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  • 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: 2015-07-18
    Description: We present infrared (IR) galaxy luminosity functions (LFs) in the AKARI North Ecliptic Pole (NEP) deep field using recently-obtained, wider Canada–France–Hawaii Telescope (CFHT) optical/near-IR images. AKARI has obtained deep images in the mid-infrared (IR), covering 0.6 deg 2 of the NEP deep field. However, our previous work was limited to the central area of 0.25 deg 2 due to the lack of optical coverage of the full AKARI NEP survey. To rectify the situation, we recently obtained CFHT optical and near-IR images over the entire AKARI NEP deep field. These new CFHT images are used to derive accurate photometric redshifts, allowing us to fully exploit the whole AKARI NEP deep field. AKARI 's deep, continuous filter coverage in the mid-IR wavelengths (2.4, 3.2, 4.1, 7, 9, 11, 15, 18, and 24 μm) exists nowhere else, due to filter gaps of other space telescopes. It allows us to estimate rest-frame 8 and 12 μm luminosities without using a large extrapolation based on spectral energy distribution fitting, which was the largest uncertainty in previous studies. Total infrared (TIR) luminosity is also obtained more reliably due to the superior filter coverage. The resulting rest-frame 8 and 12 μm, and TIR LFs at 0.15 〈  z  〈 2.2 are consistent with previous works, but with reduced uncertainties, especially at the high-luminosity end, thanks to the wide-field coverage. In terms of cosmic infrared luminosity density ( IR ), we found that the IR evolves as (1 +  z ) 4.2 ± 0.4 .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 3
    Publication Date: 2015-03-12
    Description: Myotonic dystrophy type 1 (DM1), the most prevalent muscular dystrophy in adults, is characterized by progressive muscle wasting and multi-systemic complications. DM1 is the prototype for disorders caused by RNA toxicity. Currently, no therapies exist. Here, we identify that fibroblast growth factor-inducible 14 (Fn14), a member of the tumor necrosis factor receptor super-family, is induced in skeletal muscles and hearts of mouse models of RNA toxicity and in tissues from DM1 patients, and that its expression correlates with severity of muscle pathology. This is associated with downstream signaling through the NF-B pathways. In mice with RNA toxicity, genetic deletion of Fn14 results in reduced muscle pathology and better function. Importantly, blocking TWEAK/Fn14 signaling with an anti-TWEAK antibody likewise improves muscle histopathology and functional outcomes in affected mice. These results reveal new avenues for therapeutic development and provide proof of concept for a novel therapeutic target for which clinically available therapy exists to potentially treat muscular dystrophy in DM1.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 4
    Publication Date: 2016-03-11
    Description: On human ( Homo sapiens ) chromosome 1, there is a tandem duplication encompassing Rh blood group genes (Hosa_RHD and Hosa_RHCE). This duplication occurred in the common ancestor of humans, chimpanzees ( Pan troglodytes ), and gorillas, after splitting from their common ancestor with orangutans. Although several studies have been conducted on ape Rh blood group genes, the clear genome structures of the gene clusters remain unknown. Here, we determined the genome structure of the gene cluster of chimpanzee Rh genes by sequencing five BAC (Bacterial Artificial Chromosome) clones derived from chimpanzees. We characterized three complete loci (Patr_RHα, Patr_RHβ, and Patr_RH). In the Patr_RHβ locus, a short version of the gene, which lacked the middle part containing exons 4–8, was observed. The Patr_RHα and Patr_RHβ genes were located on the locations corresponding to Hosa_RHD and Hosa_RHCE, respectively, and Patr_RH was in the immediate vicinity of Patr_RHβ. Sequence comparisons revealed high sequence similarity between Patr_RHβ and Hosa_RHCE, while the chimpanzee Rh gene closest to Hosa_RHD was not Patr_RHα but rather Patr_RH. The results suggest that rearrangements and gene conversions frequently occurred between these genes and that the classic orthology/paralogy dichotomy no longer holds between human and chimpanzee Rh blood group genes.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 5
    Publication Date: 2015-06-05
    Description: We present a kinematical study of 29 spiral galaxies included in the Spitzer Survey of Stellar Structure in Galaxies, using Hα Fabry–Perot (FP) data obtained with the Galaxy Hα Fabry–Perot System instrument at the William Herschel Telescope in La Palma, complemented with images in the R band and in Hα. The primary goal is to study the evolution and properties of the main structural components of galaxies through the kinematical analysis of the FP data, complemented with studies of morphology, star formation and mass distribution. In this paper we describe how the FP data have been obtained, processed and analysed. We present the resulting moment maps, rotation curves, velocity model maps and residual maps. Images are available in fits format through the NASA/IPAC Extragalactic Database and the Centre de Données Stellaires. With these data products we study the non-circular motions, in particular those found along the bars and spiral arms. The data indicate that the amplitude of the non-circular motions created by the bar does not correlate with the bar strength indicators. The amplitude of those non-circular motions in the spiral arms does not correlate with either arm class or star formation rate along the spiral arms. This implies that the presence and the magnitude of the streaming motions in the arms is a local phenomenon.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2016-07-28
    Description: Whole-genome sequencing data allow detection of copy number variation (CNV) at high resolution. However, estimation based on read coverage along the genome suffers from bias due to GC content and other factors. Here, we develop an algorithm called BIC-seq2 that combines normalization of the data at the nucleotide level and Bayesian information criterion-based segmentation to detect both somatic and germline CNVs accurately. Analysis of simulation data showed that this method outperforms existing methods. We apply this algorithm to low coverage whole-genome sequencing data from peripheral blood of nearly a thousand patients across eleven cancer types in The Cancer Genome Atlas (TCGA) to identify cancer-predisposing CNV regions. We confirm known regions and discover new ones including those covering KMT2C, GOLPH3, ERBB2 and PLAG1 . Analysis of colorectal cancer genomes in particular reveals novel recurrent CNVs including deletions at two chromatin-remodeling genes RERE and NPM2 . This method will be useful to many researchers interested in profiling CNVs from whole-genome sequencing data.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2016-01-10
