Difference between revisions of "Team:Newcastle/Safety"

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                 <h3>Welcome to Alternative Roots</h3>
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                 <h3>Alternative Roots</h3>
  
 
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                     Alternative Roots <br>
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                     Safety
                    Newcastle iGEM <br>
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Growing in Contained Environments
 
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                         Our Project
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                         Lab Safety
 
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                         Real World Safety
 
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                <h3 class="subhead subhead--dark">Hello There</h3>
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                            <h3 class="subhead"></h3>
                 <h1 class="display-1 display-1--light">We are Alternative Roots</h1>
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                 <h1 class="display-1">Lab Safety</h1>
 
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                <p class="about-para">Sustainability is a topic of increasing concern in the fields of agriculture, food security and rural development. There is a dire need for innovation in this field; primarily driven by predictions of substantial global population increase coupled with severe pressure on non-renewable resources. The result is a necessity to increase food production whilst reducing our impact on the environment. As such, our aim is to find sustainable solutions that address some of these issues. </p>
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                <p class="about-para">Nitrogen-fixation for fertilizer production is extremely energy-intensive, accounting for 80% of energy use in agriculture. This is due to the high temperatures and pressures involved in the Haber-Bosch process. Nitrogen is essential for plant growth but cannot be directly accessed from the atmosphere by plants despite its abundance. If an alternative to fertilizers could be developed to provide nitrogen for plant growth that is cheap, easy to use and sustainable, then energy use in the agriculture sector could be greatly reduced.</p>
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<p class="about-para">In 2018, Team Newcastle aim to engineer microbes for sustainable agriculture. The team shall build upon Newcastle University’s long and illustrious history in agriculture and food security research by engineering root colonising microbes. The microbes will attract bacteria that modify the soil's composition including nitrogen content, in a fashion that is suitable for uptake by plants via the roots.</p>
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                <div class="stats__count">10</div>
 
                <h5>BILLION PEOPLE WILL</h5>
 
                <h5>INHABIT EARTH BY 2050</h5>
 
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            <div class="col-block stats__col">
 
                <div class="stats__count">83</div>
 
                <h5>MILLION EXTRA PEOPLE</h5>
 
                <h5>NEED TO BE FED EACH YEAR</h5>
 
               
 
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                <div class="stats__count">842</div>
 
                <h5>MILLION PEOPLE SUFFER</h5>
 
                <h5>FROM HUNGER WORLDWIDE</h5>
 
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                <div class="stats__count">200</div>
 
                <h5>MILLION TONNES OF</h5>
 
                <h5>FERTILIZER USED ANNUALLY</h5>
 
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                    <p style="font-size:100%"><b>General Lab Safety</b></p>
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                    <p style="font-size:100%">We have been working alongside academics at the University while developing our project to ensure we are working safely. </p>
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                    <p style="font-size:100%">Dr. Matthew Peake is the Senior Biological Research Technician at Newcastle University and we have been working closely with him to ensure all lab protocols/safety measures are adhered to.</p>
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                    <p style="font-size:100%">Additionally, we are working with Dr. Vasilios Andriotis who has extensive knowledge on seed biochemistry, especially with Arabidopsis species, and Dr. Maxim Kapralov who currently engaged in research around plant biology and photosynthesis. Dr Maria Del Carmen Montero-Calasanz also has prior experience working with <i>Pseudomonas</i> sp., to aid us in specific areas of the project.</p>
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                    <p style="font-size:100%">Aseptic technique was used to prevent biocontamination and unintended release of organisms. Lab coats were worn in the lab at all times and were not taken outside of the lab. In addition, all waste was incinerated or autoclaved. The team used non-pathogenic strains of organisms where possible to mitigate the risks identified. </p>
  
