"
Team:Hong Kong HKU/Modeling
From 2013.igem.org
(Difference between revisions)
| (9 intermediate revisions not shown) | |||
| Line 4: | Line 4: | ||
<html> | <html> | ||
| + | |||
| + | <head> | ||
| + | <script> | ||
| + | $(window).scroll(function() { | ||
| + | var Content = $(this).scrollTop(); | ||
| + | if (Content > 525) { | ||
| + | $('.floating-menu').fadeIn(); | ||
| + | }else { | ||
| + | $('.floating-menu').fadeOut(); | ||
| + | } | ||
| + | }); | ||
| + | </script> | ||
| + | </head> | ||
| + | |||
<body> | <body> | ||
<style type="text/css"> | <style type="text/css"> | ||
| Line 28: | Line 42: | ||
} | } | ||
</style> | </style> | ||
| - | <div id="wrapper"> | + | <div id="wrapper"> |
| + | |||
| + | <image src="https://static.igem.org/mediawiki/2013/4/4d/Intro_Modeling_00000.jpg" height=auto width="960" /> | ||
| + | <br><br> | ||
| + | |||
<div id="content1"> | <div id="content1"> | ||
<font face="Impact" size="7" color="green"> | <font face="Impact" size="7" color="green"> | ||
Modeling | Modeling | ||
</font><br><br> | </font><br><br> | ||
| + | <img src="https://static.igem.org/mediawiki/2013/1/16/Ecapsiaction.png"height=280px width=auto> <br><br> | ||
| + | <font face="century gothic" size="3"> | ||
| + | Above is a schematic graph showing the desired action of E. capsi. Pi in the environment can be taken up by the bacteria through inorganic phosphate transport system (PIT) or phosphate-specific transport system (PST) which might then be converted into ATP. Since ATP is asmall molecule that can enter the MCP freely, it can be utilized by PPK1 for polyP synthesis inside the MCP. Elongated polyP will be too large to exit the MCP so it can be prevented from degradation by enzymes like PPX. Hence MCP can act as a sink for Pi. | ||
| + | </font> | ||
| + | <br><br> | ||
| + | |||
| + | <font face="century gothic" size="3"> | ||
| + | We also try to perform some statistical analysis for the reaction of PPK. | ||
| + | </font> | ||
| + | <br><br> | ||
| - | <font face=" | + | <font face="impact" size="5" color="Blue">Statistical analysis for Polyphosphate Quantification in PPK Reverse Action</font> |
| - | Statistical analysis for Polyphosphate Quantification in PPK Reverse Action | + | |
<br><br> | <br><br> | ||
| - | Introduction | + | <font face="impact" size="5" color="green">Introduction |
<br><br> | <br><br> | ||
</font> | </font> | ||
| Line 43: | Line 70: | ||
<font face="century gothic" size="3"> | <font face="century gothic" size="3"> | ||
Before analyze the efficiency of PPK1 inside the MCP, and the maintenance of polyphosphate by MCP, it is necessary that the original distribution of the length of polyphosphate is determined. Let K0 denote the lower bound of poly-pi length above which poly-pi can be maintained in MCP. MCP will effectively deter poly-pi from being degraded by PPX in the cytoplasm IFF<br><br> | Before analyze the efficiency of PPK1 inside the MCP, and the maintenance of polyphosphate by MCP, it is necessary that the original distribution of the length of polyphosphate is determined. Let K0 denote the lower bound of poly-pi length above which poly-pi can be maintained in MCP. MCP will effectively deter poly-pi from being degraded by PPX in the cytoplasm IFF<br><br> | ||
| - | <img src="https://static.igem.org/mediawiki/2013/3/34/Asdfhkuequation.png"><br> | + | <img src="https://static.igem.org/mediawiki/2013/3/34/Asdfhkuequation.png"height="50" width=auto><br> |
Where μ denotes the mean of discrete poly-pi length distribution PL(l), and ω denotes a certain coefficient, so that | Where μ denotes the mean of discrete poly-pi length distribution PL(l), and ω denotes a certain coefficient, so that | ||
| - | <img src="https://static.igem.org/mediawiki/2013/d/d5/Asdfhkuequation2.png"><br>*Peffective is a proportion large enough to make E.capsi meaningful in production.<br><br> | + | <img src="https://static.igem.org/mediawiki/2013/d/d5/Asdfhkuequation2.png"height="40" width=auto><br>*Peffective is a proportion large enough to make E.capsi meaningful in production.<br><br> |
</font> | </font> | ||
| - | <font face= | + | <font face="impact" size="5" color="green"> |
