Difference between revisions of "Team:Groningen/Engagement"

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<h3>Thijs Kouwen, DSM - 27 June</h3>
 
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<p>Thijs Kouwen works as a scientist at DSM cultures and works at starter culture development and is in
 
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particular concerned with phage resistance of these cultures.
 
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First of all he told us that there is a need for fast phage detection in the dairy industry and that
 
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phages form a significant problem. The current detection is performed by both major dairy factories
 
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themselves as companies that produce starter cultures such as DSM. Some rough estimates: ¼ of the
 
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costumers of DSM has their own testing facility (only the largest) 1/3 of the costumers sends their
 
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samples to DSM for testing and other do not test for phages. Of the samples send to DSM ~30%
 
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contains phages and in 5-10% of the cases the amount of phages reaches a critical level.
 
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Although in most cases measurements can be taken in time, sometimes a complete batch is lost due
 
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to an infection. If this happens this results in significant costs for the company, since the milk is
 
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almost as expensive as the final product.
 
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DSM performs to types of testing a ‘acidification test’ which takes 4-8 hours and during this period
 
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the acidification of the medium is measured and the curve gives information about the health of the
 
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culture. Another test is an overlaytest and this takes an overnight incubation step and is therefore
 
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quite time consuming.</p>
 
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<p>Companies themselves also make use of ‘simple’ microbiological testing techniques and the largest
 
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companies use more advance techniques such as qPCR. The main problem for dairy companies is
 
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that they usually do not have the microbiological expertise to carry out the testing themselves. Also
 
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the testing is seen as a service that starter culture producing companies such as DSM should offer.
 
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At low levels of phages the infection will result in slowing down of the fermentation process, this
 
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slowing down can also be seen if the pH is followed during the fermentation. If the pH drops to
 
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slowly a first measurement is adding more of the starter culture. This is a sign of a phage infection
 
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with a low concentration of phages.
 
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If the concentration becomes higher there are two possibilities; either clean the whole system
 
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thoroughly with acid and basic chemicals/ chlorine. (Sib sytem?). Cleaning is performed by the
 
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factories themselves. And it’s done by hand since phages can reside in small corners of the tank.
 
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Another possibility is adding another starter culture that is insensitive to the infection that is at hand.
 
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The samples DSM gets are often samples after the fermentation is performed and the results of the
 
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measurements are therefore often too late for the batch that is measured. Sometimes companies
 
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perform multiple fermentations in a day and at the end of the day the samples are send to DSM.
 
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After analysis of the samples the best of the two options mentioned above can be carried out before
 
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the next fermentations are performed.</p>
 
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<p>The source of the phage can either be from the starter culture or from the milk. The latter seems the
 
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most common. Detection can performed (raw milk) or after the fermentation (Wei). In some cases
 
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such as with Mozerella it can also be tested during the fermentation process.
 
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The measurements that can be taken also depend on the type of fermentation. Dutch cheeses such
 
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as Goude use a complex undefined blend ( hundreds of bacterial strains) starter culture. So these
 
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companies cannot easily switch to another starter cultures and they will need to clean their tanks
 
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after infection. Also these starter cultures contain many types of phages that make sure that not one
 
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strain gets the overhand over other strains. However if the production is switched to another
 
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product the phages can reside in the tanks and then they can form a problem.</p>
 
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<p>American and Australian cheeses use defined cultures of 3-5 strains, in which is strains has specific
 
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tasks. In these fermentations phage problems are much more important. In this case it would be
 
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quite easy to change the culture since there are multiple strains that are sensitive to different phages
 
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but are interchangeable for the fermentation.
 
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For the defined blends phages are the biggest problem and if they could be detected in a fast and
 
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quantitative manner companies could react on infections that are rising by adding some resistant
 
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strain against the infectious phage. To serve this purpose a detector should have the following
 
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characteristics: differentiate/ detect up to 700 species of phages, have a detection limit of 10^2
 
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phages per mL and a detection time of ½ to 1 hourA detection limit of 10^4/10^5 phages per ml
 
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would make our project a usefull detector as well, since at these levels infections become
 
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problematic. At higher concentrations the infections are too out-of control to be treated.
 
