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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 to degrade cellulose into glucose, and another for yeast to convert glucose into ethanol. The second option involved one bioreactor and a E. coli-yeast co-culture. 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 experiments.



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. (link out)







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 David Lloyd’s interview here. (link out)






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.

Safety

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:

1. is our design safe?
2. 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 organism may 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 per year.

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 market.

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 (click here to visit the outreach page), 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.