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

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<h3>Unilever Skype Call - 13 July</h3>
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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:
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∙        What is the detection limit of the method? What sample size is needed?
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∙        Can different species (or strains) be detected in parallel?
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∙        To what level of identification can the method be used: genus-species-strain?
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∙        Can the method quantify live cells in the presence of dead cells of the same genus-species-strain?
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∙        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?
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∙        How would you validate the method? How does it compare to existing methods?
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∙        How could you modify the method to allow for immediate read out (current methods take half a day up to multiple days)?
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∙        How could you modify the method to allow for read out on a factory floor (current methods require a micro/molecular lab.)?
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∙        How could you modify the method to allow for read out by non-trained people (current methods require experience in microbiology/molecular biology)?
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After this conversation 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.
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Revision as of 13:25, 10 October 2017


Human Practices

What we did for our integrated human practices

  • In short: how did we implement all the information we got from our interviews?
  • We decided to make a product that is not in contact with the end product.
  • We decided to use sequences from a SK1 bacteriophage.
  • We designed an on-site detection cartridge which is easy to use.
  • We designed a program which can determine spacers for specific bacteriophages.
  • We added a hydrogen peroxide compartment to the cartridge to ensure safe disposal.

Dairy Factory Workum - 10 August

As committed IGEM-team members do, we wanted to visit dairy companies at work, on site. To this end we were kindly invited by a major dairy company 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 damage has gone down a lot. For us, this was mostly a learning opportunity to be 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.

Dairy Research Plant Wagening - 23 August

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.

Christian Hansen, Thomas Jansen - 13 September

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. 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 Chr-Hanssen offers phage detection as a free complementary product, but if the they had a test they can offer the customer at home that would be better. As our product contains GMO’s, European regulations prevent it from being used on the factory floor, we cannot currently offer this. Instead we will make our product as safe as possible as 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.

Thijs Kouwen, DSM - 27 June

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 might 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 learned 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 dairy industry. DSM provides a free service of bacteriophage testing for their customers, for which they use plaque assays and sometimes qPCR. Thijs mentioned that these test 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.

Arla Skype Call - INPUT DATE

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Unilever Skype Call - 13 July

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 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.