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  • 1
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    Loss of function of KIAA2022 causes mild to severe intellectual disability with an autism spectrum disorder and impairs neurite outgrowth (2013)
    Oxford University Press
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    Publication Date: 2013-07-26
    Description: Existence of a discrete new X-linked intellectual disability (XLID) syndrome due to KIAA2022 deficiency was questioned by disruption of KIAA2022 by an X-chromosome pericentric inversion in a XLID family we reported in 2004. Three additional families with likely pathogenic KIAA2022 mutations were discovered within the frame of systematic parallel sequencing of familial cases of XLID or in the context of routine array-CGH evaluation of sporadic intellectual deficiency (ID) cases. The c.186delC and c.3597dupA KIAA2022 truncating mutations were identified by X-chromosome exome sequencing, while array CGH discovered a 70 kb microduplication encompassing KIAA2022 exon 1 in the third family. This duplication decreased KIAA2022 mRNA level in patients' lymphocytes by 60%. Detailed clinical examination of all patients, including the two initially reported, indicated moderate-to-severe ID with autistic features, strabismus in all patients, with no specific dysmorphic features other than a round face in infancy and no structural brain abnormalities on magnetic resonance imaging (MRI). Interestingly, the patient with decreased KIAA2022 expression had only mild ID with severe language delay and repetitive behaviors falling in the range of an autism spectrum disorder (ASD). Since little is known about KIAA2022 function, we conducted morphometric studies in cultured rat hippocampal neurons. We found that siRNA-mediated KIAA2022 knockdown resulted in marked impairment in neurite outgrowth including both the dendrites and the axons, suggesting a major role for KIAA2022 in neuron development and brain function.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    Efficient satellite quenching at z~1 from the GEEC2 spectroscopic survey of galaxy groups (2013)
    Oxford University Press
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    Publication Date: 2013-04-13
    Description: We present deep Gemini Multi-Object Spectrograph-South spectroscopy for 11 galaxy groups at 0.8 〈 z  〈 1.0, for galaxies with r AB  〈 24.75. Our sample is highly complete (〉66 per cent) for eight of the 11 groups. Using an optical–near-infrared colour–colour diagram, the galaxies in the sample were separated with a dust insensitive method into three categories: passive (red), star-forming (blue) and intermediate (green). The strongest environmental dependence is observed in the fraction of passive galaxies, which make up only ~20 per cent of the field in the mass range 10 10.3  〈 M star /M  〈 10 11.0 , but are the dominant component of groups. If we assume that the properties of the field are similar to those of the ‘pre-accreted’ population, the environment quenching efficiency ( ) is defined as the fraction of field galaxies required to be quenched in order to match the observed red fraction inside groups. The efficiency obtained is ~0.4, similar to its value in intermediate-density environments locally. While green (intermediate) galaxies represent ~20 per cent of the star-forming population in both the group and field, at all stellar masses, the average specific star formation rate of the group population is lower by a factor of ~3. The green population does not show strong H absorption that is characteristic of starburst galaxies. Finally, the high fraction of passive galaxies in groups, when combined with satellite accretion models, require that most accreted galaxies have been affected by their environment. Thus, any delay between accretion and the onset of truncation of star formation () must be 2 Gyr, shorter than the 3–7 Gyr required to fit data at z  = 0. The relatively small fraction of intermediate galaxies require that the actual quenching process occurs quickly, with an exponential decay time-scale of q 1 Gyr.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    RAID v2.0: an updated resource of RNA-associated interactions across organisms (2017)
    Oxford University Press
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    Publication Date: 2017-01-05