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                    <p style="font-size:100%"><b>Endophytic Chassis</b></p>
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                    <p style="font-size:100%">We are using <i>Pseudomonas</i> sp. (CT 364). Some strains of <i>Pseudomonas</i> species can be opportunistic pathogens after repeated exposure - resulting in infections of the mouth, stomach and lungs; however, the species we are using is not listed as a human pathogen. </p>
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                    <p style="font-size:100%">Kill curves with multiple antibiotics, including chloramphenicol, were produced for <i>Pseudomonas</i> sp., so it was vital the antibiotics were handled according to the COSHH forms. </p>
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                    <p style="font-size:100%"><b>Chemotaxis </b></p>
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                    <p style="font-size:100%">Biological  Hazards: </p>
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<ul style="list-style-type:circle; overflow:visible; display:grid; text-align:left;"><li><i>Escherichia coli</i> (DH5α).</li></ul>
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<ul style="list-style-type:circle; overflow:visible; display:grid; text-align:left;"><li><i>Herbaspirillum seropedicae</i> (Z67).</li></ul>
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<ul style="list-style-type:circle; overflow:visible; display:grid; text-align:left;"><li><i>Azorhizobium caulinodans</i> (ORS571).</li></ul>
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<ul style="list-style-type:circle; overflow:visible; display:grid; text-align:left;"><li><i>Azospirillum brasilense</i> (SP245).</li></ul>
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<br></br>
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                    <p style="font-size:100%">These are low risk; however, they may have the potential to cause low level, localised changes to soil nitrogen content. We chose non-pathogenic strains of the bacteria.</p>
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                    <p style="font-size:100%">Hazards of Flavonoids: </p>
  
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<ul style="list-style-type:circle; overflow:visible; display:grid; text-align:left;"><li>Naringenin – skin, eye, respiratory irritation.</li></ul>
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<ul style="list-style-type:circle; overflow:visible; display:grid; text-align:left;"><li>Luteolin – potential skin and eye irritation.</li></ul>
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<ul style="list-style-type:circle; overflow:visible; display:grid; text-align:left;"><li>Scutelarin – non-hazardous.</li></ul>
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<br>
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<p style="font-size:100%">To avoid any irritation or inhalation, all handling of the various flavonoids was undertaken in the fume hood. For the weighing of the flavonoids when they are in their powdered form, face masks were worn to minimise the risk of inhalation. The area surrounding was kept vacant to avoid others not wearing masks coming into contact with the powder. Safety glasses were worn to avoid eye irritation, as well as gloves and lab coats to avoid skin irritation. </p>
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                    <p style="font-size:100%"><b>Naringenin Operon Development </b></p>
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                    <p style="font-size:100%">We attempted to introduce genes encoding enzymes of flavonoid biosynthesis into <i>E. coli.</i> We used a non-pathogenic strain of <i>E. coli </i> (DH5α) for this. This involved cloning and transformation using general molecular biology procedures. Chloramphenicol was used for selection of transformants. This is reported as a potential carcinogen so suitable protective equipment was worn when handling it. </p>
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                    <p style="font-size:100%"><b>Electrical Safety – Hardware </b></p>
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                    <p style="font-size:100%">We have been working alongside qualified technicians within the school of engineering who have provided us with advice and guidance relating to safety throughout each iteration of our design of NH-1. For example, we took a modular approach, making sure to test at each stage for faults such as short circuits or faulty connections and resolving them before moving on to the next component. </p>
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                    <p style="font-size:100%"><b>Safe Shipment </b></p>
  
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                    <p style="font-size:100%">We are shipping our hydroponic system, NH-1, to Boston for the Giant Jamboree. For this, we ensured it was completely sterilised using ChemGene and 70 % ethanol in order to comply with the iGEM Headquarters safety regulations. Before shipping we carried out final tests and we identified a point within the system that was generating too much heat due to high resistance. As a result, we resoldered a connector to rectify this problem. The hardware was not sent with a power supply so the system was not live, ensuring no electrical risks.</p>
  
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                    <p style="font-size:100%">We have also shipped DNA to Boston to submit our characterised and improved parts. None of the DNA we submitted posed any risks as we ensured our DNA would comply with shipping restrictions between the UK and US when we designed our parts. To send off the DNA we used the standard submission kit requested by iGEM. </p>
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                            <h3 class="subhead">2018</h3>
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                <h1 class="display-2">The Newcastle Team</h1>
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                    <a href="https://2018.igem.org/Team:Newcastle/Team" onclick="location.href='https://2018.igem.org/Team:Newcastle/Team'"><font face="verdana" color="green">MEET FULL TEAM</font> </a>             
 
