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  • 1
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Science Ltd
    Plant, cell & environment 27 (2004), S. 0 
    ISSN: 1365-3040
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Jasmonic acid (JA) is known to be involved in the response of plants to environmental stresses such as drought, and betaine (glycinebetaine) is an osmopretectant accumulated in plants under environmental stresses including drought. However, it remains currently unclear whether JA is involved in the water-stress-induced betaine accumulation in plant leaves. The present experiment, performed with the whole pear plant (Pyrus bretschneideri Redh. cv. Suli), revealed that the exogenously applied JA induced a significant increase of the betaine level in the pear leaves when the plants were not yet stressed by drought, and when the plants were subjected to water stress, the ‘JA plus drought’ treatment induced a significant higher betaine level than did the drought treatment alone. Meanwhile, the ‘JA plus drought’ treatment induced higher levels of betaine aldehyde dehydrogenase (BADH, E C 1.2.1.8) and activities in the leaves than did the drought treatment alone. These results obtained in the whole plant experiments were supported by the results of detached leaf experiments. In detached leaves JA induced significant increases in betaine levels, BADH activities and BADH protein amounts in a time- and concentration-dependent manner. These data demonstrate that JA is involved in the drought-induced betaine accumulation in pear leaves.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Science Ltd
    Fatigue & fracture of engineering materials & structures 24 (2001), S. 0 
    ISSN: 1460-2695
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This paper examines the effects of loading rate on the Weibull stress model for prediction of cleavage fracture in a low-strength, A515-70 pressure vessel steel. Interest focuses on low-to-moderate loading rates (K˙I 〈 2500 MPa √m s−1 ). Shallow cracked SE(B) specimens were tested at four different loading rates for comparison with previous quasi-static tests on shallow notch SE(B)s and standard C(T)s. To utilize these dynamic experimental data, we assume that the Weibull modulus (m) previously calibrated using quasi-static data remains invariant over the loading rates of interest. The effects of dynamic loading on the Weibull stress model enter through the rate-sensitive material flow properties, the scale parameter (σu ) and the threshold Weibull stress (σw-min ). Rate-sensitive flow properties are modelled using a viscoplastic constitutive model with uniaxial, tension stress–plastic strain curves specified at varying plastic strain rates. The analyses examine dependencies of σw-min and σu on K˙I . Present results indicate that σw-min and σu are weak functions of loading rate K˙I for this pressure vessel steel. However, the predicted cumulative probability for cleavage exhibits a strong sensitivity to σu and, consequently, the dependency of σu on K˙I is sufficient to preclude use of the static σu value for high loading rates.
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  • 3
    Publication Date: 2015-11-20
    Description: Parameter estimation is a challenging computational problem in the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter estimation of gene circuit models from such time-series mRNA data has become an important method for quantitatively dissecting the regulation of gene expression. By focusing on the modeling of gene circuits, we examine here the performance of three types of state-of-the-art parameter estimation methods: population-based methods, online methods and model-decomposition-based methods. Our results show that certain population-based methods are able to generate high-quality parameter solutions. The performance of these methods, however, is heavily dependent on the size of the parameter search space, and their computational requirements substantially increase as the size of the search space increases. In comparison, online methods and model decomposition-based methods are computationally faster alternatives and are less dependent on the size of the search space. Among other things, our results show that a hybrid approach that augments computationally fast methods with local search as a subsequent refinement procedure can substantially increase the quality of their parameter estimates to the level on par with the best solution obtained from the population-based methods while maintaining high computational speed. These suggest that such hybrid methods can be a promising alternative to the more commonly used population-based methods for parameter estimation of gene circuit models when limited prior knowledge about the underlying regulatory mechanisms makes the size of the parameter search space vastly large.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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  • 4
    Publication Date: 2015-11-26
    Description: Human lactate dehydrogenase (LDH) has attracted attention as a potential target for cancer therapy and contraception. In this study, we reconstituted human lactic acid fermentation in Saccharomyces cerevisiae , with the goal of constructing a yeast cell-based LDH assay system. pdc null mutant yeast (mutated in the endogenous pyruvate decarboxylase genes) are unable to perform alcoholic fermentation; when grown in the presence of an electron transport chain inhibitor, pdc null strains exhibit a growth defect. We found that introduction of the human gene encoding LDHA complemented the pdc growth defect; this complementation depended on LDHA catalytic activity. Similarly, introduction of the human LDHC complemented the pdc growth defect, even though LDHC did not generate lactate at the levels seen with LDHA. In contrast, the human LDHB did not complement the yeast pdc null mutant, although LDHB did generate lactate in yeast cells. Expression of LDHB as a red fluorescent protein (RFP) fusion yielded blebs in yeast, whereas LDHA-RFP and LDHC-RFP fusion proteins exhibited cytosolic distribution. Thus, LDHB exhibits several unique features when expressed in yeast cells. Because yeast cells are amenable to genetic analysis and cell-based high-throughput screening, our pdc /LDH strains are expected to be of use for versatile analyses of human LDH.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
