260 research outputs found

    Oral administration of melatonin counteracts several of the effects of chronic stress in rainbow trout

    Get PDF
    To assess a possible antistress role of melatonin in fish, we orally administered melatonin to rainbow trout for 10 d and then kept the fish under normal or high stocking density conditions during the last 4 d. Food intake; biochemical parameters in plasma (cortisol, glucose, and lactate concentrations); liver (glucose and glycogen concentrations, and glycogen synthase activity); enzyme activities of amylase, lipase, and protease in foregut and midgut; and content of the hypothalamic neurotransmitters dopamine and serotonin, as well as their oxidized metabolites, 3,4-dihydroxyphenylacetic acid and 5-hydroxy-3-indoleacetic acid, were evaluated under those conditions. High stocking density conditions alone induced changes indicative of stress conditions in plasma cortisol concentrations, liver glycogenolytic potential, the activities of some digestive enzymes, and the 3,4-dihydroxyphenylacetic acid-to-dopamine and 5-hydroxy-3-indoleacetic acid-to-serotonin ratios in the hypothalamus. Melatonin treatment in nonstressed fish induced an increase in liver glycogenolytic potential, increased the activity of some digestive enzymes, and enhanced serotoninergic and dopaminergic metabolism in hypothalamus. The presence of melatonin in stressed fish resulted in a significant interaction with cortisol concentrations in plasma, glycogen content, and glycogen synthase activity in liver and dopaminergic and serotoninergic metabolism in the hypothalamus. In general, the presence of melatonin mitigated several of the effects induced by stress, supporting an antistress role for melatonin in rainbow trout.Ministerio de Ciencia e Innovación | Ref. AGL2010-22247-C03-03Xunta de Galicia | Ref. CN2012/ 00

    N-Benzyl-1,3-dide­oxy-1,3-imino-l-xylitol

    Get PDF
    The structure determination confirms the stereochemistry of the title compound, C12H17NO3, which contains a four-membered azetidine ring system. The absolute configuration was determined by the use of d-glucose as the starting material. In the crystal, O—H⋯O and O—H⋯N hydrogen bonds link the mol­ecules into layers in the ab plane

    Differential circadian and light-driven rhythmicity of clock gene expression and behaviour in the turbot, Scophthalmus maximus

    Get PDF
    In fish, the circadian clock represents a key regulator of many aspects of biology and is controlled by combinations of abiotic and biotic factors. These environmental factors are frequently manipulated in fish farms as part of strategies designed to maximize productivity. The flatfish turbot, Scophthalmus maximus, represents one of the most important species within the aquaculture sector in Asia and Europe. Despite the strategic importance of this species, the function and regulation of the turbot circadian system remains poorly understood. Here, we have characterized the core circadian clock genes, clock1, per1, per2 and cry1 in turbot and have studied their daily expression in various tissues under a range of lighting conditions and feeding regimes. We have also explored the influence of light and feeding time on locomotor activity. Rhythmic expression of the four core clock genes was observed in all tissues studied under light dark (LD) cycle conditions. Rhythmicity of clock gene expression persisted upon transfer to artificial free running, constant conditions confirming their endogenous circadian clock control. Furthermore, turbot showed daily cycles of locomotor activity and food anticipatory activity (FAA) under LD and scheduled-feeding, with the activity phase as well as FAA coinciding with and being dependent upon exposure to light. Thus, while FAA was absent under constant dark (DD) conditions, it was still detected in constant light (LL). In contrast, general locomotor activity was arrhythmic in both constant darkness and constant light, pointing to a major contribution of light, in concert with the circadian clock, in timing locomotor activity in this species. Our data represents an important contribution to our understanding of the circadian timing system in the turbot and thereby the optimization of rearing protocols and the improvement of the well-being of turbot within fish farming environments

