Difference between revisions of "Team:Groningen/HP/Gold Integrated"

Simon van der Els works for NIZO. NIZO is the Dutch institute for dairy research. Simon his research focusses on bacteriophages and CRISPR-Cas. We send him our project proposal and called to discuss the details. He was able to give us a better insight into the growing problem of bacteriophages in the dairy industry. We also talked about the feasibility of the project, about which steps should be working relatively easy and which steps would be really challenging. It was nice to have someone specialized in the subject talking with us and giving us an idea of where we should start. At the LAB (Lactic acid bacteria) symposium in Egmond aan Zee, we also met with Simon. We were able to talk about our research and ask technical questions. For example, he helped us with which promoter we could use.

DSM cultures is one of the main providers of dairy starter cultures and has more than 100 years of expertise in the dairy industry. As they could potentially benefit from our detection device, and have knowledge about bacteriophages we decided to get in contact with them. During a phone conversation we spoke with Thijs Kouwen, senior scientist and expert on bacteriophages and starter cultures. We learnt that bacteriophage detection is performed by both major dairy factories and companies that provide starter cultures, such as DSM. There is a need for a fast bacteriophage detection system in the dairy industry and that, indeed, bacteriophages cause a significant problem to the cheese making process. DSM provides a free service of bacteriophage testing for their customers, for which they use plaque assays and sometimes qPCR. Thijs mentioned that these tests take quite a lot of time. According to Thijs an ideal detector would have the following characteristics: · Can differentiate up to 700 species of phages · Has a detection limit of 100 phages per ml · Has a detection time of 30 minutes to one hour · A detection limit of 10.000 – 100.000 would be useful as well, because the bacteriophage level will get problematic. We are currently working very hard to ensure that our product meet these specifications as much as possible.

We had a phone call with Jan Willem Sanders, a science leader in Microbiology at Unilever. Unilever does not primarily focus on dairy products, but Jan gave us some good starting points for our project with questions such as: ∙ What is the detection limit of the method? What sample size is needed? ∙ Can different species (or strains) be detected in parallel? ∙ To what level of identification can the method be used: genus-species-strain? ∙ Can the method quantify live cells in the presence of dead cells of the same genus-species-strain? ∙ Is the method reliable to detect microbes in a complex food matrix (without enrichment), such as cheese, margarine, soups, powders containing spices, etc. and their ingredients? ∙ How would you validate the method? How does it compare to existing methods? ∙ How could you modify the method to allow for immediate read out (current methods take half a day up to multiple days)? ∙ How could you modify the method to allow for read out on a factory floor (current methods require a micro/molecular lab.)? ∙ How could you modify the method to allow for read out by non-trained people (current methods require experience in microbiology/molecular biology)? After this conversation and asking ourselves these critical questions, we decided to focus on an easy to use device that could possibly be used on the factory floor by someone without a synthetic biology background, hence the fact that we proposed a cartridge which would be doubly contained and is very easy to use. Of course, such an application gives rise to other questions, such as safety and regulation. We discussed this thoroughly **here a link or something.

When designing a product targeted towards the dairy industry, what better thing to do than visit a dairy industry ourselves? As committed IGEM-team members, we wanted to visit dairy companies at work, on site. To this end we were kindly invited by a major dairy company's technologist to get a tour of a cheese factory. Prior to our tour we got safety instructions. Afterwards we were given the opportunity to ask questions about the effect bacteriophages have on starter cultures. We learned how they measure a bacteriophage infection of starter cultures in their factory and how they proceed afterwards. When something goes wrong in the fermentation process, either by bacteriophages or something else, they will slice the cheese in blocks and use it for other purposes. She told us bacteriophage infections do happen, but due to strict cleaning measurements the impact has been greatly reduced. Through this excursion, we were able to envision the sort of environment where our final product could potentially be used and also to talk to the people who could potentially work with it.