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                     <h3 class="h2">Luke Waller</h3>
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                     <p style="text-align:center"><br></p>
                    <p><br> Luke’s my name, Conner is my game. I am the engineering part Conner wants to intertwine with. Having finished my
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                    third year I am staying on at Newcastle to complete my masters, hopefully getting into robotics.
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I took this role as I wanted to explore an avenue of engineering I was not familiar with and work with a multi-disciplined team. </p>
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                     <h3 class="h2">Frank Eardley</h3>
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                     <p style="text-align:center"><br></p>
                    <p><br>I am a 4th year MBiol Cellular & Molecular Biology student. I joined iGEM
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                    for the opportunity to work with students from other academic fields and learn
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                    more about synthetic biology. Outside of my degree, I am a scuba diving instructor
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                    and enjoy jumping in the North Sea whatever the weather.</p>
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                    <h3 class="h2">Will Tankard</h3>
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                    <p><br>I’ve just completed my second year as an Architecture student. iGEM was a step
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                    into the dark for me, the last time I did anything biology related was during my GCSE’s.  
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                    I’m interested how the architecture and biology disciplines can merge. Synthetic Biology
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                    offers a new perspective on design starting with a bottom up approach.</p>
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                 <h1 class="display-1">Real World Safety</h1>
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<h3><b>Growing in Contained Environments</b></h3>
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                    <p style="font-size:100%"><br>The use of biotechnology to modify plants has become common place in agricultural research - but we have conceptualised this as common place in agricultural practice. (See our <a href="https://2018.igem.org/Team:Newcastle/Human_Practices" class="black"> Human Practices</a>). In the context of our project, the purpose of containment is to prevent recombinant DNA from transgenic organisms being transferred to populations outside of our urban farm in Newcastle’s Victoria Tunnel (although the safety principals apply to any contained environments in which our transgenic organisms are present). </p>
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                     <p style="font-size:100%">Genetically engineered organisms are subject to special rules intended to ensure that they are used in a way that does not pose an unacceptable risk to human health - or the environment. In order to design our hydroponic urban farm to meet these biosafety standards, we referred to:</p>
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<ul style="list-style-type:circle; overflow:visible; display:grid; text-align:left;"><li><strong>Greenhouse Research with Transgenic Plants and Microbes: A Practical Guide to Containment [1] </strong><font size="2"><br>(Traynor, Patricia L, Dann Adair, Ruth Irwin) </font>
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<br>
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Methods for the safe handling of transgenic materials in contained environment are also described in the National Institutes of Health’s Guidelines for Research Involving Recombinant DNA Molecules (NIH Guidelines).</li></ul>
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<p style="font-size:100%"><br>Below we have taken extracts from the guide to containment that we referred to in order to design our own contained system: </p>
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<ul style="list-style-type:circle; overflow:visible; display:grid; text-align:left;"><li><strong>Elements of containment: </strong>
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<br>
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1. Avoid unintentional transmission of rDNA-containing plant genomes or release of rDNA-derived organisms associated with plants.
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<br>
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2. Minimise the possibility of unanticipated deleterious effects on organisms and ecosystems outside of the experimental facility.
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<br>
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3. Avoid the inadvertent spread of a serious pathogen from a greenhouse to a local agricultural crop.
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<br>
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4. Avoid the unintentional introduction and establishment of an organism in a new ecosystem.
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</li></ul>
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<p style="font-size:100%"><br>Having read the guide, we concluded our GMO was classified as <strong>BL2-P</strong>.</p>
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<ul style="list-style-type:circle; overflow:visible; display:grid; text-align:left;"><li><strong>Biosafety Level 2 for Plants (BL2-P)</strong>
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<br>
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"BL2-P is assigned to experiments with transgenic plants and associated organisms, which, if released outside the greenhouse, could be viable in the surrounding environment but would have a negligible impact or could be readily managed. BL2-P is required for transgenic plants that may exhibit a new weedy characteristic or that may be capable of interbreeding with weeds or related species growing in the vicinity."
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<li><strong>Procedures that must be followed for BL2-P:</strong></li>
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<br>
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<img src="https://static.igem.org/mediawiki/2018/f/fc/T--Newcastle--ContainmentRegs3.jpeg" width="350">
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</li></ul>
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<br>
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<h3><b>Newcastle's Victoria Tunnel - Retrofitting for Containment</b></h3>
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<p style="font-size:100%"><br>Retrofitting a structurally sound facility to meet BL2-P containment standards is far cheaper than building a new facility. Necessary modifications, if any, are usually simple, straightforward, and involve readily available materials. This is one of the reasons we have proposed a contained environment in the Victoria Tunnel - it is in a prime location running under the city centre whilst being structurally sound and accessible.</p>
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<br>
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<p style="font-size:100%"><br>Physical containment is achieved through making appropriate choices when it comes to facility design and equipment. These choices include: glazing, sealing, screening, air flow system, and other features all affect the degree to which a contained environment is capable of isolating transgenic organisms from the surrounding environment. These systems are also effective in keeping unwanted pests out of the facility.</p>
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<img src="https://static.igem.org/mediawiki/2018/3/30/T--Newcastle--ContainmentRegs1.jpeg" alt="Paris" class="center">
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<br>
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<h3><b>Layout</b></h3>
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<p style="font-size:100%"><br>When retrofitting to accommodate transgenic materials: traffic patterns, process flow, and security measures should be analysed to determine if the layout should be modified. The configuration should be optimised to provide variable levels of containment and growing conditions, control of access, and ease of movement.</p>
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<p style="font-size:100%">An efficient and manageable layout has an array of small rooms and cubicles opening off one or more common walkways; a compartmentalised arrangement of small rooms allows the facility to provide a variety of containment levels as well as individualised environmental conditions.</p>
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<p style="font-size:100%">A contained environment can be an inhospitable for people and equipment because of the humidity, temperature, light, chemicals, and soil. An enclosed area within or adjacent to the facility, provides cleaner, more comfortable space for offices, labs, equipment, supplies, and control systems.</p>
 +
 
