Spring/Summer Edition 2016

IIDR Trainee Newsletter

This quarterly newsletter is published for the students and postdoctoral fellows of the Michael G. DeGroote Institute for Infectious Disease Research (IIDR). If you have a story idea, or would like to contribute to the next edition, please contact Joel Tiller at tillej1@mcmaster.ca.

Editor: Bushra Ilyas

Contributors: Bushra Ilyas, Ryan Buensuceso, Sara Kilmury

A comprehensive list of what’s happening across the IIDR and its affiliated institutes

Upcoming events

Welcome to the spring/summer edition of the IIDR Trainee Newsletter! Written for trainees, by trainees, each edition includes news and feature stories that are relevant to us all.

This edition’s main feature tells the story of an undergraduate trainee whose achievements embody the drive and spirit of success that are central to the IIDR. Read about Yung Lee, one of this year’s winners of the Wilson Leadership Scholarship Award, and the great work he is doing in the Kaushic Lab.

This edition also includes an in-depth profile on the the Comprehensive Antibiotic Resistance Database (CARD), a one-of-a-kind bioinformatics platform developed by Drs. McArthur and Wright. Learn about the unique capabilities of CARD, and how you can use the database to bolster your research capabilities.

And if you find yourself in need of a worthwhile distraction, we have put together a short list of science-based podcasts worth checking out.

Rounding out this edition is a great article that highlights the pitfalls of celebrity science, reminding us all to be wary of letting the snazzy headlines dictate our understanding of the true science underlying them.

Finally, for the latest on what’s happening in and around the IIDR, check out our page dedicated to upcoming events.

Enjoy,

Comprehensive Antibiotic Resistance Database (CARD)

Research profile

In this issue

Don’t believe everything that you hear

Feature

Four science podcasts worth listening to

Recommendations

Trainee profile: Yung Lee

Follow the IIDR

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Bushra Ilyas, PhD Candidate

Spring/Summer Edition IIDR Trainee Newsletter

and Puja Bagri

Feature

In the arms race against antibiotic-resistant superbugs, many would argue that bacteria has the upper hand.

What is clear is our need for new tools of war to continue our collective fight, and the Comprehensive Antibiotic Resistance Database (CARD) promises to be a very powerful one. CARD has the potential to supercharge our current efforts to tackle antibiotic resistance for years to come.

CARD is a collaborative project with the goal of assembling all the known antibiotic resistance genes in a central, searchable, annotated database. Spearheaded by Drs. Andrew McArthur and Gerry Wright, the database collects known resistance gene sequences in a searchable format, organized by the Antibiotic Resistance Ontology.

CARD runs on a symbiosis with researchers at the bench and

in clinics. On the clinical front, sequencing of antibiotic resistance bugs identifies novel genes that contribute to resistance, providing CARD curators with a steady stream of new information to include in the database. Moreover, CARD provides tools to simplify the work of clinicians and researchers.

In an era where sequencing is more often the first step to defining antibiotic treatment options during clinical care, CARD allows for rapid identification of resistance determinants in a genome using the Resistance Gene Identifier.

Additionally, the Antibiotic Resistance Ontology associates the genetic information of resistance genes with extra information, including the class of resistance and other genes or drugs they are linked to, making genes, antibiotics and pathways easily searchable. This makes CARD not only a great tool to search unknown genes

in your favorite bug for resistance determinants, but also to identify classes of resistance and how they are related to each other.

In addition to content curation, which is the backbone of the McArthur Lab, trainees are involved in improving the type of data we can access, as well as the functionality of CARD. For example, the Resistance Gene Identifier uses gene homology or SNP analysis to identify resistance genes in a genome of interest.

However, these parameters alone do not cover all the types of mutations that can contribute to resistance. The lab is now focused on developing a framework to encompass the other mechanisms of resistance seen in the literature, such that CARD can incorporate these into the analysis.

Other projects include improving resistance gene identification in metagenomic data, surveillance and transmission of resistance genes, and building better tools to determine the prevalence of certain resistance determinants in the environment.

The strength of CARD is its constant updates and improvements. The team pushes out new updates monthly, and is always accessible if you have a specific research question but aren’t sure how to use CARD to answer it.

For more information on CARD, please direct your questions to Dr. McArthur, and be sure to join the CARD Mailing List for notifications on updates and improvements.

The Comprehensive Antibiotic Resistance Database (CARD)By Bushra Ilyas

Research profile:

Spring/Summer Edition IIDR Trainee Newsletter 1

Spring/Summer Edition IIDR Trainee Newsletter 2

Imagine this scenario: you’re having a conversation with a friend or colleague about an interesting, albeit questionable, health “fact” they heard on the radio the other day. You’re intrigued, but also a little skeptical – as a scientist, naturally, you want to investigate this claim further.

As trainees of the Michael G. DeGroote Institute for Infectious Disease Research (IIDR), we are fortunate that we can turn to sources like Pubmed or Google Scholar to assist us with either validating or contradicting seemingly suspicious claims.

