Team:Cambridge/HumanPractices/Overview

From 2012.igem.org

(Difference between revisions)
(Innovation)
(Overview of Human Practices and Outreach)
Line 106: Line 106:
We believe that a standardised output for biosensor experiments would be of enormous help to teams, giving them the tools to compare results, share and collaborate more effectively.
We believe that a standardised output for biosensor experiments would be of enormous help to teams, giving them the tools to compare results, share and collaborate more effectively.
 +
 +
All of these issues were discussed in our interview with Dr. <html><u><a href="http://2012.igem.org/Team:Cambridge/HumanPractices/Interview" style="color:#000066">ARSOlux kit</a></u></html> , an environmental researcher who is particularly interested in the opportunities that genetically modified biosensors can afford.
<html>
<html>

Revision as of 03:45, 27 October 2012

Parts for a reliable and field ready biosensing platform

Implementation of biosensors in real world situations has been made difficult by the unpredictable and non-quantified outputs of existing solutions, as well as a lack of appropriate storage, distribution and utilization systems. This leaves a large gap between a simple, functional sensing mechanism and a fully realised product that can be used in the field. We aim to bridge this gap at all points by developing a standardised ratiometric luciferase output in a Bacillus chassis. This output can be linked up with prototyped instrumentation and software for obtaining reliable quantified results. Additionally, we have reduced the specialized requirements for the storage and distribution of our bacteria by using Bacillus' sporulation system. To improve the performance of our biosensing platform we have genetically modified Bacillus’ germination speed. Lastly, we demonstrated the robustness of our system by testing it with a new fluoride riboswitch, providing the opportunity to tackle real life problems.

One minute tour! :)

>> Return to page
>> Return to page


Contents

Judging Form

  • Please help the judges by filling out this form. Tell them what medal you think you deserve and why. Tell them which special prizes you should win. Help them find your best parts. Show them how you thought about the safety of your project. Helping the judges will help you too.

  • Team: Cambridge
  • Region: Europe
  • iGEM Year:2012
  • Track:Foundational Advance
  • Project Name:Parts for a reliable and field ready biosensing platform
  • Project Abstract: Implementation of biosensors in real world situations has been made difficult by the unpredictable and non-quantified outputs of existing solutions, as well as a lack of appropriate storage, distribution and utilization systems. This leaves a large gap between a simple, functional sensing mechanism and a fully realised product that can be used in the field.

    We aim to bridge this gap at all points by developing a standardised ratiometric luciferase output in a Bacillus chassis. This output can be linked up with prototyped instrumentation and software for obtaining reliable quantified results. Additionally, we have reduced the specialized requirements for the storage and distribution of our bacteria by using Bacillus' sporulation system. To improve the performance of our biosensing platform we have genetically modified Bacillus’ germination speed. Lastly, we demonstrated the robustness of our system by testing it with a new fluoride riboswitch, providing the opportunity to tackle real life problems.

Back to wiki


iGEM Medals for non-software teams

  • We believe our team deserves the following medal:
    • Bronze
    • Silver
    • √Gold

Because we met the following criteria (check all that apply and provide details where needed)

Requirements for a Bronze Medal

  • √Register the team, have a great summer, and plan to have fun at the Regional Jamboree.
  • √Successfully complete and submit this iGEM 2012 Judging form.
  • √Create and share a Description of the team's project using the iGEM wiki and the team's parts using the Registry of Standard Biological Parts.
  • √Plan to present a Poster and Talk at the iGEM Jamboree.
  • √Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Standard Biological Parts. Including:
    • √Primary nucleaic acid sequence
    • √Description of function
    • √Authorship
    • Safety notes, if relevant.
    • √Acknowedgment of sources and references
  • √Submit DNA for at least one new BioBrick Part or Device to the Registry.

Additional Requirements for a Silver Medal

  • √Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected; characterize the operation of your new part/device.
  • √Enter this information and other documentation on the part's 'Main Page' section of the Registry
    Part Number(s): BBa_K911004

Additional Requirements for a Gold Medal: (one OR more)

Back to wiki

iGEM Prizes

All teams are eligible for special prizes at the Jamborees. more... To help the judges, please indicate if you feel you should be evaluated for any of the following special prizes:

  • √Best Human Practice Advance
  • √Best Experimental Measurement
  • Best Model

Please explain briefly why you should receive any of these special prizes:

Best Human Practice Advance:

We feel that we deserve this prize for three reasons:

  1. We explored the impacts, *both positive and negative*, of synthetic biology as a solution to real world problems, through interviewing professionals working in a relevant field, namely the impact of arsenic water contamination in Bangladesh.
  2. We recognized existing problems with the way the current direction of synthetic. On going through the registry we found that most of the characterization data for biosensing parts is often neither comparable nor replicable. We have worked to solve this issue, for example with our ratiometric dual channel output.
  3. *Our project doesn’t stop here*, in Chanel number 6 (Team:Cambridge/HumanPractices/FutureDirections) we considered the future implications and technological applications of our project, as well as the means by which it could be improved by subsequent users. We feel that the end to an iGEM project should not be the conclusion of an idea, but the start of it.

