Team:Manchester/Attributionstest

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          <p><i>All experimental, modelling and human practices research and work was undertaken by the team unless otherwise explicitly stated here.</i><br>
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    <p>
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We are so grateful to everyone who has helped us over the course of our project, without you all this would have been impossible! Thanks especially go to our advisors, who let us use their lab equipment and many reagents without hesitation. We really appreciate everything.<br>
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<p><i><b>Would any of your project ideas raise safety issues in terms of:</b></i></p>
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<p><i>1. researcher safety,</p>
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<p>2. public safety, or</p>
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<p>3. environmental safety</i></p> </p>
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<br>
<br>
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        <p><u>Researcher Safety:</u></p>
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Thank you, in particular, to:<br>
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<p>During the project the risk to the researcher was minimised in a number of ways. Standard lab protection was always worn (lab coat and gloves) and we adhered to COSHH forms. All team members involved in lab work attended a 2 hour safety briefing with the Safety and Risk Management Officer for the MIB (Dr. Tanya Aspinall). No eating, drinking or chewing was allowed in the lab. No shorts, skirts or dresses were allowed when in the lab. The lab we worked in is Biosafety Level 1 according to WHO Laboratory Safety Manual.</p>
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<br>
<br>
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<p><b>Organisms we used:</b></p>
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<b>Our Instructors:</b><br>
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<p><i>E. coli</i> BL21(DE3) - Standard lab strain. Used Good Microbiological Practice (GMP) when handling.</p>
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<i>Prof. Eriko Takano</i> and <i>Prof. Rainer Breitling</i>, for letting us use your lab space, helping us plan our project timeline efficiently, and giving very useful advice on how we can progress with our project both experimentally and in modelling<br>
-
<p><i>E. coli</i> DH5-alpha (used to ship and grow the FAS-module) - Another standard lab strain. Used GMP when handling.</p>
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-
<p><i>Synechocystis</i> sp. PCC 6803 - Sequences for the delta-9 and delta-12 desaturase genes were taken from here and then synthesised - we never had any contact with the strain. This cyanobacteria is found in freshwater and is not thought to be a threat.</p>
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<br>
<br>
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<p><b>Chemicals used:</b></p>
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<b>Our advisors:</b><br>
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<p><b>Ethidium Bromide:</b> Hazard statements H302-H330-H341 - Harmful if swallowed, Fatal if inhaled, Suggested of causing genetic defects. Personal protective clothing must be worn. Used fumehood when handling. Gel containing ethidium bromide was disposed of in the hazardous waste gel box in the visualiser room. All gel kits that were used in conjunction with EtBr were kept together in a space dedicated to them in the lab. Pipette tips used with EtBr were disposed of in a designated EtBr pipette tip bin in the lab.</p>
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<i>Dr. Karl Payne</i>, for assisting with gene synthesis, being an invaluable source of advice and for not getting annoyed with us constantly asking for aliquots of competent cells!<br>
<br>
<br>
-
<p><b>Chloroform:</b> Hazard statements H302-H315-H351-H373 - Harmful if swallowed, Causes skin irritation, Suspected of causing cancer, Causes damage to organs through prolonged or repeated exposure. Personal protective clothing must be worn. Used fumehood when handling. Waste containing chloroform was disposed of in halogenated waste containers.</p>
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<i>Dr. Nicholas Rattray</i>, for carrying out the quenching and extraction of metabolites from cell cultures and running our samples in the Orbitrap LC-MS<br>
<br>
<br>
-
<p><b>Methanol:</b> Hazard statements H225-H301-H311-H331-H370 - Highly flammable liquid and vapour, Toxic if swallowed, Toxic in contact with skin, Toxic if inhaled, Causes damage to organs. Personal protective clothing must be worn. Used fumehood when handling. Waste was disposed of in organic waste containers.</p>
+
<i>Dr. Vicky Jackson</i>, for assisting both in the lab and with the model<br>
<br>
<br>
-
<p><b>Liquid Nitrogen:</b> Hazard statements H281 - Contains refrigerated gas; may cause cryogenic burns or injury. Personal protective clothing must be worn, cold-proof gloves must be worn to avoid cryogenic burns.</p>
+
<i>Dr. Wayne Aubrey</i>, for providing us with basic lab training at the start of the project, and providing us with advice and reagents<br>
<br>
<br>
-
<p><u>Public and Environmental Safety:</u></p>
+
<i>Dr. Neil Swainston</i>, for offering guidance on our model, and providing introductory tutorials to the software used<br>
-
<p>GMP was also used in order to ensure public safety. Once something had come into contact with the bacteria we used, it was sterilised. Pipette tips were put into Virkon solution and then disposed of in Autoclave bags, ready for incineration. Flasks previously containing bacteria cultures were soaked in Virkon solution before being washed in the sink. As well as this, the bacteria were cultured so as to not be viable outside of a laboratory setting (due to the specific media they were grown on). This ensures that, even if living bacteria did manage to escape the lab, it would not have survived.</p>
+
<br>
<br>
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<p>The same procedures as above were also used to ensure environmental safety. In addition to this, organic solvents that are potentially dangerous to aquatic organisms were disposed of in a separate waste container and removed professionally.</p>
+
<i>Dr. Nicole Leferink</i>, for providing us restriction enzymes and competent cells<br>
<br>
<br>
-
<p>In the unlikely event that our re-engineered strains escaped our workspace, it is thought that no risk would be posed to the public or to the environment. This is because the bacteria we use is non-pathogenic and also would be at a disadvantage in any environment other than that found within the culture medium it is grown on. This disadvantage would be expected to kill the bacteria should they ever find their way into the outside environment. </p>
+
<i>Dr. Jayendra Shankar</i>, for guiding us through the fadD knockout, and providing us with lab consumables<br>
<br>
<br>
-
<p><u>Future safety implications if project was commercialised:</u></p>
+
<i>Denis Abramov</i>, for implementing our designs for the wiki<br>
-
<p>Once the methods have been sufficiently optimised, our project would have commercial potential. This would inevitably lead to further safety concerns and questions. Due to the wide range of products that the four main components of palm oil are used in, each application would have to be considered separately. For example, the use of synthetic oleic acid in cooking oils would raise concerns over whether or not this product would be safe for consumption.</p>
+
-
<p>In order to minimise any risk posed by using genetically altered <i>E. coli</i>, a number of steps would be put in place. Firstly, the vats containing the bacteria would be kept in a secure facility, with all workers fully trained in the handling of biological samples. This would ensure that the workers/researchers were not at any risk. </p>
+
-
<p>The chemical extraction of fatty acids from the <i>E. coli</i> cultures would theoretically separate all bacteria from the final product. However, at the risk of some bacteria remaining within the extractant, further methods would have to be put in place. In the case of palmitic and stearic acid, the samples would have to be separated from each other using fractional distillation. This technique involves heating the samples up and separating the compounds based on their boiling point. The high temperatures involved would kill any bacteria present in the samples. A similar technique could also be used in the case of oleic and linoleic acid too. The samples of these fatty acids could be refluxed, which would kill any bacteria present whilst keeping the sample in a sealed vessel. After these procedures have been completed, no viable bacteria would be present within the fatty acid products, and the public would not come into contact with genetically modified bacteria.</p>
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                <img src="https://static.igem.org/mediawiki/2013/0/01/2p.gif" width="100" height="100" />
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-
    <p><b><i>Do any of the new BioBrick parts (or devices) that you made this year raise safety issues? </i></b></p>
+
<br>
<br>
-
        <p>No, none of the BioBrick parts used this year are thought to be hazardous - they are all part of either the natural biosynthesis pathway of <i>E. coli</i> or were synthesised using sequences from <i>Synechocystis</i> sp. PCC6803, a cyanobacterium found in freshwater.</p>
+
<i>Beata Czajkowska</i>, for donating lab equipment and helping us order consumables from stores<br>
-
</div>
+
-
+
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<div class="text3">
+
-
                <img src="https://static.igem.org/mediawiki/2013/2/21/3p.gif" width="100" height="100" />
+
-
    <p><b><i>Is there a local biosafety group, committee, or review board at your institution?</i></b></p>
+
<br>
<br>
-
      <p>The University of Manchester has a university-wide Biological Safety Committee, whose guidelines for safe biological laboratory practices we adhered to throughout the project (<a>http://documents.manchester.ac.uk/display.aspx?DocID=14942</a>).</p>
+
<i>Nick Weise</i>, for providing us with reagents for making the FAS media, introducing us to the nanodrop machine and always being on hand if we needed any advice<br>
-
<p>A representative for the biosafety committee of the University of Manchester (Dr. Tanya Aspinall, Safety and Risk Assessment Officer of Manchester Institute of Biotechnology) gave the team a 2 hour talk about safety in the laboratory. During this safety training, the team was advised on how to handle potentially hazardous substances, such as liquid nitrogen, and how to safely dispose of certain materials. The team’s lab benches and experimental plans were also assessed and deemed safe to proceed with. Supervisors to the team were always on hand in the lab to make sure the team were working safely.</p>
+
<br>
-
 
