Welcome #TeamVirulence, left to right: Rachel Tran (Biochem 3R06), Sally Min (BiomedDC 4A15), Anatoly Miroshnichencko (BiomedDC 4A15), and Rafik El Werfalli (BiomedDC 4A15), who are collectively working on development of CARD:Virulence, a new branch of the Comprehensive Antibiotic Resistance Database dedicated to the molecular surveillance of bacterial virulence factors.
Welcome Jalees Nasir (left) and Martins Oloni (right), new M.Sc. students in the lab and the McMaster Biochemistry & Biomedical Sciences graduate program. Jalees will be working on molecular epidemiological tools for surveillance of viral infections, while Martins will be collaborating with Agriculture and Agri-Food Canada (AAFC) on making our Comprehensive Antibiotic Resistance Database stronger for mobile elements involved in drug resistance in agricultural settings. Welcome Jalees & Martins!
Vision is a crucial aspect of life for humans and animals. Impaired vision can lead to reduced quality of life along with other complications. Cataracts are a leading cause of impaired vision and blindness worldwide. Cataracts develop as a process of aging, although several environmental and lifestyle factors increase the risk of this disease. The toxic metal cadmium (Cd) has been associated with cataract formation and other ocular diseases such as macular degeneration. Cadmium exposure exper- iments were conducted to investigate potential pathways or mechanisms by which Cd may contribute to cataract formation and ocular disease. Zebrafish larvae (72, 96, and 120 hours post fertilization), adult zebrafish (6-month male, 10-month male, and 10-month female) and the B3 human lens epithelial (HLE) cell line were acutely exposed to varying concentrations of Cd. Transcriptomic changes relative to control (0 μM Cd) were determined using microarray analysis for zebrafish larvae and RNA sequencing (RNA-Seq) for adult zebrafish and HLE cells. Gene Ontology (GO) enrichment analysis for the zebrafish larvae exposure (50 μM Cd for 4 or 8 hours) enriched the “retina development in camera-type eye” term, and genes involved in enrichment (dnmt1, ccna2, fen1, mcm3 and slbp) were down-regulated. Gene set enrichment analysis (GSEA) for the 10-month male zebrafish exposure (50 μM Cd for 4 hours) enriched the “embryonic eye morphogenesis” gene set and significant genes involved in enrichment (tcf7l1a, pitx2, fzd8a, sfrp5, lmx1bb, mfap2, six3b, lum, phactr4b, and foxc1a) were down-regulated. GSEA for the 10-month female zebrafish (50 μM Cd for 4 hours) enriched the “photoreceptor cell differentiation” gene set and significant genes involved in enrichment (odc1, thrb, and ush2a) were up-regulated. GO enrichment analysis for up-regulated genes in the HLE cell exposure (10 μM Cd for 4 hours) enriched the terms “eye development” (22 genes) and “lens development in camera-type eye” (CITED2, SKIL, CRYAB, SLC7A11, TGFB2, EPHA2, BCAR3, WNT5B, and BMP4). These results show cadmium is capable of altering transcription of eye-related genes in both zebrafish and human models, which may contribute to the formation of ocular disease. Many of these genes are involved in lens and retina development, yet they are also associated with diseases in these eye structures. Future studies could assess the consequences of altered transcription of these genes which could help elucidate the mechanisms of these changes and the overall effect of cadmium exposure on ocular disease. Ultimately, our study characterized the regulation of eye-related genes in response to Cd exposure, and provided valuable knowledge setting the foundation for identification of the molecular mechanisms contributing to ocular diseases.
- Alcock, B., A.R. Raphenya, A.N. Sharma, K.K. Tsang, T.T.Y. Lau, A. Hernandez-Koutoucheva, & A.G. McArthur. 2018. Data and curation in the Comprehensive Antibiotic Resistance Database. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
- Lau, T.T.Y., A.R. Raphenya, B. Alcock, & A.G. McArthur. 2018. Optimizing antimicrobial resistance surveillance tools through biological data organization and taxonomic identification of resistance genes. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
- Maguire, F., A.R. Raphenya, B. Alcock, A.G. McArthur, F.S. Brinkman, & R.G. Beiko. 2018. The cost of speed: evaluating systematic failures in metagenomic AMR profiling. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
- Raphenya, A.R., B. Alcock, K.K. Tsang, A.N. Sharma, T.T.Y. Lau, A. Hernandez-Koutoucheva, & A.G. McArthur. 2018. The Comprehensive Antibiotic Resistance Database and the Resistance Gene Identifier – Prediction of antimicrobial resistance genes and mutations for genomic and metagenomic sequencing data. Oral presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
- Tsang, K.K., H. Zubyk, S. Chou, G.D. Wright, & A.G. McArthur. Decoding bad bags: Predicting antibiotic resistance phenotypes from genotype. Oral presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
Kara Tsang passed her graduate transfer exam today, officially moving from the McMaster Biochemistry & Biomedical Sciences Masters program to the Ph.D. program. Kara’s work focusses on the intersection of biocuration, bioinformatics, machine learning, mutant screening, and phenotypic testing for prediction antimicrobial resistance phenotype from genotype. Well done Kara!
Update: Hot on the heels of becoming a Ph.D. student, Kara has won a 2018/2019 Department of Biochemistry & Biomedical Sciences’s Fred and Helen Knight Enrichment Award!
Tammy Lau has been awarded a prestigious Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Summer Student Fellowship for her work on development of k-mer approaches to predicting pathogen-of-origin for metagenomics antimicrobial resistance gene sequences. More details here.