Life Science Centre
2350 Health Sciences
Mall
Vancouver, BC V6T 1Z3
This
summer we will be engaging in a departmental
“strategic visioning” process to assess what we
are currently doing and where we would like to
be in 5-10 years. What I learned in a leadership
class is that a good way to start this
discussion is to generate a 1-sentence mission
statement that encompasses the unit’s overall
goals, and then use this as the starting point
to articulate the department’s core values, its
raison d’être, and what makes it unique. So
here’s my attempt at a department mission
statement: “Training people to think big about
small things and to think globally about big
questions”.
The small things are
the molecules, cells, microbial communities,
tissues, and organs that we study in
detailin order to understand the mechanisms
underlying important biological, health, and
environmental issues. Thinking globally
implies both high-throughput “big data”
approaches to science but also considering the
social context of what we work on, whether it is
aimed at improving human health or improving
environmental quality. But the key words in this
mission statement are “training” and
“people”. All of our departmental
activities share the goal of preparing our
undergraduate students, graduate students, and
post-doctoral fellows to make important
contributions to society, to research, and to
training the next generation after them.And what
I think makes Microbiology & Immunology
unique is our undergraduate programs’
small-program camaraderie within the context of
a major university and all its resources, the
quality of our graduate program and research
labs, and most importantly, the outstanding
community-spirited efforts by so many people in
our program.
Multiple
events this year really highlighted this for
me. A couple of weeks ago, a number of us
faculty members had the pleasure of attending
this year’s MISA spring graduation banquet,
which was a wonderfully fun 4-hour cruise on a
party boat. For me, the best part of the
evening was seeing how our group of
undergraduates had bonded with each other to
create a supportive network of close friends who
clearly enjoy each other’s company (and like
their profs!). Building this “community”
of students was certainly facilitated by the
long hours that this cadre spent together in our
lab courses, their interactions in our capstone
discussion courses, and the many outstanding
social, academic, and outreach events that this
year’s MISA leadership organized. Much
credit goes to this year’s MISA Executive,
especially Tim Jayme who received a 2013 Faculty
of Science Achievement Award for his many
efforts. A very well deserved Faculty of
Science Achievement Award was also awarded to
Darlene Birkenhead, our graduate program
coordinator. Darlene has been a fantastic
source of support for all of our graduate
students, who number nearly 100 at any one
time. She provides our graduate students
with invaluable advice and personal
support. The exceptional efforts by our
faculty members to develop novel teaching
approaches that enhance the student experience
were also recognized this year with both Joanne
Fox and Steven Hallam being awarded UBC Killam
Teaching Prizes. As well, faculty members
in our department were recognized for their
research contributionsand thi impacts of their
research on society.Julian Davies received the
Abbott-ASM Lifetime Achievement Award, the
American Society for Microbiology’s premier
award for sustained contributions to
microbiology. Bob Hancock was awarded the
Prix Galien, which recognizes outstanding
achievements in pharmaceutical research and
development by a Canadian, and both Bob Hancock
and Brett Finlay received the Queen Elizabeth II
Diamond Jubilee Award for service to
Canada.
On a personal note, I received a
career achievement award from the Canadian
Society of Immunology and had the great pleasure
of giving a keynote lecture at this year’s
meeting. It was a great honor and great
fun to tell many amusing stories and to provide
a retrospective on the work that my lab and I
have done over the last 30+ years.
Absolutely the best part was having the
opportunity to invite present and former lab
members to join me for this event, with more
than 20 being able to attend for a lab
reunion. I enjoyed introducing different
generations of the lab to each other and
watching my former graduate student being
nervous while her graduate student (my
scientific grandchild) gave a talk. Most
all, it really drove home to me that the award
was not so much about me but that it was to, and
for, all the people from my lab. The award
was “to them" because they had done most of the
work and “for them”, because they are my most
important
accomplishments.
