Digging Deeper, Branching Out

For the past two semesters, I have had the most amazing experience being involved in Biology Research. I had been interested in research in the past, but had never gained the courage to ask how to be a part of this opportunity until the beginning of my sophomore year. We were presented all of the research opportunities at a Research Chapel, and I had felt compelled to take the chance. I decided to reach out to Dr. Brokaw, and I am extremely grateful that I did. Dr. Brokaw has gone above and beyond as a research mentor and has provided me with opportunities that have helped me grow in so many ways.

Thus far, I have been able to work with the South American rodent genus Thomasomys and along the way have learned the process of amplifying DNA through PCR, how primers anneal to DNA sequences, gel electrophoresis, DNA purification, and how to edit sequence data and acquire phylogenies from them. I was able to present some of our data at the Texas Society of Mammalogists Conference this past spring with Dr. Tom Lee and Hannah Seah and loved being able to present what we had been working on to others.

Sharing knowledge and data that you have obtained with others is something that is of great importance to me, and it was an amazing experience to be involved in. Research has taught me that experience and practice are essential in the research lab just like they are in other parts of life. When I had first started learning about the process and techniques of PCR and gel electrophoresis, there were disappointing moments when bands didn’t show up in the gels like they should. Learning these techniques required practice and patience, but the work has been well worth it.

My desire to gain more experiences working in the research lab here at ACU has led to many exciting opportunities to acquire knowledge and learn new research protocols. Toward the end of this past semester I have been able to work with cave bacterial isolates in the genus Pseudomonas and South American species of the plant genus Mentzelia, and I couldn’t be more thankful for Dr. Brokaw and Dr. Huddleston for taking the time and having the patience to work with me and mentor me in something I have found deeply interesting.

Biology Research is something I will always recommend to people interested in learning more and who love biology. I have had an amazing time learning so many new things this past year and can’t wait for all of the new experiences and opportunities to learn from in the coming years!

 

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The journey of Bacterial Identification continues…

Ben Bernanke, an economist at the Brookings Institute once said “the research itself provides an important long-run perspective on the issues that we face on a day-to-day basis.” While thinking about writing this blog, this quote reminded me of the experience I have had with my work as a biology research student. Before I began to understand and experience this statement, I was really enthusiastic about being part of research, excited to do hands-on work, work with microorganisms and use the new research gadgets available at our new lab, and to top it all to “find something.” Frankly, isn’t that we all hope to do or achieve someday? I remember starting my research work at the beginning of Fall 2016. I wanted to be a part of finding something, without anticipating the day-to-day issues and hurdles that I would be facing.

Reflecting on my experiences from the last three semesters, this semester was rather less exciting. To quickly summarized, during Spring of 2017, our team had learned a new technique of bacterial DNA extraction, which involved utilizing additional steps within the experiment compared to that of the regular bacterial DNA extraction method. We also learned and understood the PCR technique and gel electrophoresis.  In addition, the biggest lesson from this experience was to have patience and to be more focused on accuracy of experiment rather than aiming to get quick results. Once we had learned this aspect of research, we were able to actually identify a few species of cave bacteria. I can say that this was a consolation price, which I was glad to receive after numerous failed attempts.

For Fall 2017, we were looking forward to being more cautious and using reliable techniques in order to ensure we got more results during this semester. Since we were able to identify one bacterium in Fall 2016 and one in Spring 2017, our aim was to identify a set of bacteria this semester using the same technique we had mastered last semester. But as always, surprises and setbacks are an integral part of research, and this was confirmed once again this semester. We were glad to welcome a new student on our group. We felt good that we were able to show and explain to him some of the skills that we had been able to learn over the last two semesters. Hence, we spent a lot of time trying to teach the techniques of PCR, gel electrophoresis and DNA extraction; most of our lab time in the Fall of 2017 was spent in practicing these techniques rather than being focused on getting results. I am sure many would agree that good teaching and being a good researcher go hand and hand. This is because the researchers should have the ability to explain the results of their research in a way that another person can understand and interpret. I sometimes wonder if I can positively say that this statement applies to me. I know that I possess the skills to do experiments and get results despite the struggles; however, I cannot positively say that I am a good teacher yet.

