Talking with Experts
Trevor Charles, PhD, Department of Biology, University of Waterloo
Dr. Charles is an expert in functional metagenomics, as well as the co-founder of Metagenome Bio Inc, a company which makes and screens metagenomic libraries for industries like mining, and agriculture. In June of 2017 he welcomed members of Dalhousie iGEM into his lab to teach the basic of metagenomic library construction. Dr. Charles’ team are the reason we got as far as we did, offering their experience, as well as giving us their cosmid, and the bacterial host.
Su-Ling Brooks, PhD, Department of Process Engineering and Applied Science, Dalhousie University, Halifax, Canada
Dr. Brooks’ research revolves around bioprocessing, food engineering,
fermentation, extraction of natural products, and waste utilization and
treatment. For this reason, we eagerly wanted to speak to her about the
biofuel component of our project, and our ideas surrounding bioreactor
construction. We presented her with two bioreactor ideas (see images
below). The first option involved two bioreactors, one specifically for E. coli
degrade cellulose into glucose, and another for yeast to convert glucose into
ethanol. The second option involved one bioreactor and a E. coli
During the course of our presentation, Dr. Brooks
posed many insightful questions primarily surrounding the logistics of co-cultures, and the requirements of
our organisms. At the end of the meeting we came away realizing that we still had a lot to learn
about bioreactors. It was at this meeting that we began drawing up plans for future shake flask
Mark Dubé, Port Hawkesbury Paper, Cape Breton, Canada
Mr. Dubé elaborated on the cellulose waste treatment at the Port Hawkesbury pulp and paper mill
in Cape Breton and identified two main types of waste: bark chips and a mix of clay, cellulose,
and organic phosphates. All this waste goes into a biomass boiler to produce the steam needed
to dry the paper in downstream processes. “We have looked into biofuel production, but it is
too expensive…the technology isn’t efficient enough.” Currently, Port Hawkesbury Paper buys
wood waste from surrounding companies to fill it’s need for steam.
Dr. Eddy Rubin, Chief Science Officer, Metabiota, San Francisco, USA
Dr. Rubin has years of metagenomics under his belt, so we asked him which was better:
sequencing-based or functional metagenomics? “Well, functional is great but I’m a sequencing
guy... I’m interested in scalable things.” Dr. Rubin’s argument was with the advent of next
generation sequencing and better DNA synthesis, you can produce terabytes of data and
synthesize whatever you want from it. This is a much more scalable process, you don’t have to
spend years designing functional assays.
See the rest of Dr. Rubin’s interview here.
David Lloyd, Co-founder and Director, FREDsense, Calgary, Canada
David Lloyd was involved in iGEM during his undergraduate degree at University of Alberta and
as a mentor during his Masters degree at University of Calgary. During his time at the University
of Calgary he, and a team of students, developed a biosensor which morphed into the company
FREDsense. We asked for his insight on how to develop an iGEM project into a company.
“Spend your time really figuring out what the value your product is going to provide to that
customer base. Picking up the phone and having those conversations is really important. It
was through that process […] we ended up changing the sensor we were building to look at
other market opportunities.”
See the rest of Dave’s interview here.
Scott Doncaster, Vice President, Manufacturing Technologies and Engineering, BioVectra, Charlottetown, Canada
BioVectra is a contract pharmaceutical fermentation plant that using bacteria and fungi to
produce small molecule drugs or biologics. Being in charge of manufacturing and engineering,
Scott is well versed in safety practices. Although BioVectra works with BSL-1 organisms, the
volume of organisms they use requires them to treat the bacteria or fungi as if they were BSL-2.
We asked Mr. Doncaster what safety mechanisms must be in place for large scale fermentation to work.
“Containment is key! Rooms have slanted floors so [if a spill were to happen] it all goes into a
contained grate, that would get autoclaved in emergencies. The building has been built with
special air circulation, sterilization tools, air locks, temperature control and much more.”
Stephen Snobelen, PhD, Associate Professor of Humanities, University of King’s, Halifax, Canada
Some of Dr. Snobelen’s research interest include science in popular culture, and the
popularization of science, therefore we knew we wanted to meet with him to discuss our
science literacy survey. We did not have much previous survey planning experience to draw
upon, and thus it was great to get an expert opinion on how to form unbiased questions. Dr.
Snobelen advised us not to use the phrase “science illiterate” as it could potentially polarize the
audience. Furthermore, we discussed that people are not scientifically literate or illiterate. For
instance, someone could be literate in biology, but have a poor understanding about physics.
For this reason, we tried to instead paint the idea that science literacy is a spectrum.