The Perona lab opened its doors in January
2012, in the 3rd floor of the Life
Sciences Centre. Well, technically we started by
closing our doors, trying to keep our pathogens
inside, but it was in January that the journey
began –
There are things no-one tells you when you start
a new job, things an innocent immunologist may
not have suspected it would be necessary to
know. The task list for a new PI is to recruit a
team, equip the lab, bring in the funding and
grant support, teach in the classroom, teach in
the lab, to manage staff, to understand cash
flow, fiscal restraint and the fine art of
budgeting. My training was in how to culture T
cells. The first challenge was to furnish the
lab, starting with building the lab benches, and
it was then, crow bar in hand and not a
carpentry bone in my body, that I knew there was
trouble ahead. The heavy weaponry was strangely
empowering though, and I now know we have a lab
safety manual because I used it as a mallet to
assemble the pathogen shelves; Dr.Teh became my
eternal hero when I discovered his drawer of
electrical plugs, soldering wire and gaffer tape
(never ask me how I persuaded the dissecting
microscope to work). I have dodged the
consequences of posting a tender advert for lab
equipment without fully deleting the previous
user’s information from the template, even when
the last user was a UBC’s plant operations
facility manager and the tender I placed was for
a 4-laser, 12-parameter, custom built flow
cytometer to be supplied with 260 manhole
covers. I discovered that grant writing has its
comedy as well as its pressures. I learned my
trade back home in Scotland, where the
intestinal parasites I study are an important
economic problem in the livestock industry. My
first draft of a grant application here was
returned by a colleague with a terse review
written in red across the top: “No sheep in
Canada. Try
cows.”
12 months on and the
progress is tangible. The lab has equipment; I
have an excellent team; my grant proposals have
been polished up and the first data are coming.
It’s an exciting time. Our research centres on a
family of soluble, signalling molecules known as
cytokines, secreted messengers used by cells of
the immune system to
communicate with one
another. Cytokines influence the size, speed and
quality of an immune response. They are critical
to the coordinated action of the immune system,
and inappropriate and persistent cytokine
signals are hallmarks of chronic inflammatory
disease. Our research aims to uncover how far
cytokines can spread through the body in time
and in space, which cells they affect and how
target cells control their response. Cytokine
signalling has long been thought to be very
tightly restricted, requiring the producing and
the receiving cells to be in very close
proximity, if not direct contact. The image is
like a schoolgirl whispering a secret message
right into her friend’s ear behind a shielding
hand. In contrast, our data shows that T cell
cytokines can permeate a lymph node and signal
to almost every cell therein, like a teacher
with a megaphone screaming instructions across
the
playground.
These data suggest a
very different model of cytokine instruction in
vivo, one in which cytokine signals are
widespread and indiscriminate, affecting very
many cells. The most striking aspect of this
model is that such indiscriminate cytokine
signalling affects even the immune cells that
happen to be in the
lymph
node at that time for other reasons, the
innocent bystanders. They too receive the full
impact of the cytokines’ instruction. Because
these bystander cells are the principle players
of other, unrelated immune responses, such
bystander signalling provides a mechanism for
the ability of one immune response to affect
another, and to cause chronic and escalating
inflammatory disease. By studying the regulation
of these signalling patterns, our lab is
contributing to new treatment strategies for
chronic inflammation such as allergy and asthma,
and for co-infections in Canada and across the
globe. Pathogens rarely work alone – influenza
virus kills through bacterial pneumonia;
tuberculosis is cruelly exaggerated in people
with HIV/AIDS - and our studies of concomitant
infection have significant health implications.
And, I’ve learned, not just in
sheep.
Using the foundation that was
laid before us from last years Microbiology and
Immunology Students Association’s (MISA) team,
we set forth to build and continue the legacy
and provide one of the most engaging,
meaningful, and memorable experiences for our
students. This year, through many of our
continuing events and new initiatives whether on
the social or academia side, we meant to inspire
and provide the opportunity for students to get
involved in the community and get to know their
peers. It is very evident that our MBIM and MISA
community is deeply rooted in the friendships
that are made throughout the years and these
friendships are long lasting.
A huge goal of ours was to ensure a strong
social media presence. Starting with our
completely revamped webpage that is as
interactive and personal as we can get, you will
find all the information you need about us and
our events and exactly what we have to offer at ubcmisa.org. Furthermore,
with over 600 likes on facebook,
(facebook.com/ubcmisa), and
your ability to follow us on twitter @ubcmisatweets, you can keep up
to date with everything that we are doing.
We have our own Youtube and Vimeo channel under
the name ubcmisatube, where we
film and edit many of our events. We have
had over 8000 people view our videos and share
in our experiences. Watch us compete in
many of the UBC REC games, watch MISA’s jam
sessions in the student lounge, or watch our own
funny spoof videos. Check out our channel
and see for
yourself.
Our
students’ year begin on Imagine Day and MBIM’s
orientation. Students – please take
advantage of this eventful day.
Ranging from lab tours, to meeting your
professors, to meeting the wonderful MISA team;
there is no shortage of opportunity here to
start getting involved! Be sure to sign up
for your MISA membership and take advantage of
the perks that come with it.
