Difference between revisions of "Part:BBa K2797004"

Latest revision as of 15:01, 17 October 2018

Test Device 1 for the iGEM InterLab Study (mNeonGreen)

BBa_K2797004, Test device 1 (originally BBa_J364000) for the iGEM 2018 InterLab study with mNeonGreen replacing the GFP fluorescent reporter. Each mNeonGreen test device retains the same promoter, RBS and terminator of each of their corresponding InterLab test device vectors, with the only change being mNeonGreen replacing the GFPmut3b.

Usage and Biology

The mNeonGreen protein is widely used in the imaging of cellular components due to it having a fluorescence 3-5 times that of GFP. Importantly however, it is thought to be more photostable than the mut3GFP used in the InterLab study, although there is little indication in the literature that it has been used as a reporter for the characterisation of circuits. Replacing mut3GFP with mNeonGreen allowed the investigation of whether the fast folding capabilities coupled with its brightness and higher photostability could yield a lower spread of fluorescence values in regard to the original mut3GFP, making it a better tool for part characterisation.

Newcastle 2018 - Interlab Characterisation

Three further InterLab studies were carried out using mNeonGreen expressing E. coli DH5-alpha. These contained the original test devices from the iGEM 2018 distribution kit (Anderson Promoter Collection), using the same conditions as the original study. The fluorescein/OD of the mNeonGreen study was compared to the original InterLab test device data by using a fluorescein standard curve.

Figure 1 shows the fluorescein/OD values of the original InterLab devices (GFPmut3b) vs the mNeonGreen test devices. The mNeonGreen test device 1 can be seen to have a much higher fluorescein/OD and a lower spread of values, pointing towards the idea that mNeonGreen may be a better fluorescent reporter than GFPmut3b for this specific test device.

Fluorescein/OD values of the original (white boxes) and mNeonGreen (shaded boxes) test devices at 6 hours post incubation at 37°C @ 220 rpm for 2 separate colonies. Fluorescein/OD is shown on the y-axis, while the test devices and controls of both the original and mNeonGreen devices are shown on the x-axis. At hour 0, throughout the GFP and mNeonGreen devices there are large spreads of data. At hour 6, mNeonGreen devices can be seen to have a smaller spread of data when compared to GFP in both colonies 1 & 2. Also, in most cases, the fluorescence is much higher in the mNeonGreen, with mNeonGreen TD4 having the highest median fluorescein/OD value (1.57) of the whole study. The pattern of fluorescence regarding the most productive devices is the same as that of the original InterLab study. Each test device group had 4 replicates carried out with the error bars showing the standard deviation.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 39
1000
COMPATIBLE WITH RFC[1000]

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K2797004 short</partinfo>
-<partinfo>BBa_K2797004</partinfo>, Test device 1 (<partinfo>BBa_J364000</partinfo>) for the iGEM 2018 InterLab study with mneongreen replacing the GFP fluorescent reporter.
+<partinfo>BBa_K2797004</partinfo>, Test device 1 (originally <partinfo>BBa_J364000</partinfo>) for the iGEM 2018 InterLab study with mNeonGreen replacing the GFP fluorescent reporter. Each mNeonGreen test device retains the same promoter, RBS and terminator of each of their corresponding InterLab test device vectors, with the only change being mNeonGreen replacing the GFPmut3b.
@@ Line 11: / Line 11: @@
 ===Newcastle 2018 - Interlab Characterisation===
-Three further InterLab studies were carried out using mNeonGreen expressing E. coli DH5-alpha. These contained the original test devices from the iGEM 2018 distribution kit (Anderson Promoter Collection), using the same conditions as the original study. The fluorescein/OD of the mNeonGreen study was compared to the original InterLab test device data by using a fluorescein calibration curve. Two distinct errors were present in this study:
+Three further InterLab studies were carried out using mNeonGreen expressing <i>E. coli</i> DH5-alpha. These contained the original test devices from the iGEM 2018 distribution kit (Anderson Promoter Collection), using the same conditions as the original study. The fluorescein/OD of the mNeonGreen study was compared to the original InterLab test device data by using a fluorescein standard curve.
-*'''TD6 did not successfully transform'''- Unknown cause, currently thought to be due to failed assembly.
-*'''TD5 reproducibility error''' - TD5 is actually the positive control. During initial unsuccessful transformations, human error led to TD5 being replaced with the positive control.
-Nonetheless, mNeonGreen test devices did appear to show a tighter spread of data on observation.
+Figure 1 shows the fluorescein/OD values of the original InterLab devices (GFPmut3b) vs the mNeonGreen test devices. The mNeonGreen test device 1 can be seen to have a much higher fluorescein/OD and a lower spread of values, pointing towards the idea that mNeonGreen may be a better fluorescent reporter than GFPmut3b for this specific test device.
-[[Image:BBa_K2797003.png|thumb|center|500px|Fluorescence/OD values of the original (white boxes) and mNeonGreen (shaded boxes) test devices at 0 hours and 6 hours post incubation at 37°C @ 220 rpm.  Fluorescence/OD is shown on the y-axis, while the test devices and controls are shown on the x-axis. Part A and B show the fluorescence/OD values at hour 6 & 6 for colony 1, while C & D show the values for hour 0 & 6 for colony 2. At hour 0, throughout the GFP and mNeonGreen devices there are large spreads of data. At hour 6, mNeonGreen devices can be seen to have a smaller spread of data when compared to GFP in both colonies 1 & 2. Also, in most cases, the fluorescence is much higher in the mNeonGreen, with mNeonGreen TD4 having the highest median fluorescein/OD value (1.57) of the whole study. The pattern of fluorescence regarding the most productive devices is the same as that of the original InterLab study. *TD5 through error is also the positive control.]]
+[[Image:mNeongraph.png|thumb|center|500px| '''Fluorescein/OD values of the original (white boxes) and mNeonGreen (shaded boxes) test devices at 6 hours post incubation at 37°C @ 220 rpm for 2 separate colonies.'''  Fluorescein/OD is shown on the y-axis, while the test devices and controls of both the original and mNeonGreen devices are shown on the x-axis.  At hour 0, throughout the GFP and mNeonGreen devices there are large spreads of data. At hour 6, mNeonGreen devices can be seen to have a smaller spread of data when compared to GFP in both colonies 1 & 2. Also, in most cases, the fluorescence is much higher in the mNeonGreen, with mNeonGreen TD4 having the highest median fluorescein/OD value (1.57) of the whole study. The pattern of fluorescence regarding the most productive devices is the same as that of the original InterLab study. Each test device group had 4 replicates carried out with the error bars showing the standard deviation.]]
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 <span class='h3bb'>Sequence and Features</span>