Molecular and Structural Biochemistry - 2014 Hassan, H. M. (2014, October 21). The Chicken Gut Microbiome and Salmonella. Invited presentation presented at the United State Animal Health Association – Annual Meeting, Arkansas, MO. Ballou, A. L., Ali, R., Mendoza, M., Hassan, H., & Koci, M. D. (2014). Development of the chick microbiome: How early exposure influences future microbial diversity. Presented at the Symposium on Gut Health, St Louis, MO. Allali, I., Cadenas, M. B., Ballou, A., Mendoza, M., Ali, R., Hassan, H., … Azcarate-Peril, M. A. (2014, May 20). Comparative analysis of 16S amplicon sequencing data from Roche 454 and Ion Torrent PGM platforms. Presented at the UNC Research Computing Symposium. Hassan, H. (2014). A vector for vaccination against Lyme Disease and other insect transmitted diseases using a live Salmonella vaccine [Invention Disclosure]. Meilleur, F. (2014). ORNL hosts the participants of the 4thNeutrons in Structural Biology Workshop and the IMAGINE single crystal neutron diffractometer first external users. Neutron News, 25(1), 12–12. https://doi.org/10.1080/10448632.2014.870435 Meilleur, F. (2014). The Neutrons in Structural Biology Workshop celebrates its 5th edition. Neutron News, 25(4), 11–11. https://doi.org/10.1080/10448632.2014.955418 A genome-scale resource for the functional characterization of Arabidopsis transcription factors. (2014). Cell Reports. https://doi.org/10.1016/j.celrep.2014.06.033 Cheng, K., Ibrahim, A., Hensley, M. T., Shen, D., Sun, B., Middleton, R., … Marban, E. (2014). Relative Roles of CD90 and c-Kit to the Regenerative Efficacy of Cardiosphere-Derived Cells in Humans and in a Mouse Model of Myocardial Infarction. JOURNAL OF THE AMERICAN HEART ASSOCIATION, 3(5). https://doi.org/10.1161/jaha.114.001260 Cade, C., Swartz, P., MacKenzie, S. H., & Clark, A. C. (2014). 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C., Lustgarten, M., Berman, K. G., Vivrette, S., & Redding, W. R. (2014). Surgical treatment of synovial osteochondromatosis in the middle carpal joint of a pony. EQUINE VETERINARY EDUCATION, 26(8), 395–399. https://doi.org/10.1111/eve.12093 Olson, A. L., Tucker, A. T., Bobay, B. G., Soderblom, E. J., Moseley, M. A., Thompson, R. J., & Cavanagh, J. (2014). Structure and DNA-Binding Traits of the Transition State Regulator AbrB. STRUCTURE, 22(11), 1650–1656. https://doi.org/10.1016/j.str.2014.08.018 Brackett, C. M., Melander, R. J., An, I. H., Krishnamurthy, A., Thompson, R. J., Cavanagh, J., & Melander, C. (2014). Small-Molecule Suppression of beta-Lactam Resistance in Multidrug-Resistant Gram-Negative Pathogens. JOURNAL OF MEDICINAL CHEMISTRY, 57(17), 7450–7458. https://doi.org/10.1021/jm501050e Cao, J., Guenther, R. H., Sit, T. L., Opperman, C. H., Lommel, S. A., & Willoughby, J. A. (2014). Loading and Release Mechanism of Red Clover Necrotic Mosaic Virus Derived Plant Viral Nanoparticles for Drug Delivery of Doxorubicin. SMALL, 10(24), 5126–5136. https://doi.org/10.1002/smll.201400558 Loziuk, P. L., Sederoff, R. R., Chiang, V. L., & Muddiman, D. C. (2014). Establishing ion ratio thresholds based on absolute peak area for absolute