Laboratory Results<br><br> | Laboratory Results<br><br> | ||
</font> | </font> | ||
<font face="century gothic" size="3"> | <font face="century gothic" size="3"> | ||
| - | Under the restriction of laboratory conditions, here we refer to Ryo Ohtomoa, Yoko Sekiguchib, Tetsuro Mimurac, Masanori Saitoe, Tatsuhiro Ezawaf assay | + | Under the restriction of laboratory conditions, here we refer to Ryo Ohtomoa, Yoko Sekiguchib, Tetsuro Mimurac, Masanori Saitoe, Tatsuhiro Ezawaf assay <a href="http://www.sciencedirect.com/science/article/pii/S0003269704002155">results</a>, 2004.<br><br> |
| - | + | ||
Since it’s hard to look at the precise results of PPK catalysis in laboratory, as our team has tried, the reverse reaction can be considered as a reference in computing the accumulation of poly-pi.<br> | Since it’s hard to look at the precise results of PPK catalysis in laboratory, as our team has tried, the reverse reaction can be considered as a reference in computing the accumulation of poly-pi.<br> | ||
Under Ohtomoa conditions, low-sensitivity of PPK to short-chain polyphosphate has been suggested, referring to Figure 3 in Ohtomoa paper. | Under Ohtomoa conditions, low-sensitivity of PPK to short-chain polyphosphate has been suggested, referring to Figure 3 in Ohtomoa paper. | ||
| - | <br><img src="https://static.igem.org/mediawiki/2013/9/95/Asdfhkuequation3.png"><br><br> | + | <br><img src="https://static.igem.org/mediawiki/2013/9/95/Asdfhkuequation3.png"height=320px width=auto><br><br> |
Time course analysis of PPK reaction using the fractions 1 and 7 as substrate | Time course analysis of PPK reaction using the fractions 1 and 7 as substrate | ||
*The fraction 1, denoting poly-pi from from P10 to P40, diamonds; the fraction 7, denoting poly-pi from Pi to P32, circles. | *The fraction 1, denoting poly-pi from from P10 to P40, diamonds; the fraction 7, denoting poly-pi from Pi to P32, circles. | ||
<br><br> | <br><br> | ||
| - | Assay results manifest the following:<br><br> | + | <b>Assay results manifest the following:</b><br><br></font> |
| - | <img src="https://static.igem.org/mediawiki/2013/6/66/Asdfhkuequation4.png"><br><br> | + | <img src="https://static.igem.org/mediawiki/2013/6/66/Asdfhkuequation4.png"height=230px width=auto><br><br> |
| - | <br><br></font><font face=" | + | <br><br></font><font face="impact" size="5" color="green"> |
| - | Statistical Test<br></font><font face="century gothic" size="3"> | + | Statistical Test<br><br></font><font face="century gothic" size="3"> |
Here we apply a Chi-square Test by hypothesizing L ~ Poi(θ), which could be verified through normalization of length L. | Here we apply a Chi-square Test by hypothesizing L ~ Poi(θ), which could be verified through normalization of length L. | ||
*Θ could be obtained by calculating from the sample.</font> | *Θ could be obtained by calculating from the sample.</font> | ||
| - | <font face=" | + | <font face="impact" size="5" color="green"><br><br> |
| - | Conclusion<br></font> | + | Conclusion<br><br></font> |
<font face="century gothic" size="3"> | <font face="century gothic" size="3"> | ||
| - | In experiment, if we could verify that the lower boundary of MCP maintained polyphosphate length is K0≤1.44θ, then it is ensured that E.capsi is highly effective at recycling rate of 80%. | + | In experiment, if we could verify that the lower boundary of MCP maintained polyphosphate length is K0≤1.44θ, then it is ensured that E.capsi is highly effective at recycling rate of 80%.<br><br> |
</font> | </font> | ||
</div> | </div> | ||
Latest revision as of 02:54, 28 September 2013
Modeling
Above is a schematic graph showing the desired action of E. capsi. Pi in the environment can be taken up by the bacteria through inorganic phosphate transport system (PIT) or phosphate-specific transport system (PST) which might then be converted into ATP. Since ATP is asmall molecule that can enter the MCP freely, it can be utilized by PPK1 for polyP synthesis inside the MCP. Elongated polyP will be too large to exit the MCP so it can be prevented from degradation by enzymes like PPX. Hence MCP can act as a sink for Pi.
