Molecular and Structural Biochemistry - 2004 Paredes, A. M., Ferreira, D., Horton, M., Saad, A., Tsuruta, H., Johnston, R., … Brown, D. T. (2004). Conformational changes in Sindbis virions resulting from exposure to low pH and interactions with cells suggest that cell penetration may occur at the cell surface in the absence of membrane fusion. Virology, 324(2), 373–386. https://doi.org/10.1016/j.virol.2004.03.046 Hernandez, R., Nelson, S., Salm, J. R., Brown, D. T., & Alpert, A. J. (2004). Rapid preparative purification of West Nile and Sindbis virus PCR products utilizing a microbore anion-exchange column. Journal of Virological Methods, 120(2), 141–149. https://doi.org/10.1016/j.jviromet.2004.04.013 Blonder, J., Goshe, M. B., Xiao, W., Camp, D. G., Wingerd, M., Davis, R. W., & Smith, R. D. (2004). Global Analysis of the Membrane Subproteome of Pseudomonas aeruginosaUsing Liquid Chromatography-Tandem Mass Spectrometry. Journal of Proteome Research, 3(3), 434–444. https://doi.org/10.1021/pr034074w Mackenzie, J. (2004). Digital Imaging Workflow in Modern Microscopy. Microscopy and Microanalysis, 10(S02), 1256–1257. https://doi.org/10.1017/S1431927604887798 Sommer, B. J., Barycki, J. J., & Simpson, M. A. (2004). Characterization of Human UDP-glucose Dehydrogenase. Journal of Biological Chemistry, 279(22), 23590–23596. https://doi.org/10.1074/jbc.M401928200 Kundu, B., Richardson, S. D., Swartz, P. D., Matthews, P. P., Richard, A. M., & DeMarini, D. M. (2004). Mutagenicity in Salmonella of halonitromethanes: a recently recognized class of disinfection by-products in drinking water. Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 562(1-2), 39–65. https://doi.org/10.1016/j.mrgentox.2004.05.007 Kundu, B., Richardson, S. D., Granville, C. A., Shaughnessy, D. T., Hanley, N. M., Swartz, P. D., … DeMarini, D. M. (2004). Comparative mutagenicity of halomethanes and halonitromethanes in Salmonella TA100: structure–activity analysis and mutation spectra. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 554(1-2), 335–350. https://doi.org/10.1016/j.mrfmmm.2004.05.015 Naylor, S., & Cavanagh, J. (2004). Status of systems biology - does it have a future? Drug Discovery Today: BIOSILICO, 2(5), 171–174. https://doi.org/10.1016/S1741-8364(04)02421-7 Meilleur, F., Contzen, J., Myles, D. A. A., & Jung, C. (2004). Structural Stability and Dynamics of Hydrogenated and Perdeuterated Cytochrome P450cam (CYP101)†. Biochemistry, 43(27), 8744–8753. https://doi.org/10.1021/bi049418q Hanley-Bowdoin, L., Orozco, B. M., Kong, L. J., & Gruissem, W. (2004). Geminivirus resistant transgenic plants. Washington, DC: U.S. Patent and Trademark Office. Saleh-Lakha, S., Grichko, V. P., Sisler, E. C., & Glick, B. R. (2004). The effect of the ethylene action inhibitor 1-cyclopropenylmethyl butyl ether on early plant growth. JOURNAL OF PLANT GROWTH REGULATION, 23(4), 307–312. https://doi.org/10.1007/s00344-004-0011-9 Wu, J. C., Su, P., Safwat, N. W., Sebastian, J., & Miller, W. L. (2004). Rapid, efficient isolation of murine gonadotropes and their use in revealing control of follicle-stimulating hormone by paracrine pituitary factors. ENDOCRINOLOGY, 145(12), 5832–5839. https://doi.org/10.1210/en.2004-0257 Nicely, N. I., Kosak, J., Serrano, V., & Mattos, C. (2004). Crystal structures of Ral-GppNHp and Ral-GDP reveal two binding sites that are also present in Ras and Rap. STRUCTURE, 12(11), 2025–2036. https://doi.org/10.1016/j.str.2004.08.011 Kong, I. S., Bates, T. C., Hulsmann, A., Hassan, H., Smith, B. E., & Oliver, J. D. (2004). Role of catalase and oxyR in the viable but nonculturable state of Vibrio vulnificus. FEMS MICROBIOLOGY ECOLOGY, 50(3), 133–142. https://doi.org/10.1016/j.femsec.2004.06.004 Nanda, K., & Wollenzien, P. (2004). Pattern of 