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  • 1
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    A functional synonymous mutation in melanoma [Genetics] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-08-14
    Description: Synonymous mutations, which do not alter the protein sequence, have been shown to affect protein function [Sauna ZE, Kimchi-Sarfaty C (2011) Nat Rev Genet 12(10):683–691]. However, synonymous mutations are rarely investigated in the cancer genomics field. We used whole-genome and -exome sequencing to identify somatic mutations in 29 melanoma samples....
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Prolonged Antigen Presentation following an Acute Virus Infection Requires Direct and Then Cross-Presentation [INFECTIOUS DISEASE AND HOST RESPONSE] (2014)
    The American Association of Immunologists (AAI)
    Details
    Publication Date: 2014-10-04
    Description: Antiviral CD8 + T cell recognition of MHC class I–peptide complexes on the surface of professional APCs is a requisite step in an effective immune response following many potentially lethal infections. Although MHC class I–peptide production is thought to be closely linked to the continued presence of virus, several studies have shown that the persistence of Ag presentation occurs for an extended period of time following the clearance of RNA viruses. However, the mechanism responsible for Ag presentation persistence following viral clearance was unknown until now. In this study, we used a recombinant DNA virus expressing different forms of a model Ag to study the mechanism of prolonged Ag presentation in mice. We determined that the persistence of Ag presentation consists of three distinct mechanistic phases, as follows: ongoing viral replication, persistence of virally infected cells, and cross-presentation of Ag. These data will allow manipulation of the form of Ag contained within viral vectors to produce the most effective and protective CD8 + T cell response to be generated following vaccination.
    Print ISSN: 0022-1767
    Electronic ISSN: 1550-6606
    Topics: Medicine
    Published by The American Association of Immunologists (AAI)
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  • 3
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    HSP90 empowers evolution of hormone resistance [Medical Sciences] (2014)
    National Academy of Sciences
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    Publication Date: 2014-12-24
    Description: The efficacy of hormonal therapies for advanced estrogen receptor-positive breast cancers is limited by the nearly inevitable development of acquired resistance. Efforts to block the emergence of resistance have met with limited success, largely because the mechanisms underlying it are so varied and complex. Here, we investigate a new strategy...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    Paternal occupation and birth defects: findings from the National Birth Defects Prevention Study (2012)
    BMJ Publishing Group
    Details
    Publication Date: 2012-07-14
    Description: Objectives Several epidemiological studies have suggested that certain paternal occupations may be associated with an increased prevalence of birth defects in offspring. Using data from the National Birth Defects Prevention Study, the authors investigated the association between paternal occupation and birth defects in a case–control study of cases comprising over 60 different types of birth defects (n=9998) and non-malformed controls (n=4066) with dates of delivery between 1997 and 2004. Methods Using paternal occupational histories reported by mothers via telephone interview, jobs were systematically classified into 63 groups based on shared exposure profiles within occupation and industry. Data were analysed using Bayesian logistic regression with a hierarchical prior for dependent shrinkage to stabilise estimation with sparse data. Results Several occupations were associated with an increased prevalence of various birth defect categories, including mathematical, physical and computer scientists; artists; photographers and photo processors; food service workers; landscapers and groundskeepers; hairdressers and cosmetologists; office and administrative support workers; sawmill workers; petroleum and gas workers; chemical workers; printers; material moving equipment operators; and motor vehicle operators. Conclusions Findings from this study might be used to identify specific occupations worthy of further investigation and to generate hypotheses about chemical or physical exposures common to such occupations.
