Week 7: qPCR struggles and successes

This week I once again started out with a qPCR of the same plate I ran last week because the efficiency had been too low.  I made new standards and ran a full plate, yet unfortunately, when I analyzed the results the efficiency was still too low to my frustration.  The next day I used Kiley's standards for the same plate of qPCR because her standards had yielded good efficiency in her last run.  The data looked good upon analysis although some of the lower standards had to be thrown out.  We are still in the process of analyzing this data to see if the results are viable.  It is slightly concerning that our results are showing much higher abundances of amoA than were found previously when compared to other scientists' data as well as some of Lydie's old data.  We are not sure why this is the case just yet.  While the qPCR was being run I took the time to make more stock solutions of primers.  On Thursday, I ran a gel of some chosen samples that were being problematic in the qPCR runs to see if the DNA was possibly damaged in some way and impacting the results. However, most of the samples seemed to look okay after taking snapshots of the gels under UV light; there were maybe two samples that looked as if the DNA was probably damaged.  I also extracted the subsurface sediment samples I had taken during last week's sampling trip.  Upon subjecting the extracted samples to nanodrop, it seemed that the DNA was exceptionally concentrated in these particular samples.  On Thursday I got a break from lab work because the ESP was underway and had already collected several samples that needed to be recorded and logged into our sample list.  It was exciting to see that the ESP seemed to be working properly and taking good samples.  That day we also got the opportunity to observe a student give her dissertation defense, which was interesting to watch and informative in terms of giving us a glimpse of what we could potentially be looking forward to in the future.