161 research outputs found

    Expression of Annexin Al and KI-67 in histopathologically negative margins of oral squamous cell carcinoma cases with and without local recurrence

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    AIM OF THE STUDY: To evaluate the expression of the immunohistochemical markers Annexin A1 and Ki-67 in histologically negative margins of surgically treated Oral squamous cell carcinoma (OSCC) cases with and without local recurrences. MATERIALS AND METHODS: Specimens for the study will be selected from the archives of Department of Oral and Maxillofacial pathology, Vivekanandha Dental College for Women, Tiruchengode. 20 Specimens/tissue blocks of surgically treated OSCC cases histopathologically diagnosed as well, moderate and poorly differentiated with their negative margins and 10 normal buccal mucosa were selected. One section will be stained with haematoxylin and eosin, and the other two will be immunohistochemically stained with Annexin A1 and Ki-67 markers. The analysis of Annexin A1 and Ki-67 expression will be carried out on the basis of the percentage of cells showing staining in the different layers of the oral mucosa. Score 0 = no staining or unspecific staining of tumor cells; Score 1 = weak (intensity) and incomplete staining (quality) of more than 10% - 30% of tumor cells (quantity); Score 2 = moderate and complete staining of more than 30% -60% of tumor cells; Score 3 = strong and complete staining of more than 60% of tumor cells. After recording the data, expression of Annexin A1 and Ki 67 in surgically treated OSCC cases and their negative margins with and without local recurrence will be compared and statistically analysed using Chi-square test. RESULTS: On comparison of negative margins of recurrent and non-recurrent OSCC cases, a P-value of 0.0041 is obtained which is found to be more significant. On analyzing the tumor proper region between the pathologically differentiated grades of OSCC cases a significant P-value (0.041) is obtained. Annexin A1 expression decreased significantly as neoplasia progressed in OSCC cases. On comparision between the negative margins of recurrent and non-recurrent OSCC cases a P-value of <0.0001 is obtained which is found to be more significant. A significant P-value (0.041) is obtained between the pathological differentiated grades of OSCC. Expression of Ki-67 increased significantly as neoplasia progressed in OSCC cases. CONCLUSION: Anti-proliferative activity of Annexin A1 and proliferative activity of the Ki-67 nuclear antigen has been linked and investigated whether their expression can be of clinical use for prediction of locoregional recurrence exclusively in primary OSCC. The results of this study provide data on Annexin A1 and Ki-67 expression in the tumor proper region and histopathologically negative margins of well and moderately differentiated OSCC cases with and without local recurrence. Thus by predicting the local recurrence, surgeons can be intimated for wide local excision, thereby preventing treatment failures and benefiting the patients

    First draft genome sequence of a UK strain (UK99) of Fusarium culmorum

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    Fusarium culmorum is a soilborne fungal plant pathogen that causes foot and root rot and Fusarium head blight on small-grain cereals, in particular on wheat and barley. We report herein the draft genome sequence of a 1998 field strain called FcUK99 adapted to the temperate climate found in England

    Interaction of Fusarium oxysporum f. sp. ciceri and Meloidogyne javanica on Cicer arietinum

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    Interaction of Meloidogyne javanica and Fusarium oxysporum f. sp. cice~q was studied on Fusarium wilt-susceptible (JG 62 and K 850) and resistant (JG 74 and Avrodhi) chickpea cultivars. In greenhouse experiments, inoculation of M. javanicajuveniles prior to F. oxysporum f. sp. ciceri caused greater wilt incidence in susceptible culfivars and induced vascular discoloration in roots of resistant cultivars. Nematode reproduction was greatest (P = 0.05) at 25 °C. Number of galls and percentage of root area galled increased when the temperature was increased from 15 °C to 25 °C. Wilt incidence was greater at 20 °C than at 25 °C. Chlorosis of leaves and vascular discoloration of plants did not occur at 15 °C. The nematode enhanced the wilt incidence in wilt-susceptible cultivars only at 25 °C. Interaction between the two pathogens on shoot and root weights was significant only at 20 °C, and F. o. ciceri suppressed the nematode density at this temperature. Wilt incidence was greater in clayey (48% clay) than in loamy sand (85% sand) soils. The nematode caused greater plant damage on loamy sand than on clayey soil. Fusarium wilt resistance in Avrodhi and JG 74 was stable in the presence of M. javanica across temperatures and soil types

