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@IcedTea2K @actions-user
IcedTea2K authored and actions-user committed Oct 28, 2023
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Showing 1 changed file with 74 additions and 53 deletions.
127 changes: 74 additions & 53 deletions src/views/lab-validation/GroupAView.vue
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Expand Up @@ -5,18 +5,22 @@ import DoubleColumn from '@/components/lab-notebook/DoubleColumn.vue'
import CustomTable from '@/components/CustomTable.vue'
const tableOneData = {
headers: ['Buffer', 'Buffer DNase I Concentration (U/mL)', 'Volume of Buffer (µL)',
'Volume of DNase I (µL)'],
rowHeaders: ['Manufacturer’s buffer', 'TE', 'HEPES'],
rowsPerRowHeader: 2,
data: [
[0.05, 32, 4],
[0.1, 28, 8],
[0.05, 32, 4],
[0.1, 28, 8],
[0.05, 32, 4],
[0.1, 28, 8]
]
headers: [
'Buffer',
'Buffer DNase I Concentration (U/mL)',
'Volume of Buffer (µL)',
'Volume of DNase I (µL)'
],
rowHeaders: ['Manufacturer’s buffer', 'TE', 'HEPES'],
rowsPerRowHeader: 2,
data: [
[0.05, 32, 4],
[0.1, 28, 8],
[0.05, 32, 4],
[0.1, 28, 8],
[0.05, 32, 4],
[0.1, 28, 8]
]
}
const tableTwoData = {
headers: [
Expand Down Expand Up @@ -91,41 +95,38 @@ const sectionTitleStyle = 'text-subtitle-sm lg:text-subtitle text-white mb-4'
<h3 class="text-subtitle-sm lg:text-subtitle text-white mb-4">DNA I Assay</h3>
<div class="flex flex-col gap-y-4">
<p>
The DNase I assay was adapted from the standard protocol of the
Picogreen Assay kit (ThermoFisher Scientific, 2022). This kit uses a
reaction buffer containing 1 M Tris-HCl (pH 7.5), 1 M MgCl<sub>2</sub>, and 1 M
CaCl<sub>2</sub> (ThermoFisher Scientific, 2022), which will be referred to as
the manufacturer’s buffer. 0.05 U/mL and 0.1 U/mL DNase I solutions
were prepared in the manufacturer’s buffer, the TE buffer and the
HEPES buffer separately for use in the activity assay. Buffer DNase
concentration is given in units of DNase activity per mL (U/mL),
with the activity unit defined as the complete degradation of 1 µg
of plasmid DNA at 37°C by one unit of DNase I in 10 minutes
(ThermoFisher Scientific, 2011). The HEPES buffer was also used for
thiolation treatment and conjugation to the liposome.
The DNase I assay was adapted from the standard protocol of the Picogreen Assay kit
(ThermoFisher Scientific, 2022). This kit uses a reaction buffer containing 1 M
Tris-HCl (pH 7.5), 1 M MgCl<sub>2</sub>, and 1 M CaCl<sub>2</sub> (ThermoFisher
Scientific, 2022), which will be referred to as the manufacturer’s buffer. 0.05 U/mL
and 0.1 U/mL DNase I solutions were prepared in the manufacturer’s buffer, the TE
buffer and the HEPES buffer separately for use in the activity assay. Buffer DNase
concentration is given in units of DNase activity per mL (U/mL), with the activity
unit defined as the complete degradation of 1 µg of plasmid DNA at 37°C by one unit of
DNase I in 10 minutes (ThermoFisher Scientific, 2011). The HEPES buffer was also used
for thiolation treatment and conjugation to the liposome.
</p>
<p>
An aqueous working solution of the Quant-iT™PicoGreen™ dsDNA Reagent was
prepared in the TE buffer by using the buffer to dilute it 200 fold. A 2 µg/mL
stock solution of lambda dsDNA was prepared in the TE buffer as well by using
the buffer to dilute it 50 fold. In a 96 well plate, the controls were created
by adding water, the manufacturer's buffer, the TE buffer, and the HEPES buffer
to twelve wells such that each solution type had three wells of 80 µL each. For
the other treatments, 40 µL of the aqueous working solution of the Quant-iT™
PicoGreen™ dsDNA Reagent was added each well, followed by the designated amount
of buffer for each treatment shown in Table 1 as well as 4 µL of the stock
solution of lambda dsDNA. The wells were incubated for five minutes at room
temperature with protection from light before adding the corresponding volume of
DNase I indicated in Table 1. Fluorescence was measured at an excitation
wavelength of about 480 nm and an emission wavelength of about 520 nm to
determine enzyme activity using a fluorometer-spectrophotometer in kinetic mode
every 2 minutes for at least 10 minutes. These treatments were performed three
times to obtain a triplicate.
An aqueous working solution of the Quant-iT™PicoGreen™ dsDNA Reagent was prepared in
the TE buffer by using the buffer to dilute it 200 fold. A 2 µg/mL stock solution of
lambda dsDNA was prepared in the TE buffer as well by using the buffer to dilute it 50
fold. In a 96 well plate, the controls were created by adding water, the
manufacturer's buffer, the TE buffer, and the HEPES buffer to twelve wells such that
each solution type had three wells of 80 µL each. For the other treatments, 40 µL of
the aqueous working solution of the Quant-iT™ PicoGreen™ dsDNA Reagent was added
each well, followed by the designated amount of buffer for each treatment shown in
Table 1 as well as 4 µL of the stock solution of lambda dsDNA. The wells were
incubated for five minutes at room temperature with protection from light before
adding the corresponding volume of DNase I indicated in Table 1. Fluorescence was
measured at an excitation wavelength of about 480 nm and an emission wavelength of
about 520 nm to determine enzyme activity using a fluorometer-spectrophotometer in
kinetic mode every 2 minutes for at least 10 minutes. These treatments were performed
three times to obtain a triplicate.
