Hope I'm Doing this Right

Community Service Day

Unfortunately, I did not go to the NYSM today. It was the Community Service/Dr. Martin Luther King Jr. Celebration Day at Emma. I am excited to be going back next week though. As of now, no problems to report. Everything has been running smoothly.


January 18, 2012

A Brief Summary

A little while ago, Dr. Cryan gave me a report that he and Julie Urban wrote, titled "Entomologically famous, evolutionarily unexplored: The first phylogeny of the lanternfly Fulgoridae (Insecta: Hemiptera: Fulgoroidea)." The report shows the results of the first study ever of the phylogeny of the Fulgoridae lanternfly. The study was based on DNA nucleotide sequence data from five genetic loci. The report begins by explaining the uniqueness of the fulgorid species included the brilliant colors, the production of cuticular waxes, and the enlongated head function. The primary goals of the study were to reconstruct the phylogeny of the major lineages in the Fulgoridae species, test the existing classification of the Fulgoridae, and examine the evolution of the enlongated fulgorid head. Some of the tests that they do include taxon sampling, DNA extractions and PCR amplification, and sequence alignment and phylogenic analysis. In the end, the study was able to test the classification of Fulgoridae, examine the evolution of the Fulgorid head morphology, and explore the distribution patters of the fulgoridae. More research will be needed to gain a greater understanding of the fulgoridae, but this study was a great way to test old hypotheses and get a jump start on research into the fulgoridae species. When I first read it, it was all very scientific and confusing, but as I've been working with Dr. Cryan, more of this report is making sense.
Posted January 11, 2012

Something Went Wrong

Today was very much like last week. We started out by making the gel for the new DNA that we replicated in the PCR machine last week. The process was the same. We added dyes to make the DNA visible, we ran electricity through the gel and watched as the pink, blue, and purple streaks appeared. We took another picture of the gel, but the results still showed up negative. Dr. Cryan said that since the experiment had been completed successfully a while back, and since this was our second failure, there was probably something wrong with the ingredients. This means that either one of the components we added went bad or the actual DNA was messed up. Since the DNA is fairly new, we concluded that this issue must be one of the other components. In order to test the DNA and the other components, we switched out all of my ingredients for new ones, and also added another sample DNA. The new sample that we added was recently tested and was successful. This means that if the new DNA turns out positive in the photo and the others do not, then we know the DNA is bad. If all of the DNA samples turn out positive, we know it was one of the ingredients. After making a completely new mixture from scratch, we put the samples in the PCR machine and let it run. Cross your fingers all of the samples turn out positive!
Again, we finished early, so Dr. Cryan took out more insects for me to examine and categorize by species. After we finished categorizing, we placed each species in different test tubes. Each tube got filled with alcohol, I believe, and then labeled. Unfortunately, time was up so I couldn't examine more, but I'm excited to see our results of the PCR next time!

Posted JANUARY 11, 2012

Making Gels

Last time I was at the NYSM, I used the PCR machine to replicate DNA. Today, I took the samples that we replicated and made a gel with them. We assembled various substances to make the gel. One of the ingredients was this fluorescent dye that makes the DNA within the gel visible under the black light. Within the gel form, we put in combs, which are plastic comb shaped inserts that go into the gel and make about 25 grooves in the gel. We waited for 5-10 minutes for the gel to solidify. While we waited, we added this dark dye to each of the 9 samples so that they would not only be visible but also to add density. The next step took a lot of patience, precision, and a steady hand. I had to take 5 micro liters of each sample, using a pipette, and insert them individually into each groove within the gel. The gel was submerged with one liquid below it and one liquid above it. My depth perception has never been great, so placing the pipette in the exact location, making sure not to penetrate the gel was a bit tricky. After all was in place, we had to run the gel through an electrical current. DNA is negative, so by running a current that ran negative to positive, the DNA would move along with it. Because of the dyes, we could see 3 separate color lines forming. After it was done, we took the gel over to a machine that exposed the gel to the correct lighting and then could take a picture and process it through a computer. We need to do this because the picture will show bright lines on certain areas where it was positive. Unfortunately, the photo was all negative. This means that something must have gone wrong somewhere along the lines. Disappointing, but not the end of the world. In the next ten minutes, I made up new test tubes to go through the PCR machine. Next time I go, we will give the gel another shot.
Since we had an extra half an hour, Dr. Cryan went into the freezer and pulled out some insect samples. We looked through microscopes and separated the mix of all different shapes, sizes, and colors into what appeared to be categories based on species type. It was amazing to see the tiny insects under a microscope. A little weird at first, but then I got to see the different features each species had and Dr. Cryan told me what the features did. It was amazing to see some insects that had only recently evolved to have a different feature and then comparing it to the insect it used to look like.

Posted January 4, 2012

18S and 18S nDNA Replication

Dr. Cryan started off the day by giving me a little background on DNA replication and the secondary structure of protein coding versus nonprotein coding DNA. Afterwards, he showed me logs for replicating QUI54LC, I believe it was called. My first job was to replicate 18S DNA from the point a07 to bi. He showed me a list of chemicals and quantities, which we multiplied by 9 because we had 8 DNAs to replicate and one blank control. After using many different pipettes and quantities, I was able to create one test tube with all the "ingredients." Then I put 25 microlitres into each individual test tube with individual DNA. He taught me how to use the PCR machine. You place the test tubes into the machine, choose a folder, a reaction, and then let it begin. The PCR machine raises the temperature to about 95˚C then lowers it then evens out at about 54˚C. It repeats the cycle 44 times after the first cycle. We finished that one with some time to spare, so he had me do the same test with 18S on a different segment of the DNA. All in all, it was a successful day and I learned a lot about the importance of exact measurements and not contaminating different test tubes.

Posted 15th December 2011