+
<b>Others:</b><br>
-
</div>  
+
<i>Prof. Mattheos Koffas</i>, for providing us with the FAS module<br>
-
+
<br>
-
<div class="text4">
+
<i>Dr. Andy Balmer</i>, for having early discussions with us that helped us to delve deeper into the world of human practices and the knowledge deficit assumption<br>
-
                <img src="https://static.igem.org/mediawiki/2013/7/7e/4p.gif" width="100" height="100" />
+
<br>
-
    <p><b><i>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</i></b></p>
+
<i>Jérémy Férrant</i>, for providing us with software to allow us to randomly generate values for parameters for the model<br>
 +
<br>
 +
<i>Dr. Nigel Hodson of the University of Manchester BioAFM Facility</i>, for donating his time to view our samples using AFM and charging us discount price<br>
 +
<br>
 +
<i>Dr. Matthew Hickman</i>, for discussing how to do public outreach effectively, leading to our successful Science Stars and open day events<br>
 +
<br>
 +
<i>Dr. Catherine Rhodes</i>, for having a chat about economic concepts such as the impact of biofuels and patenting with us<br>
 +
<br>
 +
<i>Dr Rosalind le Feuvre and Chris Cowan</i>, for assisting with financial matters<br>
 +
<br>
 +
<i>Dr. Tanya Aspinall</i>, for providing the team with a health and safety induction<br>
 +
<br>
 +
<i>Lesley-Ann Miller</i>, for assisting with organising travel arrangements for the jamboree<br>
 +
<br>
 +
<i>Katy Denniff & colleagues</i>, for organising the community open day, where we had a stall<br>
<br>
<br>
-
        <p>To encourage safe laboratory practices, we believe it would be a good idea for completed generic COSHH/Risk Assessment forms for common procedures such as gel electrophoresis and PCR be available on the iGEM website. Having a collection of completed forms covering the most common protocols used during the iGEM competition would first ensure that teams carry out these procedures adhering to the iGEM Safety Committee’s standards, and secondly would give teams a guideline when filling out safety forms for non-standard procedures. </p>
+
<i>Rose Richardson & colleagues</i>, for organising the science stars event, where we had a workshop<br>
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Latest revision as of 16:06, 26 October 2013

