- 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.
iGEM Medals for non-software teams
- We believe our team deserves the following medal:
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
- 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)
- Improve an existing BioBrick Part or Device and enter this information back on the Experience Page of the Registry.
Part Number(s): None
- √Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.
Link to this information on your wiki. Page name: Team:Cambridge/Outreach/Collaboration
- √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.
Link to this information on your wiki.
Page name: Team:Cambridge/HumanPractices/Overview,Team:Cambridge/HumanPractices/MarketResearch,Team:Cambridge/HumanPractices/FutureDirections
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:
- 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.
- 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.
- *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:
- We designed and built Biologger, a *cheap, arduino-based, fully functional automatic rotary device* that has an incorporated ratiolumnometer
- 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.
- 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.
- 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.
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 improved part(s): None
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.
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
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
- Gel Electrophoresis A technique for separating DNA strands of different lengths.
- Gel Extraction of DNA A technique used to isolate a desired fragment of intact DNA from an agarose gel following agarose gel electrophoresis.
- Gibson Assembly A technique for ligating multiple DNA fragments in one step, compatible with standard assembly.
- PCR using a high temperature DNA polymerase A method for amplifying a section of DNA.
- Making a Biobrick A final step to put your construct into the standard biobrick format to be submitted to the registry.
- Chemically competent cells generation A technique to produce e.coli cellsreceptive to chemical transformation.
- Electocompetent cells generation A technique to produce e.coli cells receptive to transformation by electroporation
- Electroporation A method for transforming appropriately competent cells with plasmid DNA using electricity.
- Glycerol stocks A technique for long term storage of cells at -80 degrees without losing cell vitality.
- Transformation of Bacillus subtilis A technique used to introduce foreign DNA into competent Bacillus cells.
- Transformation of Escherichia coli A method for transforming competent E.coli with DNA
- Colony PCR PCR with cells as a template. Useful for checking the length of an insert in an introduced plasmid.
- Restriction Enzyme Digest A method for creating a restriction map of a plasmid.
- MiniPrep - DNA extraction A method used to extract DNA from bacterial cells.
- β-galactosidase assay Assay to qualitatively measure the amount of the enzyme β-galactosidase being produced by a population of cells. Useful as a reporter system.
- Miller assay Assay to quantify the amount of the enzyme β-galactosidase being produced by a population of cells. Useful as a quantitative reporter system.
- Production of magnesium free cells. Technique to produce cells that contain little or no magnesium, to control for this variable in tests involving the magnesium riboswitch.
- IPTG induction A technique for inducing the pSPANK promoter in E.coli cells.
Sporulation and Germination
- Imaging spores A method for seeing vegetative cells and bacillus spores under the microscope.
- Producing high yields of spores A method for obtaining high yields of spores from B. Subtilis
- BioBricks Resources for manipulation of BioBricks and information regarding the distribution.
- LB Agar Plates preparation A method used to prepare agar plate to culture common bacteria.
- Use of Antibiotic Stocks The production of Antibiotic LB agar plates and liquid medium to discriminate bacterial lineages.
- M9 minimal medium A recipe for making M9 minimal medium for use when autofluorescence must be avoided.
- Medium B A recipe for making medium B.
- CCMB80 for chemically competent cells generation A recipe for making CCMB80
- TAE buffer for gel electrophoresis A recipe for making 10xTAE buffer
- SOB growth medium A recipe for making SOB growth medium
- CDSM A Chemically Defined Media to induce sporulation in B. Subtilis
- Germination Media A Chemically Defined Media to induce Germination in B. Subtilis
mfold, DNA or RNA folding forms on the left hand side