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Sökning: WFRF:(Kim S.) > (1995-1999)

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1.
  • Dunham, I, et al. (författare)
  • The DNA sequence of human chromosome 22
  • 1999
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 402:6761, s. 489-495
  • Tidskriftsartikel (refereegranskat)
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2.
  • Andrés, E. C., et al. (författare)
  • The AMANDA neutrino telescope
  • 1999
  • Ingår i: Nuclear physics B, Proceedings supplements. - 0920-5632 .- 1873-3832. ; 77:1-3, s. 474-485
  • Tidskriftsartikel (refereegranskat)abstract
    • With an effective telescope area of order 104 m2 for TeV neutrinos, a threshold near ∼50 GeV and a pointing accuracy of 2.5 degrees per muon track, the AMANDA detector represents the first of a new generation of high energy neutrino telescopes, reaching a scale envisaged over 25 years ago. We describe early results on the calibration of natural deep ice as a particle detector as well as on AMANDA's performance as a neutrino telescope.
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  • Andres, E., et al. (författare)
  • AMANDA : Status, results and future
  • 1999
  • Ingår i: Proceedings, 8th International Workshop, Venice, Italy, February 23-26, 1999. Vol. 1, 2. ; , s. 63-79
  • Konferensbidrag (refereegranskat)abstract
    • We review the status of the AMANDA neutrino telescope. We present resultsobtained from the four-string prototype array AMANDA-B4 and describe themethods of track reconstruction and neutrino event separation. We give also firstresults of the analysis of the 10-string detector AMANDA-B10, in particular onatmospheric neutrinos and the search for magnetic monopoles. We sketch thefuture schedule on the way to a cube kilometer telescope at the South Pole,ICECUBE.
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8.
  • Wischnewski, R., et al. (författare)
  • The AMANDA neutrino detector
  • 1999
  • Ingår i: Nuclear physics B, Proceedings supplements. - : Elsevier. - 0920-5632 .- 1873-3832. ; 75:1-2, s. 412-414
  • Tidskriftsartikel (refereegranskat)abstract
    • The first stage of the AMANDA High Energy Neutrino Detector at the South Pole, the 302 PMT array AMANDA-B with an expected effective area for TeV neutrinos of ∼ 104 m2, has been taking data since 1997. Progress with calibration, investigation of ice properties, as well as muon and neutrino data analysis are described. The next stage 20-string detector AMANDA-II with ∼800 PMTs will be completed in spring 2000.
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9.
  • Choi, S. D., et al. (författare)
  • Binding Mode of [Ruthenium(II) (1,10-Phenanthroline)2L]2+ with Poly(dT*dA-dT) Triplex. Ligand Size Effect on Third-Strand Stabilization
  • 1997
  • Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 36:1, s. 214-223
  • Tidskriftsartikel (refereegranskat)abstract
    • The binding of homochiral [Ru(II)(1,10-phenanthroline)(2)L](2+) complexes {where L = 1,10-phenanthroline (phen), dipyrido[3,2-a:2',3'-c]phenazine (DPPZ) or benzodipyrido[3,2-a:2',3'-c]phenazine (BDPPZ)} to poly(dT*dA-dT) triplex has been investigated by linear and circular dichroism and thermal denaturation. Analysis of the linear dichroism spectra indicates that the extended DPPZ and BDPPZ ligands lie approximately parallel to the base-pair and base-tripler planes consistent with intercalation which is also supported by strong hypochromism in the interligand absorption bands with either duplex or tripler. The spectral properties of any of the metal complex enantiomers were similar for binding to either duplex or tripler DNA, indicating that the third strand, which occupies the major groove of the template duplex, has little effect on the binding geometries and hence supports the hypothesis that the metal complexes all bind from the minor groove with the DPPZ and BDPPZ ligands intercalated but without intercalation in the case of [Ru(phen)(3)](2+). Third-strand stabilization depended on the nature of the third substituted phenanthroline chelate ligand but was not directly related to its size, with stabilizing power increasing in the order phen
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10.
