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  • 1
    Publication Date: 2016-08-27
    Description: Actin-like MreB paralogs play important roles in cell shape maintenance, cell wall synthesis and the regulation of the D,L-endopeptidases, CwlO and LytE. The gram-positive bacteria, Bacillus amyloliquefaciens LL3, is a poly--glutamic acid (-PGA) producing strain that contains three MreB paralogs: MreB, Mbl and MreBH. In B. amyloliquefaciens , CwlO and LytE can degrade -PGA. In this study, we aimed to test the hypothesis that modulating transcript levels of MreB paralogs would alter the synthesis and degradation of -PGA. The results showed that overexpression or inhibition of MreB, Mbl or MreBH had distinct effects on cell morphology and the molecular weight of the -PGA products. In fermentation medium, cells of mreB inhibition mutant were 50.2% longer than LL3, and the -PGA titer increased by 55.7%. However, changing the expression level of mbl showed only slight effects on the morphology, -PGA molecular weight and titer. In the mreBH inhibition mutant, -PGA production and its molecular weight increased by 56.7% and 19.4%, respectively. These results confirmed our hypothesis that suppressing the expression of MreB paralogs might reduce -PGA degradation, and that improving the cell size could strengthen -PGA synthesis. This is the first report of enhanced -PGA production via suppression of actin-like MreB paralogs.
    Keywords: Biotechnology & Synthetic Biology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 2
    Publication Date: 2017-01-05
    Description: The human disease methylation database (DiseaseMeth,  http://bioinfo.hrbmu.edu.cn/diseasemeth/ ) is an interactive database that aims to present the most complete collection and annotation of aberrant DNA methylation in human diseases, especially various cancers. Recently, the high-throughput microarray and sequencing technologies have promoted the production of methylome data that contain comprehensive knowledge of human diseases. In this DiseaseMeth update, we have increased the number of samples from 3610 to 32 701, the number of diseases from 72 to 88 and the disease–gene associations from 216 201 to 679 602. DiseaseMeth version 2.0 provides an expanded comprehensive list of disease–gene associations based on manual curation from experimental studies and computational identification from high-throughput methylome data. Besides the data expansion, we also updated the search engine and visualization tools. In particular, we enhanced the differential analysis tools, which now enable online automated identification of DNA methylation abnormalities in human disease in a case-control or disease–disease manner. To facilitate further mining of the disease methylome, three new web tools were developed for cluster analysis, functional annotation and survival analysis. DiseaseMeth version 2.0 should be a useful resource platform for further understanding the molecular mechanisms of human diseases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2015-06-02
    Description: Environment reconstruction is to rebuild the physical environment in the cyberspace using the sensory data collected by sensor networks, which is a fundamental method for human to understand the physical world in depth. A lot of basic scientific work such as nature discovery and organic evolution heavily relies on the environment reconstruction. However, gathering large amount of environmental data costs huge energy and storage space. The shortage of energy and storage resources has become a major problem in sensor networks for environment reconstruction applications. Motivated by exploiting the inherent feature of environmental data, in this paper, we design a novel data gathering protocol based on compressive sensing theory and time series analysis to further improve the resource efficiency. This protocol adapts the duty cycle and sensing probability of every sensor node according to the dynamic environment, which cannot only guarantee the reconstruction accuracy, but also save energy and storage resources. We implement the proposed protocol on a 51-node testbed and conduct the simulations based on three real datasets from Intel Indoor, GreenOrbs and Ocean Sense projects. Both the experiment and simulation performances demonstrate that our method significantly outperforms the conventional methods in terms of resource efficiency and reconstruction accuracy.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 4
    Publication Date: 2014-12-17
    Description: Natural tetracyclic diterpenoid aphidicolin is a potent and specific inhibitor of B-family DNA polymerases, haltering replication and possessing a strong antimitotic activity in human cancer cell lines. Clinical trials revealed limitations of aphidicolin as an antitumor drug because of its low solubility and fast clearance from human plasma. The absence of structural information hampered the improvement of aphidicolin-like inhibitors: more than 50 modifications have been generated so far, but all have lost the inhibitory and antitumor properties. Here we report the crystal structure of the catalytic core of human DNA polymerase α (Pol α) in the ternary complex with an RNA-primed DNA template and aphidicolin. The inhibitor blocks binding of dCTP by docking at the Pol α active site and by rotating the template guanine. The structure provides a plausible mechanism for the selectivity of aphidicolin incorporation opposite template guanine and explains why previous modifications of aphidicolin failed to improve its affinity for Pol α. With new structural information, aphidicolin becomes an attractive lead compound for the design of novel derivatives with enhanced inhibitory properties for B-family DNA polymerases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2014-12-20
    Description: We present Doppler images of both components of the eclipsing binary system ER Vul, based on the spectra obtained in 2004 November, 2006 September and 2008 November. The least-squares deconvolution technique is used for enhancing the signal-to-noise ratios of the observed profiles. The new surface images reveal that both stars of ER Vul show strong starspot activities and the starspots appear at various latitudes. The surface maps of 2006 and 2008 both show the presence of large high-latitude starspots on each component of ER Vul. We find no obvious phase shift of the active regions during our observations. The longitude distributions of starspots are non-uniform on both stars. At low-to-mid latitudes, the active regions are almost exclusively found in the hemisphere facing the other star. However, we find no pronounced concentration of spots at the sub-stellar points.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2014-12-29
