Project description:Genomic content of Bordetella pertussis clinical isolates circulating in areas of intensive children vaccination. 13 isolates and one reference strain of Bordetella pertussis used.
Project description:Meningitis is a complex disease which can be caused by infection with either viral or bacterial pathogens. Viral meningitis is usually a sterile self-limiting disease with a good clinical prognosis, while bacterial meningitis is a potentially more serious disease with a higher mortality rate. Early diagnosis of bacterial meningitis is of paramount importance, as intervention with antimicrobial therapy increases the likelihood of a favourable clinical outcome. Routine diagnosis in many laboratories is still dependent to some degree on traditional methods e.g. culture, though molecular methods have been developed which can give a shorter time to diagnosis. However, there is not as yet a single test format that can detect all bacterial pathogens capable of causing meningitis. In addition, many tests e.g. real-time PCR have a finite limit for multiplexing and do not provide additional information such as strain or serogroup which is useful during outbreaks and for retrospective epidemiological surveillance. To this end we have developed a microarray probe set for detection of meningitis-associated bacterial pathogens including those in the N. meningitidis serogroups. Here we demonstrate utility of this array in specific detection of represented bacterial species and strains and in detection of pathogen signals in cerebrospinal fluid samples from patients with suspected bacterial meningitis. This method shows promise for development as a diagnostic tool; however, we discuss the technical issues encountered and suggest mechanisms to improve resolution of pathogen-specific signals in complex clinical samples. We designed as part of a larger pan-pathogen microarray a sub-set of probes to meningitis-associated bacterial pathogens. We present here data confirming the pathogen-specificity of many of these probes and their potential use in clinical diagnosis through testing on a small number of patient clinical samples using human DNA and no added nucleic acid controls. These data are from single channel Cy3-labelled nucleic acids. Four technical replicates for each feature are included on the array.
Project description:Our goal was to search for new molecular markers of the mitochondrial implication in the thyroid tumorigenesis. Using a DNA microarray (Cancerochip), we explored a collection of thyroid samples representing 4 classes of thyroid tumors. 45 thyroid tumoral and paired control tissues representing 4 classes (benign follicular tumors [FTA], oncocytic variants of follicular tumors [OT], papillary thyroid carcinomas [PTC] and tumors of uncertain malignancy potential [TUMP]) of thyroid tumors were explored for the expression of 6866 genes.
Project description:The incidence of esophageal and junctional adenocarcinoma has increased 6-fold in the west in the last 30 years and 5 year survival remains <14%. We aimed to characterize genome-wide aberrations in esophageal adenocarcinoma to further understand disease pathogenesis and ultimately identify groups with differential survivals with implications for clinical management. Oligo-array-based high-resolution analysis of copy number changes in 89 fresh frozen esophageal adenocarcinoma resection sections with long-term clinical follow-up data was performed. Good quality array comparative genomic hybridization profiles were obtained from 56/89 of the samples (63%). Our analyses confirmed known genomic aberrations in esophageal adenocarcinoma and identified 3 novel genomic regions with copy number changes. A modified T test with adjusted Bonferroni correction identified 17 genes with significantly different log2 ratios (p<4x10-7), including 6 novel genes, that characterize a group with a poorer survival. Total RNA isolated from human tissue sections was used to make fluorescently labeled cRNA that was hybridized to DNA oligonucleotide. Briefly, 4 µg of total RNA was used to synthesize dsDNA through reverse transcription. cRNA was produced by in vitro transcription and labeled postsynthetically with Cy3 or Cy5. Two populations of labeled cRNA, a reference population and an experimental population, were compared with each other by competitive hybridization to microarrays. Two hybridizations were done with each cRNA sample pair using a fluorescent dye reversal strategy. Human microarrays contained oligonucleotide probes corresponding to approximately 21,000 genes. All oligonucleotide probes on the microarrays were synthesized in situ with inkjet technology (Agilent Technologies, Palo Alto, CA). After hybridization, arrays were scanned and fluorescence intensities for each probe were recorded. Ratios of transcript abundance (experimental to control) were obtained following normalization and correction of the array intensity data. Gene expression data analysis was done with the Rosetta Resolver gene expression analysis software (version 7.0, Rosetta Biosoftware, Seattle, WA).
Project description:Transcriptional characteristics of genes in the midgut of domestic silkworms after 24 h exposure to phoxim through whole-genome oligonucleotide microarray. Transcription profiling experiments, phoxim-treated midgut (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and control samples labeled by Cy3. Three Biological replicate. No dye-swaps.
Project description:Comparing the gene expression profiling of HDGF-silenced RD-ES cells and control RD-ES cells to identify genes regulated by HDGF in RD-ES cells. Keywords: expression analysis Control RD-ES cells and HDGF-silenced RD-ES cells were profiled on 22K Human Genome Array
Project description:Microsporidia have attracted much attention because they infect a variety of species ranging from protists to mammals, including immunocompromised patients with AIDS or cancer. Aside from the study on Nosema ceranae, few works have focused on elucidating the mechanism in host response to microsporidia infection. Nosema bombycis is a pathogen of silkworm pM-CM-)brine that causes great economic losses to the silkworm industry. Detailed understanding of the host (Bombyx mori) response to infection by N. bombycis is helpful for prevention of this disease. The 23 K silkworm genome array was used to investigate host responses (i.e., Bombyx mori) occurring at 2, 4, 6 and 8 d post-infection by Nosema bombycis.We focused on elucidating the mechanism of the host response to microsporidia infection, especially for the investigation of host immune response . The third instar molted silkworm larvae were in oral infected by Nosema bombycis. In order to known the silkworm host response to Nosema bombycis infection at different time points, samples of infected larvae (i.e., the treatment set) and uninfected larvae (i.e., the control set) were collected at 2, 4, 6 and 8 dpi for RNA extraction and array hybridization. The obtained data were usd to investigate on the interplay of the genome-wide expression profile of hosts.