After some email contact we talked to Arla in Denmark via Skype. We got some tips on how to communicate our the project to the general prublic. For instance using the word ‘virus’ on the homepage of our WIKI could immediately scare people and that is definitely something you do not want. So it is best to use the word phage or bacteriophage and explain what is meant by this. We implemented this, and some other suggestions they made on our wiki. Two researchers from Arla, who also joined the conversation, were really interested in our project and had some questions prepared. Besides that, Arla also decided to sponsor our project! We explained everything got to know which are the most often occurring phage infections and how they currently detect them. .

We visited the Research facility of the same major dairy company in the Netherlands to discuss our project with Arjen Nauta (Sr. Scientist Nutritional Sciences). Since our project focusses on detecting bacteriophages which can negatively impact various dairy production lines, we were excited to talk to a bacteriophage research expert in the dairy industry such as Arjen Nauta. He kindly discussed the issues he faces in his research concerning bacteriophages and provided us with helpful advice for our project. Arjen pointed out that the use of GMOs for the dairy industry is very tricky. Even though our detection device will not get in contact with the product, the factory still needs a permit to use it. This permit is accessible by the public and as the use of GMOs in Europe is still very controversial, they do not want the risk of a NGO getting hold of it. Our detection device could however be useful in their research laboratory. Current detection techniques are not able to detect new bacteriophages. If we could implement a way that new bacteriophage sequences can be obtained, this would give new opportunities for bacteriophage research. This is not implemented in our current design due to the strict timeline which we're working with, however we've taking this into consideration in designing the future scientific outlook of our project.

During our skype call with Wouter Ghering (RIVM), who deals with biosensors and its efecton the environment, we came across a certain German scientst and the company ARSOlux that was able to work with GMO’s in a moving truck. During our talks with dairy companies, we learnt that getng a permit in order to work with GMO’s in factories is a big threshold for companies, primarily due to their public image. To this end we were interested ifit is possible for a biosensor to be used without the dairy company having to request apermit for working with GMOs. Therefore, the informaton that Wouter gave us was extremely helpful. In this scenario, we envision a dairy company that will send samples to amoving truck company where our product, IMPACT, is used to detect whether certainbacteriophages are present. In this way, the dairy company is not associated with the use ofGMO’s. Wouter also suggested that we talk to Rob Duba, a senior policy ofcer onbiotechnology at the Department of I&E, about this subject. We contacted him as part of our Human practices. We are also trying to establish communications with ARSOlux in order to analyse the logistics of our product potentially being used in a moving truck, but we currently have no response.

As part of considering the implications of our product and finding a possible potential market for it, we contacted Thomas Jansen from the Christian Hanssen company and had a skype call with him on the 13th of September. The company mostly deals with starter cultures and tests for the presence of bacterial phages. From our talk with him, we found out that the current go-to method for their company is doing a plaque assay and that when needed, they also use qPCR. Their test takes 2-3 days if everything works properly. He mentioned three points that were particularly relevant to us. First, that our product would be useful if it takes a few hours and around the same concentrations as we got from DSM. We took this into consideration and are designing a final product which will hopefully only take a few hours. Secondly, that the device will be more useful if it can detect a specific strain. This is something we’ve taken into consideration in building our final product. By imputing different plasmids into our system or adjusting the plasmid for different strains, it will be able to detect specific strains if all works properly. Thirdly, that our device can also be used on the factory floor. Currently, European regulations prevent our device from being used on the factory floor as it contains GMO's. We however still took this into consideration by designing an on site detection system which could potentially be used on the factory floor. We designed our product as safe as possible, if it would be allowed. Based on this conversation, together with the impressions we received from conversations with other factory specialists and our factory visits, we decided to broaden our horizons and look beyond the dairy industry in Europe. We tried to contact companies in some other continents which have less strict GMO standards, however, these companies never responded to our inquires. Perhaps they thought we were some sort of undercover journalists or feared the potential negative publicity, or just haven't gotten around to responding to our inquiry.

After we were told in the dairy factory we visited that they send milk samples for bacteriophage testing to their own laboratory facility we definitely needed to visit that as well! The technician of the factory kindly gave us contact information from an analyst working there. During the day we met multiple persons working at the laboratory. They do weekly bacteriophage testing for dairy factories located in the Netherlands, Belgium and Germany.