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Berlin Brandenburg

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  • 1
    Language: English
    In: Journal of the American Chemical Society, 22 June 2011, Vol.133(24), pp.9278-81
    Description: The activity of an yttrium alkoxide complex supported by a ferrocene-based ligand was controlled using redox reagents during the ring-opening polymerization of L-lactide. The oxidized complex was characterized by X-ray crystallography and (1)H NMR, XANES, and Mössbauer spectroscopy. Switching in situ between the oxidized and reduced yttrium complexes resulted in a change in the rate of polymerization of L-lactide. Synthesized polymers were analyzed by gel permeation chromatography. Polymerization of trimethylene carbonate was also performed with the reduced and oxidized forms of an indium alkoxide complex. The indium system showed the opposite behavior to that of yttrium, revealing a metal-based dependency on the rate of polymerization.
    Keywords: Mossbauer Spectroscopy -- Usage ; Oxidation-reduction Reactions -- Analysis ; Ring-opening Polymerization -- Analysis ; X-ray Crystallography -- Usage ; Yttrium Compounds -- Chemical Properties ; Yttrium Compounds -- Structure;
    ISSN: 00027863
    E-ISSN: 1520-5126
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  • 2
    Language: English
    In: Journal of Molecular Biology, 12 August 2014, Vol.426(16), pp.2901-2917
    Description: Despite the fact that DNA polymerases have been investigated for many years and are commonly used as tools in a number of molecular biology assays, many details of the kinetic mechanism they use to catalyze DNA synthesis remain unclear. Structural and kinetic studies have characterized a rapid, pre-catalytic open-to-close conformational change of the Finger domain during nucleotide binding for many DNA polymerases including DNA polymerase I (Taq Pol), a thermostable enzyme commonly used for DNA amplification in PCR. However, little has been performed to characterize the motions of other structural domains of Taq Pol or any other DNA polymerase during catalysis. Here, we used stopped-flow Förster resonance energy transfer to investigate the conformational dynamics of all five structural domains of the full-length Taq Pol relative to the DNA substrate during nucleotide binding and incorporation. Our study provides evidence for a rapid conformational change step induced by dNTP binding and a subsequent global conformational transition involving all domains of Taq Pol during catalysis. Additionally, our study shows that the rate of the global transition was greatly increased with the truncated form of Taq Pol lacking the N-terminal domain. Finally, we utilized a mutant of Taq Pol containing a disulfide bond to demonstrate that limiting protein conformational flexibility greatly reduced the polymerization activity of Taq Pol.
    Keywords: Fluorescence Resonance Energy Transfer (Fret) ; DNA Polymerase ; Enzyme Kinetics ; Protein Dynamics ; Conformational Dynamics ; Biology ; Chemistry
    ISSN: 0022-2836
    E-ISSN: 1089-8638
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  • 3
    Language: English
    In: Biochemistry, 25 March 2014, Vol.53(11), pp.1768-78
    Description: Numerous kinetic, structural, and theoretical studies have established that DNA polymerases adjust their domain structures to enclose nucleotides in their active sites and then rearrange critical active site residues and substrates for catalysis, with the latter conformational change acting to kinetically limit the correct nucleotide incorporation rate. Additionally, structural studies have revealed a large conformational change between the apoprotein and the DNA-protein binary state for Y-family DNA polymerases. In previous studies [Xu, C., Maxwell, B. A., Brown, J. A., Zhang, L., and Suo, Z. (2009) PLoS Biol. 7, e1000225], a real-time Förster resonance energy transfer (FRET) method was developed to monitor the global conformational transitions of DNA polymerase IV from Sulfolobus solfataricus (Dpo4), a prototype Y-family enzyme, during nucleotide binding and incorporation by measuring changes in distance between locations on the enzyme and the DNA substrate. To elucidate further details of the conformational transitions of Dpo4 during substrate binding and catalysis, in this study, the real-time FRET technique was used to monitor changes in distance between various pairs of locations in the protein itself. In addition to providing new insight into the conformational changes as revealed in previous studies, the results here show that the previously described conformational change between the apo and DNA-bound states of Dpo4 occurs in a mechanistic step distinct from initial formation or dissociation of the binary complex of Dpo4 and DNA.