Nonetheless, the biggest take away for me from this semester was the reminder that we are gaining a “long-run perspective,” and that, as a researcher, it is wise to keep this in our mind always.

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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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Cytochrome b Sequencing of Thomasomys

I did not join in research at ACU until my senior year. Although I do wish I had gotten involved sooner, I am glad to have gained what experience I did and know that I will carry what I have learned here into my future endeavors. It was also great to apply what I have learned in my classes here to actual hands-on experience. This allowed me to take the concepts I had learned about and turn it into something real.

In fall 2016, I joined with two others to begin work with sequencing the Cytochrome B (CytB) gene from Thomasomys specimens collected by Dr. Lee in Ecuador just the summer before. One member of the group had much more experience than me or the other member and served as a leader to both of us. In spring 2017, though, my group changed and I began working jointly with a team sequencing the RAG1 gene from the same specimens as I have been working with. They were definitely helpful to me as much as they were able to be, but this semester I have had to work more on my own and develop my independence. This was somewhat terrifying as I had no one to fall back on if I made a mistake, but also liberating as I became more able to rely on my own knowledge and skills. Most weeks I was performing either a PCR or a gel electrophoresis, but I also performed one or two other tasks, including cleaning the DNA samples.

I also got to experience the Texas Academy of Sciences conference this spring. The RAG1 team and I presented a poster together, which allowed us all to practice our presentation skills and also to learn more about the research project itself. It was especially enlightening to see the research going on at other universities. I was able to connect every oral presentation I attended and every poster I looked at to something I have learned over the past years here at ACU, which was an amazing feeling.

Hannah (2nd from right) and collaborators at the 2017 Texas Academy of Science Meetings

Overall, my experience of biology research over the past two semesters has been very positive and has taught me several skills which will be useful to me in the future. Among the most valuable lessons I picked up here, though, are working with a team as well as the importance of independence and self-reliance. I consider myself very fortunate to have had the opportunity to participate in research here.

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Identifying Bacteria Isolated from Sorcerer’s Cave

Editor’s Note: This blog was composed by Whitney Brantley and Claire Shudde through a research collaboration with Olivia Dahl and Stephanie Sariles.

Sorcerer’s Cave, deepest cave in Texas

Whitney: 

As a biology major at ACU, students are given several opportunities to get involved with the department. One of the biggest opportunities students can choose is to participate in is undergraduate research under the supervision of a biology professor. Many of my fellow classmates joined research teams their freshmen and sophomore year, but it wasn’t until my junior year that I chose to get involved with biology research. The fall of 2016, I had the privilege of joining a research team under Dr. Joshua Brokaw and Dr. Diana Flanagan in which we worked to identify unknown cave bacteria isolates that were collected from Sorcerer’s Cave in Terrel County, Texas. Our project was a small part in a larger research project conducted by Dr. Jennifer Huddleston, in which other teams used these isolates to test for antibiotic production or resistance. When I first began working on this research team, I honestly did not think I would find much interest in my work. I thought research would only be another simple extracurricular activity I am involved in. However, I was quickly proven wrong.

Our research was centered on extracting bacterial DNA and amplifying it through PCR. In the lab, Dr. Flanagan taught us several basic techniques of extracting DNA and setting up PCR reactions along with gel electrophoresis. We used these techniques every week for the next two semesters. After weeks of several hours in the lab and attempting many direct DNA extractions, we consistently received no positive bands in our gels to send for identification. To my surprise, I actually began to get frustrated with these results, and wanted to work even harder to receive positive DNA bands. After many more failed attempts by the entire team, we soon switched to a new extraction technique using a KOH-EDTA method. With high hopes about this technique, we spent more hours in the lab and continued to work diligently. However, after a few weeks, the frustration continued as our results only proved to be inconsistent and varying.

