Rodent Phylogeny Research

Hello fellow biology enthusiast, my name is Michael Maeker and this blog post is the first blog entry on the Phylogeny of Thomasomys research project. The goal of this research is to determine the structure of a phylogeny for a variety of of rodent species found by Dr. Thomas Lee and his research teams on the eastern slope of the Andes mountains in Ecuador. By using DNA from the liver tissue of the collected rodent samples we hope to conduct a phylogenetic analysis of the genus Thomasomys. The region of the Andes where the samples were collected have a wide variety of species. Studying the genetics of these species may provide insight into the history of the rodents in this area. The finding that prompted this research was a cytochrome-b sequence analysis which suggested a specimen identified as T. baeops was not most similar to previously studied T. baeops specimens. These results suggest the T. baeops may not be monophyletic.

Neighbor-joining tree of Thomasomys species based on cytochrome-b gene sequences.

See image in original publication here.

This summer I picked up work on this project with Dr. Josh Brokaw. The summer research was focused of running a series of PCR (polymerase chain reaction) experiments on a set of DNA samples from the rodents. The immediate goal is to get a PCR profile and primer set that will amplify the cytochrome-b from the mitochondrial DNA of all of our samples.  After we achieve a well amplified product, we will get it sequenced and begin the phylogenetic study.

We recently received more samples collected by Dr. Lee and Grayson Allred this summer from the western slope of the Andes. These samples will be included in the phylogeny research. I will be posting more information and findings as I go.

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Biology Students Conduct Groundbreaking Summer Research

See this latest story about our research program here.

Grayson Allred in Ecuador, Summer 2012

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Prairie Research: Background Information

I thought I would give some background information on the research Emily and I are working on. Today’s post will be the background, and my next post will explain the methods we are using in our research, hopefully breaking this into two parts will keep it from becoming too lengthy.

The Tall Grass Prairie Preserve is owned and ran by the Nature Conservancy and has over 100 oil producing wells scattered throughout the preserve. In January of 1999 a pipeline carrying oil broke and spilled about 70 barrels of crude oil over an area roughly 900 square meters down a slope from the pipeline. The area effected was contaminated with an average of 35,000 mg/kg of total petroleum hydrocarbons.

Bioremediation efforts began on the site in May of 1999 and were performed every three months until October of 2001.  The entire area had prairie hay applied and was then tilled. The research area was then divided into three sections, the top of the slope closest to the pipeline break was left unfertilized while a second area further down the slope was fertilized and a third area nearby (tilled but not effected by the spill) was set aside as a control.

This picture shows an aerial view of the unfertilized (SN1 & SN2) and fertilized (SF1 & SF2) spill areas (red) and the tilled control (TC1 and TC2; green) area containing the six quadrats (white squares) sampled for vegetation.

In 2010, after several  years of undisturbed revegitation, observations suggested that plant growth and community composition of the spill zone are still substantially different from the surrounding prairie. This observation led to the hypothesis that the plant species composition differences are associated with hydrocarbons that are persisting in the soil after the bioremediation process.

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Our Students Were on TV

Watch Here on KTAB (16 August 2012)

News Webpage

Dr. Xu watches Tori Moore prepare a gel.

Dr. Xu and Zack Morgan

For more from Dr. Xu also see KRBC 16 August 2012 (webpage) and KTAB 17 August 2012 (webpage).

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At the Nature Conservancy’s Tallgrass Prairie Preserve

This summer Dr. Brokaw and I took a trip to the Nature Conservancy’s Tall Grass Prairie Preserve to collect new data for our bioremediation research.  I enjoyed getting the experience in field research.

Samantha prepares to record vegetation data from a 10 meter square plot.

The first few days were spent collecting information on plant populations at the oil spill sites and control sites.   I learned that the fastest way to learn a plant’s name is to have to see it and say it multiple times a day. In Plant Systematics we learned how to tell similar plants apart, but the field experience I gained on this trip really cemented some of the terms and subtle differences that can be used to distinguish two very similar species from each other.

We then collected soil samples from the research sites and from several other sites across the prairie.  The tools we were using to collect the samples were more efficient than what was used last year and the soil collection did not take as long as anticipated.  The best part of soil collecting was getting to roam all over the prairie while looking for our gps points.

Before heading home we went through Stillwater and met with Dr. Mike Palmer at Oklahoma State University. Dr Palmer worked on this same project with Dr. Brokaw during his masters work. We also sat in on an informal meeting and got to hear about the research that others in the department are working on.