Unfortunately, the general public lacks sufficient access to these tools. And while I think it’s exciting to see science receive the attention it deserves from mainstream media outlets, and even Hollywood A-listers, I worry that those without access to peer-reviewed sources will get caught up in sensationalized reporting and/or groundless opinions.

Celebrity opinion-shapers like Jenny McCarthy, Jim Carrey and Dr. Oz are in a unique position to have both a platform to express their opinions and a very large audience to share them with. For example, The View, on which Jenny McCarthy was a host, garners an average of 2.7 million viewers per episode. Many of these viewers rely on the show and its hosts for current news and general tips on healthy living.

However, to have such a prominent anti-vaccination advocate like Jenny McCarthy as a host inadvertently lent credibility to her views. Celebrities are just as entitled to their own views and opinions as anyone else, but a distinction should be made in the public eye between their opinion on a topic, such as vaccination, and trying to pass that opinion off as fact.

Perhaps even more dangerous in this regard is Dr. Oz. As a former licensed medical doctor with almost 2 million viewers tuning in to his show daily, Dr. Oz appears to be a credible source for health information, and many of his viewers see him as such. He is a medical doctor after all. However, a show such as his relies heavily on sponsorship and advertisement dollars to stay afloat, and it comes as no surprise that rather than dispensing sound medical advice, Dr. Oz spends most of the show telling viewers about the latest magic pill that will cure all that ails you. With these plugs, the one thing that consistently seems to be missing is any credible source or reference for the treatment in question, often because there isn’t one. Many supplements and “natural” remedies are not regulated by any governing bodies. At best, they may have no effect whatsoever, but this isn’t always the case. What viewers deserve to know is that they are receiving advice from someone whose medical opinions can be auctioned off to the highest bidder.

On the flip sideOf course, it’s not all doom and gloom. This is not to say that fame and science can’t go hand in hand. Within the last few years, we have seen the rise of the “scientist celebrity.” Bill Nye the Science Guy and Neil deGrasse Tyson have become almost household names, taking often complex scientific concepts and making them not only accessible, but also engaging to the general public. Bill Nye, in particular, has become a powerful advocate for climate change awareness and action. Likewise, Commander Chris Hadfield, a Canadian astronaut who through his use of social media while aboard the International Space Station – and through an awesome David Bowie cover – captured the attention of people worldwide and reignited an interest and fascination in science and space travel.

In short, mainstream media can be a positive source for scientific information – if you know where and how to look for it. It’s easy to get distracted by those who speak the loudest, but fame doesn’t necessarily equal credibility, and thus it’s important to be critical of the information we take in, regardless of how high the speaker’s soapbox is.

Don’t believe everything that you hearAs Sara Kilmury points out, it’s important to remain critical of the information we take in.

Four science podcasts worth listening to

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By Ryan Buensuceso

Consistently ranked high on the iTunes Science and

Medicine podcast list, Radiolab is a show about

curiosity.

Hosts Jad Abumrad and Robert Krulwich often blur the lines between science, philosophy and the human

experience, earning Radiolab the reputation

as one of the best science podcasts available to

download.

Suggested listening: Staph Retreat

Part of the NPR family of podcasts, Invisibilia deals with the invisible things

that influence our lives on a daily basis.

Co-hosted by Lulu Miller, Hanna Rosin and Alix Spiegel, Invisibilia “interweaves narrative

storytelling with scientific research that will

ultimately make you see your own life differently.”

Suggested listening: Fearless

Originally part of the Australian Broadcasting Corporation, Science Vs is making a move to the

Gimlet Media podcasting network.

Science journalist Wendy Zukerman breaks down

the latest fad framing itself as scientific fact.

Suggested listening: Science

Radiolab Sickboy

Sickboy is a Canadian-based, round table podcast

hosted by three friends - Jeremie, Brian and Taylor

- who are determined to help others see the

positive in living with an illness or disease

Humor, the hosts have discovered, is the best way to break down the stigma

associated with illness and disease.

Suggested listening: Cystic Fibrosis

Invisibilia Science Vs

Podcasts have become an incredibly popular form of mainstream entertainment, especially those that fall within the realms of science, technology and health and well-being. But with so many great podcasts to choose from, where’s a good place to start? Here’s a list of four popular podcasts listed under the iTunes Science and Medicine category.

Trainee profile: Yung Lee By Puja Bagri

When looking at IIDR trainee Yung Lee’s curriculum vitae, it’s hard to believe he has only just completed his second year in the Bachelor of Health Sciences program at McMaster University.

His seemingly endless list of accomplishments and experiences are impressive.

From working in research labs, to acting as a photojournalist for the McMaster-run newspaper The Silhouette, and actively participating in numerous student groups, all while maintaining a nearly perfect GPA, there is little that Lee does not dabble in.

“I strive to do my best in everything I do. These are the things that make me truly happy and that is why I work hard and efficiently,” Lee says, when asked how he manages to juggle so many things at once.

