Whelan FJ, Yap NV, Surette MG, Golding GB, Bowdish DM.A Guide to Bioinformatics for Immunologists. Front Immunol. 2013 Dec 4;4:416. eCollection 2013. Click picture for .pdf.
Congratulations to Fiona Whelan (MSc, Bowdish lab; PhD student, Surette lab) for publishing the review article “A guide to bioinformatics for immunologists” in Frontiers Immunology. The idea of this article spawned from the research that Fiona conducted in the Bowdish lab on the elucidation of the evolutionary history and relationships between the members of the class A scavenger receptors, proteins required for host defense and homeostasis. During this time, Fiona used multiple bioinformatic techniques and tools to form hypotheses as to the function of one under-annotated member of this family, SCARA3. Even though most of these tools are easy-to-use and require little computational knowledge, Fiona and Dawn discovered through their interactions with other immunologists that these tools were being under utilized. Thus, they decided to write a review of how bioinformatic techniques can help the average immunologist in their quest for knowledge about the structure of their protein of interest, how to find SNPs that may correlate with disease phenotype, and how to conduct sequence alignments in order to find areas that are conserved across various genes.
This review article is written as a case study that follows Fiona’s research into SCARA3 that begins with obtaining the NCBI Reference FASTA sequence of the protein, predicting post-translational modifications, identifying conserved motifs, hypothesizing as to the structure of the protein, examining SCARA3’s transcriptomic profile in different immunological cell types, and analyzing any potential SNPs within the DNA sequence of SCARA3 that may correlate with disease. The article is written with the immunologist in mind and includes the use of only “point and click” tools that require no computational background whatsoever.
Is Fiona’s paper is Open Access? Of course it is! Enjoy reading it here and reading the description on the Surette lab website here.
The laboratories of both Dr. Bowdish and Dr. Surette are always interested in undergraduate and graduate students interested in exploring the impact bioinformatics can have on immunological and microbiological research.
Do professors seem distant & unapproachable to you? They shouldn’t be, after all they were once students themselves. A group of McMaster students created the “After Office Hours” series to profile a number of McMaster professors, including Dawn. They asked all sorts of great questions like “what do you do for fun?”, “what advice would you give yourself as an undergrad?”, “what’s the weirdest thing an undergraduate student has said to you?”.
To see Dawn’s interview, click here.
Dawn posts on all things macrophage-y and gives updates on the Bowdish lab and science life in general on her Google+ page, which has now been listed by http://onlinephdprogram.org as one of their “99 Google Plus Pages every PhD Candidate should follow.” Thanks for following everyone!
Today Mike Dorrington officially became a PhD candidate as he passed his comprehensive exam with distinction. He wrote a very interesting proposal on developing new technologies to measure serotype replacement of non-vaccine strains of Streptococcus pneumoniae in the developping world, which stemmed from his interest in global health. Well done Mike!
The winning team!
Well it was an impressive show even for our over achieving lab! Bowdish lab undergraduates (Netusha Thevaranjan, Dessi Loukov, James Han), graduate students (Kyle Novakowski, Mike Dorrington, Fan Fei), post-docs (Dr. Chris Verschoor) and associates (Fiona Whelan, Dr. Jennifer Stearns, Michelle Pinto) all got selected to present posters at the IIDR trainee day. James Han won the IIDR Award of Excellence for best poster by an undergraduate and Dr. Jennifer Stearns brought home the award for best poster by a post-doc. Avee Naidoo was selected to give a talk only 6 weeks into her graduate degree and Dr. Chris Verschoor won the Gulliver award ($1000!) for the best oral presentation by a post-doc. What a great day!
For a complete album of photos, click here.
Avee Naidoo gives her first talk on her project – 6 weeks into grad school!
Dessi Loukov presents her poster and gets lots of compliments on her story.
Dr. Chris Verschoor wins the Gulliver award for best presentation by a PDF.
Dr. Jennifer Stearns and James Han win IIDR awards of excellence for their poster presentations.
Dawn was deeply touched by her team’s nomination for the President’s Award in Graduate Supervision. This was a touching tribute to her abilities as a supervisor. Although she didn’t win the award, she won the support of the people who matter most – the Bowdish lab team.
The Bowdish lab team attends the President’s Award for Graduate Supervision Ceremony. Dawn was thrilled to be nominated for the award by her team.
Bowdish lab associate member (technically she’s supervised by Dr. Mike Surette but we think of her as one of our own), Julie Kaiser, successfully defended her MSc thesis “Host responses to the Strepotococcus Milleri Group”. To see a photo of Julie in her post exam bliss/haze click here. Julie is moving on to a PhD at UWO in Dr. Dave Heinrichs lab. We’re sending Dave on of our best & brightest – we expect a thank you card any day now.
The lab of Dr. Dawn Bowdish at the McMaster University Immunology Research Centre (MIRC) has recently begun collaboration with the Vancouver-based pharmaceutical company Qu Biologics on preclinical studies investigating the role of macrophage dysfunction in chronic inflammation.
Qu Biologics has developed Site Specific Immunomodulators (SSIs), which aim to “reboot” the body’s innate immune system in targeted organs or tissues to reverse chronic inflammation.
“Macrophages are important cells of the innate immune system. There is growing evidence that macrophage dysfunction underlies many important common chronic diseases, including cancer and autoimmune disease,” said Dr. Hal Gunn, CEO of Qu Biologics. “This collaboration will be invaluable to assist in our understanding of the benefits of SSI therapy on macrophage function as it relates to chronic inflammation and immune dysfunction.” Dr. Gunn added.
The studies will test whether a lung-specific SSI therapy can restore normal lung and bone marrow-derived macrophage function using a variety of in vivo and in vitro assays.
Dr. Bowdish adds “This is an ambitious and exciting project that takes a fundamentally different approach to tackling the problem of chronic inflammation, which has been very resistant to therapeutic intervention. My team is thrilled to be working together on a problem that affects the lives of so many Canadians.” This work capitalizes on the resources and immunology expertise of the McMaster Immunology Research Centre and Dr. Bowdish’s research interests in how inflammation impairs macrophage function.
About Qu Biologics
Qu Biologics develops Site Specific Immunomodulators (SSI), a novel class of immunotherapies that aim to reboot the body’s immune system. SSIs are designed to stimulate an immune response in targeted organs or tissues to potentially reverse the chronic inflammation underlying many conditions including cancer and autoimmune disease. The company recently launched a Phase 1/2 clinical trial to research SSI therapy for the treatment of Crohn’s disease.
Backed by a prestigious group of scientific advisors and board members, Qu Biologics is led by a management team that includes co-founder and CEO Dr. Hal Gunn, a physician and expert on the body’s immune response to chronic disease; and Chief Medical Officer Dr. Simon Sutcliffe, former CEO of the BC Cancer Agency and a distinguished clinician, scientist and leader in cancer control in Canada and internationally. For more information, visit www.qubiologics.com and www.qucrohnstrial.com.
For more details and to see the original press release here:
Keith Lee, who will be attending the University of Toronto for medical school starting August 2013 has received a very prestigious CIHR MSc graduate award. He has chosen to decline to pursue his medical studies and potentially re-apply as an MD/PhD student next year. Congratulations Keith!