With only a few weeks until our fall research presentation and no consistent data to present, Dr. Flanagan decided to run a few PCRs and gels to test the two techniques we had previously used. Surprisingly, her results came back with four positive bands for unknown isolates using the KOH-EDTA method. This proved that our current method actually did work, but our team was making technique errors that were affecting our results. We were given the option to stop research and present Dr. Flanagan’s results, or try one more set of PCR reactions and gel electrophoresis. Determined to obtain positive results ourselves, our team decided to try once more two weeks before our presentation to receive positive results. I clearly remember the change in our attitudes that research day as each member tried to focus a little extra on each pipette attempt made. Two days after our PCR reaction, we checked our results with gel electrophoresis, and all received positive bands of DNA! It was such an exciting moment in our research to feel our hard work pay off. These PCR samples were then cleaned and sent to Yale DNA Analysis to be identified just in time for our presentation.

Continuing into the 2017 spring semester, our team switched to a new extraction technique using a Zymo DNA extraction kit. We have been able to obtain several new positive results in just a short time using this accurate kit and presented eight identified cave bacteria isolates at the ACU Undergraduate Research Festival. Of all the research topics presented at the research festival, ours may have had little importance, but I along with my fellow team members were extremely proud of our work. These past two semesters of working with these cave bacteria have taught me that biology research is not the least bit uninteresting. On the other hand, research has the power to teach you lessons and spark new interests. This time spent involved with microbiology research taught me patience and determination truly do pay off. It also showed me that cave bacteria and gel electrophoresis can actually be exciting and rewarding!

2016 Fall Poster Session

Claire:

When I was five, I watched a documentary about scientists. All I remember from it were petri dishes with bacteria growing on them, but I knew I wanted to do that when I grew up. A few months before I came to ACU as a freshman, I was put in contact with Dr. Joshua Brokaw regarding the possibility of doing research with the Biology Department. Thankfully, he added me to the list of people doing research in the fall.

The semester had barely begun when Dr. Brokaw broke everyone into groups and assigned projects. My group was working with Dr. Diana Flanagan on identifying unknown cave bacteria isolated from Sorcerer’s Cave. In the group of four, I was the youngest and the least experienced. I was certain that this would be a semester of shadowing and dishwashing. However, I was completely wrong. I was immediately learning techniques right along with the other students. The process took two weeks. The first week we would attempt to replicate the bacterial DNA running a PCR, and the second week we would check to see if we had successfully replicated the DNA by running a gel electrophoresis. The first time we went through this cycle, I successfully replicated the DNA of one of my samples. This was incredibly exciting. The excitement was short-lived, as we were unable to replicate the DNA using that technique again.

After a month of unsuccessful DNA replication, Dr. Flanagan revised the experiment. This, too, was mainly unsuccessful, and I grew to be quite disappointed in both the research and in myself. This is when I learned an important lesson: research is not always easy. It can be somewhat depressing when results don’t always come about the way you would like them. However, this motivated us to find another way to make things work. A setback in research is not the end of the world, instead it is an encouragement to determine how to overcome. We overcame the obstacle of not replicating DNA at the very end of the semester. We fine-tuned our technique and were able to identify four of the cave isolates.

Using a different DNA extraction technique during the Spring semester, we were able to positively identify four more cave isolates after only one try. After preparing our poster for the Undergraduate Research Festival, we presented the research at the beginning of April. It was an exciting experience. I was able to share the things that I had learned over the past eight months, which is one of the main benefits to research. Research is hard, but definitely worth it. Undergraduate research has given me lab experience that will help in graduate school and later as a scientist. It has been a rewarding year of doing research, and I am excited to continue next semester.

 

2017 ACU Undergraduate Research Festival

 

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ACU Wildlife Society Spotlight

This January The Texas Chapter of The Wildlife Society featured the ACU Wildlife Society and our research projects in its monthly newsletter!