    Description: We present Doppler images of both components of the eclipsing binary system ER Vul, based on the spectra obtained in 2004 November, 2006 September and 2008 November. The least-squares deconvolution technique is used for enhancing the signal-to-noise ratios of the observed profiles. The new surface images reveal that both stars of ER Vul show strong starspot activities and the starspots appear at various latitudes. The surface maps of 2006 and 2008 both show the presence of large high-latitude starspots on each component of ER Vul. We find no obvious phase shift of the active regions during our observations. The longitude distributions of starspots are non-uniform on both stars. At low-to-mid latitudes, the active regions are almost exclusively found in the hemisphere facing the other star. However, we find no pronounced concentration of spots at the sub-stellar points.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
    Publication Date: 2014-02-15
    Description: We present Doppler images of RS CVn-type binary II Peg based on two data sets obtained in 2004 February and November. In order to improve signal-to-noise ratio and reliability, we apply least-squares deconvolution technique to calculate average profiles from 2032 photospheric absorption lines. Both of the resulting surface images show a wide latitude distribution of starspots. Most spots are concentrated at a high-latitude belt above 60° and a low-latitude belt near equator. The starspots evolved dramatically between two observing runs, which may indicate shorter time-scale evolution in this epoch, especially for low-latitude belt. There is no stable preferred active longitude that can be found in our images. We also find out a possible phenomenon that the intermediate-latitude spot migrated poleward and merged with the high-latitude spot to make it stronger, which may reveal a more complex behaviour of starspots on II Peg. A potential change of orbital ephemeris zero-point was detected. This may imply an orbital period change of II Peg like other active close binaries.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 8
    Publication Date: 2016-07-13
    Description: We extend our previous study of the cool gas responsible for the emission of O vii X-ray lines in the cores of clusters and groups of galaxies. This is the coolest X-ray emitting phase and connects the 10 000 K H α emitting gas to the million degree phase, providing a useful tool to understand cooling in these objects. We study the location of the O vii gas and its connection to the intermediate Fe xvii and hotter O viii phases. We use high-resolution X-ray grating spectra of elliptical galaxies with strong Fe xvii line emission and detect O vii in 11 of 24 objects. Comparing the O vii detection level and resonant scattering, which is sensitive to turbulence and temperature, suggests that O vii is preferably found in cooler objects, where the Fe xvii resonant line is suppressed due to resonant scattering, indicating subsonic turbulence. Although a larger sample of sources and further observations is needed to distinguish between effects from temperature and turbulence, our results are consistent with cooling being suppressed at high turbulence as predicted by models of active galactic nuclei feedback, gas sloshing and galactic mergers. In some objects, the O vii resonant-to-forbidden line ratio is decreased by either resonant scattering or charge exchange boosting the forbidden line, as we show for NGC 4636. Charge exchange indicates interaction between neutral and ionized gas phases. The Perseus cluster also shows a high Fe xvii forbidden-to-resonance line ratio, which can be explained with resonant scattering by low-turbulence cool gas in the line of sight.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 9
    Publication Date: 2016-06-01
    Description: : Identifying chemical probes or seeking scaffolds for a specific biological target is important for protein function studies. Therefore, we create the Annotated Scaffold Database (ASDB), a computer-readable and systematic target-annotated scaffold database, to serve such needs. The scaffolds in ASDB were derived from public databases including ChEMBL, DrugBank and TCMSP, with a scaffold-based classification approach. Each scaffold was assigned with an InChIKey as its unique identifier, energy-minimized 3D conformations, and other calculated properties. A scaffold is also associated with drugs, natural products, drug targets and medical indications. The database can be retrieved through text or structure query tools. ASDB collects 333 601 scaffolds, which are associated with 4368 targets. The scaffolds consist of 3032 scaffolds derived from drugs and 5163 scaffolds derived from natural products. For given scaffolds, scaffold-target networks can be generated from the database to demonstrate the relations of scaffolds and targets. Availability and implementation: ASDB is freely available at http://www.rcdd.org.cn/asdb/ with the major web browsers. Contact: junxu@biochemomes.com or xujun9@mail.sysu.edu.cn 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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  • 10
    Publication Date: 2017-01-19
    Description: Emetic toxin-producing Bacillus cereus (emetic B. cereus ) is the third member of B. cereus group whose toxins are encoded by megaplasmids, beside anthrax and insecticidal toxins of B. anthracis and B. thuringiensis , respectively. A total of 18 emetic isolates collected from food poisoning events, clinical and non-random food samples in Zhejiang province of China, were analyzed by plasmid screening, pulse field gel electrophoresis, multilocus sequence typing, and toxic gene identification to investigate their genotypic diversity. In this study, 13 plasmid profile types, 14 pulse types and 6 different STs from emetic isolates were detected, in which ST 1035,1038,1053,1054 and 1065 were first assigned and reported. The toxic gene ces existed on its own, or coexisted with other toxic genes bceT, cytk, entFM and nhe , but never with hbl in emetic isolates. The results demonstrated that the emetic B. cereus strains from China were heterologous at genotypic level.
    Keywords: Food Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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