Team:KU Seoul/Result

From 2009.igem.org

(Difference between revisions)
(Results)
 
(34 intermediate revisions not shown)
Line 13: Line 13:
</head>
</head>
</html>
</html>
-
 
+
{|style=  "background:#FFCC33;" align="center"  
-
{|style=  "background:#FFCC33;" align="justify"
+
|
|
== Results ==
== Results ==
-
(''Or you can choose different headings. But you must have a team page, a project page, and a notebook page.'')
+
<b>1. Synthetic Circuit - I : pSB3C5/Pars-gfp-Pznt-rfp</b>
-
Your abstract
+
 
 +
1) Pznt-rfp
 +
 
 +
{| style="color:Black; background-color:#ffffcc;" cellpadding="3" cellspacing="0" border="1"
 +
|align="center"|Zn<Sup>2+</Sup> (mM)
 +
| align="center"| 0
 +
| align="center"| 0.5
 +
| align="center"| 0.75
 +
| align="center"| 1
 +
| align="center"| 1.5
 +
| align="center"| 2
 +
|-
 +
|align="center"|OD<sub>600</sub>
 +
| align="center"| 0.490 ± 0.003
 +
| align="center"| 0.459 ± 0.004
 +
| align="center"| 0.433 ± 0.008
 +
| align="center"| 0.418 ± 0.005
 +
| align="center"| 0.275 ± 0.011
 +
| align="center"| 0.243 ± 0.008
 +
|-
 +
|align="center"|Red fluorescence (RF)
 +
| align="center"| 26628 ± 706
 +
| align="center"| 27856 ± 292
 +
| align="center"| 29333 ± 292
 +
| align="center"| 31217 ± 66
 +
| align="center"| 46044 ± 237
 +
| align="center"| 49188 ± 174
 +
|-
 +
|align="center"|OD<sub>600</sub>/RF
 +
| align="center"| 54376 ± 1203
 +
| align="center"| 60646 ± 787
 +
| align="center"| 67803 ± 573
 +
| align="center"| 74687 ± 755
 +
| align="center"| 167833 ± 7202
 +
| align="center"| 202565 ± 6428
 +
|-
 +
|align="center"|Background
 +
| align="center"| 0
 +
| align="center"| 6270 ± 520
 +
| align="center"| 13427 ± 1719
 +
| align="center"| 20311 ± 475
 +
| align="center"| 113457 ± 6016
 +
| align="center"| 148189 ± 6731
 +
|}
 +
[[Image:KU Seoul Result RFP.png]]
 +
 
 +
This parts produces red fluorosence based on the zinc ion level. The zinc detecting promoter can be
 +
induced beyond 1mM concentration of zinc ion. This range from 1mM to 2mM is enough to detect zinc level in common waste water. We need to detect the upper concentration limit of zinc ion so that we know when dilution is required. If the level curve does not change proportionally according to concentraion, you may have to dilute the concentration of sample.
 +
 
 +
[[Image:cal_red.png]]
 +
 
 +
The value of R square is 0.876. Although it is not a satisfying value for confidence,  
 +
we can make a new formula; Absorbance(fluorsence) = 17971x + 15193, x indicates the concentration of zinc ion(unit:mM).
 +
If you have a sample showing specific absorbance, you can calculate the concentration of zinc ion in an indirect way. If you presume that the sample contains large amount of zinc ion, you can try another way to measure the concentration of zinc ion. First, dilute the sample by serial dilution (ex, 10^-1, 10^-2, 10^-3 ...). Second, find the absorbance value between 1,31217 and 2,49188. Then calculate the concentration inversely.
 +
 
 +
 
 +
2) Pars-gfp
 +
Different from zinc ion, arsenic ion has more severe impact on the E.coli. When microbials are exposed to arsenic ions in even 1mM concentration, it is already fatal to cells. They are very senstive to arsenic ion, which reflects its toxicity. The interaction of arsenic ion is conducted by more than two or more groups of proteins. You can see that the curve of fluorosence of GFP shows sigmoid curve form.
 +
 
 +
It seems that the the cost of expression of arsenic ion binder is very expensive for microbial cells.
 +
In lower levels of concentraion, the fluorosence curve did not show regression curve at the initiation
 +
point. Strong inhibitor might exist at the initation of expression state.
 +
 
 +
The main point of issue is to define the possible measure range. Although the overall results show a sigmoid curve, the range from 0.15 to 0.5 mM concentration of arsenic ion shows regression. We should utilize the midpoint of this curve to measure arsenic ions instead of the endpoint. We can also use the dilution method if the sample contains too much amount of arsenic ions.
 +
 
 +
Because the population size of E.coli reflects the intensity of fluorosence, we belive that the hypothesis we have postulated is correct.  Compared to zinc ion, the arsenic ion has more harmful effect on the growth of bacteria. This is a drwaback to our detecting system cosnidering that the bacteria can be killed while measuring concentrations. It is hard to distinguish between the effect of concentration of sample or death rate of bacteria.
 +
 
