David Bates Award: Holding the Torch for Air Quality in British Columbia

Insidious adversaries

Prior to starting graduate studies, most of my academic career was focused on curbing salient health challenges that I grew up around. Because of their conspicuous manifestations, infectious diseases naturally flew onto my radar and kindled a personal propensity for medicine and research. They were relatively preventable (although not in the most affected communities in Africa), and are characterized by an identifiable causative infectious agent. At the time, endeavors like developing specific targets for conserved regions of HIV coat proteins were not only appealing, but also specific enough for me. However, considering that strides in HIV (and other infectious diseases’) treatment have been able to assure an almost normal life course for affected populations, my attention was diverted to auxiliary risk factors like antimicrobial resistance and comorbidities. This journey towards more inconspicuous yet crucial health concerns is what eventually drew my attention towards non-communicable diseases like chronic obstructive pulmonary disease (COPD) and cardiovascular diseases which are becoming increasingly responsible for worldwide mortality. Behind the increasing salience of these “insidious adversaries” are gradual changes in technology and consumption behaviours which have driven risk factors like air pollution.   

Currently, air pollution is implicated in more than 9 million death worldwide. Although natural drivers of air pollution like volcanic activity and forest fires have a role in propagating pollution, anthropogenic sources of air pollutants like transportation, manufacturing and electricity generation have been cited as significant contributors. Particulate matter (PM), which is an active component of most air pollution has been especially implicated. Because diesel exhaust is a primary contributor to traffic-related ultrafine particulate matter, I sought to learn more about its health effects as the focus of my graduate studies. 

Towards provincial recognition.

Delivering the award recipient speech at the B.C Air Quality workshop 2019

The David Bates Award is given annually in recognition of outstanding students in British Columbia who are dedicated to tackling challenges of air quality. My research thesis project that aims to understand how the human body responds to different concentrations of diesel exhaust was perfectly aligned to the objectives of this award. This research has the potential to improve public and occupational health safety guidelines around diesel exhaust exposures, as well as provide mechanistic understanding of the health effects of this prominent pollutant. The award was presented by Elisabeth Caton during the BC lung workshop at the Pinnacle Hotel Harbourfront on February 6th. It was an honor to receive this recognition for my dedication to elucidating interventions against the health effects of air pollution; it went a long way in urging me on as my first award on this exciting journey of research and discovery. Importantly, I get to be featured as one in a long line of esteemed recipients of this award.

David Bates Award bio:
Link: David Bates Award feature – 2019

“Juma is a graduate student in the Experimental Medicine program at the University of British Columbia (UBC). Having grown up in Uganda, he was fortunate to receive the MasterCard Foundation scholarship which enabled him to pursue and complete a BSc. in Microbiology and Immunology at UBC. His broad research interests included the effects of pollutants on gut bacteria, as well as infectious diseases like Kaposi’s Sarcoma and HIV/AIDS in sub-Saharan Africa. During this time, he developed a keen interest in the extensive contribution of pollution towards the instigation and exacerbation of human diseases. Under the supervision of Dr. Chris Carlsten at the Chan Yeung Center for Occupational and Environmental Respiratory Disease (COERD), Juma investigates the dose-response as a result of controlled human exposure to diesel exhaust. Specifically, he aims to identify a protein signature in the blood, urine and/or nasal lavage that can be validated as a robust biosignature. Additionally, he studies lung function and inflammation, as well as polycyclic aromatic hydrocarbon metabolites in urine which could elucidate the observed protein response. Identification of a biosignature could provide mechanistic insight into the health effects of diesel exhaust, provide therapeutic targets, and facilitate development of reliable health monitoring tools that can be used to prevent and treat lung diseases caused by diesel exhaust. Juma also has a keen interest in neurogenic inflammation, which he studies as a potential mechanism for the symptoms and effects resulting from diesel exhaust exposure. Collectively, his work is one crucial step towards protecting the health of Canadians, and other populations affected by diesel exhaust exposure.”