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Recombination Activating Gene 1 Team

Editor’s Note: This blog was composed through a research collaboration by Marissa Horne and Cameron Ludwig.

Marissa Horne:

The Abilene Christian University Biology Department caters to a host of professions. We, the students learning from these amazing professors, have been given the incredible opportunity to assist in research projects by working and learning under the guidance of our teachers. This was the case with me. One semester ago, I approached Dr. Joshua Brokaw because I was interested in doing some entry-level research as a springboard to start working on more in depth and more complicated projects in the future. As it turns out, what I thought would be entry-level research was an ongoing project that was anything but easy. I started learning the process under some upperclassmen that had worked with the material before. It felt like a guided sink or swim lesson in DNA sequencing. I eventually learned, and by my next semester I was able to help a friend of mine learn the same methods and practices that would allow us to work together on the RAG1 (recombination activating gene 1) Thomasomys project (Thomasomys is a genus of South American rodents).

Thomasomys sp. - photo by Jorge Brito M.

Thomasomys sp. – photo by Jorge Brito M.

Learning curve aside, the process and methods that we utilize in the lab are very interesting, and executing them well is crucial to obtaining good results. Every week that we came into lab we were either running a PCR or a gel electrophoresis. There is always much more to it than that, but as my fellow researchers can concur, this was the gist of daily lab work for this project. We definitely had some blunders; when two people with limited research experience are put together, some mistakes are bound to be made. However we were able to fix what needed to be fixed, and get decent results. I very much enjoyed seeing my own progress and confidence in the lab grow as the semester went on. My first time working on this project it was easy to let the more experienced researchers take the lead. This year I was the more experienced researcher, so I really had to be sure of what we were doing before we did it. The whole experience could pretty much be summed up in the word, learning. We are learning new things about our research subjects, we are learning how to conduct a proper research study, and we learn the valuable lesson of patience over and over again. Our project was almost a repetition, more like a confirmation, of previous hypotheses about relationships within Thomasomys. There was a lot of waiting and repeating steps, over and over again, in many aspects of this experience.

Poster copy

Fall 2016 Biology Research Poster Session

Towards the end of the semester, we began to prepare for our poster board presentation. Here we needed much guidance from Dr. Brokaw to put together a phylogenetic tree that showed our most recent results. This was the step that basically put together all of the small details into one big picture, or poster! One of my favorite parts of this research experience is getting to do the research festivals and the poster presentations, because I get to share a part of this interesting experience with others. I especially enjoyed talking to the first year students. They had prepared questions to ask us, but most of the time the more curious students ended up asking more than what was required of them. These events are where future researchers are found, so I really had fun talking to them about the work we had been doing.

Overall I can confidently say that Biology Research this semester was one of the most enjoyable and informative classes that I took. It was a time that I didn’t have to worry about anything else besides the task at hand. I can’t wait to see where this project will lead, and I’m hoping to continue doing research in the future.

Cameron Ludwig

I was one member of the team researching the RAG1 gene in Thomasomys.  The ultimate goal of our research was to attempt to further develop the phylogeny that has been formed for the genus.  A phylogeny is a hypothesis that attempts to explain the evolutionary history and certain relationships between different species sort of like a human geneology.  The issue is that the phylogeny is simply a hypothesis.  Our goal as researchers was to test out the hypothesis based on data that has already been produced by collecting new data to hopefully confirm previous findings.  The goal of the research is to increase confidence that this phylogeny does accurately show the relationships within this genus.  When we sequence more DNA, we will be able to gain more confidence in the phylogeny and more fully explain the relationships.  One of the issues with the previously sequenced DNA was that previous teams have been using mitochondrial DNA which is only accurate in showing the phylogeny through the female lineage.  Our research was important because we were using nuclear DNA that will help to further expand that phylogeny by including the female and male lineage.

products_thermocycler

Our main tool for collecting DNA sequence data was the PCR machine (a.k.a. thermal cycler).  The thermal cycler utilizes the polymerase chain reaction in order to copy segments of DNA for analysis.  Once we produced our data from the PCR, we separated and identified the different sizes of DNA strands using gel electrophoresis.  Once those strands were separated, we were able to send purified DNA for sequencing and use this to form our phylogenetic trees and further understand the evolutionary relationships present.