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<img src="https://static.igem.org/mediawiki/2018/7/71/T--Newcastle--VTP1.jpeg" alt="Paris" class="center">
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<br>
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<h3><b>Additional safety considerations when designing contained environments</b></h3>
 +
<br>
 +
<ul style="list-style-type:circle; overflow:visible; display:grid; text-align:left;"><li><strong>Termination and Disposal </strong>
 +
<br>
 +
"To prevent the unintended survival of GMOs outside the contained environment, all experimental materials must be rendered biologically inactive (devitalised) before disposal. Termination procedures for the safe disposal of soil and plant material should be part of the experimental plan for a research project. Devitalisation of plant material and soil should be completed before it leaves a contained facility to go to landfill."
 +
<br></br>
 +
<li><strong>Apparel and Hygiene</strong>
 +
<br>
 +
"Personnel entering BL1-P and BL2-P facilities may wear their usual street or lab clothing."</li>
 +
<br>
 +
<li><strong>Greenhouse Staff</strong>
 +
<br>
 +
"All staff should become familiar with any differences between caring for GMOs and conventional plants that may affect their own work. In most cases, a brief orientation session is sufficient to explain the nature of the plants (or other transgenic organisms) and any special practices to be employed when handling or working around them. Both the greenhouse manager and the PI should work with the staff to ensure compliance with safety procedures and standards."
 +
</li>
 +
<br>
 +
<li><strong>Signage</strong>
 +
<br>
 +
"Entryways into BL2-P and higher facilities should be posted with signs indicating that access is limited to authorised personnel only. If the facility uses organisms that pose a risk to the local ecosystem or agriculture, a sign so stating must be placed on the access doors to the facility. A description of the potential risk may be posted on the restricted access sign as long as this is not confidential information. The sign should state the name and telephone number of the responsible individual, the plants in use, and any special requirements for using the area. It may include contact information for the greenhouse manager and others to be called in case of emergency."</li>
 +
</ul>
 
                      
 
                      
 
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                 <div class="service-text">
 
                 <div class="service-text">
                     <h3 class="h2">Heather Bottomley</h3>
+
                     <img src="">
                     <img src="https://static.igem.org/mediawiki/2018/8/81/T--Newcastle--Heather.png">
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                     <p style="text-align:center"><br></p>
                    <p><br> Heather's the name, not doing the wiki is my game. I've just finished my                  third year of MBiol Cellular and Molecular Biology. I joined iGEM as an opportunity to formulate
+
                    a novel idea and work in a multi - disciplinary team enhancing my biological knowledge.</p>
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                 </div>
 
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                 <div class="service-text">
 
                 <div class="service-text">
                     <h3 class="h2">Connor Trotter</h3>
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                     <img src="">
                     <img src="https://static.igem.org/mediawiki/2018/d/dc/T--Newcastle--Connor.png">
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                     <p style="text-align:center"><br></p>
                    <p><br> Connor is the name, getting my name misspelled is the game. I'm currently entering my third year
+
                    of Biology which has, so far, been fuelled by an excess of caffeine and binge watching a lot
+
                    of Rupaul's Drag Race. I joined Newcastle's team to apply what I have learned in a unique fashion by intertwining elements of Engineering and Architecture into biological concepts.</p>
+
 
                      
 
                      
                </div>
 
            </div>
 
   
 
            <div class="col-block service-item" data-aos="fade-up">
 
                <div class="service-icon"><i class="icon-lego-block"></i></div>
 
                <div class="service-text">
 
                    <h3 class="h2">Patrycja Ubysz</h3>
 
                    <img src="https://static.igem.org/mediawiki/2018/3/30/T--Newcastle--Patrycja.png">
 
