249 research outputs found
Decays of Baryons --- Quark Model versus Large-
We study nonleptonic decays of the orbitally excited, \su6 \rep{70}-plet
baryons in order to test the hypothesis that the successes of the
nonrelativistic quark model have a natural explanation in the large- limit
of QCD. By working in a Hartree approximation, we isolate a specific set of
operators that contribute to the observed s- and d-wave decays in leading order
in . We fit our results to the current experimental decay data, and make
predictions for a number of allowed but unobserved modes. Our tentative
conclusion is that there is more to the nonrelativistic quark model of baryons
than large-.Comment: LaTeX 49pp. (38 pp. landscape), PicTex, PrePicTex, PostPicTex
required for 3 figures, Harvard Preprint HUTP-94/A008. (Two additional
operators are included, but conclusions are unchanged.
DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein
[EN] Single-stranded DNA-binding proteins (SSBs) play a key role in genome maintenance, binding and organizing single-stranded DNA (ssDNA) intermediates. Multimeric SSBs, such as the human mitochondrial SSB (HmtSSB), present multiple sites to interact with ssDNA, which has been shown in vitro to enable them to bind a variable number of single-stranded nucleotides depending on the salt and protein concentration. It has long been suggested that different binding modes might be used selectively for different functions. To study this possibility, we used optical tweezers to determine and compare the structure and energetics of long, individual HmtSSB¿DNA complexes assembled on preformed ssDNA and on ssDNA generated gradually during `in situ¿ DNA synthesis. We show that HmtSSB binds to preformed ss-DNA in two major modes, depending on salt and protein concentration. However, when protein binding was coupled to strand-displacement DNA synthesis, only one of the two binding modes was observed under all experimental conditions. Our results reveal a key role for the gradual generation of ssDNA in modulating the binding mode of a multimeric SSB protein and consequently, in generating the appropriate nucleoprotein structure for DNA synthetic reactions required for genome maintenance.We are grateful to Prof. M. Salas laboratory (CBMSO-CSIC) for generously providing the Phi29 DNA polymerase and to Juan P. García Villaluenga (UCM) for useful discussions. Spanish Ministry of Economy and Competitiveness [MAT2015-71806-R to J.R.A-G, FIS2010-17440, FIS2015-67765-R to F.J.C., BFU2012-31825, BFU2015-63714-R to B.I.]; Spanish Ministry of Education, Culture and Sport [FPU13/02934 to J.J., FPU13/02826 to E.B-H.]; National Institutes of Health [GM45925 to L.S.K.]; University of Tampere (to G.L.C.); Programa de Financiacion Universidad Complutense de Madrid-Santander Universidades [CT45/15-CT46/15 to F.C.]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [BFU2015-63714-R].Morin, J.; Cerrón, F.; Jarillo, J.; Beltran-Heredia, E.; Ciesielski, G.; Arias-Gonzalez, JR.; Kaguni, L.... (2017). DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein. Nucleic Acids Research. 45(12):7237-7248. https://doi.org/10.1093/nar/gkx395S723772484512Shereda, R. D., Kozlov, A. G., Lohman, T. M., Cox, M. M., & Keck, J. L. (2008). SSB as an Organizer/Mobilizer of Genome Maintenance Complexes. Critical Reviews in Biochemistry and Molecular Biology, 43(5), 289-318. doi:10.1080/10409230802341296Flynn, R. L., & Zou, L. (2010). Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians. Critical Reviews in Biochemistry and Molecular Biology, 45(4), 266-275. doi:10.3109/10409238.2010.488216Murzin, A. G. (1993). OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. The EMBO Journal, 12(3), 861-867. doi:10.1002/j.1460-2075.1993.tb05726.xKozlov, A. G., Weiland, E., Mittal, A., Waldman, V., Antony, E., Fazio, N., … Lohman, T. M. (2015). Intrinsically Disordered C-Terminal Tails of E. coli Single-Stranded DNA Binding Protein Regulate Cooperative Binding to Single-Stranded DNA. Journal of Molecular Biology, 427(4), 763-774. doi:10.1016/j.jmb.2014.12.020Kuznetsov, S. V., Kozlov, A. G., Lohman, T. M., & Ansari, A. (2006). Microsecond Dynamics of Protein–DNA Interactions: Direct Observation of the Wrapping/Unwrapping Kinetics of Single-stranded DNA around the E.coli SSB Tetramer. Journal of Molecular Biology, 359(1), 55-65. doi:10.1016/j.jmb.2006.02.070Lohman, T. M., & Ferrari, M. E. (1994). Escherichia Coli Single-Stranded DNA-Binding Protein: Multiple DNA-Binding Modes and Cooperativities. Annual Review of Biochemistry, 63(1), 527-570. doi:10.1146/annurev.bi.63.070194.002523Maier, D., Farr, C. L., Poeck, B., Alahari, A., Vogel, M., Fischer, S., … Schneuwly, S. (2001). Mitochondrial Single-stranded DNA-binding Protein Is Required for Mitochondrial DNA Replication and Development in Drosophila melanogaster. Molecular Biology of the Cell, 12(4), 821-830. doi:10.1091/mbc.12.4.821Ruhanen, H., Borrie, S., Szabadkai, G., Tyynismaa, H., Jones, A. W. E., Kang, D., … Yasukawa, T. (2010). Mitochondrial single-stranded DNA binding protein is required for maintenance of mitochondrial DNA and 7S DNA but is not required for mitochondrial nucleoid organisation. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1803(8), 931-939. doi:10.1016/j.bbamcr.2010.04.008Farr, C. L., Matsushima, Y., Lagina, A. T., Luo, N., & Kaguni, L. S. (2004). Physiological and Biochemical Defects in Functional Interactions of Mitochondrial DNA Polymerase and DNA-binding Mutants of Single-stranded DNA-binding Protein. Journal of Biological Chemistry, 279(17), 17047-17053. doi:10.1074/jbc.m400283200Van Tuyle, G. C., & Pavco, P. A. (1985). The rat liver mitochondrial DNA-protein complex: displaced single strands of replicative intermediates are protein coated. The Journal of Cell Biology, 100(1), 251-257. doi:10.1083/jcb.100.1.251Clayton, D. A. (1982). Replication of animal mitochondrial DNA. Cell, 28(4), 693-705. doi:10.1016/0092-8674(82)90049-6Farr, C. L., Wang, Y., & Kaguni, L. S. (1999). Functional Interactions of Mitochondrial DNA Polymerase and Single-stranded DNA-binding Protein. Journal of Biological Chemistry, 274(21), 14779-14785. doi:10.1074/jbc.274.21.14779Korhonen, J. A., Gaspari, M., & Falkenberg, M. (2003). TWINKLE Has 5′ → 3′ DNA Helicase Activity and Is Specifically Stimulated by Mitochondrial Single-stranded DNA-binding Protein. Journal of Biological Chemistry, 278(49), 48627-48632. doi:10.1074/jbc.m306981200Miralles Fusté, J., Shi, Y., Wanrooij, S., Zhu, X., Jemt, E., Persson, Ö., … Falkenberg, M. (2014). In Vivo Occupancy of Mitochondrial Single-Stranded DNA Binding Protein Supports the Strand Displacement Mode of DNA Replication. PLoS Genetics, 10(12), e1004832. doi:10.1371/journal.pgen.1004832Oliveira, M. T., & Kaguni, L. S. (2011). Reduced Stimulation of Recombinant DNA Polymerase γ and Mitochondrial DNA (mtDNA) Helicase by Variants of Mitochondrial Single-stranded DNA-binding Protein (mtSSB) Correlates with Defects in mtDNA Replication in Animal Cells. Journal of Biological Chemistry, 286(47), 40649-40658. doi:10.1074/jbc.m111.289983Williams, A. J., & Kaguni, L. S. (1995). Stimulation ofDrosophilaMitochondrial DNA Polymerase by Single-stranded DNA-binding Protein. Journal of Biological Chemistry, 270(2), 860-865. doi:10.1074/jbc.270.2.860Bogenhagen, D. F., Wang, Y., Shen, E. L., & Kobayashi, R. (2003). Protein Components of Mitochondrial DNA Nucleoids in Higher Eukaryotes. Molecular & Cellular Proteomics, 2(11), 1205-1216. doi:10.1074/mcp.m300035-mcp200BARAT-GUERIDE, M., DUFRESNE, C., & RICKWOOD, D. (1989). Effect of DNA conformation on the transcription of mitochondrial DNA. European Journal of Biochemistry, 183(2), 297-302. doi:10.1111/j.1432-1033.1989.tb14928.xYang, C., Curth, U., Urbanke, C., & Kang, C. (1997). Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 Å resolution. Nature Structural Biology, 4(2), 153-157. doi:10.1038/nsb0297-153Raghunathan, S., Ricard, C. S., Lohman, T. M., & Waksman, G. (1997). Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution. Proceedings of the National Academy of Sciences, 94(13), 6652-6657. doi:10.1073/pnas.94.13.6652CURTH, U., URBANKE, C., GREIPEL, J., GERBERDING, H., TIRANTI, V., & ZEVIANI, M. (1994). Single-stranded-DNA-binding proteins from human mitochondria and Escherichia coli have analogous physicochemical properties. European Journal of Biochemistry, 221(1), 435-443. doi:10.1111/j.1432-1033.1994.tb18756.xOverman, L. B., & Lohman, T. M. (1994). Linkage of pH, Anion and Cation Effects in Protein-Nucleic Acid Equilibria. Journal of Molecular Biology, 236(1), 165-178. doi:10.1006/jmbi.1994.1126Bhattacharyya, B., George, N. P., Thurmes, T. M., Zhou, R., Jani, N., Wessel, S. R., … Keck, J. L. (2013). Structural mechanisms of PriA-mediated DNA replication restart. Proceedings of the National Academy of Sciences, 111(4), 1373-1378. doi:10.1073/pnas.1318001111Carlini, L. E., Porter, R. D., Curth, U., & Urbanke, C. (1993). Viability and preliminary in vivo characterization of site directed mutants of Escherichia coli single-stranded DNA-binding protein. Molecular Microbiology, 10(5), 1067-1075. doi:10.1111/j.1365-2958.1993.tb00977.xGriffith, J. D., Harris, L. D., & Register, J. (1984). Visualization of SSB-ssDNA Complexes Active in the Assembly of Stable RecA-DNA Filaments. Cold Spring Harbor Symposia on Quantitative Biology, 49(0), 553-559. doi:10.1101/sqb.1984.049.01.062Morrical, S. W., & Cox, M. M. (1990). Stabilization of recA protein-ssDNA complexes by the single-stranded DNA binding protein of Escherichia coli. Biochemistry, 29(3), 837-843. doi:10.1021/bi00455a034Muniyappa, K., Williams, K., Chase, J. W., & Radding, C. M. (1990). Active nucleoprotein filaments of single-stranded binding protein and recA protein on single-stranded DNA have a regular repeating structure. Nucleic Acids Research, 18(13), 3967-3973. doi:10.1093/nar/18.13.3967Wessel, S. R., Marceau, A. H., Massoni, S. C., Zhou, R., Ha, T., Sandler, S. J., & Keck, J. L. (2013). PriC-mediated DNA Replication Restart Requires PriC Complex Formation with the Single-stranded DNA-binding Protein. Journal of Biological Chemistry, 288(24), 17569-17578. doi:10.1074/jbc.m113.478156Bell, J. C., Liu, B., & Kowalczykowski, S. C. (2015). Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function. eLife, 4. doi:10.7554/elife.08646Suksombat, S., Khafizov, R., Kozlov, A. G., Lohman, T. M., & Chemla, Y. R. (2015). Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways. eLife, 4. doi:10.7554/elife.08193Zhou, R., Kozlov, A. G., Roy, R., Zhang, J., Korolev, S., Lohman, T. M., & Ha, T. (2011). SSB Functions as a Sliding Platform that Migrates on DNA via Reptation. Cell, 146(2), 222-232. doi:10.1016/j.cell.2011.06.036Pant, K., Karpel, R. L., Rouzina, I., & Williams, M. C. (2004). Mechanical Measurement of Single-molecule Binding Rates: Kinetics of DNA Helix-destabilization by T4 Gene 32 Protein. Journal of Molecular Biology, 336(4), 851-870. doi:10.1016/j.jmb.2003.12.025Pant, K., Karpel, R. L., Rouzina, I., & Williams, M. C. (2005). Salt Dependent Binding of T4 Gene 32 Protein to Single and Double-stranded DNA: Single Molecule Force Spectroscopy Measurements. Journal of Molecular Biology, 349(2), 317-330. doi:10.1016/j.jmb.2005.03.065Robberson, D. L., & Clayton, D. A. (1972). Replication of Mitochondrial DNA in Mouse L Cells and Their Thymidine Kinase- Derivatives: Displacement Replication on a Covalently-Closed Circular Template. Proceedings of the National Academy of Sciences, 69(12), 3810-3814. doi:10.1073/pnas.69.12.3810Ciesielski, G. L., Bermek, O., Rosado-Ruiz, F. A., Hovde, S. L., Neitzke, O. J., Griffith, J. D., & Kaguni, L. S. (2015). Mitochondrial Single-stranded DNA-binding Proteins Stimulate the Activity of DNA Polymerase γ by Organization of the Template DNA. Journal of Biological Chemistry, 290(48), 28697-28707. doi:10.1074/jbc.m115.673707Lázaro, J. M., Blanco, L., & Salas, M. (1995). [5] Purification of bacteriophage φ29 DNA polymerase. DNA Replication, 42-49. doi:10.1016/0076-6879(95)62007-9Ibarra, 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.2009.219Morin, 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.1204759109Smith, S. B., Cui, Y., & Bustamante, C. (2003). [7] Optical-trap force transducer that operates by direct measurement of light momentum. Biophotonics, Part B, 134-162. doi:10.1016/s0076-6879(03)61009-8Bosco, A., Camunas-Soler, J., & Ritort, F. (2013). Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions. Nucleic Acids Research, 42(3), 2064-2074. doi:10.1093/nar/gkt1089Smith, S., Finzi, L., & Bustamante, C. (1992). Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science, 258(5085), 1122-1126. doi:10.1126/science.1439819Longley, M. J., Smith, L. A., & Copeland, W. C. (2009). Preparation of Human Mitochondrial Single-Stranded DNA-Binding Protein. Mitochondrial DNA, 73-85. doi:10.1007/978-1-59745-521-3_5Li, K., & Williams, R. S. (1997). Tetramerization and Single-stranded DNA Binding Properties of Native and Mutated Forms of Murine Mitochondrial Single-stranded DNA-binding Proteins. Journal of Biological Chemistry, 272(13), 8686-8694. doi:10.1074/jbc.272.13.8686Jarillo, J., Morín, J. A., Beltrán-Heredia, E., Villaluenga, J. P. G., Ibarra, B., & Cao, F. J. (2017). Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers. PLOS ONE, 12(4), e0174830. doi:10.1371/journal.pone.0174830Bujalowski, W., & Lohman, T. M. (1986). Escherichia coli single-strand binding protein forms multiple, distinct complexes with single-stranded DNA. Biochemistry, 25(24), 7799-7802. doi:10.1021/bi00372a003Thömmes, P., Farr, C. L., Marton, R. F., Kaguni, L. S., & Cotterill, S. (1995). Mitochondrial Single-stranded DNA-binding Protein fromDrosophilaEmbryos. Journal of Biological Chemistry, 270(36), 21137-21143. doi:10.1074/jbc.270.36.21137Rodriguez, 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.0500597102Kamtekar, 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.2004.10.019Chrysogelos, S., & Griffith, J. (1982). Escherichia coli single-strand binding protein organizes single-stranded DNA in nucleosome-like units. Proceedings of the National Academy of Sciences, 79(19), 5803-5807. doi:10.1073/pnas.79.19.5803Hamon, L., Pastre, D., Dupaigne, P., Breton, C. L., Cam, E. L., & Pietrement, O. (2007). High-resolution AFM imaging of single-stranded DNA-binding (SSB) protein--DNA complexes. Nucleic Acids Research, 35(8), e58-e58. doi:10.1093/nar/gkm147Takamatsu, C., Umeda, S., Ohsato, T., Ohno, T., Abe, Y., Fukuoh, A., … Kang, D. (2002). Regulation of mitochondrial D‐loops by transcription factor A and single‐stranded DNA‐binding protein. EMBO reports, 3(5), 451-456. doi:10.1093/embo-reports/kvf099Wang, Y., & Bogenhagen, D. F. (2006). Human Mitochondrial DNA Nucleoids Are Linked to Protein Folding Machinery and Metabolic Enzymes at the Mitochondrial Inner Membrane. Journal of Biological Chemistry, 281(35), 25791-25802. doi:10.1074/jbc.m604501200Brown, T. A. (2005). Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism. Genes & Development, 19(20), 2466-2476. doi:10.1101/gad.135210
Mechano-chemical kinetics of DNA replication: Identification of the translocation step of a replicative DNA polymerase
DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein
Quadrupolar and magnetic ordering in CeB6
The quadrupolar ordering in CeB_6 is explained in terms of the electrostatic
interaction of quadrupolar moments arranged into a simple cubic lattice. The
representation of magnetic and quadrupolar moments by means of quasispins of
two kinds is employed. A linear increase of the quadrupolar transition
temperature T_Q(H) with applied magnetic field and its further re-entrance are
described using a generalized spherical model which is well adjusted to a
particular problem of the quadrupolar ordering in CeB_6. The theory naturally
explains the growing specific heat jump at T_Q(H) with increasing magnetic
field. The role of the quadrupolar ordering in the formation of the magnetic
ordering, as well as the possible critical experiments and applications to
other rare-earth compounds, are discussed.Comment: 40 pages, 9 Postscript figures, to appear in Phys.Rev.