People of UBC

This December, I had the opportunity to be featured for “People of UBC”. This is a UBC page that selects a group of people to highlight the vibrant community at the University.  Perhaps the greatest part of this was being able to share my passion for tea, TV and represent the research community which has become my home during graduate school.  Link: https://www.ubc.ca/about/people.html?juma-orach&fbclid=IwAR2NbC9nCmoxYyN_9tDYSOYgsiUJz8hD9wtGQfg8OdFqM2WTBJ26137On28

Seattle times

February 2018: “In Vancouver, discover University of British Columbia’s delightful attractions”

The Ridington room.  (Paul Joseph – UBC Communications & Marketing)

I was involved in a photograph featured in a news article by the Seattle times focusing on travel attractions at the University of British Columbia. Particularly, I was featured in a description on the Ridington Reading Room, popularly known as “the Harry Potter room” because of its distinctive iconic design. This photograph was taken to contribute to the pool of photographs available to Universités Canada to represent remarkable institutions of higher learning in Canada.

Effects of phthalates on gut bacteria

Phthalates are organic chemicals used as plasticizers in a wide range of food packaging, containers, and other household plastic objects. Because some phthalates elicit toxicity and yet are often ingested by human beings, I was interested in how phthalates might affect human health by changing the composition of our microbiome in a dose-dependent manner. This would provide insight on how plastic pollution affects human health, and guide efforts to regulate the use of phthalates in plastics. Working as a team of three students in the experimental microbiology course (MICB 421) at UBC, we exposed E. coli BL21 (a representative of common gut bacteria) to varying doses of DEHP (a common phthalate in Canada). DEHP had no clear effect on the growth of E. coli BL21 because DEHP was insoluble in growth media, and solvents used confounded the growth data. Nevertheless, this provided insight into the challenges of using phthalates in bacterial growth assays, and leaves important future directions for applying bacterial growth assays to study plastic pollution. Our findings were published in the Journal of Experimental Microbiology.


Investigating the Effects of Bis (2-Ethylhexyl Phthalate (DEHP) on the Growth of Escherichia coli Strain BL21

SUMMARY Phthalates (also known as phthalate esters) are organic chemicals used as plasticizers in a wide range of food packaging, containers, and other household plastic objects. Humans are exposed to phthalates through the air and by ingestion. Phthalate exposure has been shown to induce changes to the microbiome, causing shifts in the resident microbiota in a dose-dependent manner. One phthalate in particular, Bis 2-ethylhexyl) phthalate (DEHP), is known to be present at high concentrations in Canadian food packaging. Previous research has found that DEHP has biphasic effects on the growth of Escherichia coli. To further investigate the effect DEHP may have on the growth of E. coli relevant to the human gut, our research set out to determine the effects of dose-dependent exposure on E. coli BL21. To do this, minimum inhibitory concentration (MIC) and growth curve assays were conducted. In the MIC assay, growth was observed at all concentrations, with a limited inhibitory effect on E. coli growth. However, phase separation between the DEHP solution and E. coli culture media made it difficult to determine whether growth inhibition was due to the DEHP or to inadequate aeration of the growing culture. The addition of ethanol reduced the phase separation between DEHP and E. coli culture media. However, subsequent growth curves showed conflicting results suggesting that the addition of ethanol may be the reason for reduced growth rate.

Citation: Brundrett, J., Orach, J., Sonderegger, L. & Yan, T. Investigating the Effects of Bis (2-ethylhexyl) Phthalate (DEHP) on the Growth of Escherichia coli strain BL21. Journal of Experimental Microbiology and Immunology (JEMI) 22, (2018).

Link to article

Humans of Vancouver (UBC)

I had the honor of sharing a piece of my story through the Humans of Vancouver (previously known as Humans of UBC) Facebook page in January 2017. This was a wonderful opportunity for me to contribute to the diverse experiences that constitute the UBC community. This public story is quoted here:

Photo: Humans of Vancouver

“I came here from Uganda, a country in East Africa from a middle income family. My mother is a nurse, and so I essentially grew up along her hospital. Growing up with a mother working in the health care system, I began to see the challenges the hospitals face each day. People didn’t have very good access to health care, civil services had issues, and people were overall not getting the care they needed. In a 3rd world country, often there was a lack of doctors and so nurses are often consulted for medical advice. I saw how hard my mother worked, and the change she was able to make in the community. I thought, if a nurse can do that much good in the world, a doctor would be able to help people so much more. I wanted to help people and make a positive change in my community, so I decided to leave home and go abroad to study medicine. Even though the road ahead may be tough, I’m holding on to my roots and my inspiration to make a positive contribution in the world.” 

