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  • 1
    Publication Date: 2016-07-28
    Description: DNA Topoisomerases are essential to resolve topological problems during DNA metabolism in all species. However, the prevalence and function of RNA topoisomerases remain uncertain. Here, we show that RNA topoisomerase activity is prevalent in Type IA topoisomerases from bacteria, archaea, and eukarya. Moreover, this activity always requires the conserved Type IA core domains and the same catalytic residue used in DNA topoisomerase reaction; however, it does not absolutely require the non-conserved carboxyl-terminal domain (CTD), which is necessary for relaxation reactions of supercoiled DNA. The RNA topoisomerase activity of human Top3β differs from that of Escherichia coli topoisomerase I in that the former but not the latter requires the CTD, indicating that topoisomerases have developed distinct mechanisms during evolution to catalyze RNA topoisomerase reactions. Notably, Top3β proteins from several animals associate with polyribosomes, which are units of mRNA translation, whereas the Top3 homologs from E. coli and yeast lack the association. The Top3β-polyribosome association requires TDRD3, which directly interacts with Top3β and is present in animals but not bacteria or yeast. We propose that RNA topoisomerases arose in the early RNA world, and that they are retained through all domains of DNA-based life, where they mediate mRNA translation as part of polyribosomes in animals.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2016-01-01
    Description: We present the infrared (IR) and X-ray properties of a sample of 33 mid-IR luminous quasars ( L 6 μm ≥ 6 x 10 44 erg s –1 ) at redshift z 1–3, identified through detailed spectral energy distribution analyses of distant star-forming galaxies, using the deepest IR data from Spitzer and Herschel in the GOODS– Herschel fields. The aim is to constrain the fraction of obscured, and Compton-thick (CT, N H 〉 1.5 x 10 24 cm –2 ) quasars at the peak era of nuclear and star formation activities. Despite being very bright in the mid-IR band, 30 per cent of these quasars are not detected in the extremely deep 2 and 4 Ms Chandra X-ray data available in these fields. X-ray spectral analysis of the detected sources reveals that the majority (67 per cent) are obscured by column densities N H 〉 10 22 cm –2 ; this fraction reaches 80 per cent when including the X-ray-undetected sources (9 out of 33), which are likely to be the most heavily obscured, CT quasars. We constrain the fraction of CT quasars in our sample to be 24–48 per cent, and their space density to be = (6.7 ± 2.2) x 10 –6 Mpc –3 . From the investigation of the quasar host galaxies in terms of star formation rates (SFRs) and morphological distortions, as a sign of galaxy mergers/interactions, we do not find any direct relation between SFRs and quasar luminosity or X-ray obscuration. On the other hand, there is tentative evidence that the most heavily obscured quasars have, on average, more disturbed morphologies than the unobscured/moderately obscured quasar hosts, which preferentially live in undisturbed systems. However, the fraction of quasars with disturbed morphology amongst the whole sample is 40 per cent, suggesting that galaxy mergers are not the main fuelling mechanism of quasars at z 2.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 3
    Publication Date: 2016-06-04
    Description: The relationship between the co-occurrence of cryptic zooplankton species and environmental variables was studied in a lake in China. Lake Jinghu was sampled for zooplankton and water chemistry at 3 or 4-day intervals over a year, and samples of the rotifer Brachionus calyciflorus were obtained at 8-day intervals and clonally cultured in the laboratory. We found that B. calyciflorus occurred in winter and spring, and was a species complex composed of cryptic species BcI and BcII based on mtDNA COI sequence divergence and the GMYC model analyses. Both cryptic species cohabited in Lake Jinghu when they were present. The densities of BcI and BcII were not correlated, indicating that there might be no strong competition between them. Based on principal component analysis (PCA) and generalized linear models (GLM), only BcII density was impacted by chlorophyll a (Chl a ) concentration (of the lake water filtered through a 25 μm net) alone with a time lag, and the interaction of temperature and Chl a concentration without a time lag. Our results suggest that a distinct response to Chl a reduces the intensity of competition between cryptic B. calyciflorus species and promotes their coexistence in Lake Jinghu over time.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
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  • 4
    Publication Date: 2016-06-01
    Description: : Runs of homozygosity (RoHs) are genomic stretches of a diploid genome that show identical alleles on both chromosomes. Longer RoHs are unlikely to have arisen by chance but are likely to denote autozygosity, whereby both copies of the genome descend from the same recent ancestor. Early tools to detect RoH used genotype array data, but substantially more information is available from sequencing data. Here, we present and evaluate BCFtools/RoH, an extension to the BCFtools software package, that detects regions of autozygosity in sequencing data, in particular exome data, using a hidden Markov model. By applying it to simulated data and real data from the 1000 Genomes Project we estimate its accuracy and show that it has higher sensitivity and specificity than existing methods under a range of sequencing error rates and levels of autozygosity. Availability and implementation : BCFtools/RoH and its associated binary/source files are freely available from https://github.com/samtools/BCFtools . Contact: vn2@sanger.ac.uk or pd3@sanger.ac.uk 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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  • 5
    Publication Date: 2016-09-10