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As long as our product contains live GMO it would probably not be used by the most companies.
 
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Since they do not have the expertise nor the will to work with GMO’s. Also if a GMO would end up in
 
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the final product it would result in immense reputational damage. Therefore our detection system
 
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should not be complicated to use and without risks of escaping GMO.
 
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At the quality labs of DSM they could use it, but for our project it would be best if it can be used at
 
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the site of the factory since that would be the quickest.</p>
 
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<p>The major companies that now use techniques such as qPCR might be possible to get an MLI lab in
 
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the factory or on the factory terrain.
 
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Further in our final product we need to use several strains of both L. lactis as S. thermophiles (these
 
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are the two major bacterial species that get infected), since the sensitivity to phages differs between
 
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each strain.
 
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Another thing that is done against phage infection is making starter cultures more phage resistant. At
 
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DSM this is done by increasing the phage resistance of the different bacterial strains. And by
 
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optimizing the combination of several strains to decrease the overlap of sensitivity. Another thing
 
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that is done by companies is rotation of starter cultures.</p>
 
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</div>
 
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<h3>Zoë Robaey - INPUT DATE</h3>
 
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<h3>Unilever Skype Call - INPUT DATE</h3>
 
<h3>Unilever Skype Call - INPUT DATE</h3>

Revision as of 13:50, 9 October 2017


Public Engagement

Here is described all the people we talked to!

European Meetup iGEM Delft - 6 July

The European iGEM meet up for the Netherlands was held in Delft this year. The meet up started with a talk by Cees Dekker, a well known physicist. It was quite interesting to hear about the common ground between physics and biology in his talk. After the break we had the talk from Denis Murphy, he is highly involved in palm oil. Palm oil is used a lot for cosmetics in richer countries, and for sustenance in poorer countries. He expanded on a specific application for genetic engineering for making sustainable palm oil plantations. The main event of the day was of course the poster presentations of all the iGEM teams themselves. We walked around a lot, talking to pretty much every team at least once. It was very nice to see all the Dutch teams again here after we had met them during the Dutch iGEM meet up in Wageningen. During all this we handed out our 3D printed phages to the teams too. The last part of the day was a BBQ with some drinks. We left together with some of the other teams and talked more about how our respective projects were going.

Ferdinand Van Der Graaf - 30 August

We met with Ferdinand van der Graaf to discus the game we are designing about synthetic biology safety. He works as a researcher at the UMCG hospital, as well as a teacher at a local highscool. In his teachings he uses a lot of educational games, and had previously designed a game to teach about natural selection. We talked about how to implement game elements in a balanced way while not giving up too much learning elements. Furthermore he recommended to stick to tried and true game elements that work, something we found to be true too.

Maakfestival - INPUT DATE

This years’ Maakfestival was held at the Groninger Forum and provided Dutch manufactures – in the broadest sense – who are living in the north of the Netherlands with the opportunity to excite teens about diverse technical projects. We had our own iGEM booth with various attributes from the laboratory, such as (properly sealed) Escherichia coli bacteria with Green Fluorescent Protein and talked about synthetic bacteria to interested people from every age group. Participants were invited to write their own opinion on bacteria, ranging from ‘cute’ to ‘useful’. Besides that Joana gave a short talk about iGEM and synthetic biology in one of the ‘maker talks’. Sometimes, we were even surprised what some children already knew about bacteria. In the end we were really excited to introduce others to the fascinating world of synthetic biology.

NBC - 16 May

On Tuesday the 16th of May 2017 the 17th edition of the Netherlands Biotechnology Conference (NBC-17) was organized by the Dutch Biotechnology Association (NBV). During this day, 135 professionals and students working in the biotechnology work field were connected to each other and informed during several interactive sessions and keynotes about the latest developments in their work field. Here, we gave a pitch about this years’ Groningen iGEM project and were allowed to present our poster together with other Dutch iGEM teams!