    Description: Motivation: Rapid advances in genotyping and genome-wide association studies have enabled the discovery of many new genotype–phenotype associations at the resolution of individual markers. However, these associations explain only a small proportion of theoretically estimated heritability of most diseases. In this work, we propose an integrative mixture model called JBASE: joint Bayesian analysis of subphenotypes and epistasis. JBASE explores two major reasons of missing heritability: interactions between genetic variants, a phenomenon known as epistasis and phenotypic heterogeneity, addressed via subphenotyping. Results: Our extensive simulations in a wide range of scenarios repeatedly demonstrate that JBASE can identify true underlying subphenotypes, including their associated variants and their interactions, with high precision. In the presence of phenotypic heterogeneity, JBASE has higher Power and lower Type 1 Error than five state-of-the-art approaches. We applied our method to a sample of individuals from Mexico with Type 2 diabetes and discovered two novel epistatic modules, including two loci each, that define two subphenotypes characterized by differences in body mass index and waist-to-hip ratio. We successfully replicated these subphenotypes and epistatic modules in an independent dataset from Mexico genotyped with a different platform. Availability and implementation: JBASE is implemented in C++, supported on Linux and is available at http://www.cs.toronto.edu/~goldenberg/JBASE/jbase.tar.gz . The genotype data underlying this study are available upon approval by the ethics review board of the Medical Centre Siglo XXI. Please contact Dr Miguel Cruz at mcruzl@yahoo.com for assistance with the application. Contact: anna.goldenberg@utoronto.ca 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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  • 8
    Publication Date: 2016-06-11
    Description: The dual market phenomenon, in which a product's market is segmented into early and main markets, has attracted much attention in the field of innovation diffusion. It is known that main market adopters, also called the majority, begin to enter the market after a certain period, based on their levels of price sensitivity, which differ from those of early market adopters. This paper proposes a new dual market model that explicitly considers the delayed entry of the majority. We empirically estimate the delayed entry time (DET) for various consumer electronic products, comparing them with two other related phenomena of the early stages of diffusion: take-off and saddle. We also examine whether the DET of a new product can be predicted before it is reached. The result shows that the DET is predictable, using the coefficients of external and internal influence of the early market, also using those of the single market estimated from limited early data. The findings are managerially helpful because being aware of DET at an early stage enables managers to make timely decisions for serving the mass market.
    Print ISSN: 1471-678X
    Electronic ISSN: 1471-6798
    Topics: Mathematics
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  • 9
    Publication Date: 2016-09-01
    Description: We present evidence of bar-induced secular evolution in galactic discs using 3.6 μm images of nearby galaxies from the Spitzer Survey of Stellar Structure in Galaxies (S 4 G). We find that among massive galaxies ( M * /M 〉 10 10 ), longer bars tend to reside in inner discs having a flatter radial profile. Such galaxies show a light deficit in the disc surrounding the bar, within the bar radius and often show a -shaped morphology. We quantify this deficit and find that among all galaxies explored in this study (with 10 9 〈 M * /M 〈 10 11 ), galaxies with a stronger bar (i.e. longer and/or with a higher Bar/T) show a more pronounced deficit. We also examine simulation snapshots to confirm and extend results by Athanassoula and Misiriotis, showing that as bars evolve they become longer, while the light deficit in the disc becomes more pronounced. Theoretical studies have predicted that, as a barred galaxy evolves, the bar captures disc stars in its immediate neighbourhood so as to make the bar longer, stronger and thinner. Hence, we claim that the light deficit in the inner disc is produced by bars, which thus take part in shaping the mass distribution of their host galaxies.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 10
    Publication Date: 2015-05-20
    Description: Post-translational modifications of core histones affect various cellular processes, primarily through transcription. However, their relationship with the termination of transcription has remained largely unknown. In this study, we show that DNA damage-activated AKT phosphorylates threonine 45 of core histone H3 (H3-T45). By genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) analysis, H3-T45 phosphorylation was distributed throughout DNA damage-responsive gene loci, particularly immediately after the transcription termination site. H3-T45 phosphorylation pattern showed close-resemblance to that of RNA polymerase II C-terminal domain (CTD) serine 2 phosphorylation, which establishes the transcription termination signal. AKT1 was more effective than AKT2 in phosphorylating H3-T45. Blocking H3-T45 phosphorylation by inhibiting AKT or through amino acid substitution limited RNA decay downstream of mRNA cleavage sites and decreased RNA polymerase II release from chromatin. Our findings suggest that AKT-mediated phosphorylation of H3-T45 regulates the processing of the 3' end of DNA damage-activated genes to facilitate transcriptional termination.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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