- Lindsay Eltis for receiving a UBC Killam Research Prize in recognition of outstanding research and scholarly contributions.
- Curtis A. Suttle
as the recipient of the 2010 A.G. Huntsman Award honouring his
significant influence on the course of marine scientific thought.
- Bob Hancock
for a 2010 Killam Award for Excellence in Mentoring recognizing his
ability to create effective working relationships and constructive
interactions with numerous graduate students over many years.
- Lindsay Eltis and Bill Mohn together with co-applicants Steven Hallam
and other UBC and SFU researchers for the award of a $7.9M Genome
Canada Applied Research Project grant for their project entitled: “Harnessing microbial diversity for sustainable use of forest biomass resources”.
- Nita Shah,
graduate student in the Fernandez lab, as the recipient of the John
Richard Turner Award that supports genetic research by students in
Microbiology and Immunology.
……and the recipients of Faculty of Science Achievement Awards
- Ninan Abraham for outstanding research and taking on major leadership roles in and for the department.
- Jody Wright,
Ph.D. student in the Hallam lab, for her exceptional efforts in science
education as an instructor, coordinator and course designer for
workshops offered by the Advanced Molecular Biology Laboratories to
grade 9 students and their science teachers. Jody was also the
recipient of a University Graduate Teaching Assistant award last year.
CONGRATULATIONS!
MESSAGE FROM THE DEPARTMENT HEAD
|
by Dr. Mike Gold
It’s hard to believe that a year has gone
by since we published our first Microbiology and Immunology
newsletter. Time seems to be accelerating, so it is important to
periodically stop and take pleasure in all that we’ve achieved over the
last year. Our students, faculty, staff, and alumni continue to
succeed and receive recognition for their great accomplishments, many
of which are highlighted in this issue of the newsletter.
Each year brings interesting new transitions and challenges. As
you’ll read about, a huge upcoming transition for our department will
be the retirements of Drs. George Spiegelman and Hung-Sia Teh. It’s
hard to imagine the department without them. They have been mentors
to all of us, as well as inspiring instructors for thousands (or maybe
tens of thousands) of students. Also, to me, they look the same
as they did 20 years ago when I first met them. Contrast that to
my then and now pictures above. Hung-Sia and George will go on to
pursue their many other interests, but I hope that we continue to see
them often at department events. They are on the invitation list
for my retirement party.
For faculty members, the greatest pleasure is seeing our former
students graduate and become successful. This year we’ve had a
number of graduate students complete outstanding PhD’s and go on to very
high profile post-doctoral positions. I now follow their
successes on Facebook. Several of my former PhD graduate students are
now faculty members at other Canadian universities and I’ve had fun
sending them nerdy lab-warming gifts like sets of fluorescently colored
test tube racks. I’m also thinking of enrolling them in the “book
of the month” club where each month I send them one of their old lab
notebooks, in an effort to clean up my lab. Mentoring your trainees
is a life-long commitment and something our department takes great
pride in. This year Dr. Bob Hancock was awarded the UBC Killam
Prize for Mentoring, his
nomination being supported by enthusiastic letters from a number of his
former students and post-docs.
Our undergraduates continue to excel and impress us with their
abilities and their desire to make the world a better place. I
attended the spring graduation banquet last year for the first time and
was very taken by the wonderful people we’ve all had the privilege of
teaching and interacting with. I was nervous about having to give a
speech to this very talented group of young people. Scientists
usually don’t give “speeches”. We give “talks” about data. So I
tried thinking about who was the wisest person I had known and any
advice they had ever given me. Probably the wisest person I ever
met was my grandmother, who always wanted to change the world for the
better. So translating her advice, my speech to the graduating
students went something like this:
Success is something we all have to define for ourselves but for my
grandmother it meant that you are using your abilities to make a
positive contribution to the world and to society. In my
grandmother’s language, it meant that you had become a
“Mensch”. The literal meaning of mensch is “a person” but it
implies much more than that. It’s a great compliment to say: “Now
there goes a real mensch”. How can you measure mensch-ness? As an
undergraduate I was a physics major, so I like to describe things using
graphs. On a mensch-ness graph, one axis would be the Albert
Einstein/Yo-Yo Ma axis. It’s how smart and accomplished you become
in the things you do. The other axis is the humanitarian axis, the
Terry Fox axis or the Rick Hansen axis. To be a mensch, you have
to score highly on both
axes. No matter how high you score on the Einstein axis, if you
haven’t moved off that axis into the humanitarian dimension, you
weren’t much of a mensch. At the same time, you need skills in
order to make an impact in the Terry Fox dimension. All of our
graduates have done extremely well on the Einstein/knowledge/ skills
axis. And from my interactions with both our undergraduate and graduate
students, I know that they have helped their classmates, friends,
community, and those less fortunate through their many activities. My
greatest pride as Department Head is that the people coming out of our
department are mensches. The challenge for all of us is not to rest
on our laurels and be a one hit wonder. You wouldn’t want my
grandmother to say, “Well, they used to be a mensch, but now
eh...”
