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Team:University of Sheffield /Project
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==The Microchip Theory== | ==The Microchip Theory== | ||
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| + | Our idea originated with the concept of a microchip that would test water for pathogen concentration. Whilst one summer wouldn’t allow us to actually build it, we still had an impression as to what it would look like. | ||
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| + | The target was for a cheap, reusable, quick and non-technical piece of equipment. At first, the microchip really was micro, and would require a microscope to look at, but in areas of natural disaster or extreme poverty this wasn’t viable. So we planned and hand-held size chip, with a number of ‘wells’ or ‘chambers’ built into it. Each chamber would contain a different pathogen-sensing E.coli colony. This presented other problems into how to keep the E.coli alive – could they survive if attached physically to the chamber? Or would they have to be frozen, or suspended in media? Frozen seemed the most likely, but not ideal, but proper design could be implemented later. | ||
| + | Then the idea was to take a sample of water, possibly contaminated, and place it on the chip. The contaminants would interact with the specially designed E.coli, and those activated by contaminants would produce a distinctive glow visible to the naked eye. The chamber that glows corresponds to an unhealthy level of a particular pathogen in the water sample. | ||
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| + | The reusable aspect came from the idea that disposable equipment is environmentally unfriendly. However, it could be cheaper than a reusable option, so if out plan were to be properly carried out, both chips should be developed to provide options. To make the chip reusable however, LVA tags are attached to the GFP in the DNA code, which attracts a housekeeping protease to cleave the GFP more rapidly than if left to degrade in the cell alone. A short burst of glow would be visible in cell, which would disappear by the time the chip dries out/the water passes through it. | ||
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| + | This approach requires absolutely no technical knowledge, and could be ideal for its purposes. A future iGEM project anyone? | ||
Revision as of 11:35, 28 October 2008
| Introduction | Our project | Modelling | Wet Lab | Our team | Timetable | Miscellaneous |
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Project Overview
Contents |
Introduction
Fusion Receptor
The Native E.coli pathway
A Green Fluorescent Reporter
Introduction
The initial plan was to introduce a Green Fluorescent reporter molecule under one of the genes controlled by small regulatory RNA called CsrA. So as not to reduce the viability of the cell as well as to avoid any possible “noise” in the engineered system, the gene choice required several attempts.
Re-usable testing kit
The plan to have a micro – chip for sensing biological water contamination ideally would include a possibility of reusing it. Thus, the aim of our project was to use GFP with an LVA tag (AANDENYALAA). This would mean that the GFP would have an amino acid tag targeted by housekeeping proteases and would be degraded within 45 minutes once there is no more stimulation for gene expression. This in turn would mean that the E.coli system sensing V.cholerae presence in water would stop fluorescing once the concentration of CAI-1 molecules decreased up to tolerable level. [2]
The idea to include degradable GFP in our project was taken from the Andersen, J.B et al. (1998) New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria. Applied and Environmental Microbiology.
pgaABCD operon control
This particular four - gene locus in E.coli is responsible for synthesis of the biofilm adhesion protein called PGA. As this is a virulence factor, i.e. non-essential for growth in supplemented media, a possible insertion of GFP and possible disruption the operon would not cause lethal effects to our cells.
As far as it is known, the pgaABCD genes are subject to post-translational inhibition by the small regulatory RNA CsrA as well as activation by the cation-responsive regulatory protein NhaR. The first fact is to our advantage. In theory, once the binding of the CAI-1 to fusion kinase occurred, the CsrA inhibition would be releaved and the GFP would be expressed . Also, according to research it has been proven that the csrA deletion mutant had an impressive 3000 fold increase compared to the wild type.
Possible “noise” in the system
As mentioned before, one of the factors to be taken into account prior choosing the gene within which the GFP would be inserted is the interference or “noise” in the system. This possibility might have caused background fluorescence or GFP expression independent from the sensing event of our interest.
The reasons underlying this “noise” are listed below:
- High salt concentrations (NhaR dependent)
- Alkaline pH (NhaR dependent)
- Ethanol ( NhaR dependent)
- Glucose presence in the media (Independent from both CsrA and NhaR)
The noise in the system appears only if the cells are grown at extreme conditions. However, if the growth media contains only 1% glucose, 1 % ethanol, 1 % NaCl the levels of the pgaABCD transcript should not be elevated by any other factors except CsrA. On the other hand, if additional NaCl or glucose are added to the medium it might cause significant increase in the pgaABCD mRNA appearance [2]
Target of insertion
As the pgaABCD is a four-gene locus another question that arose was the actual place within the operon where the insertion could take place. Another obstacle was that genes b, c and d overlap with each other.
One would theoretically suggest insertion under the promoter sequence, before the actual gene a . However, the very high inhibition with CsrA is actually due to 6 binding sites, one of which overlaps with gene a formyl-methionine codon.
Thus, the only possible way of inserting GFP, with minimal disruption of the whole operon, is at the end of gene a sequence just before the termination codon. This would give a high level of control by CsrA, as it is just after the CsrA regulatory binding sites, and would hopefully prevent extensive damage to genes b,c and d expression.
Cholera Autoinducers
The Microchip Theory
Our idea originated with the concept of a microchip that would test water for pathogen concentration. Whilst one summer wouldn’t allow us to actually build it, we still had an impression as to what it would look like.
The target was for a cheap, reusable, quick and non-technical piece of equipment. At first, the microchip really was micro, and would require a microscope to look at, but in areas of natural disaster or extreme poverty this wasn’t viable. So we planned and hand-held size chip, with a number of ‘wells’ or ‘chambers’ built into it. Each chamber would contain a different pathogen-sensing E.coli colony. This presented other problems into how to keep the E.coli alive – could they survive if attached physically to the chamber? Or would they have to be frozen, or suspended in media? Frozen seemed the most likely, but not ideal, but proper design could be implemented later. Then the idea was to take a sample of water, possibly contaminated, and place it on the chip. The contaminants would interact with the specially designed E.coli, and those activated by contaminants would produce a distinctive glow visible to the naked eye. The chamber that glows corresponds to an unhealthy level of a particular pathogen in the water sample.
The reusable aspect came from the idea that disposable equipment is environmentally unfriendly. However, it could be cheaper than a reusable option, so if out plan were to be properly carried out, both chips should be developed to provide options. To make the chip reusable however, LVA tags are attached to the GFP in the DNA code, which attracts a housekeeping protease to cleave the GFP more rapidly than if left to degrade in the cell alone. A short burst of glow would be visible in cell, which would disappear by the time the chip dries out/the water passes through it.
This approach requires absolutely no technical knowledge, and could be ideal for its purposes. A future iGEM project anyone?