Infrastructure for Detector Research and Development towards the International Linear Collider
The EUDET-project was launched to create an infrastructure for developing and
testing new and advanced detector technologies to be used at a future linear
collider. The aim was to make possible experimentation and analysis of data for
institutes, which otherwise could not be realized due to lack of resources. The
infrastructure comprised an analysis and software network, and instrumentation
infrastructures for tracking detectors as well as for calorimetry.Comment: 54 pages, 48 picture
Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment
This paper describes an analysis of the angular distribution of W->enu and
W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with
the ATLAS detector at the LHC in 2010, corresponding to an integrated
luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and
the missing transverse energy, the W decay angular distribution projected onto
the transverse plane is obtained and analysed in terms of helicity fractions
f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV
and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw
> 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour,
are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017
+/- 0.030, where the first uncertainties are statistical, and the second
include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables,
revised author list, matches European Journal of Physics C versio
Observation of a new chi_b state in radiative transitions to Upsilon(1S) and Upsilon(2S) at ATLAS
The chi_b(nP) quarkonium states are produced in proton-proton collisions at
the Large Hadron Collider (LHC) at sqrt(s) = 7 TeV and recorded by the ATLAS
detector. Using a data sample corresponding to an integrated luminosity of 4.4
fb^-1, these states are reconstructed through their radiative decays to
Upsilon(1S,2S) with Upsilon->mu+mu-. In addition to the mass peaks
corresponding to the decay modes chi_b(1P,2P)->Upsilon(1S)gamma, a new
structure centered at a mass of 10.530+/-0.005 (stat.)+/-0.009 (syst.) GeV is
also observed, in both the Upsilon(1S)gamma and Upsilon(2S)gamma decay modes.
This is interpreted as the chi_b(3P) system.Comment: 5 pages plus author list (18 pages total), 2 figures, 1 table,
corrected author list, matches final version in Physical Review Letter
Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS
We present the results of a search for new, heavy particles that decay at a
significant distance from their production point into a final state containing
charged hadrons in association with a high-momentum muon. The search is
conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV
and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS
detector operating at the Large Hadron Collider. Production of such particles
is expected in various scenarios of physics beyond the standard model. We
observe no signal and place limits on the production cross-section of
supersymmetric particles in an R-parity-violating scenario as a function of the
neutralino lifetime. Limits are presented for different squark and neutralino
masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final
version to appear in Physics Letters
Measurement of the inclusive isolated prompt photon cross-section in pp collisions at sqrt(s)= 7 TeV using 35 pb-1 of ATLAS data
A measurement of the differential cross-section for the inclusive production
of isolated prompt photons in pp collisions at a center-of-mass energy sqrt(s)
= 7 TeV is presented. The measurement covers the pseudorapidity ranges
|eta|<1.37 and 1.52<=|eta|<2.37 in the transverse energy range 45<=E_T<400GeV.
The results are based on an integrated luminosity of 35 pb-1, collected with
the ATLAS detector at the LHC. The yields of the signal photons are measured
using a data-driven technique, based on the observed distribution of the
hadronic energy in a narrow cone around the photon candidate and the photon
selection criteria. The results are compared with next-to-leading order
perturbative QCD calculations and found to be in good agreement over four
orders of magnitude in cross-section.Comment: 7 pages plus author list (18 pages total), 2 figures, 4 tables, final
version published in Physics Letters
- …