I’m taking suggestions for this year’s graduation banquet speech.
Mike
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IS THERE LIFE AFTER IMMUNOLOGY FOR HUNG SIA-TEH? |
by Dr. Hung Sia-Teh
Professor
Hung-Sia Teh has worn many hats in our department and at UBC at
large. Among them principal investigator on many research
projects, Acting Director of the Biomedical Research Centre, and Acting
Head, Department of Microbiology and Immunology. But, does he
know how to retire?
On July 1, 2011 I will have been with the Department of Microbiology
and Immunology at UBC for 34 years! During these 34 years I have been
very fortunate to be given the task of teaching the subject I love:
immunology. I find great joy in teaching this subject because it is
relevant to our daily health and a fabulous subject from the
developmental biology point of view. It is only in the recent past that
we finally figured out how the immune system tailors its defense
against specific pathogens. Of course there are miscues and when they
happen, undesirable consequences are the result. Furthermore, our
immune system can also cause autoimmune diseases, graft rejection,
asthma and allergies. It is exciting to explain these concepts to my
students. Over the past 34 years I must have instructed over 15,000
students. It is my hope that these students have learned a subject
that will be useful for the rest of their lives. It will be a big bonus
for me if a few of these students actually proceeded to do research in
immunology.
It may be of interest to ask how I became an immunologist. I came from a
very humble background in a small town in Malaysia called Teluk Anson.
I didn’t have any particular talent except to do well in my studies,
which earned me a Canadian International Development Agency (CIDA or
Colombo Plan) scholarship to the U. of Alberta in Edmonton in 1965.
Following my graduation with a B.Sc. with distinction in Agriculture in
1969 I returned to Malaysia with the intention of serving in the
Ministry of Agriculture. However, for unknown reasons, the Ministry
refused me a job. Having been relieved of my contractual requirements I
returned to the U. of Alberta in 1971 on a Medical Research Council
Studentship to do my PhD in the Biochemistry Department. My first
research supervisor, Christopher Smith, was a renowned nucleic acid
chemist. During the first four months I learned how
to sequence transfer RNA in his lab. I got my first good results after 5
months, obtaining sequences of partial digests that enabled me to
complete the sequence of lysyl transfer RNA from yeast. Unfortunately, I
could not share this nice result with Chris Smith since over the
weekend that I made this progress he was killed in a climbing accident
in Mt. Edith Cavell in February 1972. Consequently, after five months
of graduate studies I was without a research supervisor. With the
approval of the Department Head I operated Chris’s lab with the help of a
technician, got the project finished towards the end of 1972 and
published the findings in the Journal of Biological Chemistry (JBC 1973
248: 4475-85). After completion of this project I decided to do
something different. I wanted to switch to a more biological system and
the only faculty member interested in immunology in
the Biochemistry Department at that time was Vern Paetkau. Being a
biochemist, Vern suggested that I work on determining whether immune
responses can be regulated by cyclic AMP. I learned the immunological
techniques from a post-doctoral fellow, Kwok-Choy Lee. Kwok-Choy was a
fellow Malaysian and a very good friend and teacher. I was able to get
some good results in the next year and got this work published in
Nature (Nature 1974, 250: 505-507). This was how I got into immunology.
After getting my PhD in 1975 I did two years of post-doctoral training
with Rick Miller and Bob Phillips at the Ontario Cancer Institute in
Toronto and joined the Department of Microbiology as an assistant
professor in 1977.
It is reasonable to ask why I choose to retire from a subject that I
love. First, 34 years at UBC is long enough and second, I want to make
room for new talent. But is there life after immunology for me? My
colleagues often ask me what are my plans after I retire. To me the
nicest thing about retirement is that you don’t need a plan. I will
have more time for my grandchildren, tennis, golf and skiing. My wife
(Soo Jeet) and I like to travel and we will definitely travel more in
the next few years. Being of Chinese decent, I am very interested in
the Chinese language, history and culture. I plan to improve my skills
in reading and writing Chinese and tour more extensively in China.
