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  • Articles  (4)
  • Callose  (1)
  • Cell wall  (1)
  • Extrahaustorial matrix  (1)
  • Genomics  (1)
  • Springer  (3)
  • Oxford University Press  (1)
  • American Association for the Advancement of Science
  • American Chemical Society
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  • Articles  (4)
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  • Springer  (3)
  • Oxford University Press  (1)
  • American Association for the Advancement of Science
  • American Chemical Society
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  • 1
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    BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-18
    Description: Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially for ‘targeted’ resequencing efforts. This is critically important in the clinical setting where targeted resequencing is frequently being applied to rapidly assess clinically actionable mutations in tumor biopsies in a cost-effective manner. We present BreaKmer, a novel approach that uses a ‘kmer’ strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants. Relative to four publically available algorithms, BreaKmer detected SV with increased sensitivity and limited calls in non-tumor samples, key features for variant analysis of tumor specimens in both the clinical and research settings.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
    Electronic Resource
    Electronic Resource
    The herbicide dichlobenil disrupts cell plate formation: immunogold characterization (1996)
    Springer
    Protoplasma 194 (1996), S. 117-132 
    Details
    ISSN: 1615-6102
    Keywords: Cellulose biosynthesis ; Herbicides ; Cell plate formation ; Callose ; Xyloglucans
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have utilized light and transmission electron microscopy and immunocytochemistry to examine onion roots treated with the herbicide dichlobenil (2,6-dichlorobenzonitrile; DCB), a purported disrupter of cellulose biosynthesis. The most salient effect of DCB is observed on cell plate formation, the process that gives rise to new cell walls. In the presence of DCB, cell plates develop normally up to the tubular network stage. They are the result of fusion of Golgi-derived vesicles and the accumulation of callose and the first strands of cellulose. The DCB-treated cell plates retain the reticulate and malleable nature of the tubular network/early fenestrated plate stage of cell plate formation, but fail to display signs of the stiffening and straightening associated with an accumulation of cellulose. Instead, the malleable cell plates in the DCB-treated cells retain a wavy architecture, accumulate pockets of electron opaque material, and produce plasmodesmata in abnormal orientations. Immunocytochemical investigations of the abnormal cell plates formed after DCB treatment show 20-fold increase in the level of callose labelling found in the control cell plates. Xyloglucans and rhamnogalacturonans can be detected in the partially-formed cell plates, with the labelling density of xyloglucan 4–5 times greater than in the control cell plates and that of the rhamnogalacturonans being similar to the controls. These data support the hypothesis that DCB inhibits cellulose biosynthesis as a primary mechanism of action, and that in the absence of cellulose synthesis the cell plates fail to mature and to give rise to new cross walls.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01882020
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Location of cell-wall components in ectomycorrhizae ofCorylus avellana andTuber magnatum (1996)
    Springer
    Protoplasma 191 (1996), S. 55-69 
    Details
    ISSN: 1615-6102
    Keywords: Affinity techniques ; Immunogold ; Cell wall ; Corylus avellana ; Ectomycorrhizae ; Tuber magnatum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The cell-wall components in ectomycorrhizae ofCorylus avellana andTuber magnatum have been investigated by using immunocytochemistry and enzyme/lectin-gold techniques. Observations were performed in differentiated regions of hazel roots in the presence and absence of the ectomycorrhizal fungus. The results provided new information on the location of specific components in both the host and the fungal wall. The cellobiohydrolase I (CBH I)-gold complex and the monoclonal antibody (MAb) CCRC-M1 revealed cellulose and xyloglucans, respectively, in the host wall. MAb JIM 5, which detected un-esterified pectins, labelled only the material occurring at the junctions between three cells, while no labelling was found after treatment with MAb JIM 7, which detected methyl-esterified pectins. MAb CCRC-M7, which recognized an arabinosylated β-(1,6)-galactan epitope, weakly labelled tissue sections. MAb MAC 266, which detects a carbohydrate epitope on membrane and soluble glycoproteins, labelled the wall domain adjacent to the plasmamembrane. In the presence of the fungus, host walls were swollen and sometimes degraded. The labelling pattern of uninfected tissue was maintained, but abundant distribution of gold granules was found after CBH I and JIM 5 labelling. None of the probes labelled the cementing electron-dense material between the hyphae in the fungal mantle and in the Hartig net. The probes for fungal walls, i.e., wheat germ agglutinin (WGA) and concanavalin A (Con A) and a polyclonal antibody, revealed the presence of chitin, high-mannose side chains of glycoproteins and β-1,3-glucans. Con A alone led to a labelling over the triangular electron-dense material, suggesting that this cementing material may contain a fungal wall component.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01280825
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  • 4
    Electronic Resource
    Electronic Resource
    Isolation by ConA binding of haustoria from different rust fungi and comparison of their surface qualities (1992)
    Springer
    Protoplasma 170 (1992), S. 95-103 
    Details
    ISSN: 1615-6102
    Keywords: Affinity chromatography ; Biotrophy ; Concanavalin A ; Extrahaustorial matrix ; Puccinia ; Uromyces
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Rust haustoria isolated from infected leaf tissue strongly bind to ConA. This property was exploited to purify them by affinity chromatography on a ConA-Sepharose macrobead column. Haustoria were obtained with more than 90% purity and yields of up to 50%. Binding of haustoria to the column was partially inhibited by a ConA-specific sugar, methyl α-D-mannopyranoside. Compared to ConA,Lens culinaris agglutinin and wheat germ agglutinin were less efficient affinity ligands. Using ConA-Sepharose, rust haustoria from a variety of sources could be isolated with equal efficiency, indicating that they have similar carbohydrate surface properties. The haustoria maintained their typical shape after the isolation procedure, which suggests a rather rigid wall structure. The morphology of haustoria was characteristic both for a given species and the nuclear condition of the rust mycelium. Electron microscopy of isolated haustoria revealed an intact haustorial wall surrounded by a fibrillar layer presumably derived from the extrahaustorial matrix. The matrix thus appears to represent a layer with gel-like properties which is rich in ConA-binding carbohydrates and connected to the haustorial wall but not to the host-derived extrahaustorial membrane.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01378785
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    Paper (German National Licenses)
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