  • Son, G.S., et al. (författare)
  • Binding Mode of Norfloxacin to Calf Thymus DNA
  • 1998
  • Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 120:26, s. 6451-6457
  • Tidskriftsartikel (refereegranskat)abstract
    • Norfloxacin, a quinolone antibacterial reagent, has been studied with respect to its binding to calf thymus DNA using fluorescence and linear dichroism techniques and unwinding of supercoiled DNA. The fluorescence of norfloxacin is strongly quenched in the presence of DNA and using this decrease in a fluorescence titration the equilibrium constant of the complex formation was established to be 2.8 x 10(3) M-1. The electric transition moments of the norfloxacin chromophore have been analyzed using fluorescence anisotropy, magnetic circular dichroism, and linear dichroism in stretched poly(vinyl alcohol) film and INDO/S calculations. These data are then used to interpret flow linear dichroism results for the norfloxacin-DNA complex. The transition moments for the long-wavelength transitions are found to be oriented at about 65.0-85.0 degrees with respect to the DNA helix axis. A near perpendicular orientation of the norfloxacin chromophore plane makes it possible to exclude classical groove or surface binding modes. The possibility of a classical intercalation binding mode also can be ruled out from unwinding experiments. However, it is shown that the molecular plane of norfloxacin is near perpendicular relative to the DNA helix axis with a possibility of a bending of the DNA helix at the binding site.
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11.
  • Kim, H. K., et al. (författare)
  • Interactions of intercalative and minor groove binding ligands with triplex poly(dA)•[poly(dT)]2and with duplex poly(dA)•poly(dT) and poly[d(A-T)]2studied by CD, LD, and normal absorption
  • 1996
  • Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 35:4, s. 1187-1194
  • Tidskriftsartikel (refereegranskat)abstract
    • The binding of 9-aminoacridine and one bis-acridine compound to double helical poly(dA). poly(dT) and poly[d(A-T)](2) and triple helical poly(dA).[poly(dT)](2) has been investigated using linear dichroism (LD) and circular dichroism (CD). A close examination of the negative reduced LD and the induced CD for the first pi --> pi* transition absorption region leads us to conclude that the acridine moiety of the 9-aminoacridine and bis-acridine molecule intercalates with both duplex and tripler DNA. Binding geometries of the acridine moieties in the examined polynucleotides are similar to those found for the ligands with DNA (Hansen et al. (1984) J. Chem. Sec., Chern. Commun., 509-511). It is also found that both 9-aminoacridine and bis-acridine effectively enhance the thermal stability of the tripler DNA. The corresponding spectra for the complexes of the minor groove binders DAPI and Hoechst with poly(dA).[poly(dT)](2) were studied for comparison. They both show a positive LD and a mixing ratio dependent positive CD in the ligand absorption region, similar to those of their duplex complexes. This indicates that these ligands bind in the grooves of the tripler, probably to the one corresponding to the minor groove of the template duplex.
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12.
  • Kim, Y B, et al. (författare)
  • Atomic force microscopy of rubbed polyimide aligning films for liquid crystal displays
  • 1995
  • Ingår i: 15th International Liquid Crystal ConferenceBUDAPEST, HUNGARY, JUL 03-08, 1994. ; , s. 89-98
  • Konferensbidrag (refereegranskat)abstract
    • The surface of polyimide (PI) films for aligning liquid crystals were studied by means of atomic force microscopy (AFM). The surface of the unrubbed PI films consisted of polymer clusters of different sizes which are randomly distributed over the film area. After rubbing, however, these polymer clusters formed long chains along the rubbing direction. The cluster chains were separated with periodicity about 100 nm for weak rubbing strength. Deeper grooves are also present, separated with periodicity about 2 mu m that could be related to the microstructure of the fibres from the rubbing cloth. On increasing the rubbing strength further on, the cluster chains coalesce into wider ones. The rubbed PI films show optical retardation, which was increased rapidly with increased the rubbing strength and reached a constant value of about 1.4nm.