                    <p><br>I'm Pat, no game with my name. Just finished first year of Chemistry, I
 
                    probably liked it too much. I believe being interdisciplinary is crucial for research, especially
 
                    in Synthetic Biology. I want to contribute to the team using my chemical/physical approach. I
 
                    love working in the lab, however, would be happier without microbes. Basic coffee addict, bad
 
                    experience with BBQ parties. Probably follow every single NASA team account on Twitter.</p>
 
 
                      
 
                      
 
                 </div>
 
                 </div>
 
             </div>
 
             </div>
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                <div class="service-icon"><i class="icon-lego-block"></i></div>
 
                <div class="service-text">
 
                    <h3 class="h2">Lewis Tomlinson</h3>
 
                    <img src="https://static.igem.org/mediawiki/2018/0/0e/T--Newcastle--Lewis.png">
 
                    <p><br>Name: Lewis. Likes: llamas, guinea pigs, rock hyrax, all other animals, molecular biology, dungeons and dragons, science fiction and fantasy.
 
                    Life goal: llama sanctuary (including birds and rodents).</p>
 
                   
 
                </div>
 
            </div>
 
           
 
                <div class="col-block service-item" data-aos="fade-up">
 
                <div class="service-icon"><i class="icon-lego-block"></i></div>
 
                <div class="service-text">
 
                    <h3 class="h2">Sadiya Quazi</h3>
 
                    <img src="https://static.igem.org/mediawiki/2018/f/f2/T--Newcastle--Sadiya.png">
 
                    <p><br>Sadiya’s the name, which most can’t pronounce (despite it being totally phonetic). Just completed first year of Chemistry after switching from Fine Art,
 
                    and yes, it’s been a huge change, as people always exclaim when I tell them. Both benefit from having that alternative perspective and this is what drew me to
 
                      iGEM - working as part of a very cross-disciplinary team.</p>
 
                   
 
                </div>
 
            </div>
 
               
 
                <div class="col-block service-item" data-aos="fade-up">
 
                <div class="service-icon"><i class="icon-lego-block"></i></div>
 
                <div class="service-text">
 
                    <h3 class="h2">Umar Farooq</h3>
 
                    <img src="https://static.igem.org/mediawiki/2018/8/84/T--Newcastle--Umar.png">
 
                    <p><br>I'm Umar, a 1st year undergraduate studying Automation and Control Engineering. I joined IGEM for the
 
                    opportunity to work alongside a multi-disciplinary team and develop my skills outside of engineering. When
 
                    I'm not working on the project, I like swimming, playing the guitar and eating cake. Addicted to bad
 
                    jokes, allergic to onions.
 
                    </p>
 
                   
 
                </div>
 
            </div>
 
           
 
                <div class="col-block service-item" data-aos="fade-up">
 
                <div class="service-icon"><i class="icon-lego-block"></i></div>
 
                <div class="service-text">
 
                    <h3 class="h2">Chris Carty</h3>
 
                    <img src="https://static.igem.org/mediawiki/2018/e/e4/T--Newcastle--Chris.png">
 
                    <p><br>I’m Chris, 2nd year Architecture student, discovered iGEM when beginning my dissertation in the area  of Bio-Materialism. I want to take organisms that have been designed at the genetic scale and design them for use at the human scale - aiding the transition from biologically inspired to biologically engineered design. Better at architecture than Will.</p>
 
                   
 
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                <div class="col-full">
                <h3 class="subhead">Our Sponsors</h3>
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                            <br>
                 <h1 class="display-2">Newcastle iGEM is proud to be sponsored by:</h1>
+
<br>
 +
<br>
 +
<br>
 +
<h3 class="subhead"></h3>
 +
                 <h1 class="display-2">References & Attributions</h1>
 
             </div>
 
             </div>
        </div> <!-- end section-header -->
 
  
         <div class="row clients-outer" data-aos="fade-up">
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                    <a href="#sponsors" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/6/65/T--Newcastle--SAgELogo.png/600px-T--Newcastle--SAgELogo.png" /></a>
+
                    <a href="https://bbsrc.ukri.org/" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/2/21/T--Newcastle--BBSRCSquare.png/600px-T--Newcastle--BBSRCSquare.png"></a>
+
                    <a href="https://wellcome.ac.uk/home" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/b/be/T--Newcastle--Wellcomelogo.png/600px-T--Newcastle--Wellcomelogo.png"/></a>
+
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+
                    <a href="https://www.ncl.ac.uk/sage/" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/4/42/T--Newcastle--Ibidi.png/600px-T--Newcastle--Ibidi.png" /></a>
+
                    <a href="http://opentrons.com/" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/9/9a/T--Newcastle--OpenTronsLogoPNG.png/600px-T--Newcastle--OpenTronsLogoPNG.png" /></a>
+
                    <a href="https://seedcell.co.uk/" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/8/86/T--Newcastle--SeedCellSquare2.png/600px-T--Newcastle--SeedCellSquare2.png" /></a>
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                </div> <!-- end clients -->
 
