Project description:Differential DNA methylation (DNAm) in the brain is associated with many psychiatric diseases, but access to brain tissues is essentially limited to post-mortem samples. The use of surrogate tissues has become common in identifying methylation changes associated with psychiatric disease. In this study, we determined the extent to which peripheral tissues can be used as surrogates for DNAm in the brain. Blood, saliva, buccal, and live brain tissue samples from 27 medically intractable epilepsy patients undergoing brain resection were collected. Genome-wide methylation was assessed with the Infinium HumanMethylation450 (n=12) and HumanMethylationEPIC BeadChip arrays (n=21). For each CpG and each gene, levels of brain-peripheral tissue correlation varied widely. This indicates that to determine the most useful surrogate tissue for representing brain DNAm, the patterns specific to the genomic region of interest must be considered. To assist in that objective, we have developed a website, IMAGE-CpG, that allows researchers to interrogate DNAm levels and degree of cross-tissue correlation in user-defined locations across the genome.
Project description:Sewage samples were collected and concentrated for Human and animal viruses. Viruses were cultured on Buffalo Green Monkey Cells (BGMK) and their genomic DNA/RNA were extracted and labeled with Cy3 and Cy5 respectively. Labeled DNA/RNA were hybridized unto the array and signals generated were analyzed to indicate the presence of target viruses. Keywords: Detection of pathogens within environmental sample (Viruses) Environmental viruses were concentrated using organic flocculation with Beef Extract supplemented with glycine. Viruses were concentrated using 2 successive rounds of centrifugation and resuspended in Sodium Phosphate buffer. Viral nucleic acid was extracted, labeled and hybridized unto the microarray to determine the presence of target viruses within the sample.
Project description:We used the Illumina 450KMethylation BeadChip to measure DNA methylation at 485,512 loci across the genome for 40 postmortem brain samples. The purpose of our study was to identify differentially methylated regions (DMRs) associated with autism. Samples included 16 temporal cortex brain tissue samples (6 cases and 10 controls), 11 prefrontal cortex brain tissue samples (6 cases and 5 controls), and 13 cerebellum brain tissue samples (7 cases and 6 controls).
Project description:Adeno-associated viruses (AAVs) are foundational gene delivery tools for basic science and clinical therapeutics. However, lack of mechanistic insight, especially for engineered vectors created by directed evolution, can hamper their application. Here, we adapted an unbiased human cell microarray platform to determine the extracellular and cell surface interactomes of natural and engineered AAVs. We identified a naturally-evolved and serotype-specific interaction of AAV9 with human interleukin 3 (IL3), with possible roles in host immune modulation, as well as lab-evolved low-density-lipoprotein-receptor-related-protein 6 (LRP6) interactions specific to engineered capsids that cross the blood-brain barrier in non-human primates upon intravenous administration. The unbiased cell microarray screening approach also allowed us to identify off-target tissue binding interactions of engineered brain-enriched AAVs that may inform vectors’ peripheral organ tropism and side effects. These results allow confident application of engineered AAVs in diverse organisms and unlock future target-informed engineering of improved viral and non-viral vectors for non-invasive therapeutic delivery to the brain.
Project description:We performed the ATAC-seq to brain tissue from prefrontal cortex region in 6 AD Postmortem samples and 6 control non-dementia postmortem samples.
Project description:Brain metastasis is a major complication of lung cancer. An investigation of the pathogenic mechanisms of brain metastasis, as well as the identification of appropriate molecular markers, is necessary. We used microarrays to determine the expression patterns of microRNAs in lung cancer tissue with or without brain metastasis and to investigate the biological role of these miRNAs during tumorigenesis.
Project description:4 samples from 9 brain regions Brain tissue from the New South Wales Tissue Resource Centre, 9 brain regions, 4 samples each: 1 male alcoholic, 1 female alcoholic, 1 male control, 1 female control. Brain regions: pre-frontal cortex, cerebral cortex, visual cortex, thalamus, hippocampus, amygdala, caudate nucleus, putamen, cerebellum