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Team:Dundee/Notebook
From 2012.igem.org
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<h3 class="black">Week Two</h3> | <h3 class="black">Week Two</h3> | ||
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| - | + | <strong>Biology</strong><br /> | |
| + | The second week was when the project really began. The first task was to amplify the 13 type VI secretion system genes by PCR. TssA, TssE, TssF, TssM, Hcp and VgrG were all cloned individually from the prepared S. typhimurium chromosomal DNA. ClpV, VipA, VipB and TssJ, TssK (referred to hereafter at ClpV and TssJK respectively) were cloned as the original operons. Following PCR, results were analysed on a gel and showed that every gene was successfully amplified. The genes were then PCR purified and digested either BglII- HindIII or BclI- HindIII (TssM). Hcp (needle) and VgrG (needle tip) genes were cloned as fuse genes, i.e. they were cloned without a stop codon to allow the addition of another gene. These fuse genes were digested BglII- EcoRI. Digests were strata-cleaned, ligated into pUNI-PROM and transformed into DH5α cells. | ||
| + | Transformed colonies were mini-prepped, digested EcoRI-HindIII to remove the insert and products were run on a gel. Clones TssA, TssE, TssJK, Hcp and Hcp Fuse appeared correct and were sent for sequencing. TssF, VgrG, VgrG fuse and ClpV failed to show an insert on the gel so were rechecked using colony PCR. | ||
| + | <br /><br /> | ||
| + | <strong>Maths</strong><br /> | ||
| + | We continued to work on our interacting species model by including specific parameters, such as removal rates due to the natural processes in the colon, competition terms and the death rate of C. difficile due to the engineered type VI secretion system in E. coli. | ||
| + | <br /><br /> | ||
| + | <strong>Software</strong><br /> | ||
| + | Testing of a promising software modelling tool proved disappointing due to its inability to represent large cell number interactions. After consideration, the decision was made to begin development of a bespoke C++ application that could handle realistically large colonies of cells, whilst integrating the mathematical modelling aspects into the behaviour. The aim is to provide a cross-platform, cellular automata model of the project features top provide a graphical means to explore the project’s biological dynamics. Work also began on developing the team’s official Wikipedia website. | ||
</div> | </div> | ||
</div> | </div> | ||
Revision as of 14:18, 20 August 2012
Notebook
Week One
Biology
The first week for the biologists was a general introduction to the ways of the lab. We were given a health and safety briefing and attended a health and safety seminar (an experience that would terrify any undergrad new in the lab). The team was taken through all the experiments that would be crucial for the project and a general plan of attack was devised. The main achievements of this week were the production of competent DH5α E. coli cells; purification and amplification of Salmonella typhimurium LT2 chromosomal DNA and digestion of pUNI-PROM with EcoRI and BamHI or XbaI BamHI.
Maths
The Mathematics team began by looking at common modelling methods in biology. After some research, we started to piece together a system of ordinary differential equations (ODEs) representing the populations of E. coli and C. difficile using logistic growth models.
Software
The team created a template Blog website and Twitter account. To provide a graphical representation of the project, existing software modelling options were investigated to ascertain whether an existing tool could provide suitable functionality or if a bespoke solution would be preferable. Work commenced on an Android framework for a suite of mobile utilities that will be developed over the course of the project.
The first week for the biologists was a general introduction to the ways of the lab. We were given a health and safety briefing and attended a health and safety seminar (an experience that would terrify any undergrad new in the lab). The team was taken through all the experiments that would be crucial for the project and a general plan of attack was devised. The main achievements of this week were the production of competent DH5α E. coli cells; purification and amplification of Salmonella typhimurium LT2 chromosomal DNA and digestion of pUNI-PROM with EcoRI and BamHI or XbaI BamHI.
Maths
The Mathematics team began by looking at common modelling methods in biology. After some research, we started to piece together a system of ordinary differential equations (ODEs) representing the populations of E. coli and C. difficile using logistic growth models.