    Keywords: Fluorescence Resonance Energy Transfer ; Protein Conformation ; DNA Polymerase Beta -- Chemistry ; Sulfolobus Solfataricus -- Enzymology
    ISSN: 00062960
    E-ISSN: 1520-4995
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  • 4
    Language: English
    In: The Journal of biological chemistry, 13 April 2012, Vol.287(16), pp.13040-7
    Description: A major product of oxidative damage to DNA, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), can lead to genomic mutations if it is bypassed unfaithfully by DNA polymerases in vivo. However, our pre-steady-state kinetic studies show that DNA polymerase IV (Dpo4), a prototype Y-family enzyme from Sulfolobus solfataricus, can bypass 8-oxoG both efficiently and faithfully. For the first time, our stopped-flow FRET studies revealed that a DNA polymerase altered its synchronized global conformational dynamics in response to a DNA lesion. Relative to nucleotide incorporation into undamaged DNA, three of the four domains of Dpo4 undertook different conformational transitions during 8-oxoG bypass and the subsequent extension step. Moreover, the rapid translocation of Dpo4 along DNA induced by nucleotide binding was significantly hindered by the interactions between the embedded 8-oxoG and Dpo4 during the extension step. These results unprecedentedly demonstrate that a Y-family DNA polymerase employs different global conformational dynamics when replicating undamaged and damaged DNA.
    Keywords: Bacterial Proteins ; DNA Polymerase Beta ; Oxidative Stress -- Physiology ; Sulfolobus Solfataricus -- Enzymology
    E-ISSN: 1083-351X
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  • 5
    In: Chemical Communications, 2012, Vol.48(54), pp.6806-6808
    Description: An ethoxy-bridged dinuclear indium catalyst was used for the ring opening polymerization of the cyclic ester -butyrolactone to form the biodegradable polyester poly(hydroxybutyrate) (PHB). The catalyst shows remarkable activity and control during polymerization, allowing for formation of diblock polymers. Addition of high ratios of alcohols to the catalyst leads to fast chain transfer and immortal polymerization.
    Keywords: 4-Butyrolactone -- Analogs & Derivatives ; Indium -- Chemistry;
    ISSN: 1359-7345
    E-ISSN: 1364-548X
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  • 6
    Language: English
    In: Polymer, 2012, Vol.53(12), pp.2443-2452
    Description: In this study, different compositions of nearly monodispersed diblock copolymers of dl-lactide or d-lactide and l-lactide were synthesized by living ring-opening polymerization with a dinuclear indium catalyst. The effects of molecular weight and block length ratio on the rheological behavior of dl and l-lactide diblock copolymers in the disordered state were investigated. For comparison, blends of PDLLA and PLLA homopolymers of equivalent molecular weights to the diblock copolymers were prepared. We found that the time–temperature (t–T) superposition principle is applicable to the diblock copolymers PLLA-b-PDLLA and blends in the disordered state. However, the t–T superposition failed at low temperatures close to the temperature of crystallization. In contrast, diblock copolymers PLLA-b-PDLA formed stereocomplex crystallites of high melting point (slightly above 200 °C) that causes a viscosity enhancement. The failure of t–T superposition was found due to existing of micro homo or stereocomplex crystallites. The non-isothermal crystallization behavior was investigated using differential scanning calorimetry (DSC). The DSC thermograms of blends exhibited a single glass transition at 50–60 °C followed by melting point of PLLA at 177 °C. With decreasing of the PLLA content in the blends, the intensity of the melting peak decreased. In addition, different crystallization behavior was observed for diblock copolymers compared to their equivalent blends. Specifically, low temperatures and enthalpies of melting peaks were observed for diblock copolymers. These also show improvement in elongation at break and tensile strength as compared to their counterpart homopolymer blends. ; p. 2443-2452.