While I was working I often squeezed in as much fun things as possible
during the weekends. Retirement to me will be a never-ending weekend. I
am definitely looking forward to it.
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by George Spiegelman
I
have often told the story (so some of you may have heard it) that I
have worked every year of my life since I was 14. And I never had a
job outside a lab. That's I suppose not strictly true since much
of my "job" at UBC has been teaching and administration. However, I
approached both teaching and administration as "experiments" (why not
try this?).
So
here goes, a life outside the lab. True? Well not
really. It's just more expanding the thing I call the lab from
inside the walls where there are chemicals, centrifuges and biological
questions to places where there are other tools and questions.
So
what is next? The reason I focused much of my energy on teaching
is that very early in my time here at UBC I met some terrifically
smart, really nice undergraduates. It became very obvious to me
that "my job" here was to do what I could to help these people gain the
abilities to deal with the world they will enter after UBC.
This
world is not necessarily such a nice place. There are
extraordinary challenges of the injustice in almost all countries and
the increasingly difficult stresses that humans are applying to the
global ecosystems. It's very likely that the key things students
need to know are not covered by the lactose operon paradigm of gene
regulation. My wife and I decided that she would work in the
community and I would work within the university trying to promote
understanding of, and ways to meet, these challenges. So I spent
quite a fair chunk of time developing alternative education paths for
undergraduate students.
So
I'll be shifting energies to these same issues outside the
university. I suspect the details might look different- my wife and
I are thinking of some grand schemes. But the motivation will
remain. And the occasional picnic will be a bonus!
As
for what changes are needed, for me it's nicely summed up by a quote
attributed to Chief Seattle who was reported to have asked some
European settlers "When are you people going to start acting like you are intending to stay?"
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by Calvin Wong
Calvin Wong is President of MISA, graduating this May and thinking about doing a Masters in Management.
Let me introduce MISA: The Microbiology & Immunology Student Association.
In order to find out more about my own club, I went
digging through the AMS archives and found an original copy of our club
constitution, which to my tremendous amusement, was written on a
typewriter! It turns out our club was founded in 1985, and our name
wasn’t always such a mouthful, simply the Microbiology Club.
The
number of students in the program has steadily grown over the years,
and so has the club. Starting with four executives in 1985, we’ve now
grown to a team of over a dozen executives and nearly two hundred
members. The goals of the early days were simple: promote interest in
microbiology, and provide students with opportunities to interact
academically and socially. The scope and number of our activities
has increased over the years, but the basics remain.
We
usually host a handful of social events throughout the year, such as
hockey nights at the Abdul Ladha Science Student Centre, and whatever
else students suggest. MISA used to be the kind of club that held
regular bake sales to support weekend ski trips and beer gardens, a lot
of them at that. There aren't as many beer gardens these days, but we
do equally exciting things, like hosting a computer gaming tournament
this year.
On
the academic end of the spectrum, our greatest success story from the
past three years has been info sessions we call the Undergraduate
Research Nights. Grad students and faculty members are invited to speak
to undergrads about their current research. Students not only hear
about the latest advances happening right in their backyard, but also
glean valuable insight into how they themselves can get started early.
Eventually, we want to be able to invite alumni to speak at our events
as well. After all, who better to inspire and potentially mentor our
students?
New
this year, the MISA exec team offers advising to students on a variety
of matters such as a good combination of electives to take. Then
of course, there are some activities that we've been at for the better
part of twenty-six years: info sessions to guide students applying to
our program, producing our ever popular course review packages for
midterms and finals, and offering peer tutoring for Biol 112 (I hear
that course is harder now, not that I did well back when it was
"easier").
And to balance life, we add some volunteer or charity work to our
social and academic activities. This can mean working hand in hand with
the department to organize events such as World AIDS Day or World TB
Day which you've no doubt read about in last year's issue. Another fine
example was this year's welcome back barbeque in September, when
Pakistan was reeling from recent monsoon floods. In hopes of
contributing what we could, we gave students the option of making a
donation when they came by to pick up their hotdogs. No pressure, no
recommended donation amount, and we actually ended up raising over $300
that day! We'd like to thank all who came out for their generosity
and support.
