Week 4- Infection experiment and troubleshooting

 This week we started the infection experiment and continued to try and get a good PCR and gel run to be able to begin sequencing. For the infection experiment we have 18 bottles set up- 12 experimental and 6 with dye as controls. Half of the bottles are shaken to simulate turbidity and the other half are not. Half of each of the bottles in shaken/not shaken have parasites while half do not. We will take a small sample from each bottle and measure RFU values and fix the samples to do cell counts, as well as measure for chlorophylls and nutrients. We also got some results from the gels we’ve been running- but it’s still not perfect. After a lot of troubleshooting (we’re having troubles with PCR, transformation, AND cloning) we we’re able to clean up some of the DNA samples for transformation and cloning but we still have not been able to start sequencing any of the samples yet. Hopefully we will be able to send something over for sequencing next week.