Project description:Pseudomonas aeruginosa is a common bacterium in the terminal plumbing system of buildings and it is from this niche that a substantial fraction of infections are acquired. To better understand P. aeruginosa biology in this environment, we examined the transcriptomes in tap water and pond water.
Project description:Rainbow trout (Oncorhynchus mykiss) is an important aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). Fish skin is an important immune organ, however, little is known about the differences in skin immunity between WR_S and YR_S in a natural flowing water pond aquaculture environment, and very few studies were conducted to investigate the ceRNA mechanism for fish skin.
Project description:Methods currently available to estimate the post-mortem submerged interval (PMSI) of cadavers in water suffer from poor accuracy, being mostly based on morphological examination of the remains. Proteins present within bones have recently attracted more attention from researchers interested in the estimation of the post-mortem interval (PMI) in terrestrial environments. Despite the great potential of proteomic methods for PMI estimation, their application to aquatic environments has not yet been explored. In this study, we examined whether four different types of aquatic environment (tap water, saltwater, pond water and chlorinated water) affected the proteome of mice bones with increasing PMSIs (from zero to three weeks).
Project description:Clinical-grade human embryonic stem cells (hESCs) from 4 centres in the UK were cultured in self-renewal conditions Genomic DNA was isolated from low passage hESCs and submitted for SNP analysis using Illumina HumanCytoSNP-12 v2.1 BeadChip arrays
Project description:An European eel-specific microarray platform was developed to identify genes involved in response to pollutants. A comparative analysis of gene expression was conducted between European eel Anguilla anguilla individuals from lowly-polluted Wijmeers pond at Uitbergen (Belgium), highly-polluted Hazewinkel pond at Willebroek (Belgium), extremely-polluted Dessel-Schotel canal at the locations of Schotel (Belgium) and low polluted Bolsena lake (Italy) environments.
Project description:Gastric cancer is the second most common cause of cancer death worldwide, but incidence and mortality rates show large variations across different countries. Variation in risk factors between different populations, including environmental and host factors influencing gastric cancer risk, have been reported but little is known about the biological differences between gastric cancers from different geographic locations. We set out to study genomic instability patterns of gastric cancers obtained from patients from United Kingdom (UK) and South Africa (SA). DNA was isolated from 67 gastric adenocarcinomas, 33 UK patients, 9 Caucasian SA patients and 25 native SA patients. Microsatellite instability and chromosomal instability were analyzed by PCR and microarray comparative genomic hybridization, respectively. Data was analyzed by supervised univariate and multivariate analyses as well as unsupervised hierarchical cluster analysis. Tumors from Caucasian and native SA patients showed significantly more microsatellite instable tumors (p<0.05). For the microsatellite stable tumors, geographical origin of the patients correlated with cluster membership, derived from unsupervised hierarchical cluster analysis (p=0.001). Several chromosomal alterations showed significantly different frequencies in tumors from UK patients and native SA patients, but not between UK patients and Caucasian SA patients and between native and Caucasian SA patients. In conclusion, gastric cancers from South African and UK patients show differences in genetic instability patterns, indicating possible different biological mechanisms underlying the disease.
Project description:The non-tumourigenic human breast epithelial cell line MCF10A is the cell line most commonly used as a model for normal human breast cells. This dataset provides a reference genome for MCF10A. The whole genome, high-throughput sequencing was performed using the Illumina NovaSeq 6000 PE150 system. Both NGS and bioinformatic analysis were performed by Novogene (UK).