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14.
  • Kim, S.K., et al. (författare)
  • Binding Geometries of Triple Helix Selective Benzopyrido [4,3-b]indole Ligands Complexed with Double- and Triple-Helical Polynucleotides
  • 1997
  • Ingår i: Biopolymers. - 0006-3525 .- 1097-0282. ; 42:1, s. 101-111
  • Tidskriftsartikel (refereegranskat)abstract
    • The binding modes of three benzopyrido[4,3-b]indole derivatives (and one benzo[f]pyrido[4-3b]quinoxaline derivative) with respect to double helical poly(dA) . poly(dT) and poly[d(A-T)](2) and triple-helical poly(dA) . 2poly(dT) have been investigated using linear dichroism (LD) and CD: (I) 3-methoxy-11-amino-BePI where BePI = {7H-8-methyl-benzo[e]pyrido[4,3-b]indole}, (II) 3-methoxy-11-[(3'-amino)propylamino]-BePI, (III) 3-methoxy-7-[(3'diethylamino)propylamino]BgPI where BgPI = {benzo[g]pyrido[4,3-b]indole}, and (IV) 3-methoxy-11-[(3'amino)propylamino]BfPQ where BfPQ = {benzo[f]pyrido[4-3b]quinoxaline}. The magnitudes of the reduced LD of the electronic transitions of the polynucleotide bases and of the bound ligands are generally very similar, suggesting an orientation of the plane of the ligands' fused-ring systems preferentially perpendicular to the helix axis. The LD results suggest that all of the ligands are intercalated for all three polynucleotides. The induced CD spectrum of the BePI chromophore in the (II-BePI)-poly[d(A-T)](2) complex is almost a mirror image of that for the (I-BePI)-poly(dA) . poly(dT) and (I-BePI)-poly(dA) . 2poly(dT) complexes, suggesting an antisymmetric orientation of the BePI moiety upon intercalation in poly[d(A-T)]2 compared to the other polynucleotides. The induced CD of I-BePI bound to poly(dA) . 2poly(dT) suggests a geometry that is intermediate between that of its other two complexes. The concluded intercalative binding as well as the conformational variations between the different BePI complexes are of interest in relation to the fact that BePI derivatives are triplex stabilizers.
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21.
  • Kim, S J, et al. (författare)
  • Distinct "assisted" and "spontaneous" mechanisms for the insertion of polytopic chlorophyll-binding proteins into the thylakoid membrane
  • 1999
  • Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 274:8, s. 4715-4721
  • Tidskriftsartikel (refereegranskat)abstract
    • The biogenesis of several bacterial polytopic membrane proteins has been shown to require signal recognition particle (SRP) and protein transport machinery, and one such protein, the major light-harvesting chlorophyll-binding protein (LHCP) exhibits these requirements in chloroplasts. In this report we have used in vitro insertion assays to analyze four additional members of the chlorophyll-alb-binding protein family. We show that two members, Lhca1 and Lhcb5, display an absolute requirement for stroma, nucleoside triphosphates, and protein transport apparatus, indicating an "assisted" pathway that probably resembles that of LHCP. Two other members, however, namely an early light-inducible protein 2 (Elip2) and photosystem II subunit S (PsbS), can insert efficiently in the complete absence of SRP, SecA activity, nucleoside triphosphates, or a functional Sec system. The data suggest a possibly spontaneous insertion mechanism that, to date, has been characterized only for simple single-span proteins. Of the membrane proteins whose insertion into thylakoids has been analyzed, five have now been shown to insert by a SRP/Sec-independent mechanism, suggesting that this is a mainstream form of targeting pathway. We also show that PsbS and Elip2 molecules are capable of following either "unassisted" or assisted pathways, and we discuss the implications for the mechanism and role of SRP in chloroplasts.
