Journal Club 2
Hello again! The past couple of days have been spent trying to wrap up aspects of our project and get to the point where we can send off our samples for sequencing. Since we had to, unfortunately, drop the culture independent portion of our project, we’ve just been focusing on our culture-dependent samples, and luckily we have a lot of them. Friday night my partner and I went into lab to do a pre-plasmid purification preparation on our samples, Saturday we went in to do a Qiagen miniprep on them, and yesterday we started a restriction enzyme digest. At this point, we’re doing the same thing to our culture-dependent samples that we did with our culture-independent samples, so fingers crossed we have more luck this time! Today in lab we’re going to run a gel to see if everything worked, and if so we’ll actually be able to send something away for sequencing, which would be great since our poster is due just two weeks from today!
On Monday we had our second journal club, but this time my lab section presented the figures to the rest of the class. As a class we voted on which article we wanted to read, and we chose a really interesting article about carrying capacity called “Variation in Local Carrying Capacity and the Individual Fate of Bacterial Colonizers in the Phyllosphere” (I’ll include the link below if you’re interested in reading it). Carrying capacity is generally defined as the maximum number of bacteria a leaf can support. Through the use of computer models and green fluorescent protein labeled bacteria, the authors challenged the commonly accepted definition of carrying capacity (namely that the capacity was the same across the surface of a leaf) and asserted that the leaf is actually made up of different sites of high, medium and low carrying capacity, which in combination sum to give the total carrying capacity of the leaf. They demonstrate that there are a large number of sites on the leaf that have either a medium or a low local carrying capacity, and a small number of sites that have a high carrying capacity (meaning they have a lot of nutrients and bacteria that land there can divide many times). Thinking about the carrying capacity of a leaf in terms of specific sites on the leaf rather than as an average value for the leaf as a whole gives us another tool with which to analyze our own samples. Although we can’t use GFP-labeled bacteria or computer models, analyzing the plant anatomy can help us think about where on the leaf there might be sites that are better equipped to handle a large number of bacteria, and where bacteria might have trouble growing. Using our initial plates from the beginning of the semester, we can come up with the carrying capacity for our own leaves, to determine whether or not bamboo is a good habitat for bacteria. I’ll keep you posted on how that goes, and whether or not we can send samples away for sequencing!