Just
for the record, ours are "Japanese-style hot dogs" and not "Japa
Dogs", because that would be trademark infringement... And yes, there
are clear differences between the two. Mainly, ours are better :) . If
you've ever had a Japa Dog before, be sure to come by next time MISA has
a hotdog sale. I'm sure you'll agree :)
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USING A BACTERIUM TO PREVENT A VIRAL INFECTION |
by Sassan Sangsari
Sassan
is a 4th year Integrated Sciences student who has been working on the
HIV Microbicide Project in the Horwitz Lab since the summer of 2010.
His interests in HIV/AIDS span beyond research and drug development, as
this particular virus is linked to many social justice issues.
Microbiologists are combining forces
With
laboratories in the Life Sciences Centre being side by side,
departmental collaborations are strongly encouraged and easily
implemented. Microbiology Dr. Marc Horwitz, a Virologist, is getting
the crucial element to combat sexual transmission of HIV delivered by
his colleague John Smit, a Bacteriologist from the floor below.
While
HIV/AIDS constitutes one of the major public health concerns of our
time, lots of research grants are enticing researchers to come up with
creative strategies to reduce global infection rates. The virus can
primarily be transmitted both sexually and by blood contact. As for
sexual transmission, condoms are known to effectively prevent HIV
infections. The catch of course is that people don’t like to use
condoms. And here is where microbicides come into play.
An HIV microbicide is a gel or crème that can be applied topically
prior to sexual intercourse in order to reduce the chance that the
virus can be transmitted. As such, it offers several benefits over
condoms. For starters, there is no “rubber in the way of full
pleasure”. Quite to the contrary, it could even serve as a lubricant.
Second, if the microbicidal ingredient can be packaged into a
colourless and odourless gel it becomes barely noticeable by the sex
partner and one could thereby avoid any issues along the lines of “So
you don’t trust me to not have HIV?!”. Currently no microbicides have
made it to the market, though the list of candidates in the pipeline is
long.
The
main host cells of HIV are Helper T cells and Macrophages, both of
which display the crucial receptor CD4 and either co-receptor CXCR4 or
CCR5 that HIV binds to with its viral membrane proteins gp120 and gp41.
To prevent HIV from infecting a host cell, one needs to prevent these
key players from mingling with each other. For this, the bacterium
Caulobacter crescentus has been hired to do the job.
After playing with C. crescentus, a harmless gram-negative bacterium
found in soil and water, for the past three decades, Dr. Smit found a
way to make the bug produce and display any protein he wants on its
surface. So by displaying MIP-1alpha (the natural ligand of CCR5) on C.
crescentus recombinants for example, an agent is introduced that blocks
a critical host cell co-receptor from being accessible to the virus.
Similarly, expressing the peptide Fuzeon (an antiretroviral drug that
binds gp41) confines virions like a mosquito light trap. By developing
multiple recombinant bacteria that interfere with the infection process
in several ways, it becomes highly improbable for a mutant to evade
the microbicide effect.
The
team, consisting of faculty research associate Dr. John Nomellini, lab
technician Iryna Shanina and undergraduate students Evan Ailon, Lara
Robertson and Sassan Sangsari, are currently trying out different
proteins displayed on C. crescentus in the hopes of increasing the
potency of the blocking effect in vitro. Once an optimized
cocktail is determined that works on a representative sample of HIV
strains, the project will hopefully test the microbicide on non-human
primates trials.
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FINDING INSPIRATION IN AFRICA |
by Rebecca Gordon
Rebecca
Gordon is a fourth-year student in Department of Microbiology and
Immunology. After graduation this April she is pursuing a Master of
International Public Health.
I
went to Africa last summer thinking HIV/AIDS was a medical and
scientific challenge; posed to us by Mother Nature and waiting for the
adequate advances in technology and bright minds to save the day. This
view was one of the factors that had driven me to study microbiology
and immunology at UBC. I returned from Africa with a new perspective,
new goals and a new direction for the next chapter of my life as I
graduate from UBC this April.
