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  • Articles  (50)
  • Springer  (27)
  • Oxford University Press  (21)
  • Institute of Physics (IOP)  (2)
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  • Articles  (50)
Journal
  • 1
    Publication Date: 2016-05-27
    Description: Vibrio parahaemolyticus is a Gram-negative, motile, nonspore-forming pathogen that causes foodborne illness associated with the consumption of contaminated seafoods. Although many cases of foodborne outbreaks caused by V. parahaemolyticus have been reported, the genomes of only five strains have been completely sequenced and analyzed using bioinformatics. In order to characterize overall virulence factors and pathogenesis of V. parahaemolyticus associated with foodborne outbreak in South Korea, a new strain FORC_008 was isolated from flounder fish and its genome was completely sequenced. The genomic analysis revealed that the genome of FORC_008 consists of two circular DNA chromosomes of 3266 132 bp (chromosome I) and 1772 036 bp (chromosome II) with a GC content of 45.36% and 45.53%, respectively. The entire genome contains 4494 predicted open reading frames, 129 tRNAs and 31 rRNA genes. While the strain FORC_008 does not have genes encoding thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH), its genome encodes many other virulence factors including hemolysins, pathogenesis-associated secretion systems and iron acquisition systems, suggesting that it may be a potential pathogen. This report provides an extended understanding on V. parahaemolyticus in genomic level and would be helpful for rapid detection, epidemiological investigation and prevention of foodborne outbreak in South Korea.
    Print ISSN: 0928-8244
    Topics: Biology , Medicine
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  • 2
    Publication Date: 2014-08-27
    Description: Motivation: Time-evolving differential protein–protein interaction (PPI) networks are essential to understand serial activation of differentially regulated (up- or downregulated) cellular processes (DRPs) and their interplays over time. Despite developments in the network inference, current methods are still limited in identifying temporal transition of structures of PPI networks, DRPs associated with the structural transition and the interplays among the DRPs over time. Results: Here, we present a probabilistic model for estimating Time-Evolving differential PPI networks with MultiPle Information (TEMPI). This model describes probabilistic relationships among network structures, time-course gene expression data and Gene Ontology biological processes (GOBPs). By maximizing the likelihood of the probabilistic model, TEMPI estimates jointly the time-evolving differential PPI networks (TDNs) describing temporal transition of PPI network structures together with serial activation of DRPs associated with transiting networks. This joint estimation enables us to interpret the TDNs in terms of temporal transition of the DRPs. To demonstrate the utility of TEMPI, we applied it to two time-course datasets. TEMPI identified the TDNs that correctly delineated temporal transition of DRPs and time-dependent associations between the DRPs. These TDNs provide hypotheses for mechanisms underlying serial activation of key DRPs and their temporal associations. Availability and implementation: Source code and sample data files are available at http://sbm.postech.ac.kr/tempi/sources.zip . Contact: seungjin@postech.ac.kr or dhwang@dgist.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 3
    Publication Date: 2016-10-08
    Description: Retinoic acid-inducible gene I (RIG-I) recognizes specific molecular patterns of viral RNAs for inducing type I interferon. The C-terminal domain (CTD) of RIG-I binds to double-stranded RNA (dsRNA) with the 5'-triphosphate (5'-PPP), which induces a conformational change in RIG-I to an active form. It has been suggested that RIG-I detects infection of influenza A virus by recognizing the 5'-triphosphorylated panhandle structure of the viral RNA genome. Influenza panhandle RNA has a unique structure with a sharp helical bending. In spite of extensive studies of how viral RNAs activate RIG-I, whether the structural elements of the influenza panhandle RNA confer the ability to activate RIG-I signaling has been poorly explored. Here, we investigated the dynamics of the influenza panhandle RNA in complex with RIG-I CTD using NMR spectroscopy and showed that the bending structure of the panhandle RNA negates the requirement of a 5'-PPP moiety for RIG-I activation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Geo-marine letters 4 (1984), S. 177-180 
    ISSN: 1432-1157
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract Archived data, together with field observations collected between 1980 and 1982 off the west coast of Korea, suggest that the onset of winter monsoon winds in late fall initiates a residual southward flow that potentially carries large volumes of resuspended bottom sediments into the Korea Strait. During the calm conditions of summer, muds are replenished by high river discharges and reform the band of soft material, which characteristically occurs as a series of mudflats near the coast. Thus, these mudflats serve as a temporary storage facility during summer accumulation and as a source during winter erosion.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1432-0614
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Although many studies have examined the influence of culture conditions on the production and composition of polysaccharides, little is known about the factors influencing the quality of exopolysaccharides (EPS). In this work we studied the effect of yeast extract on the production, composition and molecular weight of the EPS zooglan produced by Zoogloea ramigera 115SLR. This bacterium was grown on a new completely defined synthetic medium and on a medium containing yeast extract. Growth and polysaccharide production performances were comparable on the two media with a glucose to exopolysaccharide conversion yield of 35% (g/g). The polysaccharides produced on these two media have an identical composition but a different molecular weight and molecular weight distribution. The yeast extract medium leads to a more homogeneous polysaccharide solution.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1432-0614