    Description: With the development of biotechnologies and computational prediction algorithms, the number of experimental and computational prediction RNA-associated interactions has grown rapidly in recent years. However, diverse RNA-associated interactions are scattered over a wide variety of resources and organisms, whereas a fully comprehensive view of diverse RNA-associated interactions is still not available for any species. Hence, we have updated the RAID database to version 2.0 (RAID v2.0, www.rna-society.org/raid/ ) by integrating experimental and computational prediction interactions from manually reading literature and other database resources under one common framework. The new developments in RAID v2.0 include (i) over 850-fold RNA-associated interactions, an enhancement compared to the previous version; (ii) numerous resources integrated with experimental or computational prediction evidence for each RNA-associated interaction; (iii) a reliability assessment for each RNA-associated interaction based on an integrative confidence score; and (iv) an increase of species coverage to 60. Consequently, RAID v2.0 recruits more than 5.27 million RNA-associated interactions, including more than 4 million RNA–RNA interactions and more than 1.2 million RNA–protein interactions, referring to nearly 130 000 RNA/protein symbols across 60 species.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Offset between stellar spiral arms and gas arms of the Milky Way (2015)
    Oxford University Press
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    Publication Date: 2015-09-26
    Description: Spiral arms shown by different components may not be spatially coincident, which can constrain formation mechanisms of spiral structure in a galaxy. We reassess the spiral arm tangency directions in the Milky Way through identifying the bump features in the longitude plots of survey data for infrared stars, radio recombination lines (RRLs), star formation sites, CO, high-density regions in clouds, and H i . The bump peaks are taken as indications for arm tangencies, which are close to the real density peaks near the spiral arm tangency point but often have ~1° offset to the interior of spiral arms. The arm tangencies identified from the longitude plots for RRLs, H ii regions, methanol masers, CO, high-density gas regions, and H i gas appear nearly the same Galactic longitude, and therefore there is no obvious offset for spiral arms traced by different gas components. However, we find obvious displacements of 1 $_{.}^{\circ}$ 3–5 $_{.}^{\circ}$ 8 of gaseous bump peaks from the directions of the maximum density of old stars near the tangencies of the Scutum–Centaurus Arm, the northern part of the Near 3 kpc Arm, and maybe also the Sagittarius Arm. The offsets between the density peaks of gas and old stars for spiral arms are comparable with the arm widths, which is consistent with expectations for quasi-stationary density wave in our Galaxy.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Genetic determinants of telomere length and risk of common cancers: a Mendelian randomization study (2015)
    Zhang, C., Doherty, J. A., Burgess, S., Hung, R. J., Lindstrom, S., Kraft, P., Gong, J., Amos, C. I., Sellers, T. A., Monteiro, A. N. A., Chenevix-Trench, G., Bickeboller, H., Risch, A., Brennan, P., Mckay, J. D., Houlston, R. S., Landi, M. T., Timofeeva, M. N., Wang, Y., Heinrich, J., Kote-Jarai, Z., Eeles, R. A., Muir, K., Wiklund, F., Gronberg, H., Berndt, S. I., Chanock, S. J., Schumacher, F., Haiman, C. A., Henderson, B. E., Amin Al Olama, A., Andrulis, I. L., Hopper, J. L., Chang-Claude, J., John, E. M., Malone, K. E., Gammon, M. D., Ursin, G., Whittemore, A. S., Hunter, D. J., Gruber, S. B., Knight, J. A., Hou, L., Le Marchand, L., Newcomb, P. A., Hudson, T. J., Chan, A. T., Li, L., Woods, M. O., Ahsan, H., Pierce, B. L., on behalf of GECCO and the GAME-ON Network: CORECT, DRIVE, ELLIPSE, FOCI, and TRICL
    Oxford University Press
    Details
    Publication Date: 2015-08-27
    Description: Epidemiological studies have reported inconsistent associations between telomere length (TL) and risk for various cancers. These inconsistencies are likely attributable, in part, to biases that arise due to post-diagnostic and post-treatment TL measurement. To avoid such biases, we used a Mendelian randomization approach and estimated associations between nine TL-associated SNPs and risk for five common cancer types (breast, lung, colorectal, ovarian and prostate cancer, including subtypes) using data on 51 725 cases and 62 035 controls. We then used an inverse-variance weighted average of the SNP-specific associations to estimate the association between a genetic score representing long TL and cancer risk. The long TL genetic score was significantly associated with increased risk of lung adenocarcinoma ( P = 6.3 x 10 –15 ), even after exclusion of a SNP