While curiously exploring various interests and hobbies, it was his experience as an undergraduate research assistant in the lab of Dr. Warren Foster that led Lee to realize how much he enjoyed conductingresearch. He credits Dr. Foster as one of the primary

reasons why he decided to pursue basic sciences research. “He made me feel like a scientist, and his encouragement gave me the confidence to do research,” Lee explains. It was through Dr. Foster’s guidance and recommendation that Lee met his current supervisor, Dr. Charu Kaushic. In the Kaushic Lab, Lee is working on developing a novel air-liquid interface culture to study the effects of female sex hormones on its susceptibility to herpes simplex virus-2 (HSV-2). His work has garnered positive

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I strive to do my best in everything I do. These are the

things that make me truly happy and that is why I work

hard and efficiently

Yung Lee

feedback; in fact, he was recently awarded the Best Overall Poster Presentation at the 29th Annual Ontario Biology Day, as well as the 2016 IIDR Summer Student Fellowship and the BHSc Program Summer Research Scholarship.

This past spring, Lee was also named a recipient of the newly founded Wilson Leadership Scholar Award, one of the highest valued undergraduate scholarships in Canada. The Wilson Scholar program “recognizes Canada’s promising undergraduate students, cultivating their untapped potential and preparing them to serve as the nation’s next generation of leaders.”

The award, which was presented to three McMaster students entering their last two years of undergraduate studies, includes $50,000 to cover educational expenses, along with admission to a leadership development program. When asked about the process involved in winning this prestigious award, Lee revealed that he was quite surprised by the outcome: “It was a vigorous process. I’ve never had the opportunity to reflect and learn so much about myself. Everyone involved throughout the multiple stages was kind and encouraging. I never thought I would be fortunate enough to win such an amazing scholarship award.”

When showered with compliments from his peers, Lee’s modesty tends to influence his trademark response: a simple smile followed by a quiet ‘Thank you’. His humble persona is a result of the different obstacles he has overcome to get to where he is today. His biggest challenge was having to start a new life in a new country less than eight years ago, when Lee and his family immigrated to Canada from South Korea. His parents made the difficult decision to relocate with hopes that Canada would provide Lee

and his sister with greater opportunities. With little experience with the English language, Lee regards this as the most challenging time of his life. It was a hurdle which pushed him to work harder than he ever had before. With support from his teachers and family members, Lee was able to adapt and become fluent in English. And his hardworking nature and determination enabled him to land a spot in the prestigious Health Sciences program at McMaster.

“This program was always my first choice, in terms of university undergraduate programs. I love the program, especially how everyone is tight knit. I am constantly inspired by the people I have met in this program, because everyone has something valuable to offer,” Lee explains when asked about his undergraduate experience so far.

Lee’s current plan is to pursue a career in medicine, and he hopes to incorporate clinical research in his future plans. He is gaining valuable experience within the field, as he is involved in clinical infectious disease research under the supervision of Drs. Gordon Guyatt and Reed Siemieniuk. Lee wants to help individuals on a larger scale, which he believes is “possible by not only practicing medicine, but also conducting clinical research.”

He adds: “I’m really grateful that I am here right now. Meeting new people, sharing my ideas and talents, learning different things inside and outside of the classroom makes me believe that every day is a precious learning opportunity. I’m looking forward to all the things that lie ahead and continuing this exciting journey of lifelong learning.”

There is no doubt that wherever Lee’s future takes him, he will continue to strive for excellence and work hard to chase his dreams.

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I’ve never had the opportunity to reflect and learn so much

about myself. Everyone involved throughout the

multiple stages were kind and encouraging...

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I’m looking forward to all the things that lie ahead and continuing this exciting

journey of lifelong learning

Various institutes and facilities across campus offer academic-, social- and career-oriented events throughout the year. Keep an eye on this section for a list of all upcoming events.

Upcoming events

Bedside-to-Bench Seminar Series

2016 marked the return of the IIDR Bedside-to-Bench Seminar Series, which brings together clinicians and scientists on the clinical aspects of infectious diseases and related scientific research.

Keep an eye out for emails from Joel Tiller, or check the Events section of the IIDR’s website.

Public Lecture Seminar Series

Hosted by the IIDR, this popular seminar series features invited speakers from universities from around the world. Each lecture is roughly an hour long and is open to the public.

Keep an eye out for emails from Joel Tiller, or check the Events section of the IIDR’s website.

Demystifying Medicine Series

Hosted by the Department of Pathology and Molecular Medicine, this seminar series brings together clinical diagnostic and patient cases with pathology and therapy to increase understanding of how basic biology research is used to understand human disease.

Keep an eye out for emails from Joel Tiller, or check the Demystifying Medicine website.

6th annual Trainee Day

Hosted by the IIDR, Trainee Day is the ideal forum to recognize and celebrate the innovative work being done by our students and postdoctoral fellows.

This year’s event will take place on Wednesday, October 26, and will feature Dr. Arturo Casadevall as the keynote speaker.

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