Back from the Past, Blast to the Future

Did my spicy title draw you in? Well, now for the dry stuff.

I finished my research on previous Presidential policies regarding Israel and Palestine, and have now begun applying this to current events. My goal is to analyze how Trump’s policies compare/ contrast to historical US precedence, and the effect this will have on the future of a one or two state solution.

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Fine-Tuning Our Experimental Protocols

Since my last blog post, a lot has happened. We ran a few more Western Blots, which were mostly successful. I have also been learning how to use the fluorescent microscope to examine and take pictures of the slides from our experimental trials, which unfortunately have not been very successful. Recently I’ve been having issues with cell confluency (how concentrated the cells are)– when the cells get too confluent, it provides a perfect breeding ground for fungus, as we found out a few weeks ago. When the cells aren’t confluent enough, however, we are forced to seed our six-well plates at lower than ideal concentrations. Low confluency has been the more prominent issue in recent weeks, requiring us to either seed at a lower concentration or simply wait for the cells to grow several more days.

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Experimental Troubleshooting

Our research project has been stalled because we have had multiple complications with our cell lines. First, one of our plates in which the cells were contained in grew some type of fungus while incubating. We had no idea what to do with it but unfortunately we had to toss that plate out. When we tried to restart the cell line, we tried to count the cells to get a higher concentration in the plates, but unfortunately the cells had not grown enough for us to seed them at a high concentration. These problems were interesting because we had no idea what was causing them. However, we have since continued our experiments by restarting the contaminated plates and seeding at lower concentrations. After we have completed the experiments, we look at the slides under the microscope to observe the fixed cells. Some of our slides have turned out well, but other slides have shown no cells at all. We are currently trying to troubleshoot our procedure and trying different ways to optimize it for the cells. We also realized that we had not been incubating our cells with nerve growth factor (NGF) for enough time and that might have been an issue with with not seeing neurites.

When at first you don’t succeed…

One of the most frustrating things about science is that you spend a lot of time wondering if you’re headed down the right path. Although having multiple ways of doing things can be a benefit, it can also lead to second-guessing. I have spent more time than I care to admit thinking about whether the method I’m currently using is the best way to achieve results. Unfortunately, the past few weeks have been a lot of trial and error. I spent a week trying to get my data in the correct format in order to use a package on it (PAML; Phylogenetic Analysis by Maximum Likelihood) only to realize that the package wasn’t ideal for the low read coverage data I’m working with. This meant I was forced to jump ship and start trying to figure out a completely new way of doing things.

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Losing the Battle to Win the War: Plant massacres and program fails

I’ve taken a fair few Ls in the past few weeks here in Puzey lab, but I know they’ve all been for the best. In my last post, I wrote about the measures we were taking to beat back thrips and spider mites; in this post, I must write that I was unable to control the insects on my plants, and had to make the decision to cut them all back. The spider mite populations were huge, and I was having to wipe down the leaves and stems of my plants every day to kill them. Misting with water and even bleach didn’t help, and on top of that, thrips were still present. I couldn’t use insecticidal soaps on the plants, because we had released so many predatory insects to help. So, I cut every single plant back to its roots. This sounds traumatic for the plants, but milkweed has such extensive root systems that they regrow quickly and healthily. Now I just have to wait for everything to grow—and then I can start executing my experiment!

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