residing in a known lung cancer susceptibility region ( TERT-CLPTM1L ) P = 6.6 x 10 –6 ). Under Mendelian randomization assumptions, the association estimate [odds ratio (OR) = 2.78] is interpreted as the OR for lung adenocarcinoma corresponding to a 1000 bp increase in TL. The weighted TL SNP score was not associated with other cancer types or subtypes. Our finding that genetic determinants of long TL increase lung adenocarcinoma risk avoids issues with reverse causality and residual confounding that arise in observational studies of TL and disease risk. Under Mendelian randomization assumptions, our finding suggests that longer TL increases lung adenocarcinoma risk. However, caution regarding this causal interpretation is warranted in light of the potential issue of pleiotropy, and a more general interpretation is that SNPs influencing telomere biology are also implicated in lung adenocarcinoma risk.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Structure and decoy-mediated inhibition of the SOX18/Prox1-DNA interaction (2016)
    Oxford University Press
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    Publication Date: 2016-05-06
    Description: The transcription factor (TF) SOX18 drives lymphatic vessel development in both embryogenesis and tumour-induced neo-lymphangiogenesis. Genetic disruption of Sox18 in a mouse model protects from tumour metastasis and established the SOX18 protein as a molecular target. Here, we report the crystal structure of the SOX18 DNA binding high-mobility group (HMG) box bound to a DNA element regulating Prox1 transcription. The crystals diffracted to 1.75Å presenting the highest resolution structure of a SOX/DNA complex presently available revealing water structure, structural adjustments at the DNA contact interface and non-canonical conformations of the DNA backbone. To explore alternatives to challenging small molecule approaches for targeting the DNA-binding activity of SOX18, we designed a set of five decoys based on modified Prox1 -DNA. Four decoys potently inhibited DNA binding of SOX18 in vitro and did not interact with non-SOX TFs. Serum stability, nuclease resistance and thermal denaturation assays demonstrated that a decoy circularized with a hexaethylene glycol linker and terminal phosphorothioate modifications is most stable. This SOX decoy also interfered with the expression of a luciferase reporter under control of a SOX18-dependent VCAM1 promoter in COS7 cells. Collectively, we propose SOX decoys as potential strategy for inhibiting SOX18 activity to disrupt tumour-induced neo-lymphangiogenesis.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology (2012)
    Oxford University Press
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    Publication Date: 2012-12-20
    Description: Over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice ( Oryza sativa L.) subspecies, 93-11 ( indica ) and Nipponbare ( japonica ). To integrate information from genome assemblies and annotations for better analysis and application, we now introduce a comparative rice genome database, the Rice Genome Knowledgebase (RGKbase, http://rgkbase.big.ac.cn/RGKbase/ ). RGKbase is built to have three major components: (i) integrated data curation for rice genomics and molecular biology, which includes genome sequence assemblies, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and the relevant literature; (ii) User-friendly viewers, such as Gbrowse, GeneBrowse and Circos, for genome annotations and evolutionary dynamics and (iii) Bioinformatic tools for compositional and synteny analyses, gene family classifications, gene ontology terms and pathways and gene co-expression networks. RGKbase current includes data from five rice cultivars and species: Nipponbare ( japonica ), 93-11 ( indica ), PA64s ( indica ), the African rice ( Oryza glaberrima ) and a wild rice species ( Oryza brachyantha ). We are also constantly introducing new datasets from variety of public efforts, such as two recent releases—sequence data from ~1000 rice varieties, which are mapped into the reference genome, yielding ample high-quality single-nucleotide polymorphisms and insertions–deletions.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies (2016)
    Oxford University Press
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    Publication Date: 2016-02-02
