Difference between revisions of "Team:Groningen/Safety"

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<h1> Safety </h1>
 
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When handling biological materials such as GMOs, safety measurements should be taken into account. To this end, various levels of institutes/organizations are involved to maintain all the different aspects of safety. Here, we will describe the most important organizations who are responsible for this and provide you with all the necessary information. 
 
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European Level:
 
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Most of all the Dutch legislation concerning biotechnology is derived from the European Union (EU). From a European level, a directive was made to ensure safety not only for the researcher but also for the laboratory and the environment. For more information click here (=hyperlink https://ec.europa.eu/food/plant/gmo/legislation_en).
 
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National level:
 
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The Dutch government processed these rules into nation-wide legislation, for more information click here (=hyperlink  http://wetten.overheid.nl/BWBR0035072/2017-07-01#Hoofdstuk2 ). As of 2016, the Dutch government also started the research program termed ‘Biotechnology and Safety’ with its goal to gain scientific insights into the possible long-term risks and insecurities derived from biotechnological innovation.
 
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Since our project focusses on the dairy industry we want to highlight the following legislation regarding the labelling of foods and other products with GMOs. The most important ones are highlighted here: 
 
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Legislation labelling of foods and products with GMO’s
 
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Products containing more than 0,9% of GMO’s ingredient, the manufacturer should label it on the product.
 
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Milk, meat and eggs from animals which have consumed GMO-food do not have to have labelled
 
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In the case that products do not contain any GMO’s, food manufactures are allowed to label it ‘made without gentechnology’ when they conform to the rules of ‘Warenwetbesluit Nieuwe Voedingsmiddelen’. 
 
  
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Dutch Department of Infrastructure and Environment
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In addition, the Dutch Department of Infrastructure and Environment (Ministerie van Infrastructuur en Milieu, I&M) is responsible for renewing and modernizing policy concerning biotechnology. Not only does this entail creating more opportunities for this sector, it also focused on safeguarding safety and providing support for biotechnological innovations. For more information about our talk with Sr. policy officer Rob Duba on Biotechnology at the Department I&M click here (= hyperlink..... )
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<h1 style="text-align:center;">Safety</h1>
  
