Fellowship-winners-2016-1Ten undergraduate students from the faculties of Science and Health Sciences have been awarded the prestigious Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Summer Student Fellowship, including our own Briony Lago (third from the right). This highly competitive fellowship, now in its fourth year and worth $1,000, is designed to support students working in the labs of IIDR members during their summer practicum, which runs from May to August. Briony Lago joined the lab as part of her McMaster Chemical Biology Co-Op program, working on our ‘Omic’ Responses & Inactivity in Aging project (a collaboration with colleagues in Kinesiology & Chemistry), our collaboration with Bates College on the role of Nfe2 in oxidative stress response during zebrafish development, and biocuration of our Comprehensive Antibiotic Resistance Database.

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image2Congratulations to Kara Tsang and Zachary Lin on completion of their Biomedical Discovery and Commercialization (BDC) 4A15 thesis research! Both Kara & Zachary presented their research results at the 2016 BDC Engage Symposium.

Zachary Lin: Adapting Galaxy bioinformatics to outbreak- associated Clostridium difficile

Kara Tsang: The translation of biocuration to metagenomic analysis for combatting multi-drug resistant Pseudomonas aeruginosa

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Arjun Sharma

Arjun Sharma is a 2cd year Biochemistry & Biomedical Sciences student how as a volunteer designed and created the new AMR Forums! Learn more about Arjun’s project at ‘New online AMR forum is a valuable learning resource’ or visit the AMR Forums.

 

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Andrew-judy627

Combatting Antibiotic Resistance Using Surveillance – click on the image to watch the 10 minute video. More details here.

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briony lagoBriony Lago has joined the lab as part of her McMaster Chemical Biology Co-Op program. She will be working on our ‘Omic’ Responses & Inactivity in Aging project (a collaboration with colleagues in Kinesiology & Chemistry, see here) as well as our collaboration with Bates College on the role of Nfe2 in the oxidative stress response during zebrafish development (see here).

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alcockBrian Alcock has joined the McArthur Lab to lead curation of the Comprehensive Antibiotic Resistance Database (arpcard.mcmaster.ca). Brian recently completed his MSc in the laboratory of Dr. Ben Evans in McMaster’s Biology Department. Welcome Brian!

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JoannaWilsonDr. Joanna Wilson, Department of Biology, McMaster University

I never expected a standing ovation. Especially considering that my message was “I see you.” But when I won a YWCA Hamilton Women of Distinction Award for my contributions to Science and Technology last April, that is exactly what happened.” Read the full editorial at the Hamilton Spectator.

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image1Zachary Lin – Adapting Galaxy bioinformatics to outbreak-associated Clostridium difficile

The completion of the human genome project in 2001 sparked the beginning of a sequencing revolution with applications that are only now being realized by researchers. The decreasing cost of DNA sequencing has ignited a continuous generation of genomic data with a limited number of researchers able to manipulate the output. Consequentially the demand to examine this genetic information has forced bioinformaticians to improve the analytical tools involved in sequence analysis. Galaxy is a user-friendly analytical platform where researchers without a computational background can navigate their way through an investigation and use various analytical tools and workflows to assist them with their genomic research (1). Galaxy enables the addition of novel software into the environment by individual users to fill in the gaps of tools that haven’t been created by the Galaxy team. This project will focus on a particular analytical gap concerning tools related to antibiotic resistance, phylogenetics, and bacterial virulence. Currently, the proposed software to be adapted to the galaxy setting includes a resistance gene identifier (RGI) associated with the comprehensive antibiotic resistance database (CARD) (2), a single nucleotide polymorphism identifier (BANSP) , and novel virulence factor identification software associated with the virulence factor database (VFDB) (3). The combination of Galaxy’s existing ToolShed and these unique additions will create a comprehensive analytical environment that can be applied to realistic situations. One such situation that this project will concentrate on refers specifically to the outbreaks of Clostridium difficile (C. diff) in the health care system.

karaKara Tsang – Expansion of the Antibiotic Resistance Ontology for the ESKAPE pathogens

The loss of effective antimicrobials is reducing the ability to protect the global population from infectious diseases, leading to profound impacts on the healthcare system, international trade, agriculture, and environment. The field of antibiotic drug discovery and the monitoring of the dynamic and new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. The curation and directed development of the Comprehensive Antibiotic Database (CARD) will advance the understanding of the genetics, genomics, and threat severity of antibiotic resistance, while simultaneously improving its ability to accurately predict and screen for antibiotic resistance genes within raw genomes. Strategically advancing the Antibiotic Resistance Ontology (ARO), the unique organizing principle of the CARD, allows the value of big data in disparate realms of research to be used and understood by the multidisciplinary efforts working to combat the emergence and prevalence of the ESKAPE pathogens, a critical driving force of the global health crisis.

 

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