    Keywords: Press releases
    Print ISSN: 1351-0711
    Electronic ISSN: 1470-7926
    Topics: Medicine
    Published by BMJ Publishing Group
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  • 5
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    Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-01-21
    Description: The genetics of renal cancer is dominated by inactivation of the VHL tumour suppressor gene in clear cell carcinoma (ccRCC), the commonest histological subtype. A recent large-scale screen of approximately 3,500 genes by PCR-based exon re-sequencing identified several new cancer genes in ccRCC including UTX (also known as KDM6A), JARID1C (also known as KDM5C) and SETD2 (ref. 2). These genes encode enzymes that demethylate (UTX, JARID1C) or methylate (SETD2) key lysine residues of histone H3. Modification of the methylation state of these lysine residues of histone H3 regulates chromatin structure and is implicated in transcriptional control. However, together these mutations are present in fewer than 15% of ccRCC, suggesting the existence of additional, currently unidentified cancer genes. Here, we have sequenced the protein coding exome in a series of primary ccRCC and report the identification of the SWI/SNF chromatin remodelling complex gene PBRM1 (ref. 4) as a second major ccRCC cancer gene, with truncating mutations in 41% (92/227) of cases. These data further elucidate the somatic genetic architecture of ccRCC and emphasize the marked contribution of aberrant chromatin biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030920/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030920/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Varela, Ignacio -- Tarpey, Patrick -- Raine, Keiran -- Huang, Dachuan -- Ong, Choon Kiat -- Stephens, Philip -- Davies, Helen -- Jones, David -- Lin, Meng-Lay -- Teague, Jon -- Bignell, Graham -- Butler, Adam -- Cho, Juok -- Dalgliesh, Gillian L -- Galappaththige, Danushka -- Greenman, Chris -- Hardy, Claire -- Jia, Mingming -- Latimer, Calli -- Lau, King Wai -- Marshall, John -- McLaren, Stuart -- Menzies, Andrew -- Mudie, Laura -- Stebbings, Lucy -- Largaespada, David A -- Wessels, L F A -- Richard, Stephane -- Kahnoski, Richard J -- Anema, John -- Tuveson, David A -- Perez-Mancera, Pedro A -- Mustonen, Ville -- Fischer, Andrej -- Adams, David J -- Rust, Alistair -- Chan-on, Waraporn -- Subimerb, Chutima -- Dykema, Karl -- Furge, Kyle -- Campbell, Peter J -- Teh, Bin Tean -- Stratton, Michael R -- Futreal, P Andrew -- 077012/Wellcome Trust/United Kingdom -- 077012/Z/05/Z/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- 093867/Wellcome Trust/United Kingdom -- R01 CA113636/CA/NCI NIH HHS/ -- R01 CA134759/CA/NCI NIH HHS/ -- Cancer Research UK/United Kingdom -- England -- Nature. 2011 Jan 27;469(7331):539-42. doi: 10.1038/nature09639. Epub 2011 Jan 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21248752" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carcinoma, Renal Cell/*genetics ; Cell Line, Tumor ; Disease Models, Animal ; Gene Expression Regulation ; Gene Knockdown Techniques ; Humans ; Kidney Neoplasms/*genetics ; Mice ; Mutation/*genetics ; Nuclear Proteins/*genetics/*metabolism ; Pancreatic Neoplasms/genetics ; Transcription Factors/*genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Controllable Disorder in a Hybrid Nanoelectronic System: Realization of a Superconducting Diode (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-07-25
    Description: We have studied a hybrid nanoelectronic system which consists of an AlGaAs/GaAs two-dimensional electron gas (2DEG) in close proximity (~70 nm) to an Al superconducting nanofilm. By tuning the current through the Al film, we can change the conductance of the 2DEG and furthermore vary the effective disorder in the Al superconducting film in a controllable way. When a high current is injected into the film, screening which couples the Al film and the 2DEG results in a collapse of anti-symmetric behavior in the current-voltage characteristics, V(I) ~ -V(-I), which holds true in a conventional superconductor. Our results may open a new avenue of experimentally realizing a superconducting diode. Scientific Reports 3 doi: 10.1038/srep02274
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Nature Publishing Group (NPG)
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  • 7
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    Single-cell paired-end genome sequencing reveals structural variation per cell cycle (2013)
    Oxford University Press
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    Publication Date: 2013-06-28
    Description: The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although single-cell genome analyses could resolve these problems, such analyses are error-prone because of whole-genome amplification (WGA) artefacts and are limited in the types of DNA mutation that can be discerned. We developed methods for paired-end sequence analysis of single-cell WGA products that enable (i) detecting multiple classes of DNA mutation, (ii) distinguishing DNA copy number changes from allelic WGA-amplification artefacts by the discovery of matching aberrantly mapping read pairs among the surfeit of paired-end WGA and mapping artefacts and (iii) delineating the break points and architecture of structural variants. By applying the methods, we capture DNA copy number changes acquired over one cell cycle in breast cancer cells and in blastomeres derived from a human zygote after in vitro fertilization. Furthermore, we were able to discover and fine-map a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) by sequencing a single blastomere. The methods will expedite applications in basic genome research and provide a stepping stone to novel approaches for clinical genetic diagnosis.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Multiple bidirectional EMIC waves observed by Cluster at middle magnetic latitudes in the dayside magnetosphere (2013)
