An Ongoing Journey to Identify Cave Bacteria

Transferring from a community college, the amount of lab work and experience that I had been exposed to, was always limited to the curriculum of the classes that I was enrolled to take in a given semester. In all honesty, I have to admit that I always enjoyed the labs and the hands-on experiences so much that I remember saying that I wish there was an opportunity as a student to do more in the labs. Part of this is because the best way for me to learn is by doing and applying the theory and concepts in real life scenarios. To me science is fascinating, but it’s even more exciting when I can see it taking place right in front of me. As a pre-dental student, on my first semester at ACU I started considering the possibility of applying to DDS (dental school)-PhD dual programs because I truly enjoyed working in the lab, and I came to know that ACU students had the opportunity to participate in doing research projects under the guidance and supervision of a faculty mentor in different ongoing projects in the department. As I expressed my interest to Dr. Joshua Brokaw, the following semester (Fall 2016) he allowed me to join as a volunteer in one of the teams working on a rather new microbiology project, identifying bacteria from the Sorcerer’s cave located at Terrell county, Texas.

The Fall 2016 experience was the opposite to what any of my previous experiences had been in the class setting and far opposite to what I was expecting the experience to be. I was used to following the instructions of the professor, to be told what was to be expected and if something was wrong, one knew exactly what was the problem (almost like following a cooking recipe!). But research works completely different. To start, I have to learn the PCR technique, which I learn from one of the upper classmen working in our group as well as with the help of Dr. Brokaw. The first two months we met in the lab I felt scared, intimidated and clueless with all the equipment, the steps when doing PCR, Gel electrophoresis and the work required from our group. To make things worse (or at least I thought of it this way then!) the protocol that our group was following to extract the DNA was not working, therefore we were not getting results. I have to admit that at one given point I was so frustrated and disappointed at myself that I remember thinking that after all maybe the lab work was not 100% for me and certainly there was nothing fun about it or the feeling of failure! That first semester we spent the whole time trying to figure out what was the best way to make the KOH-EDTA DNA extraction protocol work. For this, we tried different ways to take the bacterial samples, we used different amounts of bacteria samples and even different amounts of chemical used. None of the PCR’s our group did worked, it was only with Dr. Brokaw’s help that we were able to identify one species of bacteria (Pseudomonas vranovensis) after a whole semester worth of work. Even though I was somewhat disappointed at myself and thought I had been wasting my time, during the evaluation process at the end of the semester I realized six main things:

  • Things will not always be what we expect, but we decide to make adjustments and learn from the struggles.
  • It can be easy to quit out of frustration, but research takes dedication, perseverance and a lot of effort. Only by having those qualities can one continue to work despite the errors or disappointments.
  • Team work is important, but equally important is to push oneself to learn what needs to be done, to be reliable and to work independently.
  • It is ok to start all over if it’s necessary and keep trying until one gets the results one needs.
  • Most importantly, I learned to have a little bit more patience with myself, and others. Learning to be patient and relying on others can also be a humbling process.
  • The one result we got at the end of the semester was so exciting and rewarding that probably if it had been an easy task I would not have valued it as much as I did at the end.

Thus, despite the struggles I decided to keep working on the project and give myself the chance to keep learning not only science and lab techniques but also learning from others and life. I decided then to continue to work on the project the following semester.

During Spring 2017, we not only started the year with a new protocol but, to add to the excitement, we also worked in a new facility, The Halbert-Walling Research Center. Although everything was new, it was also equally frustrating to have everything disorganized, from finding the specimens to ensuring proper working of the machines and equipment. Reorganizing by itself took a couple of weeks out of our schedule and put us behind on our research. One of the things which also set us behind was the utilization of new protocol (E.Z.N.A. DNA extraction kit) that required the bacterial cultures to be incubated in LB broth. This DNA extraction method was more extensive in the required steps, and the fact that none of us had ever used or done it also added to the delay. The first time we did the extraction the whole process took around six hours, just to extract the DNA. However, after performing couple of PCRs and gel electrophoresis, we were able to see that we were obtaining some results. This was very rewarding but also frustrating as the results we got were inconclusive, indicating possible error in the PCR process (technique). At this point we were trying to work as much as we could in order to be ready for the annual Research Festival, given the length of the procedure and the need for repetitions, we were able to identify only one type of bacteria (Pseudomonas clororaffis) for this second semester. Even though we did not obtain a large amount of results, we were still able to identify an effective way to obtain the DNA required to do a PCR that will yield accurate results, which in turn led to the bacterial identification.

Our ability to identify this effective way of DNA extraction by using a new, untested protocol by our lab was perhaps the biggest success for the semester. For the next academic year, our focus will be on obtaining better quantity and quality of data which will aid in identifying all of the bacteria found in this cave.

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