    Description: : The development of the Infinium HumanMethylation450 BeadChip enables epigenome-wide association studies at a reduced cost. One observation of the 450K data is that many CpG sites the beadchip interrogates have very large measurement errors. Including these noisy CpGs will decrease the statistical power of detecting relevant associations due to multiple testing correction. We propose to use intra-class correlation coefficient (ICC), which characterizes the relative contribution of the biological variability to the total variability, to filter CpGs when technical replicates are available. We estimate the ICC based on a linear mixed effects model by pooling all the samples instead of using the technical replicates only. An ultra-fast algorithm has been developed to address the computational complexity and CpG filtering can be completed in minutes on a desktop computer for a 450K data set of over 1000 samples. Our method is very flexible and can accommodate any replicate design. Simulations and a real data application demonstrate that our whole-sample ICC method performs better than replicate-sample ICC or variance-based method. Availability and implementation : CpGFilter is implemented in R and publicly available under CRAN via the R package ‘CpGFilter’. Contact : chen.jun2@mayo.edu or xlin@hsph.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    Guilt by rewiring: gene prioritization through network rewiring in Genome Wide Association Studies (2014)
    Oxford University Press
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    Publication Date: 2014-04-18
    Description: Although Genome Wide Association Studies (GWAS) have identified many susceptibility loci for common diseases, they only explain a small portion of heritability. It is challenging to identify the remaining disease loci because their association signals are likely weak and difficult to identify among millions of candidates. One potentially useful direction to increase statistical power is to incorporate functional genomics information, especially gene expression networks, to prioritize GWAS signals. Most current methods utilizing network information to prioritize disease genes are based on the ‘guilt by association’ principle, in which networks are treated as static, and disease-associated genes are assumed to locate closer with each other than random pairs in the network. In contrast, we propose a novel ‘guilt by rewiring’ principle. Studying the dynamics of gene networks between controls and patients, this principle assumes that disease genes more likely undergo rewiring in patients, whereas most of the network remains unaffected in disease condition. To demonstrate this principle, we consider the changes of co-expression networks in Crohn's disease patients and controls, and how network dynamics reveals information on disease associations. Our results demonstrate that network rewiring is abundant in the immune system, and disease-associated genes are more likely to be rewired in patients. To integrate this network rewiring feature and GWAS signals, we propose to use the Markov random field framework to integrate network information to prioritize genes. Applications in Crohn's disease and Parkinson's disease show that this framework leads to more replicable results, and implicates potentially disease-associated pathways.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome (2014)
    Oxford University Press
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    Publication Date: 2014-11-12
    Description: The archaeal exosome is a phosphorolytic 3'–5' exoribonuclease complex. In a reverse reaction it synthesizes A-rich RNA tails. Its RNA-binding cap comprises the eukaryotic orthologs Rrp4 and Csl4, and an archaea-specific subunit annotated as DnaG. In Sulfolobus solfataricus DnaG and Rrp4 but not Csl4 show preference for poly(rA). Archaeal DnaG contains N- and C-terminal domains (NTD and CTD) of unknown function flanking a TOPRIM domain. We found that the NT and TOPRIM domains have comparable, high conservation in all archaea, while the CTD conservation correlates with the presence of exosome. We show that the NTD is a novel RNA-binding domain with poly(rA)-preference cooperating with the TOPRIM domain in binding of RNA. Consistently, a fusion protein containing full-length Csl4 and NTD of DnaG led to enhanced degradation of A-rich RNA by the exosome. We also found that DnaG strongly binds native and in vitro transcribed rRNA and enables its polynucleotidylation by the exosome. Furthermore, rRNA-derived transcripts with heteropolymeric tails were degraded faster by the exosome than their non-tailed variants. Based on our data, we propose that archaeal DnaG is an RNA-binding protein, which, in the context of the exosome, is involved in targeting of stable RNA for degradation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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