Team:Dalhousie/HP/Silver

silver int

Talking with Experts

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
Mark 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 Scott 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? and (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.