 +
 
 +
{| style="color:Black; background-color:#ffffcc;" cellpadding="3" cellspacing="0" border="1"
 +
|align="center"|AsO<Sup>3-</Sup> (mM)
 +
| align="center"| 0
 +
| align="center"| 0.00625
 +
| align="center"| 0.125
 +
| align="center"| 0.25
 +
| align="center"| 0.5
 +
| align="center"| 0.75
 +
| align="center"| 1
 +
|-
 +
|align="center"|OD<sub>600</sub>
 +
| align="center"| 0.553 ± 0.009
 +
| align="center"| 0.519 ± 0.002
 +
| align="center"| 0.480 ± 0.005
 +
| align="center"| 0.395 ± 0.007
 +
| align="center"| 0.315 ± 0.006
 +
| align="center"| 0.286 ± 0.004
 +
| align="center"| 0.273 ± 0.006
 +
|-
 +
|align="center"|Green fluorescence (GF)
 +
| align="center"| 27740 ± 226
 +
| align="center"| 26411 ± 169
 +
| align="center"| 25267 ± 267
 +
| align="center"| 25536 ± 213
 +
| align="center"| 25407 ± 259
 +
| align="center"| 24849 ± 152
 +
| align="center"| 26479 ± 149
 +
|-
 +
|align="center"|OD<sub>600</sub>/GF
 +
| align="center"| 50206 ± 1225
 +
| align="center"| 50855 ± 123
 +
| align="center"| 52606 ± 689
 +
| align="center"| 64669 ± 1684
 +
| align="center"| 80665 ± 603
 +
| align="center"| 86897 ± 1321
 +
| align="center"| 96784 ± 2165
 +
|-
 +
|align="center"|Background
 +
| align="center"| 0
 +
| align="center"| 648 ± 1314
 +
| align="center"| 2399 ± 969
 +
| align="center"| 14463 ± 2896
 +
| align="center"| 30459 ± 1631
 +
| align="center"| 36691 ± 1636
 +
| align="center"| 46578 ± 3220
 +
|}
 +
[[Image:cal_green.png]]
 +
[[Image:KU Seoul Calibrationcurve.png]]
 +
 
 +
<b>2.Synthetic circuit – II : PyodA-AMD</b>
 +
{| style="color:Black; background-color:#ffffcc;" cellpadding="3" cellspacing="0" border="1"
 +
|align="center"|Cd<Sup>2+</Sup> (mM)
 +
| align="center"| 0
 +
| align="center"| 0.05
 +
| align="center"| 0.1
 +
| align="center"| 0.2
 +
| align="center"| 0.4
 +
| align="center"| 0.8
 +
|-
 +
|align="center"|OD<sub>615</sub>
 +
| align="center"| 0.242 ± 0.005
 +
| align="center"| 0.258 ± 0.008
 +
| align="center"| 0.274 ± 0.011
 +
| align="center"| 0.284 ± 0.01
 +
| align="center"| 0.293 ± 0.011
 +
| align="center"| 0.302 ± 0.01
 +
|-
 +
|align="center"|Background
 +
| align="center"| 0
 +
| align="center"| 0.016 ± 0.004
 +
| align="center"| 0.032 ± 0.006
 +
| align="center"| 0.043 ± 0.005
 +
| align="center"| 0.052 ± 0.007
 +
| align="center"| 0.060 ± 0.007
 +
|}
 +
[[Image:KU Seoul Expression.png]]
 +
 
 +
Cadimum detector has a similar problem related to toxicity, as discussed above. Like arsenic ion, cadmium has
 +
harmful effects on bacteria. 0.2mM of concentration of cadimum is enough to inhibt cell growth of E.coli. The E.coli did not show big difference between 0.2mM and 0.4mM concentration of cadimum. We wanted to show the change in concentration with naked eye, but the difference was too subtle to be acknowledged with our eyes.Amd gene, which turns brown in the presence of aceteaminopen, demonstrates only the possiblity. We conisdered using a stronger promoter to detect heavy metals, but we did not use them due to standards issues. Some parts registered on the registry did not work, not to mention inaccurate sequencing. GFP and RFP fluorsence can be seen only with UV irritation.
 +
 
