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


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


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.


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.


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


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.


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.


White-Tailed Deer


Black-Tailed Jackrabbit


Great-Tailed Grackles

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Phylogenetic Analyses with New Nuclear Markers for Thomasomys

As my first research project as a student at Abilene Christian University, I was a member of the AP5 research team. The goal of our research was to confirm and further develop a newly constructed phylogeny of rodents in the genus Thomasomys. A phylogeny is a hypothesis of the evolutionary history and the evolutionary relationships between species. The reason that it is important to test the previously constructed phylogenetic tree is because a phylogeny is always a hypothesis.  The more DNA that is tested, the more confident we can be of the likelihood of our hypothesis. A fully resolved tree (where the exact relationships of all of the species are described) is important because it can be used to understand the impact of historical events like the formation of the Andes on the diversification history (how species separated) of Thomasomys. The phylogeny that has already been constructed was found using mitochondrial DNA, and our research was attempting to test the mitochondrial phylogeny with nuclear DNA. The mitochondrial genome comes from organelles called mitochondria (inherited from the mother) and contains anywhere from 100 to 1000 copies per cell while nuclear DNA is found in the nucleus (inherited from both parents) and contains two copies per cell.


Thomasomys caudivarius

In order to collect DNA from the AP5 (intron 2 from the acid phosphatase type V gene) region, we conducted polymerase chain reaction (PCR) on DNA samples from species of Thomasomys with primers that we learned about from previous research on rodent phylogenies. PCR is used to amplify a piece of DNA until there are millions of copies of the DNA sequence. DNA polymerase is the enzyme that replicates the DNA, and primers are short strands of DNA that are used to facilitate DNA replication because the polymerase requires an existing strand of DNA to which it can bind the replicated DNA. However, these primers didn’t work very well with Thomasomys because they were designed for other rodent species, but we were able to amplify AP5 from a few of our samples. We used the sequence that we obtained to design three new sets of primers, and two of the three sets were successful at amplifying AP5 from most of our samples. After the DNA is amplified using PCR, the product of the PCR is then tested to see whether our targeted area was present with gel electrophoresis. Electrophoresis separates different sizes of DNA strands. If there is DNA of the correct size present after the gel, then we assume that the AP5 region is probably present, and this DNA will then be cleaned and sent off to be sequenced. This sequence is what is then used to estimate evolutionary relationships between species by looking at how the sequences vary from each other.

AP5 Network

Figure 1: Genotype network representative of the AP5 sequences collected. The segments in between each oval represent a different mutation. The black ovals represent the results from primers used initially, and the red ovals represent the results from primers designed in our own labs. Although the red samples are related in a pattern congruent with mitochondrial hypotheses, they differ by only a small number of mutations in AP5.

Sequences from the AP5 gene have been both easier to obtain and easier to interpret and edit after the change in primers.  The resulting sequences from our new primers resulted in a preliminary phylogeny that was compatible with phylogenies based on mitochondrial DNA. However, the AP5 gene did not help create a more resolved phylogeny due to the lack of variability in the AP5 marker compared to the mitochondrial markers and other nuclear markers like RAG1.  Since our project began, we have learned of more promising nuclear markers that we will focus on in the future.

Other than the lack of variability of the AP5 gene, there are other potential causes of the lack of success with AP5 such as: human error in running the PCR or gel electrophoresis, the primers, or the temperature of the PCR amplification. As my time as a researcher on the AP5 team progressed, the amount of successful AP5 PCRs detected by electrophoresis increased gradually. This lends me to believe that human error caused by inexperience may have played a small role in difficulty of obtaining results. My skills in conducting PCR and gel electrophoresis improved as a result of this research, but more importantly I gained experience in applying knowledge learned in class to the real world. As a recent transfer to ACU, being a part of ACU biology research was an incredible way to feel included at a new university. There is a sense of community within research at ACU where students help each other learn and grow in a comfortable environment, which is a unique aspect not found at every institution. Towards the end of the semester, we participated in the ACU Undergraduate Research Festival with a poster presentation. As part of this presentation ACU professors circled the room asking questions of the presenters in order to test their knowledge of the research. This was my first experience at a research conference, and, being new to research, I was extremely fearful. Although initially this was a difficult experience for me, by the end I was grateful that I was a part of it. Hearing the more experienced members of our team answer questions gave me a far better understanding of our research, and I will be able to use this experience in the future.


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Phylogenetic Analyses of Species in Thomasomys (Rodentia: Cricetidae)

Picture for Blog Entry

My research experience with the biology department has certainly been a memorable part of my time here at ACU. Starting in January, I jumped in on a project of Dr. Lee’s, a portion of which he delegated to Dr. Brokaw – the continuous updating of an exhaustive taxonomic tree of a rodent genus living in Ecuador named Thomasomys. This genus of mammals living in Andes Mountains has undergone rapid adaptive radiation, occupying a variety of niches, differing in climate and elevation. Dr. Lee and Dr. Brokaw are attempting to piece together the evolutionary relationships among species within this genus.

Here are pictures of our phylogenetic trees from two different genes, cytochrome b and CO1 (both mitochondrial).

Published Image

This image includes DNA we sequenced in the spring of 2015 and was featured in a publication by Dr. Lee and Rachel Ritchie. Before getting included in publications, any DNA we sequence is submitted to GenBank and becomes accessible to researchers worldwide.