    Epigenetics as a mechanism driving polygenic clinical drug resistance

    Get PDF
    Aberrant methylation of CpG islands located at or near gene promoters is associated with inactivation of gene expression during tumour development. It is increasingly recognised that such epimutations may occur at a much higher frequency than gene mutation and therefore have a greater impact on selection of subpopulations of cells during tumour progression or acquisition of resistance to anticancer drugs. Although laboratory-based models of acquired resistance to anticancer agents tend to focus on specific genes or biochemical pathways, such 'one gene : one outcome' models may be an oversimplification of acquired resistance to treatment of cancer patients. Instead, clinical drug resistance may be due to changes in expression of a large number of genes that have a cumulative impact on chemosensitivity. Aberrant CpG island methylation of multiple genes occurring in a nonrandom manner during tumour development and during the acquisition of drug resistance provides a mechanism whereby expression of multiple genes could be affected simultaneously resulting in polygenic clinical drug resistance. If simultaneous epigenetic regulation of multiple genes is indeed a major driving force behind acquired resistance of patients' tumour to anticancer agents, this has important implications for biomarker studies of clinical outcome following chemotherapy and for clinical approaches designed to circumvent or modulate drug resistance

    Adenovirus-mediated TA-p73β gene transfer increases chemosensitivity of human malignant melanomas

    Full text link
    Malignant melanoma is the most aggressive form of skin cancer and has proven to be highly resistant to conventional chemotherapy. Intriguingly, the p53 tumor suppressor, a main mediator of chemoresistance in other tumor types, is rarely mutated in melanoma. However, we have previously shown that anti-apoptotic isoforms of p73 (ΔTA-p73), another member of the p53 family, are overexpressed in metastatic melanomas. ΔTA-p73 can oppose the pro-apoptotic functions of p53 and full length p73, and thus it could contribute to melanoma chemoresistance. In this study, we use an efficient adenoviral-based gene transfer approach to introduce a transcriptionally active form of p73 (TA-p73β) in melanoma cells, with the objective of overcoming drug resistance. Interestingly, TA-p73β significantly sensitized 5 out of 7 aggressive melanoma cell lines to the standard therapeutic agents adriamycin and cisplatin. More importantly, TA-p73β displayed a synergistic effect in vivo allowing adriamycin or cisplatin to block melanoma cell growth in mouse xenograft models ( p < 0.05). In summary, our data show that Ad-mediated TA-p73β gene expression can markedly sensitize a subset of melanoma cell lines to adriamycin and cisplatin in vitro and in vivo , suggesting a new chemosensitization strategy for malignant melanomas.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44369/1/10495_2006_Article_3407.pd

    Reduced Apaf-1 expression in human cutaneous melanomas

    Get PDF
    Malignant melanoma is a life-threatening skin cancer due to its highly metastatic character and resistance to radio- and chemotherapy. It is believed that the ability to evade apoptosis is the key mechanism for the rapid growth of cancer cells. However, the exact mechanism for failure in the apoptotic pathway in melanoma cells is unclear. p53, the most frequently mutated tumour suppressor gene in human cancers, is a key apoptosis inducer. However, p53 mutation is only found in 15–20% of melanoma biopsies. Recently, it was found that Apaf-1, a downstream target of p53, is inactivated in metastatic melanoma. Specifically, loss of heterozygosity (LOH) of the Apaf-1 gene was found in 40% of metastatic melanoma. To determine if loss of Apaf-1 expression is indeed involved in melanoma progression, we employed the tissue microarray technology and examined Apaf-1 expression in 70 human primary malignant melanoma biopsies by immunohistochemistry. Our data showed that Apaf-1 expression is significantly reduced in melanoma cells compared with normal nevi (χ2=6.02, P=0.014). Our results also revealed that loss of Apaf-1 was not associated with the tumour thickness, ulceration or subtype, patient's gender, age and 5-year survival. In addition, our in vitro apoptosis assay revealed that overexpression of Apaf-1 can sensitise melanoma cells to anticancer drug treatment. Taken together, our data indicate that Apaf-1 expression is significantly reduced in human melanoma and that Apaf-1 may serve as a therapeutic target in melanoma

    Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase

    Get PDF
    [EN] During DNA replication replicative polymerases move in discrete mechanical steps along the DNA template. To address how the chemical cycle is coupled to mechanical motion of the enzyme, here we use optical tweezers to study the translocation mechanism of individual bacteriophage Phi29 DNA polymerases during processive DNA replication. We determine the main kinetic parameters of the nucleotide incorporation cycle and their dependence on external load and nucleotide (dNTP) concentration. The data is inconsistent with power stroke models for translocation, instead supports a loose-coupling mechanism between chemical catalysis and mechanical translocation during DNA replication. According to this mechanism the DNA polymerase works by alternating between a dNTP/PPi-free state, which diffuses thermally between pre- and post-translocated states, and a dNTP/PPi-bound state where dNTP binding stabilizes the post-translocated state. We show how this thermal ratchet mechanism is used by the polymerase to generate work against large opposing loads (~50 pN).We thank Stephan Grill laboratory (MPI-CBG, Dresden) for help with data collection and E. Galburt, M. Manosas and M. De Vega for critical reading of the manuscript. Spanish Ministry of Economy and Competitiveness [BFU2011-29038 to J.L.C., BFU2013-44202 to J.M.V., BFU2011-23645 to M.S., FIS2010-17440, GR35/10-A920GR35/10-A-911 to F.J.C., MAT2013-49455-EXP to J.R.A.-G. and BFU2012-31825 to B.I.]; Regional Government of Madrid [S2009/MAT 1507 to J.L.C. and CDS2007-0015 to M.S.]; European Molecular Biology Organization [ASTF 276-2012 to J.M.L.]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [BFU2012-31825 to B.I.].Morin, J.; Cao, F.; Lázaro, J.; Arias-Gonzalez, JR.; Valpuesta, J.; Carrascosa, J.; Salas, M.... (2015). Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase. Nucleic Acids Research. 43(7):3643-3652. https://doi.org/10.1093/nar/gkv204S36433652437Steitz, T. A., & Steitz, J. A. (1993). A general two-metal-ion mechanism for catalytic RNA. Proceedings of the National Academy of Sciences, 90(14), 6498-6502. doi:10.1073/pnas.90.14.6498Nakamura, T., Zhao, Y., Yamagata, Y., Hua, Y., & Yang, W. (2012). Watching DNA polymerase η make a phosphodiester bond. Nature, 487(7406), 196-201. doi:10.1038/nature11181Kohlstaedt, L., Wang, J., Friedman, J., Rice, P., & Steitz, T. (1992). Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science, 256(5065), 1783-1790. doi:10.1126/science.1377403Steitz, T. A. (2006). Visualizing polynucleotide polymerase machines at work. The EMBO Journal, 25(15), 3458-3468. doi:10.1038/sj.emboj.7601211Zhang, H., Cao, W., Zakharova, E., Konigsberg, W., & De La Cruz, E. M. (2007). Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates. Nucleic Acids Research, 35(18), 6052-6062. doi:10.1093/nar/gkm587Wang, W., Wu, E. Y., Hellinga, H. W., & Beese, L. S. (2012). Structural Factors That Determine Selectivity of a High Fidelity DNA Polymerase for Deoxy-, Dideoxy-, and Ribonucleotides. Journal of Biological Chemistry, 287(34), 28215-28226. doi:10.1074/jbc.m112.366609Berezhna, S. Y., Gill, J. P., Lamichhane, R., & Millar, D. P. (2012). Single-Molecule Förster Resonance Energy Transfer Reveals an Innate Fidelity Checkpoint in DNA Polymerase I. Journal of the American Chemical Society, 134(27), 11261-11268. doi:10.1021/ja3038273Hariharan, C., Bloom, L. B., Helquist, S. A., Kool, E. T., & Reha-Krantz, L. J. (2006). Dynamics