From 2012.igem.org

Revision as of 12:09, 4 September 2012

Use this page to answer the questions on the safety page.

Would any of your project ideas raise safety issues in terms of:

When designing the experiments the NRPUEA team would undertake we had to consider not only the safety of the researchers and others within the lab, but also the public and the environment.We had to consider carefully the organisms and chemicals we would be using within lab, how we would handle these safely and then dispose of them after to minimize effect on environment and public.

Researcher safety

The university has safety standards which have to be met, which included having basic safety training before starting wet lab work, as well as reading, understanding and signing COSH forms.Therefore, when designing experiments we considered the risks associated and checked whether the COSH forms signed covered the procedures undertaken.The team also received training from advisors over the first few days. They learnt what to do in emergencies, where we could access the safety manual which is always within the lab, as well as being shown where to dispose of the different chemicals and used equipment. It is also vital that researchers within the university ware personal protective equipment (PPE), including lab coat, gloves and covered shoes. The members also wore protective face shields when using artificial UV light in the darkroom. The team were prohibited from eating, drinking or smoking near the lab. The team enjoyed their lunch well away from the lab, as well as being careful to wash their hands before eating and leaving.

The lab facilities were designed to be safe for the team members, providing plenty of space and clean surfaces to work on. The lab was supplied with plastic handheld pipits, and perminant pens; removing the need to use mouth during experiment eg: mouth piptets and no need to lick labels.

The team had originally thought it would be interesting to look at NO levels within salmonella, but decided later that this would result in a lot more safety concerns and complications. Therefore , the team decided to only use strains of "E.coli" (which they had all used within their university studies before and allowed to be handled within the our lab) within our projects. The organism used as a chassis, within NRPUEA iGEM teams experiments, was E.coli ( NEB 5-alpha E.coli was use to characterize existing bio bricks, as well as BL21 pLysS cells and Alpha select gold E.coli. E.coli is a well-studied type of bacteria and therefore has a fairly predictable behavior as well understood pathways. This reduces the risks of danger to the team. E.coli is a non-pathogenic bacteria which has been categorized as a biosafty level 1 bacteria. Therefore, all the students were able to use the E.coli within the university’s second year (category one and two) teaching labs.

Since the team’s project involves Nitric Oxide (NO) they had to consider the safety of the chemicals being used.It is important to note that all the chemicals within the lab are supplied with a safety advice sheet that has been generated by the company. NO has been classed as a dangerous gas which can be directly toxic to blood, lungs, pancreas and nervous system. Therefore, Cautions must be taken when using NO within the lab. It is important to use safely due to its clear appearance reducing the indication of the presence of the gas, possibly allowing the gas to be unintentionally inhaled. However, the gas has an irritating odor allowing the indication of its presence. Therefore, NO would be handled within the labs fume cupboards, as well as using chambers. This is to reduce exposure to the researcher. In reality, although the team aimed to test the hybrid promoter with NO (as required for therapeutic effects) due to time restrictions this will not be happening. similarly if the team had more time they aimed to eventually test the comparator circuit using NO after testing it with promoters which respond to safer and simpler alternatives, such as arabinose. This allows the team to test the science of the comparator circuit , as well as getting use to the procedures needed to be carried out,before using more toxic chemicals.

Another safety concern was the use of Ethidium Bromide (EtBr) during the arose gel staining. This is potentially carcinogenic, therefore having to follow the university guide (File:UEA Rules for working with carcinogens in laboratories.pdf), wearing protective equipment, gloves and disposing of waste appropriately in order to minimize the researchers expose.

When planning the project and the experiments the team discussed and considered their choices of equipment to use. They considered the equipment’s safety to the researcher, as well as the practicality and quality of results gained. Most of the equipment and procedures used within the team’s iGEM project have been previously used, by the team members during the first two years of our undergraduate degree. However, there were a few procedures such as the nanodrop and fluorometer which had not been used before. Therefore the members of the team who were using these pieces of equipment received training from experienced members of staff, in order to avoid accidents which could damage the researcher or the machine itself. Finally, there were always more experienced scientists present within the lab, such as our advisors, who the team could ask for advice on how to use equipment correctly.

Public safety

The team remove their lab coat and gloves, as well as wash their hands before leaving the lab. This is to reduce the chance of bringing anything out of the lab and in to the rest of the university. The team also keep the windows shut, in order to reduce exposure to the outside world.

All contaminated waste is autoclaved on site before being collected and disposed of under controlled conditions for cleaning for reuse.

