Human Practices

What is “human practices”?

As a team we wanted to analyse and address the society’s relationship with science, and more specifically, synthetic biology.

After researching society’s views on synthetic biology we perceived four important problems that we could solve:

1. Cooperation between scientists is lacking.

2. The public does not perceive synthetic biology to be safe.

.3. The key skills required for synthetic biology can be intimidating.

4. The general public are not as engaged as they should be.

Cooperation is lacking

We believe that cooperation and collaboration are two of the fundamental principles behind the success of synthetic biology. By always keeping these themes at the forefront of our thinking, we could allow them to permeate through our entire project whether it was working directly with another team to reach a common goal, or just making software on multiple platforms to allow more people to use it.

Tayside iGEM

We were delighted to be able to work closely with the St Andrews iGEM team, who are based just across the Tay Bridge, about 40 minutes away from Dundee. It was really useful to meet with them and share our experiences. As described later in this section, we worked with them to put on a discussion on the pros and cons of synthetic biology’s place in society to coincide with the world schools debating competition.

Towards the end of the project we found out that the St Andrews team were having troubles cloning their antimicrobial peptide generator part into the psb1c3 plasmid. We were pleased to be able to help them troubleshoot their experiments and by working together we were able to successfully clone the part.

The main problem St Andrews were having seemed to be related to the production of new plasmid backbone via PCR with the iGEM specified primer design and specified RFP part. We were able to overcome this problem by carrying out some of their cloning in our lab using their AMP generator and our plasmid backbone which we made by restriction digest of uncut plasmid followed by gel cleanup. While we were doing this St Andrews carried out the same cloning cycle in paralell but using backbone they had generated by PCR. This confirmed that the source of the odd behaviour shown by the St Andrews ligation reactions and by their transformants was likely due to the method of backbone production.

Our troubleshooting experiments led to us being able to provide the St Andrews team with a plate of bacteria containing their part on the desired backbone. Further cooperation between the teams will take place over the coming weeks in order to determine why the PCR based backbone amplification procedure was not working as it should. It was really great to share our time and resources with them, and we hope there will be a good relationship between the two teams in future iGEM competitions. We wish them the best of luck for the Jamboree.

Software Advice

Our computer scientists were able to help the TUM iGEM team by offering software advice. Having had difficulties to embed Javascript on their wiki, the TUM team tweeted for assistance. The computer scientists on the Dundee University iGEM team were very happy to help. They tweeted back giving a detailed explanation of what needed to be done. Having followed our advice they tweeted back stating that it was successful. It was interesting to interact with another iGem team we hadn’t met, following the iGEM spirit. We’re excited to meet the team in Amsterdam.

Submitting Our Parts

When submitting our biobrick parts, we took care to make the parts easily accessible to teams of the future. With new research still carried out into the way the BMC is expressed, and which features are required to form a fully functioning BMC. We hope that by submitting the structural components separately we can encourage other teams to experiment further, for example with the order and composition of the operon.

Safety Concerns

SynBin

We felt the best way to address safety concerns was to evaluate our behaviour in the laboratory, ask ourselves whether it would be acceptable to the general public, and if not, how can we make it more acceptable.

This evaluation inspired the “SynBin”, a tool to help future teams share and discuss their accidents (“Syns”). Whether it’s an embarrassing slip or a more serious “Rachelle’s set the lab on fire… again!” all incidents can be posted anonymously in the SynBin’s database. This will allow fellow synthetic biologists to learn from each other’s mistakes and adapt the way they work, creating a safer lab environment for everyone.

By demonstrating how seriously we take health and safety, we can show the public that synthetic biology is being carried out in a safe and controlled environment. We feel that practical solutions like this are the best way forward to a more engaged and accepting public.

The SynBin is in late stages of development and we hope for it to go live in the next few weeks.

Intimidating skills required

Software

One of the first problems any scientist will have on joining the world of synthetic biology is gene cloning. Gene cloning is the method by which DNA molecules can be assembled in vitro, taken up by host cells, and then replicated with the cells as they divide. By speaking with scientists within our building and by noting the problems we encountered while working, we realised that cloning can be quite intimidating!

Two problems we encountered, by no means all, with cloning were as follows:

• Different organisms use codons differently.

• Making PCR primers is confusing.

Gene Synthesiser

Many synthetic biology projects involve the heterologous expression of foreign genes in a host such as E. coli/S. cerevisiae etc. For successful and efficient translation, the codon usage of the newly introduced gene must be optimised to match the tRNA pool of the host organism. However, if one simply picked the most common codon for each amino acid, the rate of translation would be extremely fast across the entire gene. This may lead to subtle characteristics of translation being lost. For example, it has been suggested that in certain regions of the gene, the source organism may ‘choose’ a short run of rare codons, in order to slow down translation in that region. This slowing of the emerging polypeptide from the ribosome has been suggested to facilitate the correct folding of the heterologous protein and/or allow time for the insertion of essential co-factors [19]. These regions of "slow" translation, may occur in loops between different domains of the protein. It may be therefore important for certain genes, to maintain this pattern of fast to slow translation in the target organism.

“Gene Synthesiser” is a java application that makes this possible by enabling codon usage pattern matching. The application analyses the patterns of codon usage of the gene that one wants to express, in its native organism and generates new synthetic DNA sequence, optimised for the codon usage of the new target organism, yet matching any patterns of rare to common codons. Gene Synthesiser utilises codon usage data for over 35000 organisms. [20]

We also designed a number of mobile applications (Apps). With the development of smart phones, there is now a demand for simple efficient programs that can aid carrying out everyday tasks.

The Lazy scientist

The Lazy Scientist is a translation tool. The app has a number of functions including DNA to amino acid translation, back translation, reverse, complement and reverse complement. The app also contains a genetic codon lookup table allowing all corresponding codons for an amino acid to be looked up. The app is available for free in both the iPhone App Store and the Android Market.

Gene Slicer/Gene cutter

The Gene Cutter (iPhone app) and The Gene Slicer (Android app) are gene cutting tools. The apps have two functions to help restriction mapping of nucleotide sequences. The apps are able to search a sequence for a specific enzyme and can also return a list of enzymes not present in the sequence. The app is available for free in both the iPhone App Store and the Android Market.

To date there have been over 1500 downloads from all over the world. Making apps will increase the accessibility of synthetic biology, allowing scientists to have portable tools to aid them in synthetic biology wherever they are.