Phylogeny copy

Phylogeny of Thomasomys based on RAG1

Overall, I had a wonderful experience in the lab with John, Marissa, and Dr. Brokaw.  I gained more understanding of what it takes to be successful in a laboratory.  I learned from my colleagues and from the mistakes that I made and will use the experiences and knowledge that I have gained this semester to be a better researcher next semester.

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The Unknown in Sorcerer’s Cave

Editor’s Note: Many of our students in ACU Biology Research work in teams composed of members with differing levels of experience. This blog was composed through a collaboration by Samantha Studvick (2nd year) and Kathy Le (1st semester) working together on the same research project.

Sam:  I began doing research with Dr. (Josh) Brokaw at the end of the Fall 2015 semester. Initially, I was on one of the Thomasomys phylogeny projects, specifically the CO1 (Cytochrome c oxidase I) group collecting mitochondrial DNA sequences. I worked on this research for all of the Spring 2016 semester, and I got to present at the ACU Research Festival and the Texas Academy of Science and Society for the Study of Evolution conferences.

Since I enrolled in the Biology Research course this semester, I began a new project expanding on the DNA sequencing skills that I had already learned. I was a little nervous, not only to be working on an unfamiliar project, but to be working on a completely new project in a newly formed lab team. Drs. Brokaw and (Diana) Flanagan created a new research group, under the direction of Dr. (Jennifer) Huddleston, for a project to identify a set of unknown cave bacteria based on phylogenetic reconstructions.

Example phylogeny of domain Bacteria from BMC Evolutionary Biology 2005, 5:34

Example phylogeny of Domain Bacteria from BMC Evolutionary Biology 2005, 5:34

A phylogenetic tree demonstrates the interspecific relationships between organisms (like a genealogy of species). Most phylogenies are based on DNA sequences, and this requires a complex process of DNA extraction, PCR (DNA replication), gel electrophoresis, DNA purification, DNA sequencing and alignment, and computer analyses. While the goal of the project was to begin identification, most of the semester was devoted to finding the correct method for DNA extraction and running the PCR.

Kathy:  In the fall of 2016, my sophomore year, I began my first semester of research with Dr. Brokaw. We did PCRs and ran gel electrophoresis data on bacterial cave swabbings done in Terrell County’s Sorcerer’s Cave (notably the deepest cave in Texas) with the goal of identifying the bacteria in this unique isolated environment.

Overall, we used three separate methods of extracting and replicating DNA because the DNA collected was not always able to produce bands. Even though much of this semester was devoted to finding a successful technique, I learned a lot about the processes behind running PCRs and gels. It’s quite interesting seeing something you learn about in a Gen Bio lecture class actually happen in the flesh. It makes concepts easier to understand because there is tangible evidence and processes that occur to support the concepts. For instance, the process of synthesizing and denaturing DNA. Eventually, we have enough to run a gel, since the DNA is copied to more than a billion times. Once this has occurred, we run the gel and search the sequence in Genbank to begin to identify the species of the bacterium.

Sam:  We first tried to transfer portions of bacteria colonies directly into the PCR tubes without DNA extraction followed by the basic PCR protocol. The results were unsuccessful, so we implemented a new strategy for DNA extraction. Again, the results were not really worthwhile. After altering some of the quantities for the master mix (combined chemicals used in PCR), we were able to get some results, albeit inconsistent. With the DNA isolated and amplified by our successful PCRs, we were able to identify three of the isolates as Pseudomonas, which gives us a starting point for next semester; however, we will likely be switching our DNA extraction/PCR protocol yet again to hopefully yield more successful and consistent findings.