of Nucleotide Incorporation:  Snapshots Revealed by 2-Aminopurine Fluorescence Studies†. Biochemistry, 45(9), 2836-2844. doi:10.1021/bi051644sJoyce, C. M., Potapova, O., DeLucia, A. M., Huang, X., Basu, V. P., & Grindley, N. D. F. (2008). Fingers-Closing and Other Rapid Conformational Changes in DNA Polymerase I (Klenow Fragment) and Their Role in Nucleotide Selectivity†. Biochemistry, 47(23), 6103-6116. doi:10.1021/bi7021848Vande Berg, B. J., Beard, W. A., & Wilson, S. H. (2000). DNA Structure and Aspartate 276 Influence Nucleotide Binding to Human DNA Polymerase β. Journal of Biological Chemistry, 276(5), 3408-3416. doi:10.1074/jbc.m002884200Showalter, A. K., & Tsai, M.-D. (2002). A Reexamination of the Nucleotide Incorporation Fidelity of DNA Polymerases†. Biochemistry, 41(34), 10571-10576. doi:10.1021/bi026021iShah, A. M., Li, S.-X., Anderson, K. S., & Sweasy, J. B. (2001). Y265H Mutator Mutant of DNA Polymerase β. Journal of Biological Chemistry, 276(14), 10824-10831. doi:10.1074/jbc.m008680200Rothwell, P. J., Mitaksov, V., & Waksman, G. (2005). Motions of the Fingers Subdomain of Klentaq1 Are Fast and Not Rate Limiting: Implications for the Molecular Basis of Fidelity in DNA Polymerases. Molecular Cell, 19(3), 345-355. doi:10.1016/j.molcel.2005.06.032Patel, S. S., Wong, I., & Johnson, K. A. (1991). Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant. Biochemistry, 30(2), 511-525. doi:10.1021/bi00216a029Luo, G., Wang, M., Konigsberg, W. H., & Xie, X. S. (2007). Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase. Proceedings of the National Academy of Sciences, 104(31), 12610-12615. doi:10.1073/pnas.0700920104Joyce, C. M., & Benkovic, S. J. (2004). DNA Polymerase Fidelity:  Kinetics, Structure, and Checkpoints†. Biochemistry, 43(45), 14317-14324. doi:10.1021/bi048422zFiala, K. A., & Suo, Z. (2004). Mechanism of DNA Polymerization Catalyzed bySulfolobus solfataricusP2 DNA Polymerase IV†. Biochemistry, 43(7), 2116-2125. doi:10.1021/bi035746zCramer, J., & Restle, T. (2005). Pre-steady-state Kinetic Characterization of the DinB Homologue DNA Polymerase ofSulfolobus solfataricus. Journal of Biological Chemistry, 280(49), 40552-40558. doi:10.1074/jbc.m504481200Choi, J.-Y., & Guengerich, F. P. (2005). Adduct Size Limits Efficient and Error-free Bypass Across Bulky N2-Guanine DNA Lesions by Human DNA Polymerase η. Journal of Molecular Biology, 352(1), 72-90. doi:10.1016/j.jmb.2005.06.079Olsen, T. J., Choi, Y., Sims, P. C., Gul, O. T., Corso, B. L., Dong, C., … Weiss, G. A. (2013). Electronic Measurements of Single-Molecule Processing by DNA Polymerase I (Klenow Fragment). Journal of the American Chemical Society, 135(21), 7855-7860. doi:10.1021/ja311603rAllen, W. J., Rothwell, P. J., & Waksman, G. (2008). An intramolecular FRET system monitors fingers subdomain opening in Klentaq1. Protein Science, 17(3), 401-408. doi:10.1110/ps.073309208Johnson, S. J., & Beese, L. S. (2004). Structures of Mismatch Replication Errors Observed in a DNA Polymerase. Cell, 116(6), 803-816. doi:10.1016/s0092-8674(04)00252-1Yin, Y. W., & Steitz, T. A. (2004). The Structural Mechanism of Translocation and Helicase Activity in T7 RNA Polymerase. Cell, 116(3), 393-404. doi:10.1016/s0092-8674(04)00120-5Golosov, A. A., Warren, J. J., Beese, L. S., & Karplus, M. (2010). The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis. Structure, 18(1), 83-93. doi:10.1016/j.str.2009.10.014Zhang, C., & Burton, Z. F. (2004). Transcription Factors IIF and IIS and Nucleoside