Software
The team created a template Blog website and Twitter account. To provide a graphical representation of the project, existing software modelling options were investigated to ascertain whether an existing tool could provide suitable functionality or if a bespoke solution would be preferable. Work commenced on an Android framework for a suite of mobile utilities that will be developed over the course of the project.
Week Two
Biology
The second week was when the project really began. The first task was to amplify the 13 type VI secretion system genes by PCR. TssA, TssE, TssF, TssM, Hcp and VgrG were all cloned individually from the prepared S. typhimurium chromosomal DNA. ClpV, VipA, VipB and TssJ, TssK (referred to hereafter at ClpV and TssJK respectively) were cloned as the original operons. Following PCR, results were analysed on a gel and showed that every gene was successfully amplified. The genes were then PCR purified and digested either BglII- HindIII or BclI- HindIII (TssM). Hcp (needle) and VgrG (needle tip) genes were cloned as fuse genes, i.e. they were cloned without a stop codon to allow the addition of another gene. These fuse genes were digested BglII- EcoRI. Digests were strata-cleaned, ligated into pUNI-PROM and transformed into DH5α cells. Transformed colonies were mini-prepped, digested EcoRI-HindIII to remove the insert and products were run on a gel. Clones TssA, TssE, TssJK, Hcp and Hcp Fuse appeared correct and were sent for sequencing. TssF, VgrG, VgrG fuse and ClpV failed to show an insert on the gel so were rechecked using colony PCR.
Maths
We continued to work on our interacting species model by including specific parameters, such as removal rates due to the natural processes in the colon, competition terms and the death rate of C. difficile due to the engineered type VI secretion system in E. coli.
Software
Testing of a promising software modelling tool proved disappointing due to its inability to represent large cell number interactions. After consideration, the decision was made to begin development of a bespoke C++ application that could handle realistically large colonies of cells, whilst integrating the mathematical modelling aspects into the behaviour. The aim is to provide a cross-platform, cellular automata model of the project features top provide a graphical means to explore the project’s biological dynamics. Work also began on developing the team’s official Wikipedia website.
The second week was when the project really began. The first task was to amplify the 13 type VI secretion system genes by PCR. TssA, TssE, TssF, TssM, Hcp and VgrG were all cloned individually from the prepared S. typhimurium chromosomal DNA. ClpV, VipA, VipB and TssJ, TssK (referred to hereafter at ClpV and TssJK respectively) were cloned as the original operons. Following PCR, results were analysed on a gel and showed that every gene was successfully amplified. The genes were then PCR purified and digested either BglII- HindIII or BclI- HindIII (TssM). Hcp (needle) and VgrG (needle tip) genes were cloned as fuse genes, i.e. they were cloned without a stop codon to allow the addition of another gene. These fuse genes were digested BglII- EcoRI. Digests were strata-cleaned, ligated into pUNI-PROM and transformed into DH5α cells. Transformed colonies were mini-prepped, digested EcoRI-HindIII to remove the insert and products were run on a gel. Clones TssA, TssE, TssJK, Hcp and Hcp Fuse appeared correct and were sent for sequencing. TssF, VgrG, VgrG fuse and ClpV failed to show an insert on the gel so were rechecked using colony PCR.
Maths
We continued to work on our interacting species model by including specific parameters, such as removal rates due to the natural processes in the colon, competition terms and the death rate of C. difficile due to the engineered type VI secretion system in E. coli.
Software
Testing of a promising software modelling tool proved disappointing due to its inability to represent large cell number interactions. After consideration, the decision was made to begin development of a bespoke C++ application that could handle realistically large colonies of cells, whilst integrating the mathematical modelling aspects into the behaviour. The aim is to provide a cross-platform, cellular automata model of the project features top provide a graphical means to explore the project’s biological dynamics. Work also began on developing the team’s official Wikipedia website.
Week Three
Week3...
Week Four
Week4...
Week Five
Week5...
Week Six
Week6...
Week Seven
Week7...
Week Eight
Week8...
Week nine
Week9...
Week Ten
Week10...
