Tuesday, July 7, 2015
A Potential New Tool
Have you ever read a doom-and-gloom environmental biodiversity statistic touting that over half the world’s biodiversity is gone? Or have you maybe seen a graphic on the rapid rate of amphibian extinction? Did you ever wonder, how on earth researchers collect and determine this data? One of the major methods of assessing this is by capturing specimen at precise time intervals, recording data, and running statistical tests. However, quantifying this data can often be difficult, time-consuming, and expensive.
Sébastien Calvignac-Spencer, of the Robert Koch Institut in Berlin, believes that there is highly efficient alternative to this method by use of an indirect tool. I believe that Calvignac’s unconventional tool has tremendous potential in not only large-scale monitoring of ecological and biological systems, but also population disease framework. I have been fortunate enough to be given the opportunity to perform preliminary tests on the feasibility of implementing this tool.
Calvignac’s method involves collecting flies, or really any invertebrates that make contact with other organism, in a region. Detrivorous invertebrates are especially useful because they carry large amounts of DNA of organisms that inhabit the ecosystem. After collecting invertebrate samples, DNA is extracted from the invertebrate. Specific primers are then used to target certain DNA sequences in the sample. However, isolating the desired segment of DNA for sequencing is not always a straightforward process. In the case of my samples, I have had to run my PCR products through a gel, excise the desired band from the gel using a scalpel, clean the DNA, perform fusion PCR, clean the DNA using magnetic beads, add tags to the DNA, clean the DNA again, and finally sequence the DNA. The DNA sequence is then analyzed to identify the organisms that the invertebrate has been in contact with.
Thus far, conducting research at the Robert Koch Institut has been an incredible experience. Not only have I learned countless new techniques, ranging from Next Generation Sequencing to Quantification PCR, I have also been given a significant amount of independence in the lab; so much so that I have had many incredibly challenging, yet invigorating, experiences in the lab.