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Safety

All experimental, modelling and human practices research and work was undertaken by the team unless otherwise explicitly stated here.
We are so grateful to everyone who has helped us over the course of our project, without you all this would have been impossible! Thanks especially go to our advisors, who let us use their lab equipment and many reagents without hesitation. We really appreciate everything.

Thank you, in particular, to:

Our Instructors:
Prof. Eriko Takano and Prof. Rainer Breitling, for letting us use your lab space, helping us plan our project timeline efficiently, and giving very useful advice on how we can progress with our project both experimentally and in modelling

Our advisors:
Dr. Karl Payne, for assisting with gene synthesis, being an invaluable source of advice and for not getting annoyed with us constantly asking for aliquots of competent cells!

Dr. Nicholas Rattray, for carrying out the quenching and extraction of metabolites from cell cultures and running our samples in the Orbitrap LC-MS

Dr. Vicky Jackson, for assisting both in the lab and with the model

Dr. Wayne Aubrey, for providing us with basic lab training at the start of the project, and providing us with advice and reagents

Dr. Neil Swainston, for offering guidance on our model, and providing introductory tutorials to the software used

Dr. Nicole Leferink, for providing us restriction enzymes and competent cells

Dr. Jayendra Shankar, for guiding us through the fadD knockout, and providing us with lab consumables

Denis Abramov, for implementing our designs for the wiki

Beata Czajkowska, for donating lab equipment and helping us order consumables from stores

Nick Weise, for providing us with reagents for making the FAS media, introducing us to the nanodrop machine and always being on hand if we needed any advice

Others:
Prof. Mattheos Koffas, for providing us with the FAS module

Dr. Andy Balmer, for having early discussions with us that helped us to delve deeper into the world of human practices and the knowledge deficit assumption

Jérémy Férrant, for providing us with software to allow us to randomly generate values for parameters for the model

Dr. Nigel Hodson of the University of Manchester BioAFM Facility, for donating his time to view our samples using AFM and charging us discount price

Dr. Matthew Hickman, for discussing how to do public outreach effectively, leading to our successful Science Stars and open day events

Dr. Catherine Rhodes, for having a chat about economic concepts such as the impact of biofuels and patenting with us

Dr Rosalind le Feuvre and Chris Cowan, for assisting with financial matters

Dr. Tanya Aspinall, for providing the team with a health and safety induction

Lesley-Ann Miller, for assisting with organising travel arrangements for the jamboree

Katy Denniff & colleagues, for organising the community open day, where we had a stall

Rose Richardson & colleagues, for organising the science stars event, where we had a workshop

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