We also try to perform some statistical analysis for the reaction of PPK.
Statistical analysis for Polyphosphate Quantification in PPK Reverse Action
Introduction
Before analyze the efficiency of PPK1 inside the MCP, and the maintenance of polyphosphate by MCP, it is necessary that the original distribution of the length of polyphosphate is determined. Let K0 denote the lower bound of poly-pi length above which poly-pi can be maintained in MCP. MCP will effectively deter poly-pi from being degraded by PPX in the cytoplasm IFF
Where μ denotes the mean of discrete poly-pi length distribution PL(l), and ω denotes a certain coefficient, so that
*Peffective is a proportion large enough to make E.capsi meaningful in production.
Laboratory Results
Under the restriction of laboratory conditions, here we refer to Ryo Ohtomoa, Yoko Sekiguchib, Tetsuro Mimurac, Masanori Saitoe, Tatsuhiro Ezawaf assay results, 2004.
Since it’s hard to look at the precise results of PPK catalysis in laboratory, as our team has tried, the reverse reaction can be considered as a reference in computing the accumulation of poly-pi.
Under Ohtomoa conditions, low-sensitivity of PPK to short-chain polyphosphate has been suggested, referring to Figure 3 in Ohtomoa paper.
Time course analysis of PPK reaction using the fractions 1 and 7 as substrate *The fraction 1, denoting poly-pi from from P10 to P40, diamonds; the fraction 7, denoting poly-pi from Pi to P32, circles.
Assay results manifest the following:
Statistical Test
Here we apply a Chi-square Test by hypothesizing L ~ Poi(θ), which could be verified through normalization of length L. *Θ could be obtained by calculating from the sample.
Conclusion
In experiment, if we could verify that the lower boundary of MCP maintained polyphosphate length is K0≤1.44θ, then it is ensured that E.capsi is highly effective at recycling rate of 80%.
Above is a schematic graph showing the desired action of E. capsi. Pi in the environment can be taken up by the bacteria through inorganic phosphate transport system (PIT) or phosphate-specific transport system (PST) which might then be converted into ATP. Since ATP is asmall molecule that can enter the MCP freely, it can be utilized by PPK1 for polyP synthesis inside the MCP. Elongated polyP will be too large to exit the MCP so it can be prevented from degradation by enzymes like PPX. Hence MCP can act as a sink for Pi.
We also try to perform some statistical analysis for the reaction of PPK.
Statistical analysis for Polyphosphate Quantification in PPK Reverse Action
Introduction
Before analyze the efficiency of PPK1 inside the MCP, and the maintenance of polyphosphate by MCP, it is necessary that the original distribution of the length of polyphosphate is determined. Let K0 denote the lower bound of poly-pi length above which poly-pi can be maintained in MCP. MCP will effectively deter poly-pi from being degraded by PPX in the cytoplasm IFF
Where μ denotes the mean of discrete poly-pi length distribution PL(l), and ω denotes a certain coefficient, so that
*Peffective is a proportion large enough to make E.capsi meaningful in production.
Laboratory Results
Under the restriction of laboratory conditions, here we refer to Ryo Ohtomoa, Yoko Sekiguchib, Tetsuro Mimurac, Masanori Saitoe, Tatsuhiro Ezawaf assay results, 2004.
Since it’s hard to look at the precise results of PPK catalysis in laboratory, as our team has tried, the reverse reaction can be considered as a reference in computing the accumulation of poly-pi.
Under Ohtomoa conditions, low-sensitivity of PPK to short-chain polyphosphate has been suggested, referring to Figure 3 in Ohtomoa paper.
Time course analysis of PPK reaction using the fractions 1 and 7 as substrate *The fraction 1, denoting poly-pi from from P10 to P40, diamonds; the fraction 7, denoting poly-pi from Pi to P32, circles.
Assay results manifest the following:
Statistical Test
Here we apply a Chi-square Test by hypothesizing L ~ Poi(θ), which could be verified through normalization of length L. *Θ could be obtained by calculating from the sample.
Conclusion
In experiment, if we could verify that the lower boundary of MCP maintained polyphosphate length is K0≤1.44θ, then it is ensured that E.capsi is highly effective at recycling rate of 80%.
|
|
