Difference between revisions of "Team:Newcastle/Improve"
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| − | <p>Our RFP internal standard (IS) was developed to address the issue that copy number of the same plasmid is not consistent across cells. The inclusion of an IS RFP signal is therefore designed to allow measurement of variation in gene expression between cultures and transformant lines. The underpinning assumption is that because the IS devices are identical across each of the plasmids, the GFP fluorescence values of the test devices of interest can be reported relative to their internal RFP signal. RFP was cloned into the non-coding region between the chloramphenicol resistance gene and the ORI. The new plasmids were tested | + | <p>Our RFP internal standard (IS) was developed to address the issue that copy number of the same plasmid is not consistent across cells. The inclusion of an IS RFP signal is therefore designed to allow measurement of variation in gene expression between cultures and transformant lines. The underpinning assumption is that because the IS devices are identical across each of the plasmids, the GFP fluorescence values of the test devices of interest can be reported relative to their internal RFP signal. RFP was cloned into the non-coding region between the chloramphenicol resistance gene and the ORI. The new plasmids were tested and analysis of the internal standards involved comparing the original InterLab test device plasmid performance against the new internal standard plasmid performance. </p> |
<p>Results show that inclusion of the IS altered the behaviour of the test devices. The IS repressed expression of GFP from all devices and affected expression rates - particularly in devices with strong promoters. Further, the IS signal varied across plasmids though the only difference was the strength of the test device. The data generated using this approach indicates competition for cellular resources between the IS and test device. As a result, measurements and conclusions regarding the strength of strong reporters should be treated with caution.</p> | <p>Results show that inclusion of the IS altered the behaviour of the test devices. The IS repressed expression of GFP from all devices and affected expression rates - particularly in devices with strong promoters. Further, the IS signal varied across plasmids though the only difference was the strength of the test device. The data generated using this approach indicates competition for cellular resources between the IS and test device. As a result, measurements and conclusions regarding the strength of strong reporters should be treated with caution.</p> | ||
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| − | <p>From the literature, we gathered information on the potential problems associated with the GFPmut3b reporter – notably its low photostability upon exposure to natural light. Replacing the reporter to prevent such problems became an option. However, since GFPmut3b is the brightest GFP variant, it would make sense to utilise a suitably divergent fluorescent protein with similar fluorescence characteristics to GFPmut3b but a higher photostability – mNeonGreen | + | <p>From the literature, we gathered information on the potential problems associated with the GFPmut3b reporter – notably its low photostability upon exposure to natural light. Replacing the reporter to prevent such problems became an option. However, since GFPmut3b is the brightest GFP variant, it would make sense to utilise a suitably divergent fluorescent protein with similar fluorescence characteristics to GFPmut3b but a higher photostability – mNeonGreen met these requirements. The data indicated that mNeonGreen was not significantly brighter than mut3GFP as was proposed. However, the values for both replicate colonies show that the spread of fluorescence/OD<sub>600</sub> nm values for the mNeonGreen reporter is lower in each test device group. </p> |
| − | <p>The results of this experiment therefore do not support the original goal of the study. The mNeonGreen reporter, despite reports in the literature, was not seen to be significantly different to mut3GFP in its fluorescence/ | + | <p>The results of this experiment therefore do not support the original goal of the study. The mNeonGreen reporter, despite reports in the literature, was not seen to be significantly different to mut3GFP in its fluorescence/OD<sub>600</sub>nm. The mNeonGreen did, however, show a smaller range of fluorescein/OD data in comparison to GFPmut3b. Since there were no differences in fluorescence values, the smaller range of values from the mNeonGreen reporter may be due to its better photostability, or a difference in maturation time in vivo than the literature suggests. Regardless, the switch to mNeonGreen in Interlab test devices may further improve measurement reliability.</p> |
<p style="text-align:center"><a href="http://parts.igem.org/Part:BBa_K2797003" class="black">mNeonGreen coding sequence</a></p> | <p style="text-align:center"><a href="http://parts.igem.org/Part:BBa_K2797003" class="black">mNeonGreen coding sequence</a></p> | ||
<p style="text-align:center"><a href="http://parts.igem.org/Part:BBa_K2797004" class="black">mNeonGreen Test Device 1 </a></p> | <p style="text-align:center"><a href="http://parts.igem.org/Part:BBa_K2797004" class="black">mNeonGreen Test Device 1 </a></p> | ||
Revision as of 08:51, 17 October 2018
Alternative Roots
Improve
Improved Interlab measurement plasmids
Inclusion of an RFP internal standard into the 2018 Interlab test device pSB1C3 vectors.
Our RFP internal standard (IS) was developed to address the issue that copy number of the same plasmid is not consistent across cells. The inclusion of an IS RFP signal is therefore designed to allow measurement of variation in gene expression between cultures and transformant lines. The underpinning assumption is that because the IS devices are identical across each of the plasmids, the GFP fluorescence values of the test devices of interest can be reported relative to their internal RFP signal. RFP was cloned into the non-coding region between the chloramphenicol resistance gene and the ORI. The new plasmids were tested and analysis of the internal standards involved comparing the original InterLab test device plasmid performance against the new internal standard plasmid performance.
Results show that inclusion of the IS altered the behaviour of the test devices. The IS repressed expression of GFP from all devices and affected expression rates - particularly in devices with strong promoters. Further, the IS signal varied across plasmids though the only difference was the strength of the test device. The data generated using this approach indicates competition for cellular resources between the IS and test device. As a result, measurements and conclusions regarding the strength of strong reporters should be treated with caution.
Comparisons between the existing GFPmut3b test devices and a new series of mNeon green test devices
From the literature, we gathered information on the potential problems associated with the GFPmut3b reporter – notably its low photostability upon exposure to natural light. Replacing the reporter to prevent such problems became an option. However, since GFPmut3b is the brightest GFP variant, it would make sense to utilise a suitably divergent fluorescent protein with similar fluorescence characteristics to GFPmut3b but a higher photostability – mNeonGreen met these requirements. The data indicated that mNeonGreen was not significantly brighter than mut3GFP as was proposed. However, the values for both replicate colonies show that the spread of fluorescence/OD600 nm values for the mNeonGreen reporter is lower in each test device group.
The results of this experiment therefore do not support the original goal of the study. The mNeonGreen reporter, despite reports in the literature, was not seen to be significantly different to mut3GFP in its fluorescence/OD600nm. The mNeonGreen did, however, show a smaller range of fluorescein/OD data in comparison to GFPmut3b. Since there were no differences in fluorescence values, the smaller range of values from the mNeonGreen reporter may be due to its better photostability, or a difference in maturation time in vivo than the literature suggests. Regardless, the switch to mNeonGreen in Interlab test devices may further improve measurement reliability.