4-thiouridine-induced cross-linking in 16S ribosomal RNA in the Escherichia coli 30S subunit. BIOCHEMISTRY, 43(28), 8923–8934. https://doi.org/10.1021/bi049702h Brinker, M., Zyl, L., Liu, W. B., Craig, D., Sederoff, R. R., Clapham, D. H., & Arnold, S. (2004). Microarray analyses of gene expression during adventitious root development in Pinus contorta (1[w]). PLANT PHYSIOLOGY, 135(3), 1526–1539. https://doi.org/10.1104/pp.103.032235 Ulrich, D. L., Thompson, R., Bassler, B., Cavanagh, J., & Loria, J. P. (2004). H-1, N-15, and C-13 chemical shift assignments of the Vibrio harveyi histidine phosphotransferase protein LuxU. JOURNAL OF BIOMOLECULAR NMR, 29(4), 551–552. https://doi.org/10.1023/B:JNMR.0000034349.22942.e1 Egertsdotter, U., Zyl, L. M., MacKay, J., Peter, G., Kirst, M., Clark, C., … Sederoff, R. (2004). Gene expression during formation of earlywood and latewood in loblolly pine: Expression profiles of 350 genes. PLANT BIOLOGY, 6(6), 654–663. https://doi.org/10.1055/s-2004-830383 Bobay, B. G., Benson, L., Naylor, S., Feeney, B., Clark, A. C., Goshe, M. B., … Cavanagh, J. (2004). Evaluation of the DNA Binding Tendencies of the Transition State Regulator AbrB†. Biochemistry, 43(51), 16106–16118. https://doi.org/10.1021/bi048399h Mattos, C., Cohen, J. D., Green, D. F., Tidor, B., & Karplus, M. (2004). X-ray structural and simulation analysis of a protein mutant: The value of a combined approach. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 55(3), 733–742. https://doi.org/10.1002/prot.20031 Stasolla, C., Bozhkov, P. V., Chu, T. M., Van Zyl, L., Egertsdotter, U., Suarez, M. F., … Sederoff, R. R. (2004). Variation an transcript abundance during somatic embryogenesis in gymnosperms. TREE PHYSIOLOGY, 24(10), 1073–1085. https://doi.org/10.1093/treephys/24.10.1073 Hanley-Bowdoin, L., Settlage, S. B., & Robertson, D. (2004). [Review of Reprogramming plant gene expression: a prerequisite to geminivirus DNA replication]. MOLECULAR PLANT PATHOLOGY, 5(2), 149–156. https://doi.org/10.1111/J.1364-3703.2004.00214.X Morris, C. R., Scott, J. T., Chang, H. M., Sederoff, R. R., D O'Malley, & Kadla, J. F. (2004). Metabolic profiling: A new tool in the study of wood formation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 52(6), 1427–1434. https://doi.org/10.1021/jf034688l Kiss, M. Z., Sayers, D. E., Zhong, Z., Parham, C., & Pisano, E. D. (2004). Improved image contrast of calcifications in breast tissue specimens using diffraction enhanced imaging. Physics in Medicine & Biology, 49(15), 3427–3439. Paredes, A. M., Ferreira, D., Horton, M., Saad, A., Tsuruta, H., Johnston, R., … Brown, D. T. (2004). Conformational changes in Sindbis virions resulting from exposure to low pH and interactions with cells suggest that cell penetration may occur at the cell surface in the absence of membrane fusion. Virology, 324(2), 373–386. https://doi.org/10.1016/j.virus.2004.03.046 Fasina, Y. O., Swaisgood, H. E., Garlich, J. D., & Classen, H. L. (2004, May 19). Rebuttal on a semi-pilot-scale procedure for isolating and purifying soybean (Glycine max) lectin. https://doi.org/10.1021/jf0401367 Hernandez, R., Nelson, S., Salm, J. R., Brown, D. T., & Alpert, A. J. (2004). Rapid preparative purification of West Nile and Sindbis virus PCR products utilizing a microbore anion-exchange column. Journal of Virological Methods, 120(2), 141–149. https://doi.org/10.1016/j.viromet.2004.04.013 Hanley-Bowdoin, L., & Settlage, S. (2004). Geminivirus resistant transgenic plants expressing a mutant geminivirus AL3/C3 coding sequence. Washington, DC: U.S. Patent and Trademark Office. Lee, T. J., Shultz, R. W., Hanley-Bowdoin, L., & Thompson, W. F. (2004). Establishment of rapidly proliferating rice cell suspension culture and its characterization by fluorescence-activated cell sorting analysis. PLANT MOLECULAR BIOLOGY REPORTER, 22(3), 259–267. https://doi.org/10.1007/BF02773136 Kirst, M., Myburg, A. A., De Leon, J. P. G., Kirst, M. E., Scott, J., & Sederoff, R. (2004). Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus. PLANT PHYSIOLOGY, 135(4), 2368–2378. https://doi.org/10.1104/pp.103.037960 Sanjay, K. S., Singh, S. K., Gurha, P., Tran, E. J., Maxwell, E. S., & Gupta, R. (2004). Sequential 2 '-O-methylation of archaeal pre-tRNA(Trp) nucleotides is guided by the intron-encoded but trans-acting box c/D ribonucleoprotein of pre-tRNA. JOURNAL OF BIOLOGICAL CHEMISTRY, 279(46), 47661–47671. https://doi.org/10.1074/jbc.M408868200 Feeney, B., Pop, C., Tripathy, A., & Clark, A. C. (2004). Ionic interactions near the loop L4 are important for maintaining the active-site environment and the dimer stability of (pro)caspase 3. Biochemical Journal (London, England : 1984), 384(Dec 15 2004), 515–525. Bruno-Barcena, J. M., Andrus, J. M., Libby, S. L., Klaenhammer, T. R., & Hassan, H. M. (2004). Expression of a heterologous manganese superoxide dismutase gene in intestinal lactobacilli provides protection against hydrogen peroxide toxicity. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 70(8), 4702–4710. https://doi.org/10.1128/AEM.70.8.4702-4710.2004 Shapkina, T., Lappi, S., Franzen, S., & Wollenzien, P. (2004). Efficiency and pattern of UV pulse laser-induced RNA-RNA cross-linking in the ribosome. NUCLEIC ACIDS RESEARCH, 32(4), 1518–1526. https://doi.org/10.1093/nar/gkh320 Hernandez, R., Rusa, M., Rusa, C. C., Lopez, D., Mijangos, C., & Tonelli, A. E. (2004). Controlling PVA hydrogels with gamma-cyclodextrin. MACROMOLECULES, 37(25), 9620–9625. https://doi.org/10.1021/ma048375i Huggins, W., & Wollenzien, P. (2004). A 16S rRNA-tRNA product containing a nucleotide phototrimer and specific for tRNA in the P/E hybrid state in the Escherichia coli ribosome. NUCLEIC ACIDS RESEARCH, 32(22), 6548–6556. https://doi.org/10.1093/nar/gkh1001 Guenther, R. H., Sit, T. L., Gracz, H. S., Dolan, M. A., Townsend, H. L., Liu, G. H., … Lommel, S. A. (2004). Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus. NUCLEIC ACIDS RESEARCH, 32(9), 2819–2828. https://doi.org/10.1093/nar/gkh585 Farrell, H. M., Jimenez-Flores, R., Bleck, G. T., Brown, E. M., Butler, J. E., Creamer, L. K., … Swaisgood, H. E. (2004). [Review of Nomenclature of the proteins of cows' milk - Sixth revision]. JOURNAL OF DAIRY SCIENCE, 87(6), 1641–1674. https://doi.org/10.3168/jds.S0022-0302(04)73319-6 Lieberman, D. V., & Hardin, C. C. (2004). Extraction of information on the buildup and consumption of reactive intermediates from quadruplex DNA assembly time courses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION, 1679(1), 59–64. https://doi.org/10.1016/j.bbaexp.2004.03.006 Zhang, G. Y., Foegeding, E. A., & Hardin, C. C. (2004). Effect of sulfated polysaccharides on heat-induced structural changes in beta-lactoglobulin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 52(12), 3975–3981. https://doi.org/10.1021/jf035037s Wachowicz, M., Wolak, J., Gracz, H., Stejskal, E. O., Jurga, S., McCord, E. F., & White, J. L. (2004). Length scales which perturb chain packing in amorphous polymers. MACROMOLECULES, 37(12), 4573–4579. https://doi.org/10.1021/ma049263u Myburg, A. A., Vogl, C., Griffin, A. R., Sederoff, R. R., & Whetten, R. W. (2004). Genetics of postzygotic isolation in eucalyptus: Whole-genome analysis of barriers to introgression in a wide interspecific cross of Eucalyptus grandis and E-globulus. GENETICS, 166(3), 1405–1418. https://doi.org/10.1534/genetics.166.3.1405 Rose, R. B., Pullen, K. E., Bayle, J. H., Crabtree, G. R., & Alber, T. (2004). Biochemical and structural basis for partially redundant