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                    <div class="testimonials__slide">
 
  
                        <p>The iGEM Foundation is an independent, non-profit organization dedicated to the advancement of synthetic biology, education and competition,
 
                        and the development of an open community and collaboration. This is done by fostering an open, cooperative community and friendly competition.</p>
 
  
                        <img src="https://static.igem.org/mediawiki/2018/thumb/b/bb/T--Newcastle--iGEMGrey.png/600px-T--Newcastle--iGEMGrey.png" alt="Author image" class="testimonials__avatar">
 
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                    <div class="testimonials__slide">
 
                       
 
                        <p>iGEMers are building a better world by solving problems with the help of synthetic biology.
 
                        We inspire responsible innovation through our efforts in biosafety, biosecurity and public outreach.</p>
 
  
                        <img src="https://static.igem.org/mediawiki/2018/thumb/b/bb/T--Newcastle--iGEMGrey.png/600px-T--Newcastle--iGEMGrey.png" alt="Author image" class="testimonials__avatar">
 
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                            <span class="testimonials__pos"></span>
 
                        </div>
 
  
                    </div>
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<button class="collapsible">Click for References & Attributions</button>
 +
<div class="content">
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                <div class="col-full">
  
                    <div class="testimonials__slide">
 
                       
 
                        <p> This global network is leading the field, taking what they learned in the competition and expanding it to continue to build a better world.</p>
 
  
                        <img src="https://static.igem.org/mediawiki/2018/thumb/b/bb/T--Newcastle--iGEMGrey.png/600px-T--Newcastle--iGEMGrey.png" alt="Author image" class="testimonials__avatar">
 
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                            <span class="testimonials__pos"></span>
 
                        </div>
 
  
                    </div>
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<p class="about-para"><font size="2"><strong>Attributions: Sadiya Quazi & Chris Carty</strong><font></p>
  
                </div><!-- end testimonials -->
 
               
 
            </div> <!-- end col-full -->
 
        </div> <!-- end client-testimonials -->
 
  
    </section> <!-- end s-clients -->
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<p class="about-para"><font size="2">1. Traynor, P. , Adair, D. , Irwin, R. (2001) Greenhouse Research with Transgenic Plants and Microbes: A Practical Guide to Containment. Available at: https://www.conacyt.gob.mx/cibiogem/images/cibiogem/comunicacion/Eventos/CIBIOGEM/Taller-Bioseguridad-Cofinamiento/Practical-guide-containment.pdf [Accessed 12/08/2018].<font></p>
  
  
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</section>
  
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            <div class="col-full">
 
                <h3 class="subhead">Contact Us</h3>
 
                <h1 class="display-2 display-2--light">Reach out for a collaboration or just say hello</h1>
 
            </div>
 
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                <h3 class="h6">Get Involved</h3>
 
                <p><br>We are always happy to hear from individuals, groups or organisations that would like to support our project. If you wish to discuss a collaboration, sponsorship or if you just want to learn more about the project, please get in touch using the contact details on the right. Alternatively, if you would like to donate a small amount to fund our project, you can do so through <a class="link" href="https://experiment.com/projects/genetically-engineered-microbes-for-sustainable-agriculture" target="_blank">Experiment.com</a> - an online platform for discovering, funding, and sharing scientific research.
 
<br><br>
 
Any support is greatly appreciated and funds raised will be used in all areas of the iGEM project - such as lab equipment, human practices research, merchandise and travel to jamboree in Boston, USA.</p>
 
            </div> 
 
  
            <div class="contact-secondary">
 
                <div class="contact-info">
 
  
                    <h3 class="h6 hide-on-fullwidth">Contact Info</h3>
 
  
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                        <h5>Where to Find Us</h5>
 
                        <p>
 
                            Devonshire Building<br>
 
                            Newcastle University<br>
 
                            Newcastle upon Tyne<br>
 
                            NE1 7RU
 
                        </p>
 
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                        <h5>Email Us At</h5>
 
                        <p>
 
                            igem.team@newcastle.ac.uk
 
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Latest revision as of 01:43, 18 October 2018

Alternative Roots/Hardware

Alternative Roots

Safety

Lab Safety

General Lab Safety

We have been working alongside academics at the University while developing our project to ensure we are working safely.