    Keywords: Molecular Weight ; Glass Transition ; Polylactic Acid ; Polymerization ; Tensile Strength ; Temperature ; Melting ; Indium ; Viscosity ; Composite Polymers ; Crystallization ; Differential Scanning Calorimetry ; Melting Point
    ISSN: 0032-3861
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  • 7
    Language: English
    In: PLoS ONE, 01 January 2013, Vol.8(3), p.e58434
    Description: BACKGROUND: Seasonal influenza epidemics occur annually with bimodality in southern China and unimodality in northern China. Regional differences exist in surveillance data collected by the National Influenza Surveillance Network of the Chinese mainland. Qualitative and quantitative analyses...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 8
    Language: English
    In: Polymer, 25 May 2012, Vol.53(12), pp.2443-2452
    Description: In this study, different compositions of nearly monodispersed diblock copolymers of -lactide or -lactide and -lactide were synthesized by living ring-opening polymerization with a dinuclear indium catalyst. The effects of molecular weight and block length ratio on the rheological behavior of and -lactide diblock copolymers in the disordered state were investigated. For comparison, blends of PDLLA and PLLA homopolymers of equivalent molecular weights to the diblock copolymers were prepared. We found that the time–temperature (t–T) superposition principle is applicable to the diblock copolymers PLLA- -PDLLA and blends in the disordered state. However, the t–T superposition failed at low temperatures close to the temperature of crystallization. In contrast, diblock copolymers PLLA- -PDLA formed stereocomplex crystallites of high melting point (slightly above 200 °C) that causes a viscosity enhancement. The failure of t–T superposition was found due to existing of micro homo or stereocomplex crystallites. The non-isothermal crystallization behavior was investigated using differential scanning calorimetry (DSC). The DSC thermograms of blends exhibited a single glass transition at 50–60 °C followed by melting point of PLLA at 177 °C. With decreasing of the PLLA content in the blends, the intensity of the melting peak decreased. In addition, different crystallization behavior was observed for diblock copolymers compared to their equivalent blends. Specifically, low temperatures and enthalpies of melting peaks were observed for diblock copolymers. These also show improvement in elongation at break and tensile strength as compared to their counterpart homopolymer blends.
    Keywords: Polylactide ; Polylactide Block Copolymers ; Rheology ; Engineering ; Chemistry
    ISSN: 0032-3861
    E-ISSN: 1873-2291
    Source: ScienceDirect Journals (Elsevier)
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  • 9
    In: American Journal of Epidemiology, 2015, Vol. 182(8), pp.705-713
    Description: Influenza B viruses split into 2 distinct lineages in the early 1980s, commonly named the Victoria and Yamagata lineages. There are few data on the comparative epidemiology of Victoria- and Yamagata-lineage viruses. In 2007–2011, we enrolled 75 and 34 households containing index patients with acute respiratory illness who tested positive for Yamagata- and Victoria-lineage viruses, respectively, from outpatient clinics in Hong Kong, China. These index patients and their household contacts were followed up for 7–10 days. We examined overall risk of polymerase chain reaction–confirmed infection among household contacts and the risk of secondary infection within households using an individual-based hazard model that accounted for tertiary transmission and infections occurring outside the household. We found that for Victoria-lineage viruses, the risk of within-household infection among household contacts aged ≤15 years was significantly higher (risk ratio = 12.9, 95% credibility interval: 4.2, 43.6) than that for older household contacts, while for Yamagata-lineage viruses, the risk of within-household infection for household contacts did not differ by age. Influenza B Yamagata- and Victoria-lineage viruses have similar characteristics in terms of viral shedding and clinical illness. The mechanisms underlying these epidemiologic differences deserve further investigation.
    Keywords: Disease Transmission ; Influenza ; Influenza B Virus ; Victoria Lineage ; Yamagata Lineage
    ISSN: 0002-9262
    E-ISSN: 1476-6256
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  • 10
    In: PLoS ONE, 2015, Vol.10(3)
    Description: Soil salinity is a major constraint to crop growth and yield. The primary and lateral roots of Arabidopsis thaliana are known to respond differentially to a number of environmental stresses, including salinity. Although the maize root system as a whole is known to be sensitive to salinity, whether or not different structural root systems show differential growth responses to salinity stress has not yet been investigated. The maize primary root (PR) was more tolerant of salinity stress than either the crown root (CR) or the seminal root (SR). To understand the molecular mechanism of these differential growth responses, RNA-Seq analysis was conducted on cDNA prepared from the PR, CR and SR of plants either non-stressed or exposed to 100 mM NaCl for 24 h. A set of 444 genes were shown to be regulated by salinity stress, and the transcription pattern of a number of genes associated with the plant salinity stress response differed markedly between the various types of root. The pattern of transcription of the salinity-regulated genes was shown to be very diverse in the various root types. The differential transcription of these genes such as transcription factors, and the accumulation of compatible solutes such as soluble sugars probably underlie the differential growth responses to salinity stress of the three types of roots in maize.
    Keywords: Research Article
    E-ISSN: 1932-6203
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