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22.
  • Kim, S. K., et al. (författare)
  • Binding of RecA to anti-parallel poly(dA) · 2poly(dT) triple helix DNA
  • 1995
  • Ingår i: Biochimica et Biophysica Acta - Gene Structure and Expression. - : Elsevier BV. - 0167-4781. ; 1264:1, s. 129-133
  • Tidskriftsartikel (refereegranskat)abstract
    • Binding of RecA protein to conventional anti-parallel poly(dA). 2poly(dT) tripler DNA has been studied using flow linear dichroism spectroscopy. The association requires the presence of cofactor analog adenosine 5'-O-3-thiotriphosphate (ATP gamma S) and occurs with a rate similar to that for the association of RecA to double-stranded poly(dA) poly(dT) DNA. The binding of RecA to DNA stiffens the nucleotide chain, as evidenced from high orientation already at low shear rates, and the complex with tripler DNA appears to be at least as stiff as that with the duplex DNA. Therefore, the observation of a lower magnitude of the LD spectrum at 260 nm, in the triplex-RecA compared to the duplex-RecA complex, but retained magnitude of protein LD at 280 nm, indicates a markedly impaired orientation of nucleo-bases, possibly reflecting a perturbation by RecA on the third strand making its bases deviate strongly from perpendicularity. The circular dichroism spectrum: appearing immediately after dissociation of RecA by SDS, suggests an intact tripler structure, meaning that complexation with RecA has not dissociated the third strand. In conclusion, binding of RecA to tripler DNA does not modify the main organisation of the strands, but could affect the base-base interactions between them. Tilted bases could reflect a conformational change that RecA imposes also on the biological intermediate tripler structure to relax the base-base hydrogen bonding between the DNA strands.
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23.
  • Klinga-Levan, Karin, 1974, et al. (författare)
  • Chromosomal mapping of three mucin genes in the rat.
  • 1996
  • Ingår i: Mammalian genome : official journal of the International Mammalian Genome Society. - 0938-8990. ; 7:3, s. 248-50
  • Tidskriftsartikel (refereegranskat)
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24.
  • Kudryashov, V, et al. (författare)
  • Characterization of a mouse monoclonal IgG3 antibody to the tumor-associated globo H structure produced by immunization with a synthetic glycoconjugate.
  • 1998
  • Ingår i: Glycoconjugate journal. - 0282-0080. ; 15:3, s. 243-9
  • Tidskriftsartikel (refereegranskat)abstract
    • Globo H (Fuc alpha1 --> 2Galbeta1 --> 3GalNAcbeta1 --> 3Gal alpha1 --> 4Galbeta1 --> 4Glc) is a carbohydrate structure that shows enhanced expression in many human carcinomas. From mice immunized with a globo H-KLH (keyhole limpet hemocyanin) synthetic conjugate an IgG3 monoclonal antibody (mAb VK-9) was derived that recognizes the globo H structure. Serological analysis showed that the minimal structure recognized by this mAb was the tetrasaccharide sequence Fuc alpha1 --> 2Galbeta1 --> 3GalNAcbeta1 --> 3Gal. An isomeric structure with an internal alphaGalNAc linkage was also recognized but less efficiently. mAb VK-9 did not react with many related structures, such as galactosylgloboside, globoside, H type 1, H type 2 blood group structures or fucosyl-gangliotetraosyl ceramide, but did react weakly with globo A ceramide. Not only did mAb VK-9 react with carbohydrate-protein conjugates but it could also recognize globo H-ceramide and human tumor cells expressing globo H. These results suggest that globo H-KLH could be explored as a vaccine in the treatment of carcinoma patients.
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25.
  • Li, Y, et al. (författare)
  • Yeast global transcriptional regulators Sin4 and Rgr1 are components of mediator complex/RNA polymerase II holoenzyme.