Our
social events included MISA’s Welcome Back BBQ,
MISA’s 1st annual Welcome Back
Paintball Event, MISA’s Halloween Bowling,
MISA’s James Bond Movie Night, MISA goes
Skating, MISA goes Fishing, and MISA’s Year End
Pub Crawl. These events were in many ways
the catalyst that bonded our students
together…covalently.
Above/Left:
MISAs
1st annual Welcome Back Paintball
Event saw the labcoats take on the world. The
labcoats were NOT good for
camouflage
MISAs
Welcome back bbq – a mix of our 3rd and 4th year students enjoying some
dogs
MISA
gets ready to go bowling in a variety fairytale
style
Agents
001, 003, 006, 008, 009 at MISAs James Bond
Movie Night
The
highlight of our social events, however, was
NERD LOVE. MISA is always looking to
collaborate with other Science clubs in our
Faculty. And we found amazing partners in
the Science Co-op Students Association (SCOOPS),
the Biochemistry & Pharmacology &
Physiology Club (BPP), and the Biology Sciences
Society (BIOSOC). Together, we put on the
biggest and most epic
NERD PARTY thrown in
science history. Over 250 nerds across the
faculty of science, for 4 hours in Abdul Ladha
danced and showed that nerds definitely know how
to throw and have a party! Check out our promo
videos on our youtube channel.
You’ll be in for a treat! NERD LOVE is now
officially Sciences reading break Friday night
kick off. Keep that in mind. We sold out fast,
so for students next year, you’ll want to get
your tickets
ASAP!
At
many of UBC REC’s sporting events, our nerds
showed just how athletic and competitive they
are! MISA’s Contagious Canoers rowed their
hearts out and placed third in their division at
UBC REC’s Day of the Longboat. MISA’s
Cytokine Stormers and MISA’s Wildtypes battled
gloriously at UBC REC’s Gladiator which saw
MISA’s Wildtypes finish fourth in the
division. Finally, MISA tested will and
power at UBC REC’s Storm the wall and our MISA’s
Fermentation Station and MISA’s Cytokine
Stormers could not have made us more
proud. Students - join our MISA REC teams
and gain an unforgettable experience as you rise
up in glory and battle amongst the
best.
Besides
competing at UBC REC Events, MISA also competed
against other Science clubs. While BIOSOC
and MISA have a strong relationship, there isn’t
anything better than a good old fashioned sports
rivalry. MISA and BIOSOC collaborated and
challenged each other to a basketball game in
what we called: MISA vs. BIOSOC – For Nerd of
the Game. Both teams competed with passion
and pride to produce an epic event. Again,
check it out on our youtube
channel!
If
you’ve ever been cornered by a synthetic
biologist you probably know that they go on and
on about how their field will save the
environment or revolutionize the way we think
about energy. They might even mention that the
natural
flavour you’re
enjoying might only be “natural” because an
engineered bacteria made it and not an organic
chemist. In reality, synthetic biologists aim to
determine whether we can design, build
and test biological systems using principles
adopted from traditional engineering fields.
While the prospect that perhaps one day we’ll be
able to program organisms much like we can do
with integrated circuits is exciting, we’re
still in the early stages and just beginning to
figure out how to put all the pieces together…
and get them to work together.
The workflow in synthetic biology is simple:
design a system based on standardized DNA parts
(there’s even a Registry of Standard Biological
Parts that catalogues their specifications),
assemble these parts into a host organism, cross
your fingers, and test whether it works.
Recently, leaders of the field have got teams of
undergraduate students involved by competing in
the annual International Genetically Engineered
Machine (iGEM) competition.
What is iGEM?
iGEM is a unique research experience in which
teams dedicate themselves to an intense summer of designing and building biological
systems. The goal is to produce organisms with
new or unusual properties to tackle modern
problems and evolve the field of synthetic
biology. This experience leads students to think
creatively about modern biology while gaining a
wide range of technical skills. Outside of the
lab, teams are also expected to complete a human
practices component which includes assessing the
ethical and societal implications of their
technology, networking with industry professions
and engaging in outreach activities with the
local
community.
iGEM
at UBC
UBC
has been participating in iGEM since 2009 and
has consistently received regional and
international gold medal awards for their
projects. Projects have included developing
novel biosensors for detecting infectious
diseases, producing molecules to
battle
the Pine Beetle epidemic, and building
co-dependant bacterial communities. This year,
the iGEM team is based in the Hallam lab in the
Life Sciences
Center.
I want to
help!
The continued
success of iGEM at UBC relies on the generosity
of the UBC community in providing intermittent
access to research equipment, reagents and
expertise and funding. If you’d like more
information, let us know at ubcigem@gmail.com.
