit Rev Biochem Mol Biol. 3:1-15.
  • Han G.C., V. Vinayachandran, A. R. Bataille, B. Park, K. Y. Chan-Salis, C. A. Keller, M. Long S. Mahony, R. C. Hardison, B. F. Pugh. “Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution. Mol Cell Biol. 36:157-172.
  • Reja, R., V. Vinayachandran, S. Ghosh, & B. F. Pugh. “Molecular mechanisms of ribosomal protein gene coregulation.” Genes & Devel. 29:1942-1954.
  • Schneider M., D. Hellerschmied, T. Schubert, S. Amlacher, V. Vinayachandran, R. Reja, B. F. Pugh, T. Clausen, A. Köhler. “The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression.” Cell 162:1016-1028.
  • Dutta, A., V. Babbarwal, J. Fu, D. Brunke-Reese, D. M.  Libert, J. Willis and J. C.  Reese. “Ccr4-Not and TFIIS function cooperatively to rescue arrested RNA polymerase II.” Mol. Cell Biol, 35:1915-1925.
  • Salem, J. C., M. M. Reviriego-Mendoza and L. C. Santy. "ARF-GEF Cytohesin-2/ARNOregulates R-Ras and alpha5-integrin recycling through an EHD1-positive compartment." Mol Biol Cell 26:4265-4279.
  • Reviriego-Mendoza, M. M. and L. C. Santy. "The cytohesin guanosine exchange Factors(GEFs) are required to promote HGF-mediated renal recovery after acute kidney injury (AKI) in mice." Physiol Rep 3(6): e12442.
  • Quarles, K.A., D. Chadalavada, & S. A. Showalter. “Deformability in the Cleavage Site of Primary MicroRNA is Not Sensed by the Double-Stranded RNA Binding Domains in the Microprocessor Component DGCR8.” Proteins: Struct. Funct. Bioinf. 83:1165-1179. PMCID: PMC4446130.
  • Gibbs, E.B., & S. A. Showalter, “Quantitative Biophysical Characterization of Intrinsically Disordered Proteins.” Biochemistry, 54:1314-1326.
  • Acevedo, R., N. Orench-Rivera, K. A. Quarles, & S. A. Showalter. “Helical Defects in MicroRNA Influence Protein Binding by TAR RNA Binding Protein.” PLoS One, 10, e0116749.
  • Wan Y, D. W. Renner, I. Albert, M. L. Szpara. “VirAmp: a galaxy-based viral genome assembly pipeline.” GigaScience. 28:4:19.
  • Parsons L.R., Y.R. Tafuri, J. T. Shreve, C. D. Bowen, M. M. Shipley, L. W. Enquist, M. L. Szpara. “Rapid genome assembly and comparison decode intrastrain variation in human alphaherpesviruses.” MBio. Mar 31;6(2). pii: e02213-14.
  • R.K. McGinty and S. Tan. “Nucleosome structure and function.” Chem. Reviews. 115:2255-2273.
  • S. Kim, N. Chatterjee, M.J. Jennings, B. Bartholomew and S. Tan. “Extranucleosomal DNA enhances the activity of the LSD1/CoREST histone demethylase complex.” Nucl. Acid Research. 43:4868-4880.
  • Y.-M. Kuo, R.A. Ryan, S. Tan, J. Cote and A. Andrews. “Site specificity analysis of Piccolo NuA4-mediated acetylation for different histone complexes.” Biochem. J. 472:239-248.
  • Mansi Khanna, M.R., S. Crilly, K. J. Bakerink, S. Harper, D. W. Speicher, and G. H. Thomas, G.H. “Spectrin tetramer formation is not required for viable development in Drosophila.” J. Biol. Chem. 290:706–715.
  • Deng, Y, N. Nagachar, L. Fang, X. Luan, J. M. Catchmark, M. Tien, T.-h Kao. “Isolation and Characterization of Two Cellulose Morphology Mutants of Gluconacetobacter hansenii ATCC23769 Producing Cellulose with Lower Crystallinity.” TH, PLoS ONE. Volume: 10, Issue: 3
  • Y. Liu, X. Zhang, W.T. Chen, Y.L. Tan, J.W. Kelly, “Fluorescence turn-on folding sensor to monitor proteome stress in live cells.” J Am Chem Soc. 137:11303-11311.
  • Y.H. Cho, X. Zhang, Y. Liu, K. Fayer, D.L. Powers, J.W. Kelly, L. Gierasch. E.T. Powers.  “Individual and collective contributions of chaperonin and degradation to protein homeostasis in E. coli.Cell Reports. 11:321-33.

 

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