CMMT Newsletter March 2021

The Man Behind IT

Jonathan Chang is the CMMT’s Information Technology (IT) specialist. In fact, he’s the only IT person at the CMMT, a one-man shop for all things IT, and he loves it. But becoming an IT specialist was not the path he expected to take.

A self-confessed computer geek, Jonathan began tinkering with his grandfather’s Apple II computer when he was just a child. “I played with it when I first moved from Taiwan to Canada at the age of six,” he said. “Eventually, I destroyed my family’s first computer by disassembling it and putting one part in backwards. I still have that Apple II somewhere in storage.”

So, it seemed only natural that Jonathan would enroll at UBC to study cognitive systems, a computer science degree concentrating in artificial intelligence and computation. “Throughout university I made money by fixing computers for people,” Jonathan said. He also did a co-op work term at the UBC Computer Science IT department, handling their front-line help desk. “The IT help desk was a wild experience. I would often get requests to refill the vending machine, help on computer science homework, or unclog a toilet,” he said. “While it sounds ridiculous, I think this experience made me realize how many times during the day people just need help, whether or not it’s IT.”

After completing his undergraduate degree Jonathan was taken under the wing of one of his professors to pursue his Masters degree. “Due to the fallout of the 2008-2009 recession I declined the offer and instead began looking for a job,” he said.

Eventually, that led Jonathan to the CMMT. “I think that I was very lucky to find a place that fits my skills, interests and training so well. Almost every aspect of my life or academic experience had some relevance at CMMT,” he said.

Jonathan has been an IT specialist at the CMMT for 10 years. “Every day feels like a new learning day,” he said. “The CMMT provides a rare working environment for me because I feel like a participant in many of the daily workflows that happen on site.”

One of the things he likes most about working in IT is the opportunity for creative problem solving. “I can see the impact of my resourcefulness” he said. “There is a satisfaction that comes from making a direct impact to alleviate someone’s work struggle or to make their day better. I missed that when I transitioned from my freelance days of fixing computers for people to the more structured environments of my programming and other industry experiences.”

As for hobbies? Unsurprisingly, they lie with all things tech, gadgets, building computers, the latest trends. “It’s this interest that helps me stay up to date with the numerous and rapid advances being made in computer sciences.” And this translates directly to his work. “At CMMT, we are always trying to perfect our balance of industry trends with providing effective support for research groups,” he said. “I also enjoy playing badminton, though it’s hard to play these days because of COVID,” he said. “And I have started to try my hand at home improvement.”

A Process of Elimination

Phillip Richmond’s journey prior to arriving at BC Children’s Hospital (BCCH) has been an informative and interesting one. Currently a staff scientist in the newly formed Precision Health Initiative at the BC Children’s Hospital Research Institute (BCCHRI), he had originally wanted to pursue family practice alongside anaesthesiology, as his grandfather had done.

However, while doing his undergraduate degree in molecular biology in the United States, he discovered that family medicine wasn’t for him. “I learned about the reality of medicine in the US, seven minutes of patient time to 14 minutes of insurance paperwork,” he said.

While exploring his options, a friend suggested that Phillip look into the research field. This led him to find a position as an undergrad research technician working on mouse models in prenatal alcohol syndrome. Once again, however, he quickly discovered that this was not for him. Shortly thereafter, he transitioned into the lab of Dr. Robin Dowell, and his future in medicine started to take shape. He joined Dr. Dowell’s bioinformatics laboratory in 2010 as a molecular, cellular, developmental biology undergraduate student at the University of Colorado, Boulder.

“Initially hired to wash dishes, pour plates, and e-file a cabinet of papers…1235 papers to be exact, I must have proved I was serious about research,” Phillip said. Dr. Dowell began to teach him genomics and programming. “Robin taught me how to think critically about research problems, and helped spark a scientific curiosity in me,” he said.

Phillip completed his undergraduate thesis in Dr. Dowell’s laboratory, which focused on the genotypic effects of directed evolution in polyploid yeast. After graduating he continued working with her as a professional research assistant. “It was working in Dr. Dowell’s lab and seeing the impact of research on the understanding of fundamental molecular mechanisms in biology, that led me to consider graduate school,” Phillip said. “I was primarily working on projects involving basic science, and not seeing the direct impact of genomics on improving people’s lives. I wanted to pursue a PhD, and further explore how my skills in bioinformatics may translate into current medicine.”