GIVE (Global Initiative for Village Empowerment) is an organization run
by a group of volunteers made up of UBC students and alumni working in
the Kanyawagi region of Western Kenya combatting the HIV/AIDS pandemic
through projects in nutrition, business, health and education. I was
selected to travel to Kenya as part of the HIV/AIDS Education team in
December 2009. To briefly sum up the projects: theHIV/AIDS Education
team has succeeded in creating an HIV/AIDS curriculum for grades six to
eight and implementing it as an examinable subject in seventeen
schools of the Ojola School Zone. GIVE also funds the summer
examination period, hosts a celebratory Education Day and runs the
HIV/AIDS Awareness Football Cup for the students of the Ojola Zone.
The
Kanyawagi region, which includes theOjola School Zonewhere our
education projects are focused, is a community deeply affected by the
HIV/AIDS pandemic. The “Headteacher’s” office walls’ show class
summaries similar to what we see in Canadian schools with information
on grade, teacher name, classroom and number of students. The
difference in the Ojola Zone is the additional rows for the number of
half-orphans, number of orphans and number of “high-risk” students. The
number of primary school students with one or no surviving parents is
staggering. This is one of many indicators of the catastrophic effect
HIV is having on the community.
My primary role involving interaction with the students in Kenya was
teaching life-skills workshops to supplement material taught by
teachers.Misconceptions, ignorance and myths make prevention and
education initiatives challenging but extremely important. The
most difficult days were always when we set out, with our very helpful
employee and fellow educator Maurice, to teach the “Condom Use”
workshop. The use of condoms is still extremely controversial in the
region but is a required portion of our education program. Condoms are
tools not only for protection against HIV infection but also for other
sexually transmitted infections and early pregnancy, all of which pose a
considerable risk to the students of this region.
Learning
how to handle a soccerball, or at least run around in the general
vicinity of a soccer ball, creates a great environment for
gaining trust, teaching and learning from children.Our weekly soccer
tournaments were a useful venue for teaching condom demonstrations to
the students. Although there are twelve steps to correctly putting on a
condom, which I’m sure not all of you knew, the first step in this
demonstration was distracting the little kids to avoid any
inappropriate viewing of the erect prosthetic penis. This is where I,
running and a soccer ball, came in handy. Soccer tournaments also gave
us a chance to talk to the students outside of the classroom
environment and quiz them on their knowledge. Correct answers to
questions won them new school uniform shirts, which were a big deal!
These weekend talks where I could share my passion about the biology of
HIV and help students solve health and some relationship problems were
the highlight of my time in Kenya. I eventually adjusted to
situations such as havinga serious conversation with a
thirteen-year-old boy about the risks of his sexual relationship with
his new, HIV positive girlfriend.
This
summer I am very proud that GIVE will be piloting a novel project in
the Ojola Zone pioneered by myself and Martina Feldman (my peer in the
MBIM program). It has been widely recognized in the public health
community that the HIV/AIDS pandemic is undergoing a significant shift
in Sub-Saharan Africa towards females. This project will couple an
after school girls club program lead by female teachers with the
distribution of sanitary napkins. The goals of this project areto
increase female students’ school attendance and provide confidence
building life-skills to decrease risk-behaviour.
It
is very easy to get caught up in studying and forget about the big
picture, particularly as an undergraduate student in an intense program
in the Faculty of Science at UBC. Higher education and research are
driven by the big picture ideas. There is a big world out there filled
with the big issues that should be inspiring us to continue our
studies. My place of inspiration happens to be Africa but a source for
inspiration or a glimpse of the big picture does not have to be so far
from home. There are many amazing opportunities with organizations here
in Vancouver that are always thankful to have enthusiastic individuals
with a background in microbiology.
If
you would like more information about GIVE or would like to donate
time or funds to any of our projects please do not hesitate to contact
Rebecca at rebeccagordon3@hotmail.com or check out their website at www.givesociety.org
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BEHIND THE SCENES - JASON GRIGG DECODES IRON SCAVENGING |
by Dr. Sigrid Auweter
Dr. Sigrid Auweter is a post-doc in Dr. Brett Finlay's lab and generally curious about research.
Jason Grigg, graduate student (now actually a post-doc) in Dr. Michael
Murphy's lab, wants to understand how pathogenic bacteria overcome one
of the toughest challenges inside the host: extremely low
concentrations of free iron, an essential nutrient for all cells. While
at UBC, Jason has solved crystal structures of several iron uptake
systems in Staphylococcus aureus, which has laid the foundation for a
mechanistic understanding of iron acquisition by Gram-positive
bacteria. Despite his success, Jason has not forgotten how he worked
for years without measurable results. And he vividly remembers the time
when things finally reshaped in his favor.