Triphosphate Substrates as Dynamic Probes of the Human RNA Polymerase II Mechanism. Journal of Molecular Biology, 342(4), 1085-1099. doi:10.1016/j.jmb.2004.07.070Nedialkov, Y. A., Gong, X. Q., Hovde, S. L., Yamaguchi, Y., Handa, H., Geiger, J. H., … Burton, Z. F. (2003). NTP-driven Translocation by Human RNA Polymerase II. Journal of Biological Chemistry, 278(20), 18303-18312. doi:10.1074/jbc.m301103200Gong, X. Q., Zhang, C., Feig, M., & Burton, Z. F. (2005). Dynamic Error Correction and Regulation of Downstream Bubble Opening by Human RNA Polymerase II. Molecular Cell, 18(4), 461-470. doi:10.1016/j.molcel.2005.04.011Guajardo, R., & Sousa, R. (1997). A model for the mechanism of polymerase translocation 1 1Edited by A. R. Fersht. Journal of Molecular Biology, 265(1), 8-19. doi:10.1006/jmbi.1996.0707Thomen, P., Lopez, P. J., & Heslot, F. (2005). Unravelling the Mechanism of RNA-Polymerase Forward Motion by Using Mechanical Force. Physical Review Letters, 94(12). doi:10.1103/physrevlett.94.128102Larson, M. H., Zhou, J., Kaplan, C. D., Palangat, M., Kornberg, R. D., Landick, R., & Block, S. M. (2012). Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II. Proceedings of the National Academy of Sciences, 109(17), 6555-6560. doi:10.1073/pnas.1200939109Bar-Nahum, G., Epshtein, V., Ruckenstein, A. E., Rafikov, R., Mustaev, A., & Nudler, E. (2005). A Ratchet Mechanism of Transcription Elongation and Its Control. Cell, 120(2), 183-193. doi:10.1016/j.cell.2004.11.045Bai, L., Fulbright, R. M., & Wang, M. D. (2007). Mechanochemical Kinetics of Transcription Elongation. Physical Review Letters, 98(6). doi:10.1103/physrevlett.98.068103Abbondanzieri, E. A., Greenleaf, W. J., Shaevitz, J. W., Landick, R., & Block, S. M. (2005). Direct observation of base-pair stepping by RNA polymerase. Nature, 438(7067), 460-465. doi:10.1038/nature04268Dangkulwanich, M., Ishibashi, T., Liu, S., Kireeva, M. L., Lubkowska, L., Kashlev, M., & Bustamante, C. J. (2013). Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism. eLife, 2. doi:10.7554/elife.00971Lieberman, K. R., Dahl, J. M., Mai, A. H., Cox, A., Akeson, M., & Wang, H. (2013). Kinetic Mechanism of Translocation and dNTP Binding in Individual DNA Polymerase Complexes. Journal of the American Chemical Society, 135(24), 9149-9155. doi:10.1021/ja403640bLieberman, K. R., Dahl, J. M., Mai, A. H., Akeson, M., & Wang, H. (2012). Dynamics of the Translocation Step Measured in Individual DNA Polymerase Complexes. Journal of the American Chemical Society, 134(45), 18816-18823. doi:10.1021/ja3090302Dahl, J. M., Mai, A. H., Cherf, G. M., Jetha, N. N., Garalde, D. R., Marziali, A., … Lieberman, K. R. (2012). Direct Observation of Translocation in Individual DNA Polymerase Complexes. Journal of Biological Chemistry, 287(16), 13407-13421. doi:10.1074/jbc.m111.338418Rodriguez, I., Lazaro, J. M., Blanco, L., Kamtekar, S., Berman, A. J., Wang, J., … de Vega, M. (2005). A specific subdomain in  29 DNA polymerase confers both processivity and strand-displacement capacity. Proceedings of the National Academy of Sciences, 102(18), 6407-6412. doi:10.1073/pnas.0500597102Morin, J. A., Cao, F. J., Valpuesta, J. M., Carrascosa, J. L., Salas, M., & Ibarra, B. (2012). Manipulation of single polymerase-DNA complexes: A mechanical view of DNA unwinding during replication. Cell Cycle, 11(16), 2967-2968. doi:10.4161/cc.21389Morin, J. A., Cao, F. J., Lazaro, J. M., Arias-Gonzalez, J. R., Valpuesta, J. M., Carrascosa, J. L., … Ibarra, B. (2012). Active DNA unwinding