Kathy:  Initially, it was a tough semester since I was coming in totally uninformed. I constantly had to learn as we went, continuing to ask questions about the protocol and materials used for PCR prep and gel-running. Gradually, I got the hang of it, as I’m sure everyone else who was a seasoned researcher in the lab had, since the research is basically student-run with supervision from their research advisors. My main goal was to just learn how to do the process and then become good at it. Seeing as we were failing to have bands on our gels, it was a bit discouraging to say the least. I felt that I was doing the procedure wrong or perhaps botching it on the filling of the wells in the agarose. We plan to correct this by using DNA extraction kits next semester to increase the likelihood of bacteria identification.

Sam:  Doing research can be a frustrating process at times, especially with ineffective protocol. Nonetheless, I really do enjoy conducting research with a team. As a hopeful Pre-Med student, this research is not directly related to my intended field; however, there are some implications as this project may begin to look into the development of antibiotic resistance (in a distant future). The techniques used in the lab are invaluable resources, though, and are important for a foundation in any topic of research. Being concurrently enrolled in Microbiology (lecture and lab) has broadened my appreciation of the study of bacteria. Moving forward, I am excited to continue working on this project, and I look forward to presenting my findings at various conferences.

Preparing bacteria for PCR for the last time in the Clark Stevens Lab.

Preparing bacteria for PCR for the last time in the Clark Stevens Lab.

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Mentzelia to Micro

Research did not cross my mind before coming to ACU because I didn’t enjoy labs in high school, so I wasn’t interested. However, my freshman year I had classes with several sophomores, who would often talk about the research they were doing. They made it sound intriguing and fun yet challenging, which was quite the opposite of my concept on research. As I walked by all the posters and different labs in the Foster Science Building (now known as Onstead Science), my curiosity grew, and, when Dr. (Josh) Brokaw sent an email for research applications, I signed up not really sure what I was getting myself in to. I was assigned to the Mentzelia research team, and I was extremely intimidated. I had no clue as to what Mentzelia was, which turned out to be a flowering plant, or the specific end goal for the research team. I showed up the first day of research completely clueless, but this is an aspect of research that I have grown to love. I started with little knowledge of my topic, but slowly developed skills and knowledge throughout the year. Most of the work that was done with the Mentzelia team was to run PCRs and gel electrophoreses because the end goal was to compare several Mentzelia species’ phylogenetic relationships and determine if there were any patterns of homoplasy (misleading similarities) in the DNA sequence data or morphology.  I realized that patience was a key characteristic to acquire during research.  As a team, we ran over 50 PCR reactions and gel electrophoreses with few positive results. It was frustrating, however, I was able to practice basic technique that has been valuable in my current research.

Hofsommer et al., 2016b

The end goal of any research is to be able to present your findings to an audience, and I had to give an oral presentation along with one of my team members. This was a hard task because most of our results were negative. Also, I did not believe that I had the knowledge to give a well-informed presentation, but with Dr. Brokaw’s guidance, we were able to develop a well-formed presentation. I still remember the question one of judges asked me, “Why is this research important?” I blanked. I was able to come up with a quick response, but I had not thought about the importance of the research that I was conducting before this moment.

IMGP0969

I may still not completely understand the impact this research with the Mentzelia team had on plant biology, but I learned so much during my first year of participating in research. I learned that consistency, patience, and determination are key characteristics that are developed during lab work. I also learned that I enjoy research. I began clueless, and, by the end of the year, I was able to give an oral presentation over the information. The journey of research is exciting. The end results are unknown and anything can happen. This is why I decided to continue research.