Enter Vancouver, where Phillip’s mother’s side of the family lives. “I spent many summers visiting Vancouver growing up, and I fell in love with the beauty of the Pacific Northwest” Phillip said, explaining why he considered the University of British Columbia as an option for his doctorate. His ideal project would involve medicine or healthcare plus genomics. “That search led me to Dr. Wyeth Wasserman’s lab at the CMMT,” Phillip said. That was 2015. He began his PhD in bioinformatics, focusing on ways to expand the utility of whole genome sequencing in the diagnosis of rare genetic disorders.

“I have a special interest in improving and benchmarking methods for variant detection and interpretation, with an emphasis on short tandem repeat expansions,” Phillip said. The interest in short tandem repeats emerged from the discovery of a novel short tandem repeat disorder in the 5’UTR of glutaminase, which he and the TIDE team (specifically Dr. Britt Drögemöller) detected from whole genome sequencing data in an international study led by Dr. Clara van Karnebeek. This discovery led to the development of a novel short tandem repeat software package called ExpansionHunter Denovo.

“I have also explored the rare disease modifier space in an international collaboration which focused on finding prognostic markers of cerebral demyelination in X-linked Adrenoleukodystrophy,” he said. “The multi-omic space is the future of rare disease diagnosis, and I was lucky enough to collaborate with Emma Graham and Dr. Sara Mostafavi on a tool which leverages genomic and metabolomic data called metPropagate. I was also able to participate curation of the JASPAR Transcription Factor database, a staple of the Wasserman lab and a useful tool for understanding gene regulation at the sequence level.”

In his new role with the BCCHR Precision Health Initiative, Phillip will be exploring the use of multi-omic technology in the diagnosis of complex and challenging cases emerging from the clinical domain that lack diagnosis. Additionally, he will be supporting education and training around genomics and multi-omics for both research and clinical audiences.

Beyond his research and teaching Phillip has co-founded and co-chaired the BCCHR Trainee Omics Group, an initiative which focuses on training programming and analysis methods for “omics” data. As he has a passion for building community and improving trainee experiences at BCCHR, he has also served as the BCCHR Trainee Council chair since 2017. “In my free time I’m mostly walking and hiking with my dog Sherlock, going on Vancouver foodie adventures with my girlfriend, or watching sports. I look forward to traveling again when the pandemic ends,” he said.

Splitting the Difference

Lured by the mountains, the skiing and most importantly, the science program at UBC, Austin Taylor, a PhD candidate in Dr. Bruce Verchere’s laboratory, decided to head west and pursue a career in biochemistry.

Originally from Brockville, a small town an hour out of Ottawa, in Ontario, Austin left behind a possible career in ski racing. He began skiing shortly after he learned to walk – at one and a half years old. He was ski racing while in school. “I only went to school a couple of days a week,” he said. His parents ensured that as long as he kept an A average, he could keep skiing. This worked, until it was time for university and he had to decide what he wanted to do next. “I looked at chemical engineering, music, and biology and split the difference – and it was biochemistry,” he said.

Austin credits one of his professors at UBC for helping him connect with the CMMT. “Luckily, I had some great advice from Dr. Scott Covey as I was finishing up a biochemistry undergraduate degree, and he pointed me in Dr. Verchere’s direction.”

Interested in diabetes, metabolism, aggregating proteins, and protein processing, Austin found someone studying all of these areas in Dr. Verchere’s lab. “Along with a group of kind, outgoing and fun scientists,” he said.

Upon joining the Verchere lab, Austin began looking at the intersection of diabetes and pancreatic cancer. “In diabetes, there is altered biosynthesis and secretion of peptides in the islet, including the well known hormone insulin,” he said. “We looked at how loss of one of these peptide hormones islet amyloid polypeptide might be influencing pancreatic cancer development and progression.” This led to further work on the biosynthesis of these peptide hormones. “Most of my work for the last few years has been focused within the insulin-producing beta cells, and how the altered processing of peptides, after they are initially made, impacts these cells and the body as a whole,” he said.