    Description: We exploit the 7 Ms Chandra observations in the Chandra  Deep Field-South (CDF-S), the deepest X-ray survey to date, coupled with CANDELS/GOODS-S data, to measure the total X-ray emission arising from 2076 galaxies at 3.5 ≤ z 〈 6.5. This aim is achieved by stacking the Chandra data at the positions of optically selected galaxies, reaching effective exposure times of ≥10 9 s. We detect significant (〉3.7) X-ray emission from massive galaxies at z 4. We also report the detection of massive galaxies at z 5 at a 99.7 per cent confidence level (2.7), the highest significance ever obtained for X-ray emission from galaxies at such high redshifts. No significant signal is detected from galaxies at even higher redshifts. The stacking results place constraints on the BHAD associated with the known high-redshift galaxy samples, as well as on the SFRD at high redshift, assuming a range of prescriptions for X-ray emission due to X- ray binaries. We find that the X-ray emission from our sample is likely dominated by processes related to star formation. Our results show that low-rate mass accretion on to SMBHs in individually X-ray-undetected galaxies is negligible, compared with the BHAD measured for samples of X-ray detected AGN, for cosmic SMBH mass assembly at high redshift. We also place, for the first time, constraints on the faint-end of the AGN X-ray luminosity function (logL X ~ 42) at z 〉 4, with evidence for fairly flat slopes. The implications of all of these findings are discussed in the context of the evolution of the AGN population at high redshift.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2015-02-17
    Description: Long non-coding RNA HOX transcript antisenseRNA ( HOTAIR ) has been widely identified to participate in tumour pathogenesis, acting as a promoter in colorectal cancer carcinogenesis. However, the association between genetic variants in HOTAIR and cancer risk has not yet been reported. In the present study, we performed a two-stage case–control study to investigate the association between HOTAIR tagSNPs and the risk of colorectal cancer. We found that individuals with rs7958904 CC genotype had a significantly decreased risk of colorectal cancer in both Stage 1 and 2, compared with those carrying GG genotype [odds ratio (OR) = 0.70, 95% confidence interval (CI) = 0.51–0.97 in Stage 1; OR = 0.58, 95% CI = 0.37–0.91 in Stage 2; OR = 0.67, 95% CI = 0.51–0.87 in combined stage]. The subsequently stratified analyses showed that the protective effect of rs7958904 was more pronounced in several subgroups. In summary, our study showed that genetic variants in HOTAIR were associated with risk of colorectal cancer and rs7958904 may act as a potential biomarker for predicting the risk of colorectal cancer.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2015-07-12
    Description: The AF4/FMR2 proteins AFF1 and AFF4 act as a scaffold to assemble the Super Elongation Complex (SEC) that strongly activates transcriptional elongation of HIV-1 and cellular genes. Although they can dimerize, it is unclear whether the dimers exist and function within a SEC in vivo . Furthermore, it is unknown whether AFF1 and AFF4 function similarly in mediating SEC-dependent activation of diverse genes. Providing answers to these questions, our current study shows that AFF1 and AFF4 reside in separate SECs that display largely distinct gene target specificities. While the AFF1-SEC is more potent in supporting HIV-1 transactivation by the viral Tat protein, the AFF4-SEC is more important for HSP70 induction upon heat shock. The functional difference between AFF1 and AFF4 in Tat-transactivation has been traced to a single amino acid variation between the two proteins, which causes them to enhance the affinity of Tat for P-TEFb, a key SEC component, with different efficiency. Finally, genome-wide analysis confirms that the genes regulated by AFF1-SEC and AFF4-SEC are largely non-overlapping and perform distinct functions. Thus, the SEC represents a family of related complexes that exist to increase the regulatory diversity and gene control options during transactivation of diverse cellular and viral genes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 8
    Publication Date: 2015-10-08
    Description: : Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure. Availability and implementation: The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org . Contact: renjian.sysu@gmail.com or xueyu@hust.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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  • 9
    Publication Date: 2015-01-16
    Description: Transcription factors (TFs) are key regulators for gene expression. Here we updated the animal TF database AnimalTFDB to version 2.0 ( http://bioinfo.life.hust.edu.cn/AnimalTFDB/ ). Using the improved prediction pipeline, we identified 72 336 TF genes, 21 053 transcription co-factor genes and 6502 chromatin remodeling factor genes from 65 species covering main animal lineages. Besides the abundant annotations (basic information, gene model, protein functional domain, gene ontology, pathway, protein interaction, ortholog and paralog, etc.) in the previous version, we made several new features and functions in the updated version. These new features are: (i) gene expression from RNA-Seq for nine model species, (ii) gene phenotype information, (iii) multiple sequence alignment of TF DNA-binding domains, and the weblogo and phylogenetic tree based on the alignment, (iv) a TF prediction server to identify new TFs from input sequences and (v) a BLAST server to search against TFs in AnimalTFDB. A new nice web interface was designed for AnimalTFDB 2.0 allowing users to browse and search all data in the database. We aim to maintain the AnimalTFDB as a solid resource for TF identification and studies of transcription regulation and comparative genomics.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 10
    Publication Date: 2015-01-16
    Description: We reported an updated database of MiCroKiTS 4.0 ( http://microkit.biocuckoo.org ) for proteins temporally and spatially localized in distinct subcellular positions including midbody, centrosome, kinetochore, telomere and mitotic spindle during cell division/mitosis. The database was updated from our previously developed database of MiCroKit 3.0, which contained 1489 proteins mostly forming super-complexes at midbody, centrosome and kinetochore from seven eukaryotes. Since the telomere and spindle apparatus are critical for cell division, the proteins localized at the two positions were also integrated. From the scientific literature, we curated 1872 experimentally identified proteins which at least locate in one of the five positions from eight species. Then the ortholog detection was performed to identify potential MiCroKiTS proteins from 144 eukaryotic organisms, which contains 66, 45 and 33 species of animals, fungi and plants, respectively. In total, 87 983 unique proteins with corresponding localization information were integrated into the database. The primary references of experimentally identified localizations were provided and the fluorescence microscope figures for the localizations of human proteins were shown. The orthologous relations between predicted and experimental localizations were also present. Taken together, we anticipate the database can serve as a useful resource for further analyzing the molecular mechanisms during cell division.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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