Dr. Matthew Peake is the Senior Biological Research Technician at Newcastle University and we have been working closely with him to ensure all lab protocols/safety measures are adhered to.

Additionally, we are working with Dr. Vasilios Andriotis who has extensive knowledge on seed biochemistry, especially with Arabidopsis species, and Dr. Maxim Kapralov who currently engaged in research around plant biology and photosynthesis. Dr Maria Del Carmen Montero-Calasanz also has prior experience working with Pseudomonas sp., to aid us in specific areas of the project.

Aseptic technique was used to prevent biocontamination and unintended release of organisms. Lab coats were worn in the lab at all times and were not taken outside of the lab. In addition, all waste was incinerated or autoclaved. The team used non-pathogenic strains of organisms where possible to mitigate the risks identified.

Endophytic Chassis

We are using Pseudomonas sp. (CT 364). Some strains of Pseudomonas species can be opportunistic pathogens after repeated exposure - resulting in infections of the mouth, stomach and lungs; however, the species we are using is not listed as a human pathogen.

Kill curves with multiple antibiotics, including chloramphenicol, were produced for Pseudomonas sp., so it was vital the antibiotics were handled according to the COSHH forms.

Chemotaxis

Biological Hazards:

  • Escherichia coli (DH5α).
  • Herbaspirillum seropedicae (Z67).
  • Azorhizobium caulinodans (ORS571).
  • Azospirillum brasilense (SP245).


These are low risk; however, they may have the potential to cause low level, localised changes to soil nitrogen content. We chose non-pathogenic strains of the bacteria.

Hazards of Flavonoids:

  • Naringenin – skin, eye, respiratory irritation.
  • Luteolin – potential skin and eye irritation.
  • Scutelarin – non-hazardous.

To avoid any irritation or inhalation, all handling of the various flavonoids was undertaken in the fume hood. For the weighing of the flavonoids when they are in their powdered form, face masks were worn to minimise the risk of inhalation. The area surrounding was kept vacant to avoid others not wearing masks coming into contact with the powder. Safety glasses were worn to avoid eye irritation, as well as gloves and lab coats to avoid skin irritation.

Naringenin Operon Development

We attempted to introduce genes encoding enzymes of flavonoid biosynthesis into E. coli. We used a non-pathogenic strain of E. coli (DH5α) for this. This involved cloning and transformation using general molecular biology procedures. Chloramphenicol was used for selection of transformants. This is reported as a potential carcinogen so suitable protective equipment was worn when handling it.

Electrical Safety – Hardware

We have been working alongside qualified technicians within the school of engineering who have provided us with advice and guidance relating to safety throughout each iteration of our design of NH-1. For example, we took a modular approach, making sure to test at each stage for faults such as short circuits or faulty connections and resolving them before moving on to the next component.

Safe Shipment

We are shipping our hydroponic system, NH-1, to Boston for the Giant Jamboree. For this, we ensured it was completely sterilised using ChemGene and 70 % ethanol in order to comply with the iGEM Headquarters safety regulations. Before shipping we carried out final tests and we identified a point within the system that was generating too much heat due to high resistance. As a result, we resoldered a connector to rectify this problem. The hardware was not sent with a power supply so the system was not live, ensuring no electrical risks.

We have also shipped DNA to Boston to submit our characterised and improved parts. None of the DNA we submitted posed any risks as we ensured our DNA would comply with shipping restrictions between the UK and US when we designed our parts. To send off the DNA we used the standard submission kit requested by iGEM.



Real World Safety

Growing in Contained Environments


The use of biotechnology to modify plants has become common place in agricultural research - but we have conceptualised this as common place in agricultural practice. (See our Human Practices). In the context of our project, the purpose of containment is to prevent recombinant DNA from transgenic organisms being transferred to populations outside of our urban farm in Newcastle’s Victoria Tunnel (although the safety principals apply to any contained environments in which our transgenic organisms are present).