I am now working with Dr. (Diana) Flanagan on the identification of unknown bacterial isolates from Sorcerer’s Cave. At first it seemed like this semester of research was going to be similar to my previous experience because the gel electrophoreses was negative or as a team we had inconsistent results. We had to use different methods to isolate DNA in addition to running new PCR reactions and gel electrophoreses. But after changes to the methods, we had positive results that could be sequenced, and we were able to present our findings to the ACU Biology Research Club at the fall research poster session. This research has been exciting because we are working alongside Dr. (Jennifer) Huddleston’s research teams, who are testing for antibiotic resistance in the same unknown bacterial isolates. It has been a good semester of research so far, but as a team, we hope to identify more unknown bacterial isolates before the ACU Spring Research Festival and the Texas ASM (American Society for Microbiology) Meetings. I am so glad I decided to join a research team, because it has been a rewarding experience that I would have not had doing any other extracurricular activity.

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Monitoring Wildlife in the Southern Rolling Plains Using a Camera-Trap at Water Catchment Stations

In the spring semester of 2016 I joined in a research project, which was just starting to formulate, with another student. Other than classroom-based research and presentations, this was my first time being involved in a research project. This particular project is just in the preliminary stages as we’re collecting our first data. Eric Dolezalik, the other student involved, had recently studied water catchment systems in depth and decided he wanted to apply that knowledge for wildlife research. The Abilene area had seen a scarcity of water in recent years. Therefore, wildlife in the area have been spreading out to fulfill their water needs. This research project is designed to determine the various wildlife species that are present and what their population and density is in the Abilene area, while providing another water source collected by a catchment system and measuring its impact on wildlife distribution. So through the guidance of Dr. Josh Brokaw, we decided to conduct a trail camera survey with and without the presence of water sources on the 402 acres of the ACU Rhoden Farm of the Agricultural and Environmental Sciences Department in Hamby, Texas.

Rolling Plains

Location of Rhoden Farm in the Southern Rolling Plains

Grid

Camera Trap Grid

With our study site determined, we set up a rectangular grid using Universal Transverse Mercator (UTM) coordinates on Google Earth. The reason we used UTM was to eliminate any variation in distance between coordinates (like with longitude) from the curvature of the earth, but once we got in the field, we realized our handheld GPS device did not have the UTM option on it, so we had to convert our points to longitude and latitude. With the grid established, we positioned trail cameras at evenly spaced locations throughout the farm, and we eliminated any points that were too close to a large manmade object or a sizable body of water or would interfere with any normal operations of the Rhoden Farm.  We ended up with twenty locations in all.  At these locations, we mounted trail cameras on T-posts to capture any animals that wander by. We are still in the process of building water catchment systems with the guidance of professor Billy Kniffen, a water resource expert, so all the data being collected on the cameras now will be used to establish a baseline of the wildlife presence before we put these catchment systems in place.

Catchment

Incomplete Water Catchment System

The catchment systems are small shed-like structures that are only about 3 feet high, 3 feet wide, and 6 feet long. It has a slanted roof to direct all the collected water to a 55 gallon barrel where it will be stored and then will proceed to concrete watering station just in front of the camera. Once we get the catchment systems in place, only ten of the camera locations will have them, and the other ten will be considered a control of water absence for our data collection. This preliminary stage has been useful because, after the first week of data being collected, we realized that our cameras were too high to capture much of anything smaller than a coyote, so we decided to lower all the cameras to about two and half feet off the ground, in hopes of catching more animals on camera. Thus far, without the water catchment systems, we have only been able to identify a few wildlife animals that have wandered in front of our cameras. We have positively identified white-tailed deer, black-tailed jackrabbits, great-tailed grackles, coyotes, scissor-tailed flycatchers, and a few others. Though in the future and with access to a supplemental water source, we foresee capturing a lot more wildlife on camera where we can compile the data and determine the species population richness, density, and diversity and measure the impacts of the water-catchment system. I look forward to seeing which species we’ll get on cameras and to see how they react to the increased water access.

deer

White-Tailed Deer

rabbit

Black-Tailed Jackrabbit

grackle

Great-Tailed Grackles

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