    Wiley-Blackwell
    Details
    Publication Date: 2013-10-04
    Description: [1]  It is well accepted that the propagation of electromagnetic ion cyclotron (EMIC) waves are bidirectional near their source regions and unidirectional when away from these regions. The generally believed source region for EMIC waves is around the magnetic equatorial plane. Here we describe a series of EMIC waves in the Pc1 (0.2-5 Hz) frequency band above the local He + cyclotron frequency observed in situ by all four Cluster spacecraft on 9 April 2005 at mid-magnetic latitudes (MLAT = ~33°-49°) with L = 10.7-11.5 on the dayside (MLT = 10.3-10.4). A Poynting vector spectrum shows that the wave packets consist of multiple groups of packets propagating bidirectionally, rather than unidirectionally, away from the equator, while the local plasma conditions indicate that the spacecraft are entering into a region sufficient for local wave excitation. One possible interpretation is that, while part of the observed waves are inside their source region, the others are either close enough to the source region, or mixed with the wave packets from multiple source regions at different latitudes.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley-Blackwell on behalf of American Geophysical Union (AGU).
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  • 9
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    Body Mass Index May Modify Asthma Prevalence Among Low-Birth-Weight Children (2012)
    Oxford University Press
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    Publication Date: 2012-06-29
    Description: Childhood asthma, a growing health concern, has been associated with low birth weight and elevated body mass index. This study tested the hypothesis that overweight and obese adolescents with a history of low birth weight are at even greater risk of developing asthma. A cohort of 75,871 junior high school students was screened for asthma during 1995–1996 in Taiwan. Birth weight and estimated gestational age were obtained from the birth registry. Logistic regression and simple regression analyses were adjusted for confounding variables. Asthma was more prevalent in those with birth weights below 3,000 g and higher adolescent body mass indexes. Furthermore, those with both characteristics were consistently most likely to have asthma. Whether the asthma diagnosis among low-birth-weight subjects was assigned by physicians or medical questionnaire, the risks were elevated for both overweight (physician diagnosis: odds ratio = 1.41; medical questionnaire: odds ratio = 1.25) and obese (physician diagnosis: odds ratio = 1.38; medical questionnaire: odds ratio = 1.47) boys as well as overweight (physician diagnosis: odds ratio = 1.63; medical questionnaire: odds ratio = 1.30) and obese (physician diagnosis: odds ratio = 1.44; medical questionnaire: odds ratio = 1.32) girls ( P 〈 0.05). Low birth weight predisposes one to develop asthma, and excess body mass amplifies the risk. A sex difference was observed. This study suggests that prenatal care and nutritional counseling could reduce asthma prevalence.
    Print ISSN: 0002-9262
    Electronic ISSN: 1476-6256
    Topics: Medicine
    Published by Oxford University Press
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  • 10
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    Meander: visually exploring the structural variome using space-filling curves (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-08
    Description: The introduction of next generation sequencing methods in genome studies has made it possible to shift research from a gene-centric approach to a genome wide view. Although methods and tools to detect single nucleotide polymorphisms are becoming more mature, methods to identify and visualize structural variation (SV) are still in their infancy. Most genome browsers can only compare a given sequence to a reference genome; therefore, direct comparison of multiple individuals still remains a challenge. Therefore, the implementation of efficient approaches to explore and visualize SVs and directly compare two or more individuals is desirable. In this article, we present a visualization approach that uses space-filling Hilbert curves to explore SVs based on both read-depth and pair-end information. An interactive open-source Java application, called Meander , implements the proposed methodology, and its functionality is demonstrated using two cases. With Meander , users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference. The application was developed using Java version 1.6 and Processing.org and can be run on any platform. It can be found at http://homes.esat.kuleuven.be/~bioiuser/meander .
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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