The Crowe
Geomicrobiology lab opened in March 2013 on the
2nd floor of the Life Sciences Centre
and also in the new ESB. So, what is
Geomicrobiology? Broadly speaking,
geomicrobiologists concern themselves with the
role of microorganisms in geochemical and
geological processes. Microorganisms underpin
Earth’s major biogeochemical cycles, which
support and sustain life on our planet. This
intimate relationship between microorganisms and
their environments was forged deep in Earth’s
history, perhaps some 3.8 billion years ago as
revealed by isotopic signatures left in marine
sedimentary rocks. Since that time, microbes and
Earth surface chemistry have continued to evolve
in concert, establishing a network of coupled
microbial-biogeochemical feedbacks. Over
geological time,microorganisms have catalysed
dramatic changes in Earth surface chemistry,
like the oxygenation of the atmosphere, which
ultimately allowed the evolution and
proliferation of aerobic life and animals.
Exactly when and how microorganisms oxygenated
the Earth is still uncertain, as are many of the
important changes microbes have made to our
planet. Geomicrobiologists are using new and
powerful tools including transition metal stable
isotope proxies, molecular biomarkers, and whole
genome molecular clocks to search for clues in
the geological and genomic records of Earth-life
evolution.Now, during the Anthropocene, human
activities rapidly alter many of the Earth’s
well-balanced biogeochemical cycles, but can the
microbial stewards of these cycles keep pace?
This is another question at the forefront of
geomicrobiological
research.
In
the Crowe lab, we are excited by problems in
both ancient and contemporary geomicrobiology.
In particular, we are interested in the ecology
of ancient ferruginous (iron-rich) oceans.
Throughout most of Earth’s history, the oceans
were oxygen free and contained high
concentrations of ferrous iron. This is
very
different
to the oxygen-rich oceans of today, and though
oxygen-free marine waters can still be found,
these are invariably rich in hydrogen sulfide
and not iron. This is due to the high abundance
of sulfate in the modern oceans, which is
converted to hydrogen sulfide in microbial
respiration when oxygen is absent. Due to the
rarity of extant iron-rich environments, we have
a very poor understanding of how such ecosystems
function,and therefore, we have little
ecological context for microbial evolution
throughout most of Earth’s history. To fill in
this context, we are taking a transdisciplinary
approach. We search the modern Earth for
environments, such as unusual stratified lakes
with iron rich waters, and examine microbial
ecology in these analogues for the ancient
oceans. We also study the physiology and
genetics of iron-based metabolisms in the lab,
and weconstrain ancient environmental conditions
using geochemical fingerprints left in the rock
record. Combining these approaches opens a
window into the ecology and physiology ofour
ancestral iron-centric
microbes.
We
are currently very excited to have obtained the
first isolate of a photoferrotrophic Chlorobi (an anoxygenic phototrophic
bacteria) enriched from the water column of a
newly discovered ferruginous lake in the heart
of East Africa. Photoferrotrophs use sunlight to
fix carbon, but in the process convert ferrous
iron to ferric iron rather than, like plants,
converting
water
to oxygen. Photoferrotrophs were likely
important contributors to global biological
production throughout much of Earth’s history
and would therefore have played an important
role in the evolution of the biosphere and Earth
surface chemistry. Photoferrotrophs may also
have been critical contributors to the
deposition of Banded Iron Formations (BIFs),
which are massive iron ore deposits that supply
most of the world’s iron for steel. We are
optimistic that physiological studies of our
isolate will yield new clues into the roles
photoferrotrophic bacteria played in Earth
evolution. The genome of our isolate is
currently being sequenced in collaboration with
Steven Hallam, and it will be very interesting
to see what secrets we can uncover about the
antiquity of photoferrotrophy and the possible
metabolic capacity of these iron oxidizing Chlorobi. Kate Thompson will be
starting her M.Sc. this summer to continue this
work.