  • 1995
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 92:24, s. 10864-8
  • Tidskriftsartikel (refereegranskat)abstract
    • Sin4 and Rgr1 proteins, previously shown by genetic studies to play both positive and negative roles in the transcriptional regulation of many genes, are identified here as components of mediator and RNA polymerase II holoenzyme complexes. Results with Sin4 deletion and Rgr1 truncation strains indicate the association of these proteins in a subcomplex comprising Sin4, Rgr1, Gal11, and a 50-kDa polypeptide. Taken together with the previous genetic evidence, our findings point to a role of the mediator in repression as well as in transcriptional activation.
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  • Moon, J. H., et al. (författare)
  • DNA structural features responsible for sequence-dependent binding geometries of Hoechst 33258
  • 1996
  • Ingår i: Biopolymers. - 0006-3525 .- 1097-0282. ; 38:5, s. 593-606
  • Tidskriftsartikel (refereegranskat)abstract
    • The complexes of Hoechst 33258 with poly[d(A-T)(2)], poly[d(I-C)(2)], poly[d(G-C)(2)], and poly[d(G-m(5)C)(2)] were studied using linear dichroism, CD, and fluorescence spectroscopies. The Hoechst-poly[d(I-C)(2)] complex, in which there is no quanine amino group protruding in the minor groove, exhibit spectroscopic properties that are very similar to those of the Hoechst-poly[d(A-T)(2)] complex. When bound to both of these polynucleotides, Hoechst exhibits an average orientation angle of near 45 degrees relative to the DNA helix axis for the long-axis polarized low-energy transition, a relatively strong positive induced CD, and a strong increase in fluorescence intensity-leading us to conclude that this molecule also binds in the minor groove of poly[d(I-C)(2)]. By contrast, when bound to poly[d(G-C)(2)], Hoechst shows a distinctively different behavior. The strongly negative reduced linear dichroism in the ligand absorption region is consistent with a model in which part of the Hoechst chromophore is intercalculated between DNA bases. From the low drug:base ratio onset of excitonic effects in the CD and fluorescence emission spectra, it is inferred that another part of the Hoechst molecule may sit in the major groove of poly[d(G-C)(2)] and poly[d(G-m(5)C)(2)] and preferentially stacks into dimers, though this tendency is strongly reduced for the latter polynucleotide. Based on these results, the importance of the interactions of Hoechst with the exocyclic amino group of guanine and the methyl group of cytosine in determining the binding modes are discussed.
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  • Olofsson, K, et al. (författare)
  • High-speed, highly fluorous organic reactions
  • 1999
  • Ingår i: Journal of Organic Chemistry. - Uppsala Univ, BMC, Dept Organ Pharmaceut Chem, SE-75123 Uppsala, Sweden. Univ Pittsburgh, Dept Chem, Pittsburgh, PA 15260 USA. : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 64, s. 4539-
  • Tidskriftsartikel (refereegranskat)
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30.
  • Poon, D, et al. (författare)
  • Identification and characterization of a TFIID-like multiprotein complex from Saccharomyces cerevisiae.
  • 1995
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 92:18, s. 8224-8
  • Tidskriftsartikel (refereegranskat)abstract
    • Although the mechanisms of transcriptional regulation by RNA polymerase II are apparently highly conserved from yeast to man, the identification of a yeast TATA-binding protein (TBP)-TBP-associated factor (TAFII) complex comparable to the metazoan TFIID component of the basal transcriptional machinery has remained elusive. Here, we report the isolation of a yeast TBP-TAFII complex which can mediate transcriptional activation by GAL4-VP16 in a highly purified yeast in vitro transcription system. We have cloned and sequenced the genes encoding four of the multiple yeast TAFII proteins comprising the TBP-TAFII multisubunit complex and find that they are similar at the amino acid level to both human and Drosophila TFIID subunits. Using epitope-tagging and immunoprecipitation experiments, we demonstrate that these genes encode bona fide TAF proteins and show that the yeast TBP-TAFII complex is minimally composed of TBP and seven distinct yTAFII proteins ranging in size from M(r) = 150,000 to M(r) = 25,000. In addition, by constructing null alleles of the cloned TAF-encoding genes, we show that normal function of the TAF-encoding genes is essential for yeast cell viability.
