Congratulations to this year’s crop of BiomedDC 4A15 thesis students for 8 month research projects well done! From left to right:

Suman Virdee – Developing a Galaxy based Pipeline for RNA-Seq Analysis in Stem Cell Biology

Kirill Pankov – The Cytochrome P450 (CYP) Superfamily in the Cnidarian Phylum

Jonsson Liu – Clinical virulence detection and Clostridium difficile clonality

Annie Cheng – Predicting Plasmid-Mediated Antimicrobial Resistance from Whole Genome Sequencing

Godwin Chan – Using the Galaxy Platform to Increase Accessibility for Structure Determination via Cryo-Electron Microscopy

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Congratulations to 4th Year Biomedical Discovery & Commercialization student and McArthur lab member Suman Virdee for her CIHR Undergraduate Summer Studentship Award for her summer project “Development and implementation of computational tools to dissect cancer stem cell circuitry”, a joint project between our laboratory and that of Dr. Kristin Hope!

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tammy-lau3rd year Biochemistry & Biomedical Sciences student Tammy Lau has joined us for her Biochem 3A03 (Biochemical Research Practice) course. Tammy will be collaborating with Dr. Lesley MacNeil in development of a bioinformatics pipeline for a new technology for tissue-specific expression profiling in the important model organism C. elegans. Support from this project comes from a new Michael G. DeGroote Institute for Infectious Disease Research (McMaster) Research Grant. Welcome Tammy!

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briony lagoThis month we say farewell to Briony Lago as she returns to her undergraduate studies in Chemical Biology at McMaster. Briony joined us as part of her Chemical Biology Co-Op program and worked on both human muscle atrophy and zebrafish toxicology transcriptome studies, as well a curation of the Comprehensive Antibiotic Resistance Database. Her publications are below, with more on the way. Briony was also awarded a 2016 IIDR Summer Student Fellowship for her work. Good luck Briony!

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Arjun Sharmakirill-pankov suman annie jonsson godwin

Biochem 3R06 Project Students – Arjun Sharma

BiomedDC 4A15 Thesis Students – Kirill Pankov, Suman Virdee, Annie Cheng, Jonsson Liu, Godwin Chan

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Kara Tsang krishna

Kara Tsang (graduate, McMaster BDC) – Kara did her BiomedDC 4A15 thesis in the lab, focused on Pseudomonas resistome prediction and cystic fibrosis-associated metagenomic sequencing and starts September 2016 as MSc student in the area of clinical AMR analytics, particularly metagenomics. Her work will be part of our recently funded Genome Canada grants, as well as part of McMaster’s clinical genome sequencing efforts.

Krishna Srinivasan (graduate, McMaster Biology) – Krishna just finished his undergraduate degree in McMaster’s Biology department, with a thesis in environmental toxicology. He starts as a MSc student September 2016, collaborating with the Jenny lab (UAlabama) on our recently funded NIH grant examining the role of MTF-1 in lens development and cataractogenesis.

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Sachin Biren Dave

The McArthur Lab bids farewell and good luck to Biren Dave and Sachin Doshi! Sachin left mid-summer for a fellowship at Harvard and now is off to the UToronto Medical School! Biren finished his 3rd year Biochemistry Co-Op position and joins McMaster’s Stem Cell and Cancer Research Institute for his fourth year thesis. Thanks to you both!

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briony lago alcockZachary LinKara TsangBiren Davejjiaamospearl
McMaster Interdisciplinary Research Exposition (MIREx); Ontario Biology Day; Biomedical Discovery and Commercialization Engage Symposium; Rapid Microbial NGS and Bioinformatics: Translation Into Practice (Germany); Canadian Food Inspection Agency Forum on Genomics and Antimicrobial Resistance; New Antibacterial Discovery & Development Gordon Research Conference (Italy); McMaster Women in Science and Engineering (WISE) Current Research in Engineering, Science & Technology (CREST) Meeting; 6th Biennial National IDeA Symposium of Biomedical Research Excellence (USA).

Presenter underlined, trainees in bold.

  • Dave, B.M., J.A. Klein, L.A. Knodler, A.R. Raphenya, & A.G. McArthur. 2016. A phylogenetic analysis of Inv/Mxi-Spa proteins and implications for functional complementation. Poster presentation at McMaster Interdisciplinary Research Exposition (MIREx), Hamilton, Ontario, Canada.
  • Dave, B.M., J.A. Klein, L.A. Knodler, A.R. Raphenya, & A.G. McArthur. 2016. A phylogenetic analysis of Inv/Mxi-Spa proteins and implications for functional complementation. Poster presentation at Ontario Biology Day 2016, Toronto, Ontario, Canada.
  • Lin, Z. & A.G. McArthur. 2016. Adapting Galaxy bioinformatics to outbreak-associated Clostridium difficile. Poster presentation at McMaster’s Biomedical Discovery and Commercialization Engage Symposium, Hamilton, Ontario, Canada.
  • McArthur, A.G.B. Jia, A.R. Raphenya, P. Guo, K. Tsang, B. Dave, B. Alcock, B. Lago, N. Waglechner, & G.D. Wright. 2016. The Comprehensive Antibiotic Resistance Database – A Platform for Antimicrobial Resistance Surveillance. Invited presentation at the 2nd Conference Rapid Microbial NGS and Bioinformatics: Translation Into Practice, Hamburg, Germany.
  • McArthur, A.G. 2016. Bioinformatic resources for antimicrobial resistance. Invited presentation at Canadian Food Inspection Agency (CFIA) Forum on Genomics and Antimicrobial Resistance, Ottawa, Ontario, Canada.
  • McArthur, A.G. 2016. Combatting Antibiotic Resistance Using Surveillance. Invited presentation at McMaster Interdisciplinary Research Exposition (MIREx), Hamilton, Ontario, Canada.
  • Pawlowski, A.C., W. Wang, K. Koteva, H.A. Barton, B. Jia, A.R. Raphenya, P. Guo, A.G. McArthur, G.D. Wright. 2016. A multi-antibiotic resistant genotype is maintained for millions of years. Presentation at the New Antibacterial Discovery & Development Gordon Research Conference, Lucca, Italy.
  • Tsang, K. & A.G. McArthur. 2016. Translation of biocuration to metagenomic analysis. Poster presentation at McMaster Interdisciplinary Research Exposition (MIREx), Hamilton, Ontario, Canada.
  • Tsang, K. & A.G. McArthur. 2016. Translation of biocuration to metagenomic analysis. Poster presentation at Ontario Biology Day 2016, Toronto, Ontario, Canada.
  • Tsang, K. & A.G. McArthur. 2016. Translation of biocuration to metagenomic analysis. Poster presentation at McMaster Women in Science and Engineering (WISE) Current Research in Engineering, Science & Technology (CREST) Meeting, Hamilton, Ontario, Canada.
  • Tsang, K. & A.G. McArthur. 2016. Translation of biocuration to metagenomic analysis. Poster presentation at McMaster’s Biomedical Discovery and Commercialization Engage Symposium, Hamilton, Ontario, Canada.
  • Williams, L., A.G. McArthur, B. Lago, A.R. Raphenya, N. Pray, N. Saleem, S. Salas, K. Paulson, R. Mangar, Y. Liu, A. Vo, & J. Shavit. 2016. Nuclear factor, erythoid 2 (Nfe2) is a transcriptional regulator of oxidative stress during zebrafish development. Presentation at the 6th Biennial National IDeA Symposium of Biomedical Research Excellence, Washington, DC.
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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.

See: Q&A with IIDR Summer Fellowship recipient Briony Lago

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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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