Best BioBrick Measurement Approach:

It is absolutely vital that a quantitative, numerical, robust, and flexible measurement approach exists to relay information to a user that is an accurate representation of the input processed by a biological device. Working from these principles, the following was done:

  1. We designed and built Biologger, a *cheap, arduino-based, fully functional automatic rotary device* that has an incorporated ratiolumnometer
  2. Our project is entirely open-sourced and open-platform. We have published source code for the two applications which serve to operate the device, one for PCs and the other for Android devices, as well as the open source circuit design that provides this ratiometric reading. Furthermore, the Android app is able to receive its data wirelessly, which we feel is a great advance in BioBrick measurement.
  3. Our dual-channel luciferase reporter was successfully tested with a dilution series of E.coli transformed with the Lux Operon (under pBAD) biobrick (Part BBa_K325909) of the Cambridge iGEM 2010 team. It can detect, with good accuracy, both different light intensities, as well as the percentages of blue or orange frequencies in a sample.
  4. Our device was successfully tested using artificial light to detect different frequencies (colours) as well.

Having done all the above, we believe that this fully open-sourced instrumentation kit (mechanical) chassis, electronics, software code), estimated at *$35.00* (or $85.00 if a Bluetooth modem is required), is a complete BioBrick measurement solution for any and all BioBricks with a light output.

Back to wiki

Team_Parts

To help the judges evaluate your parts, please identify 3 of your parts that you feel are best documented and are of the highest quality.

  • Best new BioBrick part (natural)
    BBa_K911003
    Best new BioBrick part (engineered)
    BBa_K911004
  • Best improved part(s): None

List any other parts you would like the judges to examine:BBa_K911001, BBa_K911009, BBa_K911008

Please explain briefly why the judges should examine these other parts:

  • Magnesium Sensitive Riboswitch BBa_K911001
    As a riboswitch sensing construct, this part is an entirely new type of biosensor (along with the fluoride construct) that could potentially change the way we think about designing input genetic circuits. Unlike the fluoride riboswitch, it is a derepression system and therefore serves to demonstrate the principle that riboswitches can be used regardless of whether they turn on or off their reporter.
  • Fluorescent ratiometric construct for standardizing promoter output BBa_K911009
    Fluorescence is a major cornerstone for biosensors in the registry, however, most parts do not involve the use of a ratiometric output, which has been shown in the literature to provide much more reliable and meaningful data. This part not only furthers the development of ratiometric measurements in molecular biology but due to the choice of promoters and terminators it can be used to characterize the difference in activity between E. coli and B. Subtilis
  • Fast Germination (B. subtilis) BBa_K911008
    This part is entirely novel for the registry and fully utilizes the recombination machinery inherent in the Bacillus chassis. Have spores that can germinate at a faster rate is certainly a worthy achievement and could help with experiments with B. Subtilis that any future iGEM teams may wish to perform.

Back to wiki

iGEM Safety

For iGEM 2012 teams are asked to detail how they approached any issues of biological safety associated with their projects.

The iGEM judges expect that you have answered the four safety questions Safety page on your iGEM 2012 wiki.

Please provide the link to that page: Page name: Team:Cambridge/Safety

Attribution and Contributions

For iGEM 2012 the description of each project must clearly attribute work done by the team and distinguish it from work done by others, including the host labs, advisors, and instructors.

Please provide the link to that page, or comments in the box below: Page name: Team:Cambridge/Attributions

Comments

If there is any other information about your project you would like to highlight for the judges, please provide a link to your wiki page here: Team:Cambridge/Overview/DesignProcess

Overview of Human Practices and Outreach

iGEM criterion: Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.


Our human practices this year has been a driving force of our project from the start, defining many of its key features. This part of our project has drawn on the safety, sharing and innovation criteria in a three part sub-project as well as incorporating outreach. In the safety category, we go beyond the iGEM requirement of the safety questions to present our idea of the standard of obvious safety consciousness that teams should provide. In sharing, we explain how the desire to produce a system that would encourage sharing between iGEM teams and allow collaborative projects with greater ease was one of the factors that helped define our project from the start and how the necessity for this became increasingly obvious as the project continued and we faced problems trying to build on the research of other teams.