dynamics during processive DNA replication. Proceedings of the National Academy of Sciences, 109(21), 8115-8120. doi:10.1073/pnas.1204759109Ibarra, B., Chemla, Y. R., Plyasunov, S., Smith, S. B., Lázaro, J. M., Salas, M., & Bustamante, C. (2009). Proofreading dynamics of a processive DNA polymerase. The EMBO Journal, 28(18), 2794-2802. doi:10.1038/emboj.2009.219Bustamante, C., Chemla, Y. R., Forde, N. R., & Izhaky, D. (2004). Mechanical Processes in Biochemistry. Annual Review of Biochemistry, 73(1), 705-748. doi:10.1146/annurev.biochem.72.121801.161542Jahnel, M., Behrndt, M., Jannasch, A., Schäffer, E., & Grill, S. W. (2011). Measuring the complete force field of an optical trap. Optics Letters, 36(7), 1260. doi:10.1364/ol.36.001260Soengas, M. S., Esteban, J. A., Lázaro, J. M., Bernad, A., Blasco, M. A., Salas, M., & Blanco, L. (1992). Site-directed mutagenesis at the Exo III motif of phi 29 DNA polymerase; overlapping structural domains for the 3′-5′ exonuclease and strand-displacement activities. The EMBO Journal, 11(11), 4227-4237. doi:10.1002/j.1460-2075.1992.tb05517.xSoengas, M. S., Gutiérrez, C., & Salas, M. (1995). Helix-destabilizing Activity of φ29 Single-stranded DNA Binding Protein: Effect on the Elongation Rate During Strand Displacement DNA Replication. Journal of Molecular Biology, 253(4), 517-529. doi:10.1006/jmbi.1995.0570De Vega, M., Lazaro, J. M., Salas, M., & Blanco, L. (1996). Primer-terminus stabilization at the 3′-5′ exonuclease active site of phi29 DNA polymerase. Involvement of two amino acid residues highly conserved in proofreading DNA polymerases. The EMBO Journal, 15(5), 1182-1192. doi:10.1002/j.1460-2075.1996.tb00457.xVisscher, K., Schnitzer, M. J., & Block, S. M. (1999). Single kinesin molecules studied with a molecular force clamp. Nature, 400(6740), 184-189. doi:10.1038/22146Pandey, M., & Patel, S. S. (2014). Helicase and Polymerase Move Together Close to the Fork Junction and Copy DNA in One-Nucleotide Steps. Cell Reports, 6(6), 1129-1138. doi:10.1016/j.celrep.2014.02.025Truniger, V. (2002). A positively charged residue of phi29 DNA polymerase, highly conserved in DNA polymerases from families A and B, is involved in binding the incoming nucleotide. Nucleic Acids Research, 30(7), 1483-1492. doi:10.1093/nar/30.7.1483Berman, A. J., Kamtekar, S., Goodman, J. L., Lázaro, J. M., de Vega, M., Blanco, L., … Steitz, T. A. (2007). Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. The EMBO Journal, 26(14), 3494-3505. doi:10.1038/sj.emboj.7601780Thomen, P., Lopez, P. J., Bockelmann, U., Guillerez, J., Dreyfus, M., & Heslot, F. (2008). T7 RNA Polymerase Studied by Force Measurements Varying Cofactor Concentration. Biophysical Journal, 95(5), 2423-2433. doi:10.1529/biophysj.107.125096Keller, D., & Bustamante, C. (2000). The Mechanochemistry of Molecular Motors. Biophysical Journal, 78(2), 541-556. doi:10.1016/s0006-3495(00)76615-xHerbert, K. M., Greenleaf, W. J., & Block, S. M. (2008). Single-Molecule Studies of RNA Polymerase: Motoring Along. Annual Review of Biochemistry, 77(1), 149-176. doi:10.1146/annurev.biochem.77.073106.100741Wong, I., Patel, S. S., & Johnson, K. A. (1991). An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics. Biochemistry, 30(2), 526-537. doi:10.1021/bi00216a030Lowe, L. G., & Guengerich, F. P. (1996). Steady-State and Pre-Steady-State Kinetic Analysis of dNTP Insertion Opposite 8-Oxo-7,8-dihydroguanine byEscherichia coliPolymerases I exo-and II exo- †. Biochemistry, 35(30), 9840-9849. doi:10.1021/bi960485xKirmizialtin, S., Nguyen, V., Johnson, K. A., & Elber, R. (2012). How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations. Structure, 20(4), 618-627. doi:10.1016/j.str.2012.02.018Donlin, M. J., Patel, S. S., & Johnson, K. A. (1991). Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction. Biochemistry, 30(2), 538-546. doi:10.1021/bi00216a031Li, Y. (1998). Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. The EMBO Journal, 17(24), 7514-7525. doi:10.1093/emboj/17.24.7514Lieberman, K. R., Dahl, J. M., & Wang, H. (2014). Kinetic Mechanism at the Branchpoint between the DNA Synthesis and Editing Pathways in Individual DNA Polymerase Complexes. Journal of the American Chemical Society, 136(19), 7117-7131. doi:10.1021/ja5026408Subuddhi, U., Hogg, M., & Reha-Krantz, L. J. (2008). Use of 2-Aminopurine Fluorescence To Study the Role of the β Hairpin in the Proofreading Pathway Catalyzed by the Phage T4 and RB69 DNA Polymerases†. Biochemistry, 47(23), 6130-6137. doi:10.1021/bi800211fShamoo, Y., & Steitz, T. A. (1999). Building a Replisome from Interacting Pieces. Cell, 99(2), 155-166. doi:10.1016/s0092-8674(00)81647-5Lamichhane, R., Berezhna, S. Y., Gill, J. P., Van der Schans, E., & Millar, D. P. (2013). Dynamics of Site Switching in DNA Polymerase. Journal of the American Chemical Society, 135(12), 4735-4742. doi:10.1021/ja311641bKamtekar, S., Berman, A. J., Wang, J., Lázaro, J. M., de Vega, M., Blanco, L., … Steitz, T. A. (2004). Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage φ29. Molecular Cell, 16(4), 609-618. doi:10.1016/j.molcel.2004.10.019Hogg, M., Wallace, S. S., & Doublié, S. (2004). Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site. The EMBO Journal, 23(7), 1483-1493. doi:10.1038/sj.emboj.7600150Seifert, U. (2012). Stochastic thermodynamics, fluctuation theorems and molecular machines. Reports on Progress in Physics, 75(12), 126001. doi:10.1088/0034-4885/75/12/126001Cao, F. J., & Feito, M. (2009). Thermodynamics of feedback controlled systems. Physical Review E, 79(4). doi:10.1103/physreve.79.041118Cao, F. J., Dinis, L., & Parrondo, J. M. R. (2004). Feedback Control in a Collective Flashing Ratchet. Physical Review Letters, 93(4). doi:10.1103/physrevlett.93.040603Bier, M. (2007). The stepping motor protein as a feedback control ratchet. Biosystems, 88(3), 301-307. doi:10.1016/j.biosystems.2006.07.013Astumian, R. D. (1997). Thermodynamics and Kinetics of a Brownian Motor. Science, 276(5314), 917-922. doi:10.1126/science.276.5314.917Komissarova, N., & Kashlev, M. (1997). Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3’ end of the RNA intact and extruded. Proceedings of the National Academy of Sciences, 94(5), 1755-1760. doi:10.1073/pnas.94.5.1755Brueckner, F., & Cramer, P. (2008). Structural basis of transcription inhibition by α-amanitin and implications for RNA polymerase II translocation. Nature Structural & Molecular Biology, 15(8), 811-818. doi:10.1038/nsmb.145

    Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set

    Get PDF
    We report a measurement of the bottom-strange meson mixing phase \beta_s using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of \beta_s and the B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2, -1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +- 0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +- 0.009 (syst) ps, which are consistent and competitive with determinations by other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012
    corecore