For the public safety, it is important that we give them the opportunity to understand and ask about what we are doing within the lab, as well as making the advantages and disadvantages clear. The team took the opportunity at the future of science to explain the procedures, such as wearing lab coats that are undertaken.

When the team took transformed E.coli samples to the forum event, we has to consider the public safety. Therefore, we had the plates in a UV box behind a sheet of plastic so that the public did not such them. the plates were also sealed up. Finally, they were kept on a different stand well away form any food ect.

Environmental safety

What are risks if safety measures such as containment procedures go wrong and organisms or parts are released? What are risks to security from malicious misuse? How are you addressing such risks?

The materials data safety sheets that come with chemicals explain how to dispose of the chemicals correctly. This is also important as Anglia water carry out random samples on what is poured down the sink drains, and if a certain volume (volume is unknown to university, which encourages them not to put any waste down the sink) of listed chemicals are found, then the university is fined.

There is a very low risk of damage to the environment as all bacteria will be stored safely within the lab. However, if the bacteria was to unexpectedly be released, there is very little threat on the environment, since the bacteria are standard autotrophic laboratory stains and therefore unlikely to survive. The “E.coli” stains used are also unlikely to replicate and therefore spread. Finally, due to using plasmids with a narrow host range horizontal gene transfer between bacteria within the environment is also very unlikely, as plasmids would not replicate if transferred to other organisms.

Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,

The first bio bricks made by the NRPUEA iGEM team are hybrid promoters which are composed of a mammalian promoter fused to a bacteria promoter. The team has done this in both orientations. Since this is a new concept they are not well characterized therefore providing saftey concerns , as it is not fully known how the promoters will interact together. However, the team have not submitted any issues in the registry as no issues have arisen yet, and there are no specific concerns within the DNA sequence and both individual promoters are well characterized and understood.

The comparator circuit biobrick is also a new construct, therefore again not well characterized,this could potentially join to functional genes and effect their gene regulations. however, as with the hybrid promoter these biobricks are being placed in standard BSL1 laboratory autotrophic strains of "E.coli", and therefore unlikely to be able to survive outside the lab. therefore the team has not entered issues in to the registry, as no evidence of concern has arisen yet. but if issues arise during characterization of the comparator circuit, these will be submitted.

The team handled these saftey issues by following and being in compliance with both the government saftey standards, as well as the university saftey standards. Also the team insert the biobricks in to the narrow host range plasmid, produced by iGEM, reducing chances of horizontal gene transfer.

future iGEM teams could increase chances of saftey, by connecting the hybrid promoter to suicide gene, therefore meaning that if the unlikely happened and the transformed cells were released in the the environment and the plasmid containing the biobricck was taken up up by another bacteria, this bacteria would be destroyed and therefore reduce chance of spreading.

Is there a local biosafety group, committee, or review board at your institution?

UEA considers both staff and student safety and has its own health and safety polices and biosaftey rules that must be followed:File:UEA GMO rules.pdf,File:UEA statment of health and saftey policy.pdfandFile:UEA Microbiological saftey rules.pdf. These have been created to follow the guidelines and biosafty rules that have to be considered in the united kingdom as seen here http://www.hse.gov.uk/biosafety/gmo/law.htm . All our projects are in compliance with both the university requirements and national regulations.The university has its own biosafety committee in which the responsibilities of different aspects of safety are split between departments and staff.Dr Andrew Hemmings is the BIO safety officer at UEA. Andrew spoke to members of the team about the project and discussed whether our COSH forms covered the processes carried out. The team then discussed their project further with other members of staff including Dr Mark Coleman, university GMO safety officer, and Dr Gabriella Kelemen, university microbial safety officer.

When speaking to the UEA biosafty team there was no concern with the processes being carried out and the bacteria being used. when the team talked to GMO safety officer,Dr Mark Coleman, about the safety of the biobricks they intended to create he said "there is a highly improbable chance this project poses a significant risk to either human health or the environment".

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?

Since the team started looking at NO, and we soon became clear of the dangers of unintentional exposure to NO. Therefore, we would hope that using systems similar to our comparator sensor, NO sensors will be produced that are in the form of a sheet of paper and can be placed on the wall of labs, and buildings ect, to indicate excess levels of NO.

Future iGEM teams could aim to reduce the chance of horizontal gene transfer further by reducing the adherence between the transformed cells and others, or via the Prevention of transformations without inducing competency. This would be a procedure to prevent some cases of antibiotic genes being passed through between bacterial species.