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<p id="pp">InterLab study began by measuring the standard LUDOX Abs600. Pipetted LUDOX and water into two separate columns of a 96 well plate and measured the absorbance of the 4 replicates at 600 nm on the standard Tecan mode.</p>

<p id="pp">A serial dilution of FITC provided in the interkab kit was prepared using PBS. Fluorescence of all samples was measured in standard measurement modes. Measurements were repeated to produce a series of standard curves. The fluorescence readings were taken at 26.4°C at 477 nm and 515 nm excitation and emission respectively. Gain setting measured at 46, 56, 66. A setting change of 10 units makes a significant difference to the fluorescence data (Fig. 1). The fluorescence was measured at the optimum gain setting. This set the gain to 76, which was too high for these measurements as the weakest dilution had a lower fluorescence than the pure PBS. We ran the reader at 37°C and 56 gain to produce our optimal standard curve (Fig. 2).</p>

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<img style="max-width:100%;padding: 5px 30% 5px 30%;" src="https://static.igem.org/mediawiki/2016/6/61/T--Exeter--GainFluorescencechangeinterlab.jpg">

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<div class="col-xs-6"><span class="caption" style="padding: 5px 30% 5px 30%;">Fig. 1 Change in fluorescence for varied gain settings </span></div>

 

<img style="max-width:100%;padding: 5px 30% 5px 30%;" src="https://static.igem.org/mediawiki/2016/a/ab/T--Exeter--FITCstandardcurveinterlabeglloyd.png">

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<div class="col-xs-6"><span class="caption" style="padding: 5px 30% 5px 30%;">Fig. 2 FITC standard curve of fluorescence </span></div>

<p id="pp">Competent cells of E.coli DH5α were prepared following the provided <a href="https://2016.igem.org/Team:Exeter/Project #COMPcellsprot">protocol</a>.</p>

<p id="pp">The InterLab measurement kit contained 5 devices; (1) J23101+I13504, (2) J23106+I13504, (3) J23117+I13504, Positive and Negative control. The first attempt to transform 5µL of each device into our competent cells found no liquid in the tubes provided. The provided tubes were re-suspended using elution buffer from a Qiagen mini-prep kit.  A transformation of plasmids used in the lab under a strong promoter and GFP was performed mirroring the Interlab protocol to determine if the cells were competent. Spread plates were made and incubated at 37°C.</p>

<p id="pp">Competent cells containing the previously described strong promoter and GFP coding sequence showed strong expression of GFP. However the competent cells transformed with the iGEM parts showed no growth. A new interlab kit was ordered from iGEM.</p>

<p id="pp">The new plasmid constructs arrived and positive and negative controls were obtained from the kit plate provided. We resuspended DNA from the iGEM registry plates in 10μl of MiliQ water. 5μl of each resuspension solution was used for the transformation protocol. Original competent cells served as an additional negative control. The transformations were completed and the cells were plated onto 80μl/ml chloramphenicol plates. </p>

<p id="pp">All the colonies had grown, however the positive and negative controls had a weak fluorescence intensity. The positive control had the fewest colonies and lowest fluorescence intensity. The ranking of strongest to weakest fluorescence intensity for the constructs followed the following order: P1, P2, P3. Consequently, 5ml overnights of all the successful transformations were produced and left to grow overnight in the 37℃, 220 rpm shaking incubator.</p>

<p id="pp"> Cultures were removed from the incubator and 100μl of each overnight was pipetted into the 96 well plate in order to obtain their OD at the calibration setting.</p>

Measurements were then taken each hour for 6 hours by pipetting 100µl of each culture into the 96 well plate according to the iGEM layout for Abs600 and Fluorescence measurement. We then also used the calibrated Tecan spectrometer.</p>

<p id="pp"> The protocol was improved by using a latin rectangle arrangement in another 96 well plate. A lab robot was used to pipette out the corresponding cultures to their wells according to our preset programme linked to a descrambling spreadsheet. The Latin rectangle is designed so that no sample gets pipetted more than once in any row or column. The order in which the samples get arranged was worked out using the random number function of Microsoft Excel. Sterile LB was loaded into peripheral wells to lessen edge effects which can skew results due to high evaporation at the periphery. These adaptations aim to provide more accurate data by reducing plate effects, samples were spread randomly around the plate as to minimise differences in results due to irregularities in plate temperature.</p>

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<div class="col-xs-6"><span class="caption" style="padding: 5px 30% 5px 30%;">Fig. 3 Latin rectangle, schematic representation of a 10 sample culture layout on a 96 well-plate. The different colours and patterns represent the different aliquots that were measured. The peripheral wells in red represent sterile LB media in order to reduce edge effects.</span></div>

 

<p id="pp">The measurements were taken using the same calibration settings as before on the Tecan plate reader every hour for 6 hours. The plate was placed into mini shaking incubator at 37°C between plate readings. A scratch was noticed on the plate lid and was replaced. This lid was cold compared to the incubated plate and so condensation formed this could have affected the results. The lid was placed in an incubator briefly in order to warm it up. The results were compiled into graphs using the iGEM Interlab excel document (Fig. 4 and Fig. 5).</p>

            <span class="caption">Fig. 4 Fluoresce/Abs 600 measurements using iGEM Interlab layout</span>

        <img src="https://static.igem.org/mediawiki/2016/a/a6/T--Exeter--latinrectangleinterlabgraphforpart1egl.png"

            <span class="caption">Fig. 5 Fluoresce/Abs 600 measurements using Latin Rectangle layout</span>

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<p id="pp"> Part two of the InterLab study was started on the 31/8. Overnight cultures of the devices and controls were grown from glycerol stocks inside a 15ml falcon tube with 5ml of LB media and 5μl of 0.1M chloramphenicol.</p>

<p id="pp">An initial OD600 reading was taken using a cuvette reader. Inoculation calculations were then carried out and the cultures of the constructs were grown in new 15ml falcon tubes with 5ml of fresh LB and 5μl of 0.1M chloramphenicol from a starting OD of 0.02 for 6 hours in a 37°C incubator.</p>

<p id="pp">The measurements for fluorescence were taken using a BD FACSAria II and the calibration as well as measurement protocols were followed according to the 2016 InterLab Worksheet for Flow Cytometry that is available on the iGEM website. 10,000 events were acquired from calibration beads and from each biological sample. Samples were excited using a 488 nm laser, the filter used was 530/30. Resulting graphs from the FACS measurements are shown below (Fig. 6 - Fig. 11)</p>

<p id="pp">Our results along with the completed worksheet were submitted on the 1/9. No problems were encountered using the provided protocol or FACS machine. </p>

 

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