1-s2.0-S0166685114X00101-cov150hAuthors: Ferella M, Davids BJ, Cipriano MJ, Birkeland SR, Palm D, Gillin FD, McArthur AG, Svärd S.

Mol Biochem Parasitol. 2014 Oct;197(1-2):21-3.

Serial Analysis of Gene Expression (SAGE) was used to quantify transcriptional changes in Giardia intestinalis during its interaction with human intestinal epithelial cells (IECs, HT-29) in serum free M199 medium. Transcriptional changes were compared to those in trophozoites alone in M199 and in TYI-S-33 Giardia growth medium. In total, 90 genes were differentially expressed, mainly those involved in cellular redox homeostasis, metabolism and small molecule transport but also cysteine proteases and structural proteins of the giardin family. Only 29 genes changed their expression due to IEC interaction and the rest were due to M199 medium. Although our findings generated a small dataset, it was consistent with our earlier microarray studies performed under different interaction conditions. This study has confined the number of genes in Giardia to a small subset that specifically change their expression due to interaction with IECs.

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full_colour_fhsThe McArthur lab in McMaster’s Department of Biochemistry & Biomedical Sciences is seeking a Systems Administrator / Information Technologist to help establish a new bioinformatics laboratory at McMaster, plus develop the next generation of the Comprehensive Antibiotic Resistance Database (CARD; arpcard.mcmaster.ca). The candidate will configure BLADE and other hardware for general bioinformatics analysis, development of a GIT version control system, construction of an in house Galaxy server (usegalaxy.org), and development of a new interface, stand-alone tools, APIs, and algorithms for the CARD (based on Chado; www.gmod.org/wiki/chado). Outside of server and software development, the candidate will perform a variety of bioinformatics analyses as well as be responsible for effective provisioning, installation/configuration, operation, and maintenance of systems hardware and software and related infrastructure. Genomics and bioinformatics training will be provided.

 

The candidate is expected to have knowledge and experience of LINUX operating system installation and management, network management, RAID and other storage technologies, database skills (SQL, postgreSQL), software for hosting advanced websites (Apache, PHP, Javascript, JQuery), and the computer languages common to bioinformatics (Python, Perl).  Knowledge of bioinformatics would be advantageous to the candidate. Experience with Flask, SQLAlchemy, and JSON would be beneficial. Skills in text mining and/or controlled vocabularies would be welcome, but not mandatory.
For more information, contact Dr. Andrew McArthur at mcarthua@mcmaster.ca
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plosAuthors: Hahn ME, McArthur AG, Karchner SI, Franks DG, Jenny MJ, Timme-Laragy AR, Stegeman JJ, Woodin BR, Cipriano MJ, Linney E.

PLoS One. 2014 Nov 17;9(11):e113158.

Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis and to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing oxidative stress. The developmental expression and inducibility of anti-oxidant defenses through activation of NF-E2-related factor 2 (NRF2) affect susceptibility to oxidants, but the embryonic response to oxidants is not well understood. To assess the response to chemically mediated oxidative stress and how it may vary during development, zebrafish embryos, eleutheroembryos, or larvae at 1, 2, 3, 4, 5, and 6 days post fertilization (dpf) were exposed to DMSO (0.1%), tert-butylhydroquinone (tBHQ; 10 µM) or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD; 2 nM) for 6 hr. Transcript abundance was assessed by real-time qRT-PCR and microarray. qRT-PCR showed strong (4- to 5-fold) induction of gstp1 by tBHQ as early as 1 dpf. tBHQ also induced gclc (2 dpf), but not sod1, nqo1, or cyp1a. TCDD induced cyp1a but none of the other genes. Microarray analysis showed that 1477 probes were significantly different among the DMSO-, tBHQ-, and TCDD-treated eleutheroembryos at 4 dpf. There was substantial overlap between genes induced in developing zebrafish and a set of marker genes induced by oxidative stress in mammals. Genes induced by tBHQ in 4-dpf zebrafish included those involved in glutathione synthesis and utilization, signal transduction, and DNA damage/stress response. The strong induction of hsp70 determined by microarray was confirmed by qRT-PCR and by use of transgenic zebrafish expressing enhanced green fluorescent protein (EGFP) under control of the hsp70 promoter. Genes strongly down-regulated by tBHQ included mitfa, providing a molecular explanation for the loss of pigmentation in tBHQ-exposed embryos. These data show that zebrafish embryos are responsive to oxidative stress as early as 1 dpf, that responsiveness varies with development in a gene-specific manner, and that the oxidative stress response is substantially conserved in vertebrate animals.