    Theoretical evidences for enhanced superconducting transition temperature of CaSi2_2 in a high-pressure AlB2_2 phase

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    By means of first-principles calculations, we studied stable lattice structures and estimated superconducting transition temperature of CaSi2_2 at high pressure. Our simulation showed stability of the AlB2_2 structure in a pressure range above 17 GPa. In this structure, doubly degenerated optical phonon modes, in which the neighboring silicon atoms oscillate alternately in a silicon plane, show prominently strong interaction with the conduction electrons. In addition there exists a softened optical mode (out-of-plan motion of silicon atoms), whose strength of the electron-phonon interaction is nearly the same as the above mode. The density of states at the Fermi level in the AlB2_2 structure is higher than that in the trigonal structure. These findings and the estimation of the transition temperature strongly suggest that higher TcT_{\rm c} is expected in the AlB2_2 structure than the trigonal structures which are known so far.Comment: 6 pages and 11 figure

    PhytoPath: an integrative resource for plant pathogen genomics

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    PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species

    Ensembl Genomes 2013: scaling up access to genome-wide data

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    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future

    Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features.

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    The value of genome-wide over targeted driver analyses for predicting clinical outcomes of cancer patients is debated. Here, we report the whole-genome sequencing of 485 chronic lymphocytic leukemia patients enrolled in clinical trials as part of the United Kingdom's 100,000 Genomes Project. We identify an extended catalog of recurrent coding and noncoding genetic mutations that represents a source for future studies and provide the most complete high-resolution map of structural variants, copy number changes and global genome features including telomere length, mutational signatures and genomic complexity. We demonstrate the relationship of these features with clinical outcome and show that integration of 186 distinct recurrent genomic alterations defines five genomic subgroups that associate with response to therapy, refining conventional outcome prediction. While requiring independent validation, our findings highlight the potential of whole-genome sequencing to inform future risk stratification in chronic lymphocytic leukemia

    A Gene in the Process of Endosymbiotic Transfer

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    BACKGROUND: The endosymbiotic birth of organelles is accompanied by massive transfer of endosymbiont genes to the eukaryotic host nucleus. In the centric diatom Thalassiosira pseudonana the Psb28 protein is encoded in the plastid genome while a second version is nuclear-encoded and possesses a bipartite N-terminal presequence necessary to target the protein into the diatom complex plastid. Thus it can represent a gene captured during endosymbiotic gene transfer. METHODOLOGY/PRINCIPAL FINDINGS: To specify the origin of nuclear- and plastid-encoded Psb28 in T. pseudonana we have performed extensive phylogenetic analyses of both mentioned genes. We have also experimentally tested the intracellular location of the nuclear-encoded Psb28 protein (nuPsb28) through transformation of the diatom Phaeodactylum tricornutum with the gene in question fused to EYFP. CONCLUSIONS/SIGNIFICANCE: We show here that both versions of the psb28 gene in T. pseudonana are transcribed. We also provide experimental evidence for successful targeting of the nuPsb28 fused with EYFP to the diatom complex plastid. Extensive phylogenetic analyses demonstrate that nucleotide composition of the analyzed genes deeply influences the tree topology and that appropriate methods designed to deal with a compositional bias of the sequences and the long branch attraction artefact (LBA) need to be used to overcome this obstacle. We propose that nuclear psb28 in T. pseudonana is a duplicate of a plastid localized version, and that it has been transferred from its endosymbiont

    Ensembl Genomes: Extending Ensembl across the taxonomic space

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    Ensembl Genomes (http://www.ensemblgenomes.org) is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community, which we consider as essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimised data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site
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