</p>
<div class="overflow-x-scroll w-full md:overflow-clip">
<CustomTable :table-data="tableOneData"/>
<CustomTable :table-data="tableOneData" />
<p class="text-center text-sm">
Table 1: Designated buffer and DNA volumes for each treatment.
Table 1: Designated buffer and DNA volumes for each treatment.
</p>
</div>
</div>
Expand Down Expand Up @@ -237,49 +238,69 @@ const sectionTitleStyle = 'text-subtitle-sm lg:text-subtitle text-white mb-4'
<p>
Dische, Z. (1953). Qualitative and quantitative colorimetric determination of
heptoses. Journal of Biological Chemistry, 204(2), 983–997.
<a href="https://doi.org/10.1016/S0021-9258(18)66101-0">https://doi.org/10.1016/S0021-9258(18)66101-0</a>
<a href="https://doi.org/10.1016/S0021-9258(18)66101-0"
>https://doi.org/10.1016/S0021-9258(18)66101-0</a
>
</p>
<p>
Lahiri, D., Nag, M., Banerjee, R., Mukherjee, D., Garai, S., Sarkar, T., Dey, A.,
Sheikh, H. I., Pathak, S. K., & Edinur, H. A. (2021). Amylases: Biofilm inducer or
biofilm inhibitor? Frontiers in Cellular and Infection Microbiology, 11, 660048.
<a href="https://doi.org/10.3389/fcimb.2021.660048">https://doi.org/10.3389/fcimb.2021.660048</a>
<a href="https://doi.org/10.3389/fcimb.2021.660048"
>https://doi.org/10.3389/fcimb.2021.660048</a
>
</p>
<p>
Nijland, R., Hall, M. J., & Burgess, J. G. (2010). Dispersal of biofilms by secreted,
matrix degrading, bacterial DNase. PloS One, 5(12), e15668.
<a href="https://doi.org/10.1371/journal.pone.0015668">https://doi.org/10.1371/journal.pone.0015668</a>
<a href="https://doi.org/10.1371/journal.pone.0015668"
>https://doi.org/10.1371/journal.pone.0015668</a
>
</p>
<p>
Panda, B. B., Meher, A. S., & Hazra, R. K. (2019). Comparison between different
methods of DNA isolation from dried blood spots for determination of malaria to
determine specificity and cost effectiveness. Journal of Parasitic Diseases, 43(3),
337–342.
<a href="https://doi.org/10.1007/s12639-019-01136-0">https://doi.org/10.1007/s12639-019-01136-0</a>
337–342.
<a href="https://doi.org/10.1007/s12639-019-01136-0"
>https://doi.org/10.1007/s12639-019-01136-0</a
>
</p>
<p>
Preiss, J., & Ashwell, G. (1962). Alginic acid metabolism in bacteria: I. Enzymatic
formation of unsaturated oligosaccharides and 4-deoxy-L-erythro-5-hexoseulose uronic
acid. Journal of Biological Chemistry, 237(2), 309–316.
<a href="https://doi.org/10.1016/S0021-9258(18)93920-7">https://doi.org/10.1016/S0021-9258(18)93920-7</a>
<a href="https://doi.org/10.1016/S0021-9258(18)93920-7"
>https://doi.org/10.1016/S0021-9258(18)93920-7</a
>
</p>
<p>
Scopes, R. K. (2001). Enzyme activity and assays. Encyclopedia of Life Sciences.
<a href="https://doi.org/10.1038/npg.els.0000712">https://doi.org/10.1038/npg.els.0000712</a>
<a href="https://doi.org/10.1038/npg.els.0000712"
>https://doi.org/10.1038/npg.els.0000712</a
>
</p>
<p>
Sigma-Aldrich. (2014). Amylase Activity Assay Kit.
<a href="https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/377/793/mak009bul.pdf">https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/377/793/mak009bul.pdf</a>
<a
href="https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/377/793/mak009bul.pdf"
>https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/377/793/mak009bul.pdf</a
>
</p>
<p>
ThermoFisher Scientific. (2022). Quant-iTTM PicoGreenTM dsDNA Reagent and Kit.
<a href="https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fmp07581.pdf">https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fmp07581.pdf</a>
<a
href="https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fmp07581.pdf"
>https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fmp07581.pdf</a
>
</p>
<p>
Zhu, B., & Yin, H. (2015). Alginate lyase: Review of major sources and classification,
properties, structure-function analysis and applications. Bioengineered, 6(3),
125–131.
<a href="https://doi.org/10.1080/21655979.2015.1030543">https://doi.org/10.1080/21655979.2015.1030543</a>
125–131.
<a href="https://doi.org/10.1080/21655979.2015.1030543"
>https://doi.org/10.1080/21655979.2015.1030543</a
>
</p>
</div>
</template>
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