It was the week before Christmas in 2005, and Jason was one of the last
students left on campus. With his plane home to Ontario departing
early the next morning, Jason decided to spend the night in the lab,
frantically setting up crystal trays. He was desperate for some good
science news. His 4th year thesis work at the University of Western
Ontario was not much of a success and after not getting any results in
his first six months at UBC, he was now working on his second project
in Michael’s lab. All the hard work made him pass out on the couch,
dreaming of a first paper, and he missed his plane to Toronto. But, a
few hundred dollars poorer after rescheduling a flight just before
Christmas, things finally turned around for quiet, determined Jason. An
email arrived and an excited Mike Murphy presented Jason with the best
Christmas present crystallography has to offer: a
picture of a big, beautiful, reddish crystal, grown on one of the
plates Jason had set up that night.
Back in Vancouver, Jason used the crystals to solve the structure of
the NEAT domain, a haem binding protein domain, which is part of an
iron uptake system that allows S. aureus to scavenge this cherished
metal from the host (1). This iron import system contributes
significantly to S. aureus virulence and the NEAT domain contains some
of the most important antigenic epitopes present in vaccines against
the opportunistic bacterium. Jason’s findings have provided a molecular
understanding of how haem is moved into Gram-positive bacteria, have
impacted vaccine development, and have been cited over 30 times since
being published in the fall of 2006. Since then, Jason has gone on to
also solve the 3D structures of SirA, HtsA, and IsdE, receptor
components of three other bacterial iron uptake systems (2-4).
Besides his work in the lab, Jason plays volleyball and loves
exploring the city. He plans to stay in academic science, as he enjoys
the creativity and freedom that come with the profession. Jason is
currently applying for post-doctoral positions in the USA.
References:
1. Grigg, J. C., Vermeiren, C. L., Heinrichs, D. E., and Murphy, M. E. (2007) Mol Microbiol 63, 139-149
2. Grigg, J. C., Vermeiren, C. L., Heinrichs, D. E., and Murphy, M. E. (2007) J Biol Chem 282, 28815-28822
3. Grigg, J. C., Cooper, J. D., Cheung, J., Heinrichs, D. E., and Murphy, M. E. J Biol Chem 285, 11162-11171
4. Grigg, J. C., Cheung, J., Heinrichs, D. E., and Murphy, M. E. J Biol Chem 285, 34579-34588
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by Dr. Rachel Fernandez
The Fernandez lab studies Bordetella pertussis,
the bacterium that causes “whooping cough”. There are effective
vaccines for pertussis, but every year, about 20 million people in the
world – mostly children– suffer from pertussis and almost 300,000 of
them die. B. pertussis is an exclusively human pathogen with
no environmental reservoir. Neither natural infection nor vaccinations
provide life-long immunity. Adults and adolescents whose immunity has
waned are the source of the infection. We are working to understand the
reasons for this and to develop the next generation of pertussis
vaccines.
The research in our lab has two themes: bacterial cell biology and bacterial pathogenesis.
The bacterial cell biology program looks at how proteins,
specifically virulence factors, cross the Gram-negative outer membrane.
We focus on a class of proteins called autotransporters, which are key
virulence factors in Gram-negative bacteria; our research addresses
periplasmic trafficking of B. pertussis autotransporters and
the folded state of the proteins prior to, during, and after
translocation across the outer membrane. We have discovered that B. pertussis
can subtly modify the lipid A part of its lipooligosaccharide (LOS)
and we are further investigating how the bacterium does that.
The bacterial pathogenesis program addresses immune evasion and immune modulation tactics used by B. pertussis. B. pertussis
uses several mechanisms to evade our immune defenses. One key
defense is the complement system, which plays an important role in
marshalling both innate and adaptive immune responses. A pathogen’s
ability to control complement activation shapes the host’s integrated
immune response to it. Our lab investigates how B. pertussis evades the complement system. We have discovered that autotransporter proteins play a significant role in this process.
Toll-like
receptors (TLRs) are a critical component of innate immune responses.