Visit this story here.

Warrior in the white coat

Back in the battle against infectious disease..

2017 summer found me back in Uganda, and back at the Infectious Disease Institute – Makerere University. This being my second internship at this organization, I had a warm welcome from very familiar faces in a familiar space. But for a single staff change or two, nothing about the laboratory had changed. This time, knowing more about the lab gave me more precision in choosing the nature of work I did.

What was different
Cell pelleting

Prior introduction to several labs at Mulago steered me away from high performance liquid chromatography (Pharmacokinetics lab), towards molecular biology, immunology, and microbiology. Therefore, I spent the entirety of my internship in the translational research lab. It also helped that I was familiar with the staff in this lab and some of the work they were doing, so I spent less time adjusting to the environment. Like my previous internship here, the nature of work available and duration of my internship did not allow me to develop or latch onto a research project for a more holistic research experience. I eased into the routine lab work and fortunately this time I had more experience in the lab from my third-year microbiology lab courses. I was ready to suit up in the white coat and dive deeper into the wet lab than before.

The work.
Drug sensitivity testing(right) with Emmanuel M. (left).

This internship offered fuller days, and more complex tasks. There was a lot to confect and more to practice. I slotted into tasks that were already being conducted by the staff, and two contributions especially stood out for me. Between these major tasks, I did trivial tasks within experiments and assays, processed and stored components of whole blood, and breast milk samples. One of the prominent studies in which I spent ample time supporting the staff was the gonorrhea study. Funded by the Center for Disease Research, the study was aimed at studying the trends of antibiotic resistance and susceptibility at select health centers around Kampala. The work I did included receiving urethral swabs, gram staining and streaking the bacteria on selective media. I also helped subculture, and set drug sensitivity tests and minimum inhibitory concentration test strips. By honing these techniques, I am more equipped to investigate antimicrobial resistance which was one of the targets in my Clinton Global Initiative University (CGIU) commitment to action.

Taking the fight to leukemia

Half way into my placement, the Texas Children’s hospital introduced a project to enhance leukemia diagnosis and treatment using flow cytometry. This was aimed at using fluorescent markers to identify abnormal cell populations that would be targeted during treatment. Work done under this diagnosis felt meaningful to me because it augmented treatment and provided useful data for future cancer research. More importantly for me, this was an unforeseen opportunity to develop a skill I had been fascinated by for a long time.

Far from home, yet far from dismay
Using the FACS canto for flow cytometry.

In the way of luck, the leukemia study gave me an unforeseen opportunity to interact with Mike Cubbage, the lab manager of the Texas Children’s hospital core laboratories. A master of flow cytometry, he possessed a wealth of insight into flow cytometry data analysis. Having done research/diagnosis work around Africa, he was a resource in my efforts to learn more about laboratory-based work done on the continent but instigated from overseas. I learnt that if the capacity to conduct research was available, the costs were similar on and off the continent, for different reasons. Limitations to research in Africa arose from equipment and accessibility to reagents, while limitations to research overseas arose from high wages for complex work.

Setting up PCR (right) with Joshua M. (left).

At about the same time, Megan Neary, a PhD student from the University of Liverpool launched part of her pharmacogenetics project in the lab. Her work was focused on investigating the relationships between genes involved in HIV Antiretroviral drug metabolism and contraceptives in African populations. This was a rich opportunity for me to learn more about PCR. Although I did not seize this opportunity to the extent I did flow cytometry, I had shadowed and conducted each part of the experiment. My conversations with Megan contributed to my understanding of international research. From her, I learnt that collaborations between universities tremendously eased research in Africa. And aside from limitations like unstable electricity supply and reagent shortages, some research was better off done in Africa. This leaves an opportunity for domestic researchers to use the samples for further studies in the future.

Not withstanding challenges like my personal health and interpersonal adjustments, this internship was a success. I appreciate the time that the staff invested in training me in the skills I required, and relish their patience in moments where I was proffered the opportunity to work without supervision. It has left me a lot to ruminate about, and certainly enriched my proficiency in research and the work place. The translational lab has been a place I can learn from enthusiastic colleagues and enjoy diverse conversations with friends. This is an organization I would recommend to scientists who seek involvement in infectious disease research in Africa.