My next task is to complete the data entry of what plants were found so that this year’s data can be compared to last year’s.

Pink flags designating the corners of vegetation plots at the site of a 1999 oil spill at the Nature Conservancy's Tallgrass Prairie Preserve.

Here are some of the technical details of our methods:

To test the hypothesis that the plant species composition differences we observed were associated with persisting hydrocarbons in the soil after the bioremediation process, plant species cover was quantified and soil samples were collected from 2010-2012 from the spill zone and the adjacent tilled control plot.

Plant species cover was quantified in June of 2011 and 2012 from four 10 × 10 m quadrats in the spill zone and two 10 × 10 m quadrats in the tilled control.  Plant species cover was recorded at five spatial scales: 0.01, 0.1, 1.0, 10, and 100 m2 in each of the four corners of each 100 m2 square quadrat, and species were assigned to a percent cover class at the 100 m2 level. For use as a replicated control, 38 plots were selected randomly from a total of 151 that were located at the intersections of the 1 km x 1 km UTM grid in the TGPP, and plant species cover was recorded using the same methods as in the spill plots. We compared the species composition in the spill plots to the 38 plots on the preserve using Detrended Correspondence Analysis.

Ten soil samples were taken from the six quadrats in 2010, and soil samples were taken from each corner of each quadrat in 2011 and 2012.   Each sample was composed of five composited soil cores. The soil samples were analyzed by Continental Analytical Services Inc. in 2010 for total semivolatile petroleum hydrocarbons so that we could compare hydrocarbon levels to the corresponding plant data for each site.  We are now working on analyzing the 2011 and 2012 soils in collaboration with Dr. Kim Pamplin from the ACU Department of Chemistry and Biochemistry.

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July Reflection of Microbiology Research

Wow!  The month of July has been full of learning experiences.  The first day I started my research, I was extremely nervous.  I did not know what to expect, and I definitely did not want to mess up anything that was going on.  Now, as I look back, I had nothing to worry about because research is all about making mistakes and learning from them.

Kristin Goodwin examines DNA in a gel with a UV transilluminator.

I have learned to go with the flow because the research protocols hardly ever stay true to form or go as expected.  As long as a detailed research notebook is kept, so that awareness of the changes made is known, trial and error teaches valuable skills.  Thankfully, I overcame my initial pipetting issue and transitioned into the repetition of confidently performing PCR after PCR.  I was extremely slow at forming the master mix for the PCR protocol my first week, but now, I am much faster, while continuing my efficiency.  I have been able to amplify the tapY1 gene sequence several times now, but the gel extraction protocol continues to be a thorn in my side.  I have learned not to become frustrated, but to look at the situation optimistically.  Dr. Huddleston has been wonderful in encouraging me and patiently teaching me the skills I need to know to be effective in research.  I am an extremely organized person and pay precise attention to details.  My notes, over the protocols I have completed, are helpful in remembering what worked and what failed.  Not only is research full of performing procedures, but also, research demands the responsibility of cleaning up after oneself and learning how to run the autoclave to sterilize equipment that the whole research lab uses.  I have had to learn how to make different solutions that are used in the laboratory equipment, so that when supplies are running low, I can make more to keep the research running efficiently.  I have been challenged lately with performing the work of three people.  I enjoy working with my research team and miss them thoroughly when they are gone.  It is helpful to have someone to collaborate with on ideas and ask for advice when stuck on a procedure.  Knowing my teammates trust me enough to perform their work while they are away has been very encouraging.  I am excited to see what the future holds and how the research I am conducting will advance.  I will continue to work my hardest by learning from my mistakes, paying attention to all the steps needing to be performed, and collaborating with my teammates to find solutions to problems.

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Blog Launch

This blog was inspired by a provocative open science blog by Rosie Redfield called RRResearch.  While gaining fame during the recent debate over arsenic-based DNA (listen), RRResearch also introduced blogging as a new component of the scientific method.  Unlike a typical peer-reviewed journal publication, a blog can more fully describe the entire scientific process.  For example, many non-scientists don’t realize that scientists spend a lot of their time just trying to figure out why their experiments don’t work.  Clearly the humble blog is not intended to supplant our established peer-review process.  However, science is only as strong as our methods to exchange information, and the blog may be the next great advancement in the equitable exchange of information.

While scientific colleagues may turn to this blog to learn about biology research at ACU, we hope that many of our readers will be young students considering a career in science.  Our undergraduate research program is designed to train the next generation of researchers using real research experiences.  So if you are considering a future in science, take a look at some of the experiences our students are having and picture yourself having them too.

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