Benelux Meetup - INPUT DATE

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KIVI Lecture - INPUT DATE

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Richel Bilderbeek - INPUT DATE

We contacted Richel Bilderbeek to give us some tips about preparing lessons for children from 10 to 12 years old. He is highly experienced in educating 7 till 18 year-olds. We are working together with the Scholieren Academie to educate kids. The general goal is informing the kids about the university. What do students do? What am I, a molecular biology student, doing in a laboratory? The Scholieren Academie wants to start this project, because research has shown that kids from the eastern part of the province Groningen, choose less for higher education. By starting really early with informing these kids about the possibilities of the university, the Scholieren Academie hopes that children will choose more often for higher education after primary school. We went to some schools to give a guest lecture. A few days later, the children came to the lab to do some experiments themselves.

LAB Egmond aan Zee - 28 August

We attended the 12th LAB Symposium in Egmond aan Zee on the 28th of August. This is a yearly one week event about Lactic Acid Bacteria. Thanks to the organising committee we were able to attend the symposium for one day with three people of the team. This was a really great experience. It gave us the opportunity to present our poster during the poster sessions and to talk to researchers who are specialized in working with CRISPR-Cas, bacteriophages and Lactococcus lactis.

GBB Symposium - INPUT DATE

The Groningen Biomolecular Sciences and Biotechnology Institute (GBB) is the centre for biomolecular sciences at the University of Groningen. We were invited to give a presentation of our project and show our poster in the poster sessions. During the event we got the opportunity to explain our project to other researchers from the university.

J. Hille - INPUT DATE

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Wouter Ghering - INPUT DATE

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Rob Duba - INPUT DATE

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Jeantine Lunshof - INPUT DATE

Jeantine Lunshof works as a bioethicist at the Church laboratory in Boston. We contacted her in the beginning of our project to get a general view on ethics in the field of synthetic biology. After explaining the general idea of our project, she told us something about her work at the Church lab. Together we thought about a story which would be interesting for the public and would not scare them of. Jeantine also mentioned that the consumer of dairy products is in our case a very low stakeholder. This definitely does not mean we should set them aside. It is important to inform them and think about the story you will tell them. Why is our project important for the consumer? Does it ensure better/safer dairy products or will the dairy products be of a higher quality? The most important and helpful thing she told us was to make clear at all cases that our diagnostic tool will not get into the food! Only one small mentioning of this of one of the team members could make the headlines and break your story. Possibly the team’s project would only get remembered by the negative attention it got. Ultimately, chances of getting the product on the market would be close to zero. Tip: one team, one voice!

Siger - INPUT DATE

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Simon van der Els, NIZO - INPUT DATE

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 And telling where we should At the LAB symposium in Egmond aan Zee we met with Simon. We were able to talk about our research and ask questions. For example, he helped us with which promoter we could use.

Arla Skype Call - INPUT DATE

How are you currently combating phages? How frequent and in which way are you currently testing for phages? What are the parameters you are monitoring? Are phages infection a big problem for your company? How long does it take you to get result, starting from probe taking to getting the results in the company? We are very interested in the current situation in different dairy production plants so that we can adjust our final product which would suit the current wishes of the industry.

In what way will our product be most useful to the end user? What are desired characteristics (in terms of design and implementation) that you would value the most? Through other talks, we learned that you cannot work with GMOs directly on the factory floor. This makes it that samples have to be taken to another testing place, either within or outside the production facility/plant. This way, our ideal goal is to deliver a system that, with simple maintenance, can continuously survey samples from the main production line for contamination with phages. However, another option is to design a portable device which uses our reporter strain in a contained matter, so you would not need a GMO regulated area. This makes its implementation potentially viable in other settings besides the dairy industry.

What are the parameters for phage infection in a factory (pH, OD600nm, MOI etc.) How does this translate to detection sensitivity? With this information, we could get a better view of the desired environment for our detection system.

On the 22th of August we talked to Arla in Denmark via Skype. We got some tips on how to communicate about the project. 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. Two researchers from Arla, who also joined the conversation, were really interested in our project and had some questions prepared. We explained everything and also asked questions, because we are really interested in the point of view of the company to our project.

Unilever Skype Call - INPUT DATE

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Goedhardt, Maaike de Heij - INPUT DATE

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Cogem Symposium - INPUT DATE

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