We
are also very interested in the role of microbes
in the modern nitrogen cycle. As one of the
great biogeochemical cycles, the nitrogen cycle
intimately interacts with the carbon cycle
playing an important role in global biological
productivity and climate dynamics. Nitrogen
indeed is the limiting nutrient for most
continental and marine ecosystems. The nitrogen
cycle has been severely altered by human
activities, notably by the transfer of abundant
nitrogen gas from the atmosphere to soils and
water through the production of ammonium using
the Haber-Bosch process and its application to
soils as fertilizer. Once in the environment,
ammonium is oxidized to nitrate, which is mobile
and accumulates in streams, lakes, and the
coastal ocean leading to harmful algal blooms
and eutrophication. The most important natural
sink for this fixed nitrogen is by microbial
conversion of nitrate back to nitrogen gas
through a combination of canonical
denitrification and the recently discovered
anammox process, which isconducted by a group of
Planctomycetes who generate rocket fuel as an
intermediate. There is, however, a microbial
short circuit in this part of the nitrogen cycle that leads to a recycling of nitrate back to
ammonium. This dissimilatory reduction of
nitrate to ammonium (DNRA) is poorly understood,
but it may operate to maintain nitrogen in
waters, soils and sediments limiting its
transfer back to the atmosphere. This, of
course, has important implications both for the
management of fertilized agricultural land and
the mitigation of nitrate contamination in our
waterways. Ph.D. student Celine Michielsis
working hard to learn what regulates the
activity of DNRA in natural marine and
terrestrial environments as well as in
engineered ecosystems, including wastewater
treatment facilities.
As our lab
grows we are looking forward to collaboratively
explore new directions in Geomicrobiology, such
as the interface between minerals and the human
microbiome or the role of pathogens in
biogeochemical
cycles.
LEFT:
Outcrop of the Hamersley Basin banded iron
formation, among the world’s largest iron ore
deposits, and possibly formed by
photoferrotrophic bacteria (Photo courtesy of
Simon Poulton, University of
Leeds).
We are proud
to say that we have initiated the first
Influenza clinic hosted by a student
organization. We gave over 250
vaccinations to professors, staff, and
students. Be sure to look for us next year
for your vaccination!
Our
department has always shown MISA a tremendous
amount of support. Evidence of this is their
donation of a room in Wesbrook which we turned
into MBIM’s very first student lounge. With
three leather couches, a microwave, a fridge,
tables, and yes, TWO foosball tables, this is a
place for all you nerds to escape and get away
from the stresses of
school.
It
is important to MISA that we contribute to the
community in any way possible. A part of
this is raising awareness and funds for various
charitable initiatives. This year, we
supported Movember. A team of 12 MISA
students grew their moustaches to raise money
and awareness for prostate cancer. After
one month of fundraising, we are proud to say we
raised over $2100. We look to support this
and more charitable initiatives next
year!
Our academic events
such as our Undergrads Guide to Research gave
our students the opportunity to see first hand
what the research life entails. Various
workshops allowed them to listen to professors
and students talk about their experiences in
research. Other workshops allowed students
to learn how to talk to professors about
research positions, how to get NSERC grants, or
how to get into co-op. The night was
capped by a mix and mingler which saw professors
and graduate students come down and share a bit
of pizza while they talked about their work – a
perfect opportunity to network for our
students. Our other academic event,
4th year and beyond, saw various MBIM
alumni with different career backgrounds such as
law, medicine, research, and public health sit
at a round table with students and answer
questions.
We
wanted to show that with an MBIM degree, there
are various opportunities out there that our
students may not have known about. Finally, we
initiated MISA’s first mentorship program which
saw over 20 1st and 2nd year mentees and 20 3rd and
4th year mentors come together and
bond. Our goal was to give our 1st and 2nd years the support and advice
they need in planning out their
future.
Lastly,
but certainly not least, we had the most
successful and meaningful spring/graduation
banquets ever thrown. Oh, and did we
mention, it was on a BOAT! This night was
full of memories, laughter, and a whole lot of
dancing… from both students AND profs! We
also initiated MISA’s first annual awards
ceremony. We gave out an award of
dedication for students to Dr. William
Ramey, and an award for
teaching to Dr. Kenneth Harder.
This banquet has become more than just a party –
it’s a meaningful event that has students,
faculty, and professors come together in
celebration of the year.
MISA
takes pride that we accomplished all this as a
team, moreover, as a family, dedicated to each
other. We worked hard with purpose – to
create the most unforgettable year for the
students full of opportunity and passion.
What made us strong is our faith in each
other. It wasn’t always a smooth road, but
nothing worth accomplishing ever comes easy, and
we only get stronger and better through
learning. I couldn’t be more proud of this
fine MISA executive team. And as this year
comes to a close, we definitely look forward to
the next year and to the next MISA team.
MISA and MBIM could not be in better hands as
the new executive team carries on the MISA
legacy and the MISA
experience.
The most
important people MISA will ever thank for such
an incredible year are our students. We
truly believe that MBIM produces the most
passionate and dedicated bunch of
students. MISA couldn’t be anything
without your consistent support. For all
you incoming students next year, we truly
endeavor to become a member, get involved, and
enrich your student experience. Be proud
of the program you are in. Be proud to be
MISA.