After speaking with Scott Doncaster from the fermentation company, BioVectra, it was
clear that there were a few safety aspects to consider if our project were to make it to the
bioreactor stage. In this section, we hope to address two questions:
- is our design safe?
- What are the major concerns for companies?
Whenever organisms are genetically modified to do something they wouldn’t normally
do, safety is definitely something worth considering. Furthermore, because genetic
modification is such a contentious topic it is important to be very clear about the control
mechanisms and safe-guards surrounding these organisms. While we are not yet at the stage of
introducing our bacteria into a bioreactor we have been thinking about possible ways to make
our project safer. During our tour of the bioreactors at BioVectra the most obvious safety
feature was the slanted floors to collect any fluid that may leak. All of this collected
biohazardous material could then be correctly disposed of via an autoclave. There are
additional ways to safe-guard our biofuel design that do not involve infrastructure, and instead
involve the organism itself. We first brainstormed potential “kill switches” which would ensure
that if our organism escapes it would not be able to survive long in the wild. The problem with
kill switches, however, is that they can sometimes suffer from selective pressure. We were then
inspired by the publication by Mandell et al. (2015) where the researchers altered the genetic
code of an organism to confer metabolic dependency on nonstandard amino acids.
Furthermore, the system these researchers developed blocked incoming and outgoing
horizontal gene transfer with natural organisms. Whether it be by controlling the environment,
controlling the organism, or both, we have been thinking about safety since the start of our
project. We are eager to ensure that our cellulose-degrading E. coli
offers a safe and efficient
alternative to current biofuel systems.
In talking to representatives at BioVectra we learned about biosafety in an industrial
environment. While the people we spoke to did not voice any concerns regarding the current
state of our project, they did provide us with things to consider if we were to scale-up our
project for their reactors. Firstly, there bioreactors do not support a co-culture system and
therefore our design would have to include multiple reactors. Secondly, an E. coli
be just BSL-1, but when it is found in large quantities, such as in a 3000 L bioreactor, it has to be
treated as a BSL-2 organism. Finally, biosafety is not just to protect us and the outside from the
organism, but to also protect the organism from us.
In speaking with representatives from BioVectra we gained valuable insight into the
logistics of running a large biofuel-production system. In the future when we are prepared to
scale-up our safe system, and when we have thoroughly tested the efficiency of our organism,
we will know what to expect when approaching companies.
How We Fit In: Researching Companies
There are five major biofuel companies in Canada each doing something slightly
different. Here are summaries of those five major companies.
Iogen Corporation is one of the longest withstanding biofuel companies in Canada. They
were founded in 1975, in East Ottawa, and have been producing cellulosic ethanol since 2004.
They focus on plant fiber and enzymatic hydrolysis in order to produce a dilute ethanol stream,
which is further concentrated to commercial-grade fuel.
The St. Clair ethanol plant from Suncor Company, has been producing 400 million tons
of biofuel per year. This facility in the Sarnia-Lambton region has been running since 2006, and
it has been named the largest ethanol plant in Canada. Suncor uses corn fiber to produce their
strain of ethanol. They have partnered with Petro-Canada to blend their ethanol with Petro-
Canada’s gasoline. Although this does not diminish greenhouse gases completely, the use of
blended ethanol-gasoline fuel has been reported to reduce CO 2 emissions by up to 300,000 tons
Evoleum Biofuel is located in Saint-Jean- sur-Richelieu, Quebec. It is a major producer
for biofuels from second generation raw material. At Evoleum, the second generation materials
used are exclusively vegetable oil. They have created 95% biodegradable biodiesel, that
produces no greenhouse gas emission. Since 2010, the use of the recycled materials for biofuel
in Montreal, from Evoleum, showed a decrease of 4.8 cents a liter on biodiesel.
In Nova Scotia, the CelluFuel Company uses low-value wood fiber to convert into
renewable diesel. They receive their wood fiber from Freeman’s Lumber in Greenfield, Nova
Scotia. The wood fiber undergoes a series of catalytic induced depolymerisation’s to produce
the renewable diesel. Today, CelluFuel is currently in its demonstration phase, and once they
have successfully completed this project they will begin producing commercial-grade fuel.
Another upcoming company for biofuel production in Canada, is Woodland Biofuel,
Incorporation. They are currently in their demonstrative phase with their start up plant located
in Sarnia, Ontario. Woodland is interested in cellulosic ethanol production, using agriculture
and forestry waste. The President, Greg Nuttal, states that it will be one of the lowest fuel
productive costs, not just for ethanol but other fuel industries, including gasoline. He suggests
the company will produce 200 million gallons per year. As of now, this company is looking into
another plant location in Merritt, British Columbia.