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31.
  • Sheng, Dong Yuan, et al. (författare)
  • Water model study on convection pattern of molten steel flow in continuous casting tundish
  • 1998
  • Ingår i: ISIJ International. - 0915-1559 .- 1347-5460. ; 38:8, s. 843-851
  • Tidskriftsartikel (refereegranskat)abstract
    • Natural convection will obviously influence the liquid steel flow in continuous casting (CC) tundish, which cannot be neglected in tundish metallurgical process. Through the theoretical analysis, the dimensionless number, Gr/Re 2, is adopted to determine the convection pattern in tundish system. Validity of this criteria in a reduced scale water model are also discussed in this paper. Non-isothermal water model experiment with the temperature variation of inlet stream, has been simulated to see the effect of temperature variation of ladle stream. The convection pattern of molten steel flow in continuous casting tundish is also studied numerically by using the commercialized computational fluid dynamic (CFD) software package, CFX4. From the results of theoretical analysis, physical and mathematical model simulation, it can be stated that the convection pattern of molten steel flow in tundish is controlled by the combined nature convection and forced convection.
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32.
  • Shi, L X, et al. (författare)
  • Characterisation of the PsbX protein from Photosystem II and light regulation of its gene expression in higher plants
  • 1999
  • Ingår i: Plant Molecular Biology. - 0167-4412 .- 1573-5028. ; 40:4, s. 737-744
  • Tidskriftsartikel (refereegranskat)abstract
    • The location and expression of the previously uncharacterised photosystem II subunit PsbX have been analysed in higher plants. We show that this protein is a component of photosystem II (PSII) core particles but absent from light-harvesting complexes or PSII reaction centres. PsbX is, however, localised to the near vicinity of the reaction centre because it can be cross-linked to cytochrome b559, which is known to be associated with the D1/D2 dimer. We also show that the expression of this protein is tightly regulated by light, since neither protein nor mRNA is found in dark-grown plants.
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  • Tuite, Eimer, 1966, et al. (författare)
  • Effects of intercalators on complexation of RecA with duplex DNA
  • 1995
  • Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 34:50, s. 16365-16374
  • Tidskriftsartikel (refereegranskat)abstract
    • To elucidate the binding mode of recombination protein A (RecA) to double-stranded (ds) DNA, the effects on the RecA-DNA interaction of several mono- and bisintercalators of the acridine, phenanthridine, and cyanine classes have been investigated by linear dichroism spectroscopy. Simple monointercalators lacking side chains efficiently promoted the binding of RecA to dsDNA in the absence of nucleotide cofactor, which is otherwise required. Bisintercalators varied in their ability to induce RecA binding, while monointercalators with aminoalkyl side chains proved inefficient. Modification of DNA structure by the intercalator appears to be necessary for induction of RecA binding, but if the intercalator has a bulky minor-groove-binding side chain, it does not induce RecA binding. In detailed studies with acridines, neither the binding geometry of intercalators nor the structure of DNA was significantly modified upon binding of RecA without cofactor. Judged by circular dichroism, similar ReA conformational changes accompanied bis-9-aminoacridine- and ATPyS-induced RecA association with DNA. In the presence of ATPyS, the intercalators inhibited the rate of RecA binding to dsDNA and were extruded from DNA upon binding of RecA. This competitive aspect may suggest that intercalation of some amino acid residue(s) plays a role in nucleotide-induced RecA binding. The stoichiometry of the RecA-DNA-intercalator filament was determined; in the fully formed filament the base pair:intercalator ratio is 2, and the base pair:RecA ratio also 2. This contrasts with a base pair:RecA ratio of 3 in the ATPyS-induced filament, although in both cases the DNA experiences 50% extension.
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