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National Institute of Health and Environment (RIVM)
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<h5 style="text-align:center;">Save our L.A.B.</h5>
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In turn, the Department of I&M requests advise of the National Institute of Health and Environment (Rijksinstituut voor Volksgezondheid en Milieu, RIVM), a national institute who writes a large amount of advisory rapports for the Dutch government concerning biotechnological innovations. The RIVM focuses on safeguarding consumer health and promoting a healthy environment for all Dutch citizens. Fortunately for us, the RIVM is highly involved in the iGEM completion and aids all Dutch IGEM teams. In turn for financial support they designed the so-called ‘Think before doing’ assignment by which Dutch teams were compelled to, as the name implies, think about biosafety at the start of our project. In collaboration with the RIVM we made a game regarding safety in synthetic biology called ‘Outbreak!’. (link)
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We already spoke to various employees of the RIVM who were so kind to give us advice.  For more information about our talk with Wouter Ghering click here (=hyperlink).
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Rathenau Institute 
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The Rathenau institute, an institute who focuses on stimulating the public and political opinion with regard to social aspects of science and technology in the Netherlands, launched the ‘IGEM-ers guide to the future’ together with SYNENERGENE, a Mobilisation and Mutual Learning Action Plan funded by the European Commission’s FP7 Science in Society Work Program. The guide that was designed was an extremely helpful tool for our human practices-related activities and you can see the results from assignments throughout our website! Curious about our talks with Zoë Robaey? Please click here (=hyperlink)
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The Dutch Commission on Modification (COGEM)
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Moreover, the Dutch government is advised by the Dutch Commission on Modification (COGEM). This organization consists of experts in different fields who write scientific reports about the possible risks of either production or use of GMO’s for humans and environment and informs the government about ethical and social aspects related to genetic modification as well. For more information, please visit the COGEM (=hyperlink http://www.cogem.net/index.cfm/nl/over-ons/missie-visie) website.
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To learn more about our visit to the COGEM symposium regarding gene editing, *click here *
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�University of Groningen
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At our university, guidelines are set up by the Arbo- and Milieu Dienst (AMD; translated Occupational Health & Safety and Environmental Service) and the concerning departments of the university. Together they assign biosafety officers at various research groups and institutes. To view the biosafety officers of the Groningen Biomolecular Sciences and Biotechnology Institute (GBB) please click here (here = hyperlink to; http://www.rug.nl/research/gbb/gbbsafetyofficers/).
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To ensure safety, iGEM Groningen 2017 team members received training from a RUG-biosafety officer about working in the lab with GMOs. Other team members already gained a certificate in Safe Microbial Techniques during their studies (primarily students Biology and Life Science & Technology) demonstrating that they are able to work safely in a lab environment. The training included learning about disinfection and sterilization but primarily focused on the general lab rules (clothing e.g.) and safe microbiological techniques. To handle biological materials such as GMO’s we used biosafety cabinets and open benches.
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10 COMMANDMENTS for Safe Microbiological Techniques (or Veilige Microbiologische Technieken)
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The present day dairy industry heavily relies on the use of lactic acid bacteria like Lactococcus lactis. However these bacteria are particularly vulnerable to bacteriophages. And phage infections  can lead to lysis of the cell culture which leads to a downgraded or even unsellable product. In the worst cases the infected milk is discarded entirely. This results in huge financial losses, stress on staff and problems in obtaining a consistent quality product. So preventing phages infections within dairy production culture is essential in the present day industry. Currently multiplex PCR is used to detect the presence of common phages species, which require regular sampling. The aim of this year’s iGEM project is to simplify this detection and make it more continuous by linking a CRISPR detection system to a fluorescent signal and in parallel a restriction fragment length polymorphism analysis.
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Our systems works in several steps, which are explained in more detail below.
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All VMT related work can only be performed by those people that have permission from the Biological Safety Officer (BVF). Work according to the rules, even if you believe there is no apparent risk.
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During VMT related work all doors and windows have to be closed. Verify that insects and other pests are not present in the lab.
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  <li><b>Infection:</b> Since our system is built in the same organism as used for the fermentation, phages will infect our system automatically.</li>
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Wear a closed laboratory coat. Do not take this lab coat outside the VMT area unless it is absolutely necessary for the experiment. In case of a contamination of the labcoat, sterilize the lab coat first, with bleach or by autoclaving, before washing.
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  <li><b>Spacer acquisition:</b> After infection the CRISPR/Cas complex will recognize the phage DNA and harvest a 25-30 nt spacer and incorporate it into the CRISPR array.</li>
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Clean and sterilize spills immediately. Report serious contamination immediately to the BVF.
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  <li><b>Specific nuclease:</b> The phage specific spacer is turned into a guide RNA which together with Cas9 forms a nuclease that targets a sequence specific for the phage.</li>
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It is absolutely prohibited to eat, drink or smoke, or to have cups, plates, mugs or silverware in the VMT area.
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<li><b>Signal:</b> Our signalling plasmid contains a sequence homologous to the phage DNA in a repressor/promotor region of a GFP gene. Cutting by Cas9 leads to either expression or loss of expression of GFP, which gives an easy to detect signal. </li>
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Pipetting by mouth is prohibited. Used pipettes are collected in a disinfecting solution.
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<li><b>Multiplexed:</b> If our signalling plasmid would contain multiple sequences homologous to different phages we can detect and distinguish multiple phages. We want to do this by incorporating restriction enzyme recognition sites around our phage sequences. Cutting of these sites will result in a change of restriction pattern after a restriction analysis. </li>
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Prevent aerosols. These may be created by -splashing drops; -pouring of liquids; - discharging pipettes; -opening of moist plugs; - using inoculating loops that are too hot. Use needles only if there is absolutely no alternative.
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Glassware and instruments that have been in contact with GMO's (Genetically Modified Organisms, GGO’s in Dutch) have to be sterilized or disinfected before being washed, reused or discarded. Biological waste has to be collected in autoclavable plastic bags, which are autoclaved before discarding (use indicator tape to demonstrate that the bag was autoclaved).
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Wash hands with soap and water after work and before leaving the room. Bench surface areas have to be cleaned and disinfected daily. Keep area clean and organized.
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Record the general nature of the work clearly in a lab journal.
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We think dairy industry would benefit most from the real-time detection of the 10 most common phages using the GFP signal, since they have the means and knowledge to perform a multiplexed PCR to determine the type of infection after getting the signal. However we think our system can also be used for other applications where they don’t have the money and means to carry out multiplexed PCR.
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Revision as of 15:59, 14 October 2017


Safety

Save our L.A.B.

The present day dairy industry heavily relies on the use of lactic acid bacteria like Lactococcus lactis. However these bacteria are particularly vulnerable to bacteriophages. And phage infections can lead to lysis of the cell culture which leads to a downgraded or even unsellable product. In the worst cases the infected milk is discarded entirely. This results in huge financial losses, stress on staff and problems in obtaining a consistent quality product. So preventing phages infections within dairy production culture is essential in the present day industry. Currently multiplex PCR is used to detect the presence of common phages species, which require regular sampling. The aim of this year’s iGEM project is to simplify this detection and make it more continuous by linking a CRISPR detection system to a fluorescent signal and in parallel a restriction fragment length polymorphism analysis. Our systems works in several steps, which are explained in more detail below.

  • Infection: Since our system is built in the same organism as used for the fermentation, phages will infect our system automatically.
  • Spacer acquisition: After infection the CRISPR/Cas complex will recognize the phage DNA and harvest a 25-30 nt spacer and incorporate it into the CRISPR array.
  • Specific nuclease: The phage specific spacer is turned into a guide RNA which together with Cas9 forms a nuclease that targets a sequence specific for the phage.
  • Signal: Our signalling plasmid contains a sequence homologous to the phage DNA in a repressor/promotor region of a GFP gene. Cutting by Cas9 leads to either expression or loss of expression of GFP, which gives an easy to detect signal.
  • Multiplexed: If our signalling plasmid would contain multiple sequences homologous to different phages we can detect and distinguish multiple phages. We want to do this by incorporating restriction enzyme recognition sites around our phage sequences. Cutting of these sites will result in a change of restriction pattern after a restriction analysis.

We think dairy industry would benefit most from the real-time detection of the 10 most common phages using the GFP signal, since they have the means and knowledge to perform a multiplexed PCR to determine the type of infection after getting the signal. However we think our system can also be used for other applications where they don’t have the money and means to carry out multiplexed PCR.

Next: Parts