protein quantification using protein cleavage isotope dilution mass spectrometry. ANALYST, 139(21), 5439–5450. https://doi.org/10.1039/c4an00567h Vandergriff, A. C., Hensley, T. M., Henry, E. T., Shen, D., Anthony, S., Zhang, J., & Cheng, K. (2014). Magnetic targeting of cardiosphere-derived stem cells with ferumoxytol nanoparticles for treating rats with myocardial infarction. BIOMATERIALS, 35(30), 8528–8539. https://doi.org/10.1016/j.biomaterials.2014.06.031 Shen, W., Dallas, M. B., Goshe, M. B., & Hanley-Bowdoin, L. (2014). SnRK1 Phosphorylation of AL2 Delays Cabbage Leaf Curl Virus Infection in Arabidopsis. JOURNAL OF VIROLOGY, 88(18), 10598–10612. https://doi.org/10.1128/jvi.00761-14 Simmons, J. K., Dirksen, W. P., Hildreth, B. E., III, Dorr, C., Williams, C., Thomas, R., … Rosol, T. J. (2014). Canine Prostate Cancer Cell Line (Probasco) Produces Osteoblastic Metastases In Vivo. PROSTATE, 74(13), 1251–1265. https://doi.org/10.1002/pros.22838 Cheng, K., Shen, D., Hensley, M. T., Middleton, R., Sun, B., Liu, W., … Marban, E. (2014). Magnetic antibody-linked nanomatchmakers for therapeutic cell targeting. NATURE COMMUNICATIONS, 5. https://doi.org/10.1038/ncomms5880 Huang, B.-W., Miyazawa, M., & Tsuji, Y. (2014). Distinct regulatory mechanisms of the human ferritin gene by hypoxia and hypoxia mimetic cobalt chloride at the transcriptional and post-transcriptional levels. CELLULAR SIGNALLING, 26(12), 2702–2709. https://doi.org/10.1016/j.cellsig.2014.08.018 Bodenheimer, A. M., Cuneo, M. J., Swartz, P. D., He, J., O'Neill, H. M., Myles, D. A., … Section, F. (2014). Crystallization and preliminary X-ray diffraction analysis of Hypocrea jecorina Cel7A in two new crystal forms. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 70(Pt 6), 773–776. https://doi.org/10.1107/s2053230x14008851 Lin, Y.-C., Li, W., Chen, H., Li, Q., Sun, Y.-H., Shi, R., … Chiang, V. L. (2014). A simple improved-throughput xylem protoplast system for studying wood formation. NATURE PROTOCOLS, 9(9), 2194–2205. https://doi.org/10.1038/nprot.2014.147 Li, W., Lin, Y.-C., Li, Q., Shi, R., Lin, C.-Y., Chen, H., … Chiang, V. L. (2014). A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue. NATURE PROTOCOLS, 9(9), 2180–2193. https://doi.org/10.1038/nprot.2014.146 Ma, C. X., MacKenzie, S. H., & Clark, A. C. (2014). Redesigning the procaspase-8 dimer interface for improved dimerization. Protein Science, 23(4), 442–453. Briggs, C. M., Smith, K. M., Piper, A., Huitt, E., Spears, C. J., Quiles, M., … Hernandez, R. (2014). Live Attenuated Tetravalent Dengue Virus Host Range Vaccine Is Immunogenic in African Green Monkeys following a Single Vaccination. JOURNAL OF VIROLOGY, 88(12), 6729–6742. https://doi.org/10.1128/jvi.00541-14 Ahmed, S., Grant, K. G., Edwards, L. E., Rahman, A., Cirit, M., Goshe, M. B., & Haugh, J. M. (2014). Data-driven modeling reconciles kinetics of ERK phosphorylation, localization, and activity states. MOLECULAR SYSTEMS BIOLOGY, 10(1). https://doi.org/10.1002/msb.134708 Theil, E. C., Turano, P., Ghini, V., Allegrozzi, M., & Bernacchioni, C. (2014). Coordinating subdomains of ferritin protein cages with catalysis and biomineralization viewed from the C (4) cage axes. JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 19(4-5), 615–622. https://doi.org/10.1007/s00775-014-1103-z Bass, H. W., Wear, E. E., Lee, T.