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract New secretion vectors containing the Bacillus sp. endoxylanase signal sequence were constructed for the secretory production of recombinant proteins in Escherichia coli. The E. coli alkaline phosphatase structural gene fused to the endoxylanase signal sequence was expressed from the trc promoter in various E. coli strains by induction with IPTG. Among those tested, E. coli HB101 showed the highest efficiency of secretion (up to 25.3% of total proteins). When cells were induced with 1 mM IPTG, most of the secreted alkaline phosphatase formed inclusion bodies in the periplasm. However, alkaline phosphatase could be produced as a soluble form without reduction of expression level by inducing with less (0.01 mM) IPTG, and greater than 90% of alkaline phosphatase could be recovered from the periplasm by the simple osmotic shock method. Fed-batch cultures were carried out to examine the possibility of secretory protein production at high cell density. Up to 5.2 g/l soluble alkaline phosphatase could be produced in the periplasm by the pH-stat fed-batch cultivation of E. coli HB101 harboring pTrcS1PhoA. These results demonstrate the possibility of efficient secretory production of recombinant proteins in E. coli by high cell density cultivation.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1432-2048
    Keywords: Arginine decarboxylase ; Auxin in somatic embryogenesis ; Cell culture (polyamines) ; Dnucus (polyamines in embryogenesis) ; Embryogenesis somatic ; Polyamine ; S-Adenosylmethionine decarboxylase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Polyamine levels and the activities of two polyamine biosynthetic enzymes, arginine decarboxylase (EC 4.1.1.19) and S-adenosylmethionine decarboxylase (EC 4.1.1.50), were determined during somatic embryogenesis of carrot (Daucus carota L.) cell cultures. Embryogenic cultures showed severalfold increases in polyamine levels over nondifferentiating controls. A mutant cell line that failed to form embryos but grew at the same rate as the wild-type line also failed to show increases in polyamine levels, thus providing evidence that this increased polyamine content was in fact associated with the development of embryos. Furthermore, inhibition of these increases in polyamines caused by drugs inhibited embryogenesis and the effect was reversible with spermidine. The activities of arginine decarboxylase and Sadenosylmethionine decarboxylase were found to be suppressed by auxin; however, the specific effects differed between exogenous 2,4-dichlorophenoxyacetic acid and endogenous indole-3-acetic acid. The results indicate that increased polyamine levels are required for cellular differentiation and development occurring during somatic embryogenesis in carrot cell cultures.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1432-0614
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Pseudomonas 135, a facultative methylotroph, was cultivated on methanol as a sole carbon and energy source for the accumulation of poly-β-hydroxybutyric acid (PHB). The cells grew fairly well on minimal synthetic medium containing 0.5% (v/v) of methanol at pH 7.0 and 30° C. The maximum specific growth rate was determined to be 0.26–0.28 h−1 with a growth yield of 0.38 in the optimized growth medium. For stimulation of PHB accumulation in the cells, deficiency of nutrients such as NH inf4 sup+ , Mg2+ and PO inf4 sup3− was crucial even though cell growth was significantly suppressed. The PHB content of a 40-h culture was determined to be 37% of the total cell mass in NH inf4 sup+ -limited medium, 42.5% on Mg2+-deficient medium, and 34.5% on PO inf4 sup3− -deficient medium. The maximum content of PHB in the cells could reach 55% in NH inf4 sup+ -limited fed-batch culture. The average relative molecular eight determined by gel permeation chromatography was 3.7 × 105 in NH inf4 sup+ -limited culture, 2.5 × 105 in Mg2+-deficientmedium, and 3.1 × 105 in PO inf4 sup3− -deficient medium. Polydispersity determined in each culture was relatively high (about 10–11). The solid PHB had a melting temperature of 173° C.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Colloid & polymer science 278 (2000), S. 1198-1204 
    ISSN: 1435-1536
    Keywords: Key words Aging ; Poly(vinyl alcohol) ; Gel ; Syndiotacticity ; High molecular weight
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The properties of the aged gels of high molecular weight syndiotacticity-rich poly(vinyl alcohol)s (HMW S-PVAs) with different syndiotactic diad (s-diad) contents were investigated. HMW S-PVA gels with s-diad content of 61.5% and 58.2% showed the rapid increases of the syneresis and the turbidity from the early stage of aging time, which is ascribable to the phase separation, while that with s-diad content of 55.7% did not. From the morphological study, it was confirmed that the phase separation in HMW S-PVA gel with s-diad content of 61.5% occurred without the liquid-liquid phase separation in sol state, whereas both the liquid-liquid phase separation in sol state and the subsequent phase separation in gel state occurred in the case of HMW S-PVA gel with s-diad content of 58.2%. On the other hand, HMW S-PVA gel with s-diad content of 55.7% showed neither the liquid-liquid phase separation in sol state nor the phase separation in gel state in the long period of time. It was also confirmed from wide angle X-ray diffractogram that the crystallization was accompanied by the phase separation in gel state in the aging process of PVA gel. However, the crystallization was hindered by the fast network formation at the initial stage of time. Later the syndiotacticity promoted the crystallization. The tensile modulus of HMW S-PVA gel with higher syndiotacticity increased more significantly with time.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Multibody system dynamics 2 (1998), S. 145-168 
    ISSN: 1573-272X
    Keywords: tolerance ; clearance ; optimization ; mechanical error ; mechanism ; lubricated joint
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract This paper addresses an analytical approach to tolerance optimization for planar mechanisms with lubricated joints based on mechanical error analysis. The mobility method is applied to consider the lubrication effects at joints and planar mechanisms are stochastically defined by using the clearance vector model for mechanical error analysis. The uncertainties considered in the analysis are tolerances on link lengths and radial clearances and these are selected as design variables. To show the validity of the proposed method for mechanical error analysis, it is applied to two examples, and the results obtained are compared with those of Monte Carlo simulations. Based on the mechanical error analysis, tolerance optimizations are applied to the examples.
    Type of Medium: Electronic Resource
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