Life of a Biologist
From the Field to the Lab
Cassandra Ziegler
Cassandra Ziegler
As a PhD student, we’re not only doing our own research and lab work but also taking classes and teaching classes. As part of the program, PhD students are sometimes paid to be a teaching assistant (TA) for undergraduate classes so that we work solely at the university. For example, 1st year PhD students are all assigned to TA for general biology I lab for mostly freshman undergraduate students in the first fall semester. From there, you might continue teaching general biology II lab, or a variety of other classes that have labs. In my time here thus far, I have TAed for general biology I lab, advanced general biology II lab (for biology majors), anatomy and physiology I & II labs, and am now TAing for what we call “superlab.” These are Capstone Lab courses designed for upper level biology majors to learn advanced laboratory techniques while working on projects. There are several different Capstone Labs that students can take and this semester, I’m TAing for the Capstone IV: Microbiology lab. Now, I don’t know if you’ve potentially noticed up to this point, but I am not a microbiologist. When I was asked by a faculty member to TA for this class, they had every confidence in me based on my skills and knowledge in molecular biology (the PhD in biology program here at Duquesne is very focused on molecular biology). However, I also provided a fair warning that I hadn’t done any microbiology techniques in quite some time…about 14 years, to be exact, when I was in a microbiology class as an undergraduate at IUP. Knowing that, there was no problem. I was told that the faculty mainly teaching the lab would provide any assistance along the way and to never be afraid to ask questions, specifically that it would be worse if I didn’t understand and didn’t ask the questions. Never be afraid to ask questions, especially in science! Anyway, I’m going into all of this because we’re now approaching our spring break and the halfway point of the semester. The main teaching instructors for this superlab will be transitioning from one to another, and so will the types of techniques and projects that the students (and myself) will be working on. I figured that this would be a good opportunity to talk about and provide some pictures from part of a project that students were working on. I’m going to give yinz the cliff note version of the background so you have an idea of what is going on, because it can get pretty crazy. First off, we were working with a non-toxic strain of Eschererichia coli, commonly abbreviated as E. coli, a type of bacteria that can be a good model system to use for certain studies. One of the experiments the student were working on was to observe a specific transposon (Tn5), a piece of DNA that can move itself from one piece of DNA to another, go from one strain of E.coli to another strain by something called conjugal transfer. In our experiment, we know that the Tn5 transposon will insert itself somewhere into the lac operon. Some of you may know about the lac operon and some may not, so here is a crash course. Basically, the lac operon has the genes that allow us to metabolize lactose. Here is an image and link to a YouTube video from a channel called the Amoeba Sisters that always do an amazing job explaining biological concepts. From the image above, you can see that the lac operon has 3 main genes: lacZ, lacY, and lacA. After the students did the conjugal transfer experiment from one strain of E.coli with Tn5 (donor) with another strain of E.coli (recipient without Tn5…yet!), the students then spread E.coli on petri dishes that had specific media (this provides the bacteria with specific nutrients and/or antibiotics to either encourage or discourage growth) and allowed colonies of the bacteria to grow for a couple of days. One of the ways to determine if the Tn5 transferred into genes of the lac operon is to look for mutants. When Tn5 inserts into the DNA, the insertion can disrupt the gene and cause a mutation. How are they able to find the mutations, you ask? We used two specific types of media for the bacteria to grow on that will turn certain lac operon mutations different colors!. Let me show you an example of a final demonstration plate a student is using for their lab report: In the picture labeled “Xgal”, the wild type (no Tn5 transposon) is light blue (upper right). If Tn5 is inserted into the lacI gene, the colonies are dark blue (upper left) and if it is inserted into the lacZ gene, the colonies are white (bottom left). Now, you might have noticed that the last area for lacY mutants is also light blue. How can you tell the lacY mutants for the wild type? Glad you asked! That’s where the other plate comes into play, labeled “Mac Lac.” This stands for MacConkey agar and lactose, serving as a pH indicator. If the bacteria do not ferment the lactose, the colonies are white and indicate that they are lacY mutants. Bacteria that ferment lactose cause a decrease in pH (more acidic) and the resulting colonies are pink/red in color. These plates can help to find those last mutants. The plates you see above are the beautiful final demonstration plates after finding the mutants in a sea of wild type (non mutant) colonies and streaking them onto new plates to truly isolate the colonies. Here is what one of the initial plates looks like: You can see that almost every one of the colonies is light blue but there are one or two spots on the left area of the plate that are white. These are lacZ mutants! How cool is that? Science is crazy! In summary, that’s only a small portion of what the class was working on for the first half of the semester and they all did a great job. Even though this is not a comfortable area of biology for me, I definitely learned a lot and have had a great time with the students along the way. Hope you learned something cool from this too!
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AuthorBird Enthusiast and Graduate Student Archives
February 2024
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