Now, six years on, Austin is at the end of this particular journey. “It’s time to finish,” he said. “I’ve enjoyed my time here and getting to know people,”

Possible new frontiers could include Europe. “There’s some good research centres in Switzerland that seem very attractive. My partner’s doing her PhD in political science so being close to the United Nations in Geneva would be helpful for her as well. And it would be nice to do some travelling before signing up to work,” he said.

While the Covid 19 pandemic is slowing travel plans, Austin admits Vancouver is good place to be right now. “Outside of the lab I keep myself busy with a few too many hobbies,” he said. “I’m an avid backcountry skier, skiing plays a big part in my life. In the summer months I stay busy and active with mountain biking, rock climbing, and hiking. When I need a bit more relaxed time off I enjoy brewing beer, or enjoying a homebrew and some homemade pizza.”

Awards

Drs. Blair Leavitt & Sylvia Stockler, BCCHRI Brain, Behaviour & Development Theme Catalyst Grant Award, “Preclinical testing of a novel therapy for pyridoxine-dependent epilepsy due to ALDH7A1 deficiency: L-ornithine supplementation as an alternative to lysine-restricted diet“.

Drs. Dan Goldowitz & Michael Kobor, BCCHRI Brain, Behaviour & Development Theme Catalyst Grant Award in support of a Fetal Alcohol Spectrum Disorder (FASD) project.

Amirah Aly (Hayden Lab), BCCHRI Brain, Behaviour & Development Trainee Boost Award 2021

Bethany Adair (Simpson Lab), BCCHRI Brain, Behaviour & Development Trainee Boost Award 2021

Joanna Yeung (Goldowitz Lab), BCCHRI Brain, Behaviour & Development Trainee Boost Award 2021

Publications

Galvan, A., Petkau, T.L., Hill, A.M., Korecki, A.J., Lu, G., Choi, D., Rahman, K., Simpson, E.M., Leavitt, B.R., and Smith, Y. (Accepted). Intracerebroventricular Administration of AAV9-PHP.B SYN1-EmGFP Induces Widespread Transgene Expression in the Mouse and Monkey CNS. Human Gene Therapy, PMID. TBD.

Korecki, A.J., Cueva-Vargas, J.L., Fornes, O., Agostinone, J., Farkas, R.A., Hickmott, J.W., Lam, S.L., Mathelier, A., Zhou, M., Wasserman, W.W., Polo, A.D., and Simpson, E.M. (2021). Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells. Gene Therapy. PMID 33531684

Petkau TL, Life B, Lu G, Yang J, Fornes O, Wasserman W, Simpson EM, Leavitt B. Human progranulin-expressing mice as a novel tool for the development of progranulin-odulating therapeutics. Neurobiol Dis. 2021 Feb 23;105314. doi: 10.1016/j.nbd.2021.105314. Online ahead of print. PMID: 33636385

Ravalia AS, Lau J, Barron J, Purchase S, Southwell AL, Hayden MR, Nafar F, Parsons MP. Super-resolution imaging reveals extrastriatal synaptic dysfunction in presymptomatic Huntington disease mice. Neurobiol Dis. 2021 Feb 5:105293. doi: 10.1016/j.nbd.2021.105293. Online ahead of print. PMID: 33556538

Naia L, Ly P, Mota S, Lopes C, Maranga C, Gershoni-Emek N, Geva M, Hayden MR, Rego AC. The Sigma-1 receptor mediates pridopidine rescue of mitochondrial function in Huntington disease models. Neurotherapeutics.

Did You Know?

April 22 is Earth Day.
George Washington was inaugurated as the First President of the United States on April 30, 1789.
John Macdonald was commissioned on 24 May 1867 to form the first government of the Canadian Confederation.
May 24 is Victoria Day in Canada. This holiday celebrates the birthday of Queen Victoria, who was born on May 24, 1819.

Our next newsletter will be published in late June 2021.
Submit storyline suggestions to media@cmmt.ubc.ca by May 31, 2021.
Submit awards, events, publications, kudos, etc. to media@cmmt.ubc.ca up to until June 15, 2021.