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| ==Problems with current methodology==
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| The data we got from our experiments didn't seem to fit in with what we expected from our models and prior knowledge. We have come up with a few considerations for our experimental design that might give us better results from our experiments
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| ===Problems===
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| #Evaporation - is a major problem as:
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| #*changes the flourescence of the samples
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| #*changes the context
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| #Mixing of the samples - was not done regularly or constantly (i.e. was done manually), which:
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| #*affects reactions - disruptions the reaction mixture
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| #*affects the fluorescence
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| #Temperature regualtion - the temperature of the sample kept varying due to the sampling:
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| #*about 5mins to get one reading - sampling time of 10mins means sample not in a steady temperature - therefore need a bigger sampling time or reduce time to get readings
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| ===Solutions===
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| #Mineral oil - to reduce evaporation of samples. Need to test as:
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| #*Might affect the reading of the fluorometer, can probably be calibrated?
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| #*May block the oxygen needed by the reaction mixture
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| #*Need to get optimum volume of mineral oil which minimises evaporation whhile not blocking all oxygen and allowing fluoromemter readings
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| #Double the volume of sample - would mean that less of the sample is evaporated in proportion to the total volume, but:
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| #*doesn't minimise the evaporation
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| #PCR - put the samples in PCR tubes - the heated lid would prevent condensation, but:
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| #*would need to keep pipetting the samples from the PCR machine to the fluorometer and back for the readings - big problem for 24hr experiments
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| #Humidity - increase the humidity around the samples to reduce evaporation
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| #*Fill the wells surrounding the wells, with the samples, with water
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| ===Tests===
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| #Test for difference in fluorescence and the volume of samples wrt mineral oil being added
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| #*GFP vs GFP + mineral oil
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| #Test for rate of evaporation wrt volume of mineral oil being used
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| #*H<sub>2</sub>O vs H<sub>2</sub>O + mineral oil (different volumes)
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| #Test for chromophore formation - ie test if oxygen still reaching the sample
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| #*Cell extract + DNA vs cell extract + DNA + Mineral oil
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