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Team:Cambridge/Attributions
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| - | + | Please see below for the attributions of work carried out as part of our project. | |
===Sporage and Distribution=== | ===Sporage and Distribution=== | ||
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The magnesium riboswitch was amplified up, using primers of our own design, from a prepared ''B. subtilis'' genome sample. This sample was provided by PJ Steiner of the Haseloff lab. Oliver Meacock, from the team, then pieced this amplified DNA into pJS130, a shuttle vector also provided by PJ Steiner. Oliver Meacock also carried out the characterisation assay for the magnesium riboswitch. | The magnesium riboswitch was amplified up, using primers of our own design, from a prepared ''B. subtilis'' genome sample. This sample was provided by PJ Steiner of the Haseloff lab. Oliver Meacock, from the team, then pieced this amplified DNA into pJS130, a shuttle vector also provided by PJ Steiner. Oliver Meacock also carried out the characterisation assay for the magnesium riboswitch. | ||
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| + | All relevant primers for each riboswitch were designed by Jolyon Martin and Oliver Meacock in parallel. All PCR reactions, restriction digests, and other experiments using these parts were carried our by the pair. | ||
===Ratiometrica=== | ===Ratiometrica=== | ||
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James Brown from the Haseloff Lab, Cambridge has offered us invaluable advice in collecting and analysing data from our ratiometric fluorescent construct. | James Brown from the Haseloff Lab, Cambridge has offered us invaluable advice in collecting and analysing data from our ratiometric fluorescent construct. | ||
| - | PJ Steiner from the Haseloff Lab has provided the original E. coli and B. subtilis shuttle vector pJS130 on which we worked | + | PJ Steiner from the Haseloff Lab has provided the original E. coli and B. subtilis shuttle vector pJS130 on which we worked. |
| - | Paul Mallaband, Emmy Tsang and Thomas Whittaker from the team | + | Paul Mallaband, Emmy Tsang and Thomas Whittaker from the team designed and assembled the final ratiometric fluorescent construct using PCR and Gibson assembly. The component biobricks (other than the backbone) came from the Registry's Spring Distribution Kit. We designed the original primers for Gibson and ligation, optimised the PCR, gel and PCR extraction, and Gibson assembly protocols, and tested the construct. |
Fernan Federici from the Haseloff Lab provided the original mOrange DNA template, while the fischeri LuxBrick (K325909) is from the Parts Registry. Tom and Emmy from the team have assembled the construct using Gibson assembly and PCR. | Fernan Federici from the Haseloff Lab provided the original mOrange DNA template, while the fischeri LuxBrick (K325909) is from the Parts Registry. Tom and Emmy from the team have assembled the construct using Gibson assembly and PCR. | ||
Revision as of 01:30, 27 September 2012
Contents |
Attributions
Please see below for the attributions of work carried out as part of our project.
Sporage and Distribution
The fast promoter swap over strains we used in sporage and distribution were developed based on work by Peter Setlow from the Setlow lab at the University of Connecticut (see references in the project section). Furthermore Barbara and Peter Setlow sent us the two E. coli plasmids used for transformation of B. Subtilis as well as the finalised spores we used in testing the construct. They also provided us with information on sporulation and germination protocols and help with designing primers for biobricking the part.
Paul Mallaband and Stuart Bell from the team made up sporulation and germination medium and carried out imaging of the spores. They also carried out all relevant pcr, gibson and restriction ligation reactions to make a biobrick of the part.
Paul Grant from the Haseloff lab was instrumental in helping with imaging spores and gave advice on staining, slide preparation and microscopy.
Instrumentation
Andreas Petrides from the team led the development of the instrumentation kit along with Paul Mallaband. Electronics and Arduino code was tackled by Andreas, python code by Paul whilst both took part in the mechanical design and sourcing of materials. The testing of the instrumentation was done by Andreas with the aid of Thomas Whittaker who prepared the biological samples.
The python code was based on that submitted at http://www.blendedtechnologies.com/realtime-plot-of-arduino-serial-data-using-python/231. All arduino code was developed by Andreas and Paul. The android application was implemented by Andreas, based on [http://www.amarino-toolkit.net/index.php/home.htmlAmarino] projects' open-source code (General Public License).
Mr. Tim Love from the engineering department gave advice on software design and the Engineering department helped with supplying some of the materials required. The actual assembly of the kit was done entirely by Andreas and Paul.
Ribosense
The fluoride riboswitch, with β-galactosidase reporter, was generously supplied, both in plasmid form, and as transformed cells, by the Breaker laboratory (See references in the project page as well as the special thanks page) at the University of Yale.
The plasmid supplied was then transformed into 168 strain B. subtilis, and Top10 E. coli, by Jolyon Martin from the team. He also carried out the β-galactosidase and Miller Assays.
The magnesium riboswitch was amplified up, using primers of our own design, from a prepared B. subtilis genome sample. This sample was provided by PJ Steiner of the Haseloff lab. Oliver Meacock, from the team, then pieced this amplified DNA into pJS130, a shuttle vector also provided by PJ Steiner. Oliver Meacock also carried out the characterisation assay for the magnesium riboswitch.
All relevant primers for each riboswitch were designed by Jolyon Martin and Oliver Meacock in parallel. All PCR reactions, restriction digests, and other experiments using these parts were carried our by the pair.
Ratiometrica
James Brown from the Haseloff Lab, Cambridge has offered us invaluable advice in collecting and analysing data from our ratiometric fluorescent construct.
PJ Steiner from the Haseloff Lab has provided the original E. coli and B. subtilis shuttle vector pJS130 on which we worked.
Paul Mallaband, Emmy Tsang and Thomas Whittaker from the team designed and assembled the final ratiometric fluorescent construct using PCR and Gibson assembly. The component biobricks (other than the backbone) came from the Registry's Spring Distribution Kit. We designed the original primers for Gibson and ligation, optimised the PCR, gel and PCR extraction, and Gibson assembly protocols, and tested the construct.
Fernan Federici from the Haseloff Lab provided the original mOrange DNA template, while the fischeri LuxBrick (K325909) is from the Parts Registry. Tom and Emmy from the team have assembled the construct using Gibson assembly and PCR.
Tom from the team has designed the harveii Lux-mOrange2 construct, which was then synthesised and codon optimised by DNA 2.0.
Wiki
The javascript and css style sheets used in this wiki are based on those made by Haydn King from the Cambridge 2011 team.
Emmy from the team designed the graphics while Paul and Andreas tweaked the javascripts and css.
Social media icons from "Vintage Icon Set for Bloggers": http://webexpedition18.com/articles/vintage-icon-set-for-bloggers/
Interface and graphics are designed using Adobe CS5 Photoshop, Illustrator and Dreamweaver. Some of the PS brushes used:
- http://www.brusheezy.com/brushes/27476-dbd---swooshpack-lite
- http://differentxdreamz.deviantart.com/art/Delicate-Praise-Brushes-134841016
- http://www.brusheezy.com/brushes/18307-pretty-designs
Human Practices
Charlotte Bransfield-Garth from the team corresponded with international NGOs, conducting market research and reporting on the real world situation.
Oli from the team interviewed Dr. Konrad Siegfried, a member of the ARSOlux team testing for water contamination in Bangladesh, and also explored the future directions of the our project.