Genetically engineered organisms are subject to special rules intended to ensure that they are used in a way that does not pose an unacceptable risk to human health - or the environment. In order to design our hydroponic urban farm to meet these biosafety standards, we referred to:

  • Greenhouse Research with Transgenic Plants and Microbes: A Practical Guide to Containment [1]
    (Traynor, Patricia L, Dann Adair, Ruth Irwin)

    Methods for the safe handling of transgenic materials in contained environment are also described in the National Institutes of Health’s Guidelines for Research Involving Recombinant DNA Molecules (NIH Guidelines).


Below we have taken extracts from the guide to containment that we referred to in order to design our own contained system:

  • Elements of containment:
    1. Avoid unintentional transmission of rDNA-containing plant genomes or release of rDNA-derived organisms associated with plants.
    2. Minimise the possibility of unanticipated deleterious effects on organisms and ecosystems outside of the experimental facility.
    3. Avoid the inadvertent spread of a serious pathogen from a greenhouse to a local agricultural crop.
    4. Avoid the unintentional introduction and establishment of an organism in a new ecosystem.


Having read the guide, we concluded our GMO was classified as BL2-P.

  • Biosafety Level 2 for Plants (BL2-P)
    "BL2-P is assigned to experiments with transgenic plants and associated organisms, which, if released outside the greenhouse, could be viable in the surrounding environment but would have a negligible impact or could be readily managed. BL2-P is required for transgenic plants that may exhibit a new weedy characteristic or that may be capable of interbreeding with weeds or related species growing in the vicinity."
  • Procedures that must be followed for BL2-P:


Newcastle's Victoria Tunnel - Retrofitting for Containment


Retrofitting a structurally sound facility to meet BL2-P containment standards is far cheaper than building a new facility. Necessary modifications, if any, are usually simple, straightforward, and involve readily available materials. This is one of the reasons we have proposed a contained environment in the Victoria Tunnel - it is in a prime location running under the city centre whilst being structurally sound and accessible.



Physical containment is achieved through making appropriate choices when it comes to facility design and equipment. These choices include: glazing, sealing, screening, air flow system, and other features all affect the degree to which a contained environment is capable of isolating transgenic organisms from the surrounding environment. These systems are also effective in keeping unwanted pests out of the facility.

Paris

Layout


When retrofitting to accommodate transgenic materials: traffic patterns, process flow, and security measures should be analysed to determine if the layout should be modified. The configuration should be optimised to provide variable levels of containment and growing conditions, control of access, and ease of movement.

An efficient and manageable layout has an array of small rooms and cubicles opening off one or more common walkways; a compartmentalised arrangement of small rooms allows the facility to provide a variety of containment levels as well as individualised environmental conditions.

A contained environment can be an inhospitable for people and equipment because of the humidity, temperature, light, chemicals, and soil. An enclosed area within or adjacent to the facility, provides cleaner, more comfortable space for offices, labs, equipment, supplies, and control systems.

Paris

Additional safety considerations when designing contained environments


  • Termination and Disposal
    "To prevent the unintended survival of GMOs outside the contained environment, all experimental materials must be rendered biologically inactive (devitalised) before disposal. Termination procedures for the safe disposal of soil and plant material should be part of the experimental plan for a research project. Devitalisation of plant material and soil should be completed before it leaves a contained facility to go to landfill."

  • Apparel and Hygiene
    "Personnel entering BL1-P and BL2-P facilities may wear their usual street or lab clothing."

  • Greenhouse Staff
    "All staff should become familiar with any differences between caring for GMOs and conventional plants that may affect their own work. In most cases, a brief orientation session is sufficient to explain the nature of the plants (or other transgenic organisms) and any special practices to be employed when handling or working around them. Both the greenhouse manager and the PI should work with the staff to ensure compliance with safety procedures and standards."

  • Signage
    "Entryways into BL2-P and higher facilities should be posted with signs indicating that access is limited to authorised personnel only. If the facility uses organisms that pose a risk to the local ecosystem or agriculture, a sign so stating must be placed on the access doors to the facility. A description of the potential risk may be posted on the restricted access sign as long as this is not confidential information. The sign should state the name and telephone number of the responsible individual, the plants in use, and any special requirements for using the area. It may include contact information for the greenhouse manager and others to be called in case of emergency."







References & Attributions

Attributions: Sadiya Quazi & Chris Carty

1. Traynor, P. , Adair, D. , Irwin, R. (2001) Greenhouse Research with Transgenic Plants and Microbes: A Practical Guide to Containment. Available at: https://www.conacyt.gob.mx/cibiogem/images/cibiogem/comunicacion/Eventos/CIBIOGEM/Taller-Bioseguridad-Cofinamiento/Practical-guide-containment.pdf [Accessed 12/08/2018].