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Graham, C., D. Boreham, T. Glenn, S. Lance, J. Martino, R. Manzon, A.G. McArthur, S. Rogers, J.Y. Wilson, & C. Somers. 2014. Low quality DNA affects double digest restriction associated DNA sequencing (ddRADSeq). Poster presentation at Genomics: The Power & the Promise, Ottawa, Canada.

dasilvaTo improve the power of Learning Portfolios to enable long-term peer-to-peer mentoring between McMaster students and alumni, this Learning Portfolio Fellowship will establish a centralized database which can be used by students to formulate effective learning and career action plans based on current and past student experiences. The research question for this Learning Portfolio Fellowship is: “Can a meta-analysis based Learning Portfolio database contribute towards the undergraduate student career action plan?” While Learning Portfolios are effective qualitative measures of student outcomes, the proposed research will analyze current portfolios and capture quantitative metrics pertaining to the courses, experiential placements, volunteer opportunities, and extracurricular opportunities obtained by students pursuing various programs and career paths. Once the meta-analysis is conducted, the database will allow students to enter search queries, which will link them to collected repositories of information on their prospective career path.

This project is a collaboration with Dr. Rosa da Silva of McMaster’s Biology Department (pictured).

imageMcMaster Innovation Showcase 2014 is an opportunity for the University to demonstrate the exciting technologies that have been developed at McMaster, feature the initiatives underway relating to entrepreneurship, and engage with the community.

When: November 12, 2014; 8:00am – 5:00pm Where: McMaster Innovation Park Atrium, First Floor

More information on Keynote address, roundtable discussion, and Open Doors can be found here.

BznF4UsCQAActU5.jpg-largeToday was the annual Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Research Trainee Day, a great day of presentations and posters. Congratulations to the Award Winners.

ATW-2014-favicon-v34Smith, E.M., A.G. McArthur, M. Galus, S. Higgins, N. Kirischian, J. Jeyaranjaan, & J.Y. Wilson. 2014. Transcriptional responses of zebrafish to pharmaceutical and wastewater exposure: are single compound exposures predictive of mixtures? Keynote presentation at the Aquatic Toxicology Workshop 2014, Ottawa, Canada.

Human pharmaceuticals have been well documented in receiving waters yet their impacts on aquatic species are not clear. We have exposed adult zebrafish for 6 weeks to waterborne acetaminophen, gemfibrozil, venlafaxine, and carbamazepine at two doses (0.5 and 10 μg L-1). Fish were then exposed to a mixture of all four pharmaceuticals or wastewater effluent (5 and 25%) to assess whether transcriptional responses are similar with mixtures.. For all exposures, reproduction was significantly reduced and histopathological changes induced in kidney with at least the high dose exposure. Livers were pooled to provide sufficient RNA for microarray analyses. Hepatic transcriptional responses were determined with a modified Agilent 44K zebrafish microarry using a single channel approach. Significantly different probes were identified with a 2-way ANOVA (sex and treatment) and rank product analyses with a 10% false discovery rate. Transcriptional responses were particularly marked with acetaminophen exposure and there was broad overlap in the significant probes found between doses and across gender for this compound. 52 probes were at least 20 fold up- or down- regulated in acetaminophen exposed fish; 3 probes were 100 fold up-regulated (apolipoprotein Eb precursor, cdc73, and a hypothetical protein). Unique probes were identified for all exposures suggesting a unique transcriptional response may occur for each pharmaceutical, the pharmaceutical mixture, and wastewater effluent. Interestingly, there was almost no overlap in the transcriptional response found with single pharmaceutical exposure and either the mixture or wastewater effluent exposure. Indeed, the large transcriptional response from acetaminophen exposure was largely absent in fish exposed to the pharmaceutical mixture and wastewater effluent. This suggests that identifying individual or clusters of genes that may be useful in effects based monitoring may be difficult for pharmaceutical compounds.

McMaster_Uniersity_Health_Sciences_entranceAndrew McArthur will be returning to academia in September 2014 to join McMaster University as the Cisco Chair in Bioinformatics and Associate Professor in the Department of Biochemistry & Biomedical Sciences in the Faculty of Health Sciences. Read more about the McMaster – Cisco collaboration at: McMaster and Cisco collaborate to further bioinformatics research and build institutional research cloud.