-J., Hoffman, G. G., Gumber, H. K., Allen, G. C., … Hanley-Bowdoin, L. (2014). 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GENOME BIOLOGY, 15(3). https://doi.org/10.1186/gb-2014-15-3-r59 Schweitzer, M. H., Zheng, W. X., Cleland, T. P., Goodwin, M. B., Boatman, E., Theil, E., … Fakra, S. C. (2014). A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time. Proceedings of the Royal Society of London. Series B, 281(1775). Chen, H.-C., Song, J., Wang, J. P., Lin, Y.-C., Ducoste, J., Shuford, C. M., … Chiang, V. L. (2014). Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid: Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling. PLANT CELL, 26(3), 876–893. https://doi.org/10.1105/tpc.113.119685 Wang, H., Larson, M., Jablonka-Shariff, A., Pearl, C. A., Miller, W. L., Conn, P. M., … Kumar, T. R. (2014). Redirecting intracellular trafficking and the secretion pattern of FSH dramatically enhances ovarian function in mice. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111(15), 5735–5740. https://doi.org/10.1073/pnas.1321404111 Behera, R. K., & Theil, E. C. (2014). Moving Fe2+ from ferritin ion channels to catalytic OH centers depends on conserved protein cage carboxylates. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111(22), 7925–7930. https://doi.org/10.1073/pnas.1318417111 Pascuzzi, P. E., Flores-Vergara, M. A., Lee, T.-J., Sosinski, B., Vaughn, M. W., Hanley-Bowdoin, L., … Allen, G. C. (2014). In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts. PLANT CELL, 26(1), 102–120. https://doi.org/10.1105/tpc.113.121194 Bobay, B. G., Thompson, R. J., Milton, D. L., & Cavanagh, J. (2014). Chemical shift assignments and secondary structure prediction of the phosphorelay protein VanU from Vibrio anguillarum. BIOMOLECULAR NMR ASSIGNMENTS, 8(1), 177–179. https://doi.org/10.1007/s12104-013-9478-2 Stowe, S. D., Olson, A. L., Losick, R., & Cavanagh, J. (2014). Chemical shift assignments and secondary structure prediction of the master biofilm regulator, SinR, from Bacillus subtilis. BIOMOLECULAR NMR ASSIGNMENTS, 8(1), 155–158. https://doi.org/10.1007/s12104-013-9473-7 Olson, A. L., Thompson, R. J., Melander, C., & Cavanagh, J. (2014). Chemical shift assignments and secondary structure prediction of the C-terminal domain of the response regulator BfmR from Acinetobacter baumannii. BIOMOLECULAR NMR ASSIGNMENTS, 8(1), 67–70. https://doi.org/10.1007/s12104-012-9454-2 Golla, J. P., Zhao, J., Mann, I. K., Sayeed, S. K., Mandal, A., Rose, R. B., & Vinson, C. (2014). Carboxylation of cytosine (5caC) in the CG dinucleotide in the E-box motif (CGCAG vertical bar GTG) increases binding of the Tcf3 vertical bar Ascl1 helix-loop-helix heterodimer 10-fold. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 449(2), 248–255. https://doi.org/10.1016/j.bbrc.2014.05.018 Zhao, J., Serrano, V., & Franzen, S. (2014). A Model for the Flexibility of the Distal Histidine in Dehaloperoxidase-Hemoglobin A Based on X-ray Crystal Structures of the Carbon Monoxide Adduct. BIOCHEMISTRY, 53(15), 2474–2482. https://doi.org/10.1021/bi5001905 Khan, M. A., Ma, J., Walden, W. E., Merrick, W. C., Theil, E. C., & Goss, D. J. (2014). Rapid kinetics of iron responsive element (IRE) RNA/iron regulatory protein 1 and IRE-RNA/eIF4F complexes respond differently to metal ions. NUCLEIC ACIDS RESEARCH, 42(10), 6567–6577. https://doi.org/10.1093/nar/gku248 Schweitzer, M. H., Schroeter, E. R., & Goshe, M. B. (2014). Protein Molecular Data from Ancient (> 1 million years old) Fossil Material: Pitfalls, Possibilities and Grand Challenges. ANALYTICAL CHEMISTRY, 86(14), 6731–6740. https://doi.org/10.1021/ac500803w Cruz, F. B., Yelle, D. J., Gracz, H. S., & Barlaz, M. A. (2014). Chemical Changes during Anaerobic Decomposition of Hardwood, Softwood, and Old Newsprint under Mesophilic and Thermophilic Conditions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 62(27), 6362–6374. https://doi.org/10.1021/jf501653h Rojas-Silva, P., Graziose, R., Vesely, B., Poulev, A., Mbeunkui, F., Grace, M. H., … Raskin, I. (2014). Leishmanicidal activity of a daucane sesquiterpene isolated from Eryngium foetidum. PHARMACEUTICAL BIOLOGY, 52(3), 398–401. https://doi.org/10.3109/13880209.2013.837077 Lustgarten, M., Redding, W. R., Labens, R., Morgan, M., Davis, W., & Seiler, G. S. (2014). ELASTOGRAPHIC CHARACTERISTICS OF THE METACARPAL TENDONS IN HORSES WITHOUT CLINICAL EVIDENCE OF TENDON INJURY. VETERINARY RADIOLOGY & ULTRASOUND, 55(1), 92–101. https://doi.org/10.1111/vru.12104 Kwak, Y., Schwartz, J. K., Haldar, S., Behera, R. K., Tosha, T., Theil, E. C., & Solomon, E. I. (2014). Spectroscopic Studies of Single and Double Variants of M Ferritin: Lack of Conversion of a Biferrous Substrate Site into a Cofactor Site for O-2 Activation. BIOCHEMISTRY, 53(3), 473–482. https://doi.org/10.1021/bi4013726 Gruene, T., Hahn, H. W., Luebben, A. V., Meilleur, F., & Sheldrick, G. M. (2014, January). Refinement of macromolecular structures against neutron data with SHELXL2013. JOURNAL OF APPLIED CRYSTALLOGRAPHY, Vol. 47, pp. 462–466. https://doi.org/10.1107/s1600576713027659 Munshi, P., Snell, E. H., Woerd, Mj, J., Ra, M., Da, R., … D. (2014). Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 70(Pt 2), 414–420. https://doi.org/10.1107/s1399004713029684 Troxell, B., Zhang, J.-J., Bourret, T. J., Zeng, M. Y., Blum, J., Gherardini, F., … Yang, X. F. (2014). Pyruvate Protects Pathogenic Spirochetes from H2O2 Killing. PLoS ONE, 9(1), e84625. https://doi.org/10.1371/journal.pone.0084625 Husain, M., Jones-Carson, J., Liu, L., Song, M., Saah, J. R., Troxell, B., … Vazquez-Torresa, A. (2014). Ferric Uptake Regulator-Dependent Antinitrosative Defenses in Salmonella enterica Serovar Typhimurium Pathogenesis. INFECTION AND IMMUNITY, 82(1), 333–340. https://doi.org/10.1128/iai.01201-13 Kearney, B. N., Johnson, C. W., Roberts, D. M., Swartz, P., & Mattos, C. (2014). DRoP: A Water Analysis Program Identifies Ras-GTP-Specific Pathway of Communication between Membrane-Interacting Regions and the Active Site. JOURNAL OF MOLECULAR BIOLOGY, 426(3), 611–629. https://doi.org/10.1016/j.jmb.2013.10.036