Innovation

We took the idea of considering our project as a product. Clearly in its current state it is not a product ready to go to market, but could be considered as a prototype for one that might be. Our system is designed to be used in a huge variety of circumstances, but for the sake of this exercise we have used just one.

The idea was to consider the process of taking our ‘product’ and putting it in a ‘market'. We have considered a suitable market for the product – in this case groundwater contamination in rural India, weighed up the strengths and weaknesses of currently available systems that cater for this market and how our system differs.

We then consider the likely problems that would be faced were we attempting to attempt this now, ranging from mistrust of GMOs to bacterial disposal.

Why is this relevant?

The majority of us, whether we pursue careers in research or industry will probably at some point be involved with the production or release of a product. We have tried to use this as a trial run, to show teams what they might expect to come up against. We hope that this might inspire teams to consider human practices as a foundation for their projects as we did. Fluoride contamination was a major factor in the decision to design a system from start to finish that could quantifiably test for fluoride. We hope that this might encourage teams to think innovatively about their project when in the design phase, to consider a real world problem to which their project could be a solution and to consider the problems they might encounter in the course of applying that solution so that they can be tackled in the course of the project.

Our innovation project can be found here.

Safety

Safety is core to the iGEM competition and all teams must complete a series of safety questions on their wiki to qualify for a medal to prove that they have considered the safety implications of their project as a whole and have set about working in compliance with good laboratory practice. In addition to this criterion we have also produced protocols for reference for all of the techniques we use in the lab. These also have risk assessments for the major risks associated with them and precaution suggestion where appropriate as well as MSDS sheets for all reagents used available in the safety section of our wiki.

We assume that, like us, most iGEMers do not relish the thought of vast quantities of paperwork to accompany their projects. Our safety criteria do not impose this, but do demand further proof of safety consciousness than current requirements.

Why is this relevant?

The current team has found having this information readily accessible on the wiki (where it cannot be lost or tidied away) to be extremely useful and we consider it the duty of iGEM teams to leave their project in a sufficiently well documented state that future teams could pick up more or less where the previous team stopped.

Where teams choose to modularise their project into several sub-projects, different teams may be working with different experiments at any given time. It may be weeks before certain teams use techniques that others utilised on their first day. This is where having reliably accessible information comes into its own. Which reagent comes next? It’s on the wiki. Waste disposal? On the wiki. Do I need a mask for this? On the wiki. Is it supposed to go that colour? It’s on the wiki.

Perhaps more importantly, we have found that constantly updating and adding to the safety element of our project prevented it from slipping to the back of mind. We have found that we spent more time than anticipated considering the safety implications of experiments as we were planning and doing them, in the knowledge that we would be written up formally.

The provision of detailed protocols, MSDS and at least basic risk assessments can be hugely helpful to future teams, especially students coming to the iGEM competition from non-biological disciplines. Even those of us thoroughly familiar with techniques like PCR found the last team’s notes useful for reference in the early weeks of our project. Many excellent projects have been stopped short because of time constraints. If another team wanted to build on it, they might be able to ask the previous team if it is the next year and at the same institution, but if it is several years before the project catches the imagination of another team, then the wiki is probably all they’ll have to work with.

Sharing

Early in the summer, when we were trying to define our project, we started thinking about what we wanted it to do. We eventually settled on one of the key principles of synthetic biology – standardisation (strongly promoted by the engineers on the team). Biological research is currently a highly bespoke process with predominantly non-standardised biosensors – a multitude of output systems with a plethora of sensitivity curves exist. This renders individual sets of results amost meaningless as research from different teams is not directly comparable. This limits the capacity for sharing and collaboration as teams are effectively working on their own and this in turn limits the rate of progress.

To this end our project was focussed on producing a standardised output system with instrumentation for biosensor experiments to promote facilitate sharing and collaboration between iGEM teams, with a myriad of possible applications. A ratiometric system was chosen to provide a reliable quantification system, it was decided that the system should be portable so that it could be used for field research as well as laboratory based research and relatively cheap, to make it accessible to other iGEM teams. We felt it important that the code used in the instrumentation be open source like the rest of the project, so that it could be tweaked by future users to match their needs.

Why is this relevant?

iGEM is open source and high value is placed on sharing, collaboration and building on the work of previous teams. Where there is a lack of standardisation however, it is hard for teams to know what they can expect when working with another team’s project. We have attributed at least some of the problems we have experienced when trying to work with previous teams’ biobricks this summer to this problem.

We believe that a standardised output for biosensor experiments would be of enormous help to teams, giving them the tools to compare results, share and collaborate more effectively.

All of these issues were discussed in our interview with Dr. ARSOlux kit , an environmental researcher who is particularly interested in the opportunities that genetically modified biosensors can afford.