 +
[[Image:amd_cal.png]]
 +
 
|}
|}

Latest revision as of 16:42, 21 October 2009






Results

1. Synthetic Circuit - I : pSB3C5/Pars-gfp-Pznt-rfp

1) Pznt-rfp

Zn2+ (mM) 0 0.5 0.75 1 1.5 2
OD600 0.490 ± 0.003 0.459 ± 0.004 0.433 ± 0.008 0.418 ± 0.005 0.275 ± 0.011 0.243 ± 0.008
Red fluorescence (RF) 26628 ± 706 27856 ± 292 29333 ± 292 31217 ± 66 46044 ± 237 49188 ± 174
OD600/RF 54376 ± 1203 60646 ± 787 67803 ± 573 74687 ± 755 167833 ± 7202 202565 ± 6428
Background 0 6270 ± 520 13427 ± 1719 20311 ± 475 113457 ± 6016 148189 ± 6731

KU Seoul Result RFP.png

This parts produces red fluorosence based on the zinc ion level. The zinc detecting promoter can be induced beyond 1mM concentration of zinc ion. This range from 1mM to 2mM is enough to detect zinc level in common waste water. We need to detect the upper concentration limit of zinc ion so that we know when dilution is required. If the level curve does not change proportionally according to concentraion, you may have to dilute the concentration of sample.

Cal red.png

The value of R square is 0.876. Although it is not a satisfying value for confidence, we can make a new formula; Absorbance(fluorsence) = 17971x + 15193, x indicates the concentration of zinc ion(unit:mM). If you have a sample showing specific absorbance, you can calculate the concentration of zinc ion in an indirect way. If you presume that the sample contains large amount of zinc ion, you can try another way to measure the concentration of zinc ion. First, dilute the sample by serial dilution (ex, 10^-1, 10^-2, 10^-3 ...). Second, find the absorbance value between 1,31217 and 2,49188. Then calculate the concentration inversely.


2) Pars-gfp Different from zinc ion, arsenic ion has more severe impact on the E.coli. When microbials are exposed to arsenic ions in even 1mM concentration, it is already fatal to cells. They are very senstive to arsenic ion, which reflects its toxicity. The interaction of arsenic ion is conducted by more than two or more groups of proteins. You can see that the curve of fluorosence of GFP shows sigmoid curve form.

It seems that the the cost of expression of arsenic ion binder is very expensive for microbial cells. In lower levels of concentraion, the fluorosence curve did not show regression curve at the initiation point. Strong inhibitor might exist at the initation of expression state.

The main point of issue is to define the possible measure range. Although the overall results show a sigmoid curve, the range from 0.15 to 0.5 mM concentration of arsenic ion shows regression. We should utilize the midpoint of this curve to measure arsenic ions instead of the endpoint. We can also use the dilution method if the sample contains too much amount of arsenic ions.

Because the population size of E.coli reflects the intensity of fluorosence, we belive that the hypothesis we have postulated is correct. Compared to zinc ion, the arsenic ion has more harmful effect on the growth of bacteria. This is a drwaback to our detecting system cosnidering that the bacteria can be killed while measuring concentrations. It is hard to distinguish between the effect of concentration of sample or death rate of bacteria.


AsO3- (mM) 0 0.00625 0.125 0.25 0.5 0.75 1
OD600 0.553 ± 0.009 0.519 ± 0.002 0.480 ± 0.005 0.395 ± 0.007 0.315 ± 0.006 0.286 ± 0.004 0.273 ± 0.006
Green fluorescence (GF) 27740 ± 226 26411 ± 169 25267 ± 267 25536 ± 213 25407 ± 259 24849 ± 152 26479 ± 149
OD600/GF 50206 ± 1225 50855 ± 123 52606 ± 689 64669 ± 1684 80665 ± 603 86897 ± 1321 96784 ± 2165
Background 0 648 ± 1314 2399 ± 969 14463 ± 2896 30459 ± 1631 36691 ± 1636 46578 ± 3220

Cal green.png KU Seoul Calibrationcurve.png

2.Synthetic circuit – II : PyodA-AMD

Cd2+ (mM) 0 0.05 0.1 0.2 0.4 0.8
OD615 0.242 ± 0.005 0.258 ± 0.008 0.274 ± 0.011 0.284 ± 0.01 0.293 ± 0.011 0.302 ± 0.01
Background 0 0.016 ± 0.004 0.032 ± 0.006 0.043 ± 0.005 0.052 ± 0.007 0.060 ± 0.007

KU Seoul Expression.png

Cadimum detector has a similar problem related to toxicity, as discussed above. Like arsenic ion, cadmium has harmful effects on bacteria. 0.2mM of concentration of cadimum is enough to inhibt cell growth of E.coli. The E.coli did not show big difference between 0.2mM and 0.4mM concentration of cadimum. We wanted to show the change in concentration with naked eye, but the difference was too subtle to be acknowledged with our eyes.Amd gene, which turns brown in the presence of aceteaminopen, demonstrates only the possiblity. We conisdered using a stronger promoter to detect heavy metals, but we did not use them due to standards issues. Some parts registered on the registry did not work, not to mention inaccurate sequencing. GFP and RFP fluorsence can be seen only with UV irritation.

Amd cal.png