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  • 5
    Publication Date: 2015-06-14
    Description: Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are key s to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a ‘ blackbox preprocessing ’ to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein – DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the ‘ blackbox preprocessing ’ ). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein – DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein – protein complex and a protein – RNA complex, which is biologically known as a protein – RNA mimicry case. Availability and implementation: The PROSTA-inter web-server is publicly available at http://www.cbrc.kaust.edu.sa/prosta/ . Contact: xin.gao@kaust.edu.sa
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 6
    Publication Date: 2016-05-06
    Description: Despite over 3300 protein–DNA complex structures have been reported in the past decades, there remain some unknown recognition patterns between protein and target DNA. The silkgland-specific transcription factor FMBP-1 from the silkworm Bombyx mori contains a unique DNA-binding domain of four tandem STPRs, namely the score and three amino acid peptide repeats. Here we report three structures of this STPR domain (termed Bm STPR) in complex with DNA of various lengths. In the presence of target DNA, Bm STPR adopts a zig-zag structure of three or four tandem α-helices that run along the major groove of DNA. Structural analyses combined with binding assays indicate Bm STPR prefers the AT-rich sequences, with each α-helix covering a DNA sequence of 4 bp. The successive AT-rich DNAs adopt a wider major groove, which is in complementary in shape and size to the tandem α-helices of Bm STPR. Substitutions of DNA sequences and affinity comparison further prove that Bm STPR recognizes the major groove mainly via shape readout. Multiple-sequence alignment suggests this unique DNA-binding pattern should be highly conserved for the STPR domain containing proteins which are widespread in animals. Together, our findings provide structural insights into the specific interactions between a novel DNA-binding protein and a unique deformed B-DNA.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2015-05-13
    Description: XTE J1810-189 underwent an outburst in 2008, and was observed over ~100 d by RXTE . Performing a time-resolved spectral analysis on the photospheric radius expansion burst detected on 2008 May 4, we obtain the source distance in the range 3.5–8.7 kpc for the first time. During its outburst, XTE J1810-189 did not enter into the high/soft state, and both the soft and hard colours decreased with decreasing flux. The fractional rms remained at high values (~30 per cent). The RXTE /PCA spectra for 3–25 keV can be described by an absorbed power-law component with an additional Gaussian component, and the derived photon index increased from 1.84 ± 0.01 to 2.25 ± 0.04 when the unabsorbed X-ray luminosity at 3–25 keV dropped from 4 10 36 to 6 10 35 erg s –1 . The relatively high flux, dense observations and broad-band spectra are strong evidence that the softening behaviour detected in the outburst of XTE J1810-189 originates from the evolution of a non-thermal component rather than the thermal component (i.e. neutron star surface emission).
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 8
    Publication Date: 2016-01-07
    Description: Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal ( www.cbrc.kaust.edu.sa/desm ). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4 538 278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2016-07-06
    Description: To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/ .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 10
    Publication Date: 2015-10-10
    Description: The cancer epigenome exhibits global loss of DNA methylation, which contributes to genomic instability and aberrant gene expression by mechanisms that are yet to be fully elucidated. We previously discovered over 3300 long non-coding (lnc)RNAs in human cells and demonstrated that specific lncRNAs regulate gene expression via interactions with chromatin-modifying complexes. Here, we tested whether lncRNAs could also associate with DNA methyltransferases to regulate DNA methylation and gene expression. Using RIP-seq, we identified a subset of lncRNAs that interact with the DNA methyltransferase DNMT1 in a colon cancer cell line, HCT116. One lncRNA, TCONS_00023265, which we named DACOR1 (DNMT1-associated Colon Cancer Repressed lncRNA 1), shows high, tissue-specific expression in the normal colon (including colon crypts) but was repressed in a panel of colon tumors and patient-derived colon cancer cell lines. We identified the genomic occupancy sites of DACOR1, which we found to significantly overlap with known differentially methylated regions (DMRs) in colon tumors. Induction of DACOR1 in colon cancer cell lines significantly reduced their ability to form colonies in vitro , suggesting a growth suppressor function. Consistent with the observed phenotype, induction of DACOR1 led to the activation of tumor-suppressor pathways and attenuation of cancer-associated metabolic pathways. Notably, DACOR1 induction resulted in down-regulation of Cystathionine β-synthase, which is known to lead to increased levels of S-adenosyl methionine—the key methyl donor for DNA methylation. Collectively, our results demonstrate that deregulation of DNMT1-associated lncRNAs contributes to aberrant DNA methylation and gene expression during colon tumorigenesis.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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