CO1 ML Tree With Bootstrap Values 27-Nov-15

This image is a phylogeny based on our latest sequencing of the CO1 gene.

These are our results after the meticulous processes of running PCRs, gel electrophoresis, DNA purification, DNA quantification by NanoDrop, and sequence editing and alignment. During my participation in this project, we added two new species to our trees, T. ucucha and T. rhoadsi, found out that T. cinnameus may actually consist of two different species, and elucidated the confusing geographic distributions of the closely related sister species, T. baeops and T. taczanowskii.

Although the principal goal of the project isn’t entirely fascinating to me nor directly relevant to my future career, the experience I’ve gained working in the lab is something that I can take with me for the rest of my life. Extracting DNA, using a thermal cycler during the PCR process, running an electrophoresis gel, purifying DNA, and editing sequences have all been extremely useful techniques that I’ve learned. It’s also been fun getting to work with fellow classmates, and I learned a lot from other students like Tina Johnson, who was Dr. Brokaw’s lab mentor in the spring. Also, presenting at the ACU Research Festival was a fantastic experience, even though it was a little nerve-wracking.

One of the difficulties that I initially came across was the fact that I had no idea what was going on scientifically when I first started. I didn’t even know what “PCR” stood for until the day before presenting at the festival [The polymerase chain reaction is used to replicate DNA]. Creating a “master mix” for the PCR and loading the gel are meticulous processes that require complete focus, and I made silly errors at first because I wasn’t careful enough. This semester, my group had to repeat two steps, PCR and gel electrophoresis, multiple times, and it felt a little rote at times. We made a lot more progress in the spring semester, probably because the goal of presenting at the ACU Research Festival was more imminent. I also learned that research doesn’t turn out the way you plan it a lot of times – things go wrong more often than expected, like the way our PCR’s have turned out this semester.

Doing research while taking classes such as Cell Biology, Biostatistics, and General Biology II is a great way to apply what you’ve learned in a hands-on way. It’s also a great way to get to know the professor that you’re working for and to have the opportunity to ask him or her questions outside of the classroom. I believe that doing research for the biology department at ACU is an experience you don’t want to miss.

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Reflections on 2013/2014

It’s hard to believe the school year has finally come to an end—and even harder to believe that I began working on my summer research project about a year ago (oh, how the time flies). At the beginning of the summer, we were designing primers, and now we’re in the process of identifying specimens using SNP haplotyping. While we haven’t made as much progress as we initially envisioned (due to technical difficulties, among other things), we still identified quite a few and have made quite a dent in this continuing project (which we look forward to working on more). If nothing else, analysis of our soil collections suggested edaphic specialization in Mentzelia monoensis, which was a really exciting result to share with the world.

This semester I was not able to spend as much time in the lab, but I did present a 15-minute oral presentation at 3 different conferences. In January, we (Dr. Brokaw, Christian Hofsommer, and I) presented our work in Austin at the conference for the Society for Integrative and Comparative Biology. It was scary presenting my work in front of an audience—but it helped me to realize that I am fully capable of presenting information to a scientific community. In March, I  (in addition to several other biology and English students) presented at Alpha Chi’s National Conference in St. Louis—which was quite different from the Evolution and the SICB conferences. This conference focused primarily on undergraduate research and had presentations in over 26 different categories! So, it was really a unique experience to be exposed to so many different disciplines. I shared my work to an audience (that included my wonderful friends!) during the Organismal and Ecological Biology section. Elisa Wyrick (who researches British Literature) and I won best presentations in our categories—which came as quite a surprise! Finally, I presented my work for the last time at the ACU Undergraduate Research Festival at the beginning of April. By the end, it felt like I had come a full circle–presenting my research to my teachers and peers. Additionally, we (Dr. Brokaw, Christian Hofsommer, and I) are working on a publication, so stay tuned for more on that!
Ultimately, I feel I learned quite a lot during this past year. Slowly (but surely), I’m morphing into a scientist: I’ve learned to think more critically, ask more questions, and take more risks. And, as I’ve mentioned before, I’ve learning that failure is part of the process. Things don’t always turn out the way we’d like them to—not to mention everyone messes up from time to time. I definitely didn’t envision the primers or the specimen from different herbaria to give us difficulties, but unfortunately they did, and we had to troubleshoot around them. Despite these challenges, I’ve developed more independence and confidence in my research abilities as well as myself. I never could have imagined I would be able to explain my ideas to a room full of people—yet here I am on the other side.

A year later and I have presented at 3 national conferences, conducted field work, experimented with new methodology (primer design, allele-specific PCR, etc.), and won an award for my presentation (this one I still can’t believe)—not to mention I made many new friends! It’s difficult to articulate really just how much I have benefitted from this entire process, and I am so grateful for the opportunities research has given me (and many others) during my time at ACU. Unfortunately, this summer I will not be continuing my M. monoensis work, but instead I will be researching molecular and cell biology at Pepperdine! It’s a bit intimidating to be moving into a new lab with new people, ideas, and methodology—but ultimately, I know my experiences at ACU have well prepared me for this new adventure. Also, during the fall I will be working as a research tutor—which I honestly couldn’t be more excited about. It will be truly awesome to teach other students about research and share my passion with them.

All of the ACU Alpha Chi members attending the conference in St. Louis!
All of the ACU Alpha Chi leadership attending the conference in St. Louis!
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