They engage bacterial structures such as LPS and DNA and trigger the
production of cytokines and other molecules involved in generating
adaptive immunity. We have discovered that B. pertussis has
the capacity to modulate immune responses by adding a glucosamine
molecule to each phosphate group on its lipid A. This process is
controlled by the Bordetella Bvg virulence regulon. The presence or
absence of the glucosamine decoration dramatically changes how the host
responds to B. pertussis
with respect to the induction of pro-inflammatory cytokines. These
cytokines are important for generating adaptive immunity, although too
high an induction leads to high fevers and possibly other deleterious
effects. It turns out that only human TLR4 receptor complexes can
discriminate between lipid A that is or is not modified with
glucosamine; mice are blind to this change. We are investigating the
mechanism underlying this finding. We are examining the significance of
this modification with respect to pathogenesis and working to
understand the host’s ability to mount long-lasting immune responses.
Our work has implications for improving pertussis vaccines, especially
the killed whole-cell pertussis vaccine still being used in low and
middle-income countries.
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by Dr. Jennifer Gardy
Self-described
asscientist, nerd girl, person on TV, panda enthusiast….Dr. Jennifer
Gardy leads BCCDC’s Genome Research Laboratory and is an Adjunct
Professor in M&I
On March 24th, for the second year in a row, the Centre for
Tuberculosis Research organized a fantastic program to commemorate
World TB Day, with short talks from local researchers and a keynote
address, this year delivered by Pam Chedore, on the challenges and
opportunities associated with improving TB lab capacity in the
developing world. These events, held in the Life Sciences Centre at UBC
and reaching out to the local community in the Downtown
Eastside,reminded us all that TBremains a health issue of tremendous
importance, not just in the developing world but also here in
low-incidence countries like Canada. British Columbia has, on average,
about 300 cases of TB a year, with many of these occurring in
vulnerable populations, like the street-involved. Since 2006, BC has
seen two large outbreaks of TB in marginalized populations – one
lasting from 2006-2008 on Vancouver
Island, and one that’s been going on since 2008 in the Okanagan area.
The
2006-2008 outbreak was recently the subject of a groundbreaking study
led by M&I Adjunct Professor Dr. Jennifer Gardy and Pathology &
Laboratory Medicine Assistant Professor Dr. Patrick Tang, which also
involved former M&I postdoc (and current SFU Professor) Dr. Fiona
Brinkman and a host of other local TB researchers. Published in the
February 24 issue of the New England Journal of Medicine, the study combined whole-genome sequencing of 36
M. tuberculosis isolates from the outbreak with social network
analysis. By merging genomic, epidemiological, and clinical data, the
researchers were able to reconstruct the outbreak, identifying its
origins and stepwise spread throughout the community.
Interestingly, the epidemic curve of the outbreak and cocaine-related
RCMP files in the outbreak community suggests that the outbreak
co-occured with a spike in cocaine prevalence in the community.
The study, which has been highlighted in prestigious scientific
journals such as ScienceDaily, as well as local, national, and
international newspapers, is one of the first examples of the emerging
field of “genomic epidemiology”, in which whole genome sequences are
used as an epidemiological tool to follow the spread of a pathogen
during an outbreak. This type of study only became possible recently,
with the dramatic reduction of sequencing time and costs brought about
by next-generation sequencing platforms, and is poised to yield amazing
new insights into how infectious diseases behave within populations.
By using genomics to reconstruct other outbreaks across a range of
populations, we will be able to build a knowledgebase describing how
different pathogens behave in different types of social networks –
information that is critical to designing effective
intervention and control strategies.
The BC Centre for Disease Control, where Drs. Gardy and Tang are both
based, is already using the NEJM study’s findings to guide how they
investigate other outbreaks. One of the most striking results to come
out of the paper was the fact that rather than a chain of transmission,
in which Person A infects Person B who infects Person C and so on,
this outbreak occurred in “bursts” of transmission, with Person A
infecting many other people, most of who did not go on to spread the
disease further. The superspreaders identified by the reconstruction
were all socially well-connected, suggesting that in BCCDC’s future
outbreak investigations, it is most practical to try to identify, test,
and treat the people who are most “popular” in their social network.
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CURRICULA UPDATES FOCUS ON FIRST YEAR |
by Dr.Joanne Fox
Dr.
Joanne Fox has a cross-appointment as instructor in M&I and the
Advanced Molecular Biology Laboratory (AMBL), the educational
facilities of the Michael Smith Laboratories exploring creative ways to
get people excited about Science. She seems to have many, many
balls in the air. To see that colourful array, check her website
at http://www.msl.ubc.ca/faculty/fox .
