Project description:Microarray comparative genome hybridization (mCGH) data was collected from one Neisseria cinerea, two Neisseria lactamica, two Neisseria gonorrhoeae, and 48 Neisseria meningitidis isolates. For N. meningitidis, these isolates are from diverse clonal complexes, invasive and carriage strains, and all major serogroups. The microarray platform represented N. meningitidis strains MC58, Z2491, and FAM18 and N. gonorrhoeae FA1090.
Project description:DNA copy number profiling of 32 glioblastoma orthotopic xenografts Descriptive experiment, comparison of 39 glioblastoma tumors as orthotopic xenografts flow sorted for anueploidy
Project description:A comparative genomic hybridisation experiment using Affymetrix YG-S98 arrays to study the genetic background of S. Boulardii compared to S. Cerevisiae strain BY4743. Background: Saccharomyces boulardii, a yeast that was isolated from fruit in Indochina has been used as a remedy for diarrhoea since 1950, and is now a commercially available treatment throughout Europe, Africa and South America. Though initially classified as a separate species of Saccharomyces, recent publications have shown that the genome of S. boulardii is so similar to Saccharomyces cerevisiae that the two should be classified as conspecific. This raises the question of the distinguishing molecular and phenotypic characteristics present in S. boulardii that make it perform more effectively as a probiotic organism compared to other strains of S. cerevisiae. This investigation reports some of these characteristics including enhanced ability for pseudohyphal switching upon nitrogen limitation and increased resistance to acidic pH. However, these differences did not correlate with increased adherence to epithelial cells or transit through mouse gut. Pertinent characteristics of the S. boulardii genome such as trisomy of chromosome IX, altered copy number of a number of individual genes and sporulation deficiency have been revealed by comparative genome hybridisation using oligonucleotide-based microarrays coupled with a rigorous statistical analysis. The contributions of the different genomic and phenotypic features of S. boulardii to its probiotic nature are discussed.
Project description:Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens.
Project description:Comparison of chromosome region copy number changes accompanying progression of immortalized MLL-ENL expressing cells into leukaemic cells
Project description:The coccolithoviruses contained within the Plymouth Virus Collection (PVC) were screened for genomic content using a microarray. The diversity in genomic content was assessed for twelve strains: EhV-86, on which the microarray is based; EhV-84, EhV-88, EhV-163, EhV-V2, EhV-201, EhV-202, EhV-205, EhV-206, EhV-207, EhV-208 and EhV-209. A direct labelling method was employed to label each virus' genomic DNA which was hybridised onto a separate microarray slides.
Project description:Since Japanese quail and chicken belong to the same order Galliforms, DNA sequence of both species are highly conserved and proved to be applicable for various analyses each other. Quail are commonly used to address physiological questions for reasons of economy. To test whether chicken microarrays are useful to quail samples, we compared hybridization signals of chicken and quail genomic DNA on Affymetrix chicken genome array. Experiment Overall Design: Genomic DNA of female chicken and quail were extracted individually from liver of three birds and hybridized on Affymetrix microarrays. Samples were analyzed in triplicate set of array (three biological replicates).