enzymatic and ranscriptional functions of DCoH and DCoH2. BIOCHEMISTRY, 43(23), 7345–7355. https://doi.org/10.1021/bi049620t Busov, V. B., Johannes, E., Whetten, R. W., Sederoff, R. R., Spiker, S. L., Lanz-Garcia, C., & Goldfarb, B. (2004). An auxin-inducible gene from loblolly pine (Pinus taeda L.) is differentially expressed in mature and juvenile-phase shoots and encodes a putative transmembrane protein. PLANTA, 218(6), 916–927. https://doi.org/10.1007/s00425-003-1175-4 Stasolla, C., Belmonte, M. F., Zyl, L., Craig, D. L., Liu, W. B., Yeung, E. C., & Sederoff, R. R. (2004). The effect of reduced glutathione on morphology and gene expression of white spruce (Picea glauca) somatic embryos. JOURNAL OF EXPERIMENTAL BOTANY, 55(397), 695–709. https://doi.org/10.1093/jxb/erh074 Kojetin, D. J., Thompson, R. J., & Cavanagh, J. (2004, February 27). Sub-classification of response regulators using the surface characteristics of their receiver domains (FEBS 27785) (vol 554, pg 231, 2003). FEBS LETTERS, Vol. 560, pp. 227–228. https://doi.org/10.1016/s0014-5793(04)00063-8 Mucha, P., Szyk, A., Rekowski, P., & Agris, P. F. (2004). Sequence-altered peptide adopts optimum conformation for modification-dependent binding of the yeast tRNA(Phe) anticodon domain. PROTEIN JOURNAL, 23(1), 33–38. https://doi.org/10.1023/B:JOPC.0000016256.20648.0f Phelps, S. S., Malkiewicz, A., Agris, P. F., & Joseph, S. (2004). Modified nucleotides in tRNA(Lys) and tRNA(Val) are important for translocation. JOURNAL OF MOLECULAR BIOLOGY, 338(3), 439–444. https://doi.org/10.1016/j.jmb.2004.02.070 Gryko, D., Gryko, D. T., Sierzputowska-Gracz, H., Piatek, P., & Jurczak, J. (2004). Factors influencing the course of the macrocyclization of alpha,omega-diamines with esters of alpha,omega-dicarboxylic acids. HELVETICA CHIMICA ACTA, 87(1), 156–166. https://doi.org/10.1002/hlca.200490004 Agris, P. F. (2004). [Review of Decoding the genome: a modified view]. NUCLEIC ACIDS RESEARCH, 32(1), 223–238. https://doi.org/10.1093/nar/gkh185 Truong, V. D., Clare, D. A., Catignani, G. L., & Swaisgood, H. E. (2004). Cross-linking and rheological changes of whey proteins treated with microbial transglutaminase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 52(5), 1170–1176. https://doi.org/10.1021/jf034397c Feng, X. Q., Apelbaum, A., Sisler, E. C., & Goren, R. (2004). Control of ethylene activity in various plant systems by structural analogues of 1-methylcyclopropene. PLANT GROWTH REGULATION, 42(1), 29–38. https://doi.org/10.1023/B:GROW.0000014900.12351.4e Arguello-Astorga, G., Lopez-Ochoa, L., Kong, L. J., Orozco, B. M., Settlage, S. B., & Hanley-Bowdoin, L. (2004). A novel motif in geminivirus replication proteins interacts with the plant retinoblastoma-related protein. JOURNAL OF VIROLOGY, 78(9), 4817–4826. https://doi.org/10.1128/JVI.78.9.4817-4826.2004 Castillo, A. G., Kong, L. J., Hanley-Bowdoin, L., & Bejarano, E. R. (2004). Interaction between a geminivirus replication protein and the plant sumoylation system. JOURNAL OF VIROLOGY, 78(6), 2758–2769. https://doi.org/10.1128/JVI.78.6.2758-2769.2004 Murphy, F. V., Ramakrishnan, V., Malkiewicz, A., & Agris, P. F. (2004). The role of modifications in codon discrimination by tRNA(Lys) UUU. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 11(12), 1186–1191. https://doi.org/10.1038/nsmb861 Chen, Y. R., & Clark, A. C. (2004). Kinetic traps in the folding/unfolding of procaspase-1 CARD domain. PROTEIN SCIENCE, 13(8), 2196–2206. https://doi.org/10.1110/ps.03521504 Tran, E., Brown, J., & Maxwell, E. S. (2004, July). Evolutionary origins of the RNA-guided nucleotide-modification complexes: from the primitive translation apparatus? TRENDS IN BIOCHEMICAL SCIENCES, Vol. 29, pp. 343–350. https://doi.org/10.1016/j.tibs.2004.05.001