Seminar in Science (SCIE113). Offering a small-class experience and
extensive faculty member interaction, SCIE113 aims to get students
thinking about, “What is science?” and, “Where does science fit in my
life?” These first year seminars explore science as a comprehensive
way of knowing with curriculum that aims to strengthen critical
thinking and communication skills. The Department of Microbiology and
Immunology is actively involved in helping this new initiative grow at
UBC. Drs. Joanne Fox and Steven Hallam taught two of the very first
seminars offered in the 2010 academic year – the first year this course
was offered. The 2011/2012 academic year will see this new course
expand to offer ~400 first year students access to the program.
Throughout the term, all students from the small-group seminars come
together for a “Science and Society” speaker series, resulting in an
audience of several hundred first year undergraduate students. The goal
for this speaker series is to help students place science in the broad
context of their lives, the university environment and global society
at large. In 2010, our series included talks from faculty and graduate
students in the Department of Microbiology and Immunology. Dr. Brett
Finlay – named by Canadian Living magazine as one of the 10 Canadian
scientists “most likely to save your life” – talked about his passions
for research and Jody Wright, a graduate student from the Department
shared her story of the path to her Ph.D.
If
you’re interested in getting involved, we’re actively recruiting young
alumni to participate in our Science and Society speaker series. We’re
looking for engaging speakers to deliver a 30-35min talk that helps
expand students' horizons so they think widely about their future and
what they can do with a science degree.
To
find out more about this new course, you can visit the Faculty of
Science website and/or contact Dr. Joanne Fox, Director, First Year
Seminars (SCIE113) at: joanne@msl.ubc.ca or check out http://www.science.ubc.ca/students/new/courses/113
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FROM THE FRONT LINES IN M&I |
by Dr. Julian Davies
Dr.
Julian Davies is Professor Emeritus at the University of British
Columbia, Fellow of the Royal Society, and a former President of the
American Society for Microbiology.
Click here to read more about Julian.
Nature Biotechnology 26, 727 (2008)
And, yes, Julian is still in his lab every day :)
Nature Biotechnology 26, 727 (2008) doi:10.1038/nbt0708-727
http://www.nature.com/nbt/journal/v26/n7/full/nbt0708-727.html
Microbiology,
having begun in the late 19th century, is a relatively young science
compared to Chemistry and Physics. However, in its short lifetime
microbiology has become the most important of the life sciences; this
is due to several factors:
- microbes are the most ancient of living organisms
- they are the most numerous and universal
- they define the survival limits of life (temperature, pressure, etc.)
- all living beings depend on microbes for their existence
Since we as humans, are contigent on microbial beings for almost
everything we do (“bugs are us”), it is not surprising that we tend to
treat them as equals (why not indeed?) and even endow them with human
characteristics (anthropomorphism). This is no more evident than in
publications about bacteria and other microbes. The common journals in
the field are littered with statements that are adopted from our own
life styles. Authors clearly regard bacteria in the way they would
their pets or children; microbes have been given pseudo-human
characteristics. Bacterial behaviour is frequently described in terms
of a war metaphor (weapons, fighting, defence, competition, etc); we
are led to believe that microbial communities in the environment are in
a constant state of fighting to the death. As other examples of
humanizing bacterial properties, here are a few statements
taken from the current literature:
“making a choice to utilize a particular substrate”
“the decision to make a compound”
“bacteria as predators, prey, or even invaders”
But seriously, how* and why are all living beings so dependent on
bacteria? For one thing they are the oldest living organisms and for
another they possess an unimaginable number of metabolic functions that
permit the synthesis and breakdown of almost any organic molecule.
Recent studies have shown that microbes in the human gut (and
elsewhere) respond to a variety of human hormones; this includes
unlikely compounds such as insulin, adrenaline and others. Conversely,
the bacterial communities (or microbiomes) produce chemicals that
trigger certain events in neighboring human cells. A new field of
investigation is developing, called microbial endocrinology, that
attempts to elucidate the chemical signaling that is involved in inter-
and intra-kingdom communication within complex structures. Humans
consume plant products, what are the effects of phytohormones on
chemical
communication in the gut? There must be an enormous number of
interactions going on down there!
To
conclude this scientific ramble, how about a little consideration of
ethics and philosophy? Since microbes are so important to all life, do
they have any rights? Do you realize that when you bake a loaf of bread
100s of millions of yeast cells die? I suppose I should have said
“murdered”!
* “How?” is not a biological question, it is something that one asks a priest; but you know what I mean.
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