Clearly biofuel production is a popular industry sector with each of the aforementioned
companies carving out a particular niche for themselves. We believe that in this competitive
field, our project could have potential to hold its own. Firstly, our project would utilize
cellulose-containing waste from various industries and therefore our feedstock substrate would
not be limited to one particular area. This could be important in the future when certain
resources become scarce. As long as our substrate contained cellulose we could convert it!
Secondly, these companies still seem dependent on chemicals, water, or heat to aid in the
production process. Our project would utilize the enzymatic capabilities of microorganisms to
convert cellulose into glucose. Furthermore, we could modify this process to enhance for
production, for example, by modifying our organism. While we are a while away from making a
name for ourselves in the Canadian biofuel game, we have found our own niche within the
Practising Science Communication
We did not want our research to only reach the eyes and ears of those partaking in
iGEM, therefore we practised tailoring our project description for different members of the
community. When writing these “elevator pitches” we were surprised to discover how difficult
it can be to modify language to fit the audience. Children in particular were a difficult group to
target as they could have varying degrees of understanding and varying interest levels. Writing
pitches for discussions with companies and financial supporters was easier because the
objective of the talk was clear: how can we demonstrate to companies that we are worth
investing in? We ended up using many of these “elevator pitches” in our outreach events as
well as when talking to potential financial supporters. Here are a few examples of those pitches.
Media: Story Oriented
The International Genetically Engineered Machine (iGEM) is a global initiative that aims
to get students tackling real world problems using synthetic biology. Competitors get to choose
which problem to address. We wanted to focus our project on something that was close to
home, yet could also have a big impact. One of our first ideas was to develop an easier way to
make biofuel. While this idea is not particularly novel, we managed to put our own spin on it.
We’re creating biofuel from forestry waste. Why? The forestry industry is a major source of
cellulose waste. Cellulose can actually be converted into ethanol -- which is a potent biofuel.
There are already ways to convert cellulose into ethanol but they are not exactly efficient. After
a lot of research, we think we have found a way to make the conversion process more efficient.
Lots of animals eat wood and they have to digest it somehow, right? Most animals can’t
do this themselves and instead rely on bacterial enzymes found in their gut to help them. One
of these animals is the porcupine. We decided to take the cellulose-degrading enzymes from
one of the porcupine gut bacteria to see if we could make it work for us. In the future we are
going to try to streamline the process so that we can make large amounts of ethanol in an
efficient, waste-free way. We’ve been working throughout the whole summer to make this
happen, and are now getting ready to present our research at the global iGEM conference in
Boston. In front of a global audience we will be the only team representing Atlantic Canada!
The message: Team of undergraduate students participating in an international competition in
which they are developing a novel biofuel production system.
Technical difficulty: Limited scientific jargon, accessible to a general audience.
Corporations: Economically Oriented
iGEM is a global initiative encouraging students to use synthetic biology to solve real
world problems. Our project tackles two major problems facing Atlantic Canada: sustainable
fuel and forestry waste. We’re using synthetic biology to convert cellulose waste from the
forestry industry into ethanol, a potent biofuel. Our team is comprised of eager and passionate
undergraduate students and graduate mentors from all disciplines. iGEM is currently the only
opportunity in Atlantic Canada for students to obtain hands on synthetic biology research
experience. We’ll be traveling to Boston in November to represent Atlantic Canada at the 2017
iGEM jamboree where we will be presenting our findings to researchers, corporations, and
students from around the world.
The message: Our project tackles two issues for Atlantic Canada and could offer an
economically viable solution. Furthermore, students part of iGEM have training that is not
found elsewhere in the province.
Technical difficulty: Limited scientific jargon. Very short and concise.
A 6-Year Old: Fun Oriented
Within your stomach are millions of very tiny bugs called bacteria that help you out in all
sorts of ways such as breaking down the food you eat. It is not just people who have these
helpful bacteria, lots of other animals do as well. For example, the spiky animal called the
porcupine has bacteria in its stomach which help it break down the wood it likes to eat. We
wanted to see if we could get the parts of the bacteria responsible for breaking down the wood
to function outside of the porcupine stomach. That way we could break down left over wood
into helpful things such as fuel.
The message: We are attempting to harness the different abilities of the bacteria found on and
in the body.
Technical difficulty: No scientific jargon. Not focused too much on our project.
As communication is the major theme to our outreach efforts , it was imperative that we practiced and attempted to better our own
communication habits. Writing these elevator pitches served as an important exercise in
learning how best to convey our project.