Mentzelia and DNA

Posted on January 31, 2014 by Christian Hofsommer

During the last year, I’ve been doing research with Dr. Brokaw on the genetics of species in the genus Mentzelia. This research involves sequencing the DNA of these plants and looking for similarities and differences between multiple species in this genus in order to see if the regions we’re using are a definitive indicator of a difference between the species. In addition, we’re using it to compare a few species in particular, with a special focus on Mentzelia monoensis. This species, thus far, has only been found in one region in Mono county, California. Because the traditional means of differentiating it from other species, it’s seeds, is not always feasible depending on the season and the presence of seeds in a particular sample, it’s important to be able to identify it through alternative means. To this end, we are comparing the chloroplast DNA in Mentzelia monoensis to species that are difficult to differentiate by sight alone.

christian
My time in the lab has primarily been dedicated to the extraction of the DNA and interpreting the results of this DNA. The first step in the process is the collecting of a sample from a pressed plant, and grinding the plant matter so that the plant cell proteins don’t interfere with the DNA extraction process. This is probably the most tedious step in the process, especially when working with many samples at once. Often the pressed samples are difficult to get any leaves from, and moving the leaves takes some precision. The grinding itself can be pretty tiring on the fingers, as the leaf samples are rather small and therefore necessitate using a very small pestle to grind them, which can strain one’s fingers after a while. Even though this step can be boring, it’s also very interesting. The samples we use often are from very different geographic regions, given to us by herbariums across the area that we’re studying. In addition, the samples are very frequently older than myself; of the oldest samples we discovered was over 100 years old!

The rest of the process often goes much smoother, with enough to do to remain interesting. After extracting the DNA by grinding it, we have to purify the DNA and then amplify it through a polymerase chain reaction that essentially copies the DNA several times. We then send the DNA off to a lab for them to sequence, and we receive the results, correct any errors, and compare them to previous samples. The entire process has been fairly exciting. It’s been great to see our results accumulating over the last six months and supporting our hypotheses about the plants we’re studying. I’ve learned quite a bit about the research process, especially how to avoid mistakes (it can be rather difficult to figure out what a sample is when you rub half the label off!), and I’ve gotten a lot of valuable lab experience working with machines and processes that I might encounter later in my life. While we haven’t been able to get many results recently because we haven’t quite mastered our new extraction process, I’m looking forward to continuing to proceed and eventually get more done. Our results have thus far been interesting, and I’m excited to see where they go in the future.

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Biology prof discovers new animal species

Posted on October 10, 2013 by Amber

As originally posted in “ACU News” on October 08, 2013:

While leading a student expedition in Ecuador’s Sangay National Park in 2010 Dr. Tom Lee, professor of biology, discovered a new species of opossum. Lee, along with one ACU student and one Ecuadorian student, were the first people to ever see the species.

The shrew opossum is making its scientific debut next month. It will be listed in the Oct. 2013 issue of the Journal of Mammalogy.

“It’s exciting to go to Ecuador to see new things that people have never seen before,” says Lee. “Ecuador is one of the most diverse places in the world, and taking students there is very rewarding.”

Lee’s Ecuador discoveries can often be found in ACU classrooms. In Lee’s ecology, animal biology and mammalogy science classes, students see pictures from his expeditions, if not the actual specimen itself.

Four specimens of the rat possum belong to ACU and are used for undergraduate research.

On another Ecuador trip, Lee had photographed an unknown mammal. One year later, the animal is now recently classified as the olinguito.

Every other summer, Lee takes students to examine Ecuador’s ecosystems. The Ecuador project started in 2000 when Lee went to Ecuador with a friend who was carrying out separate research in the Galapagos Islands. The excitement of undiscovered species in the area pulled Lee to keep coming back, inviting students to learn alongside him.

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A genetically expressible summer!

Posted on October 1, 2013 by Lydia Brown

This summer Dr. Hunter gave me the opportunity to join her Marine Biology research team. While Dr. Hunter is a part of a larger team in the process of assembling the tree of life for echinoderms as a whole, her research is primarily focused on determining the phylogenetic tree for Ophiuroidea (brittle stars).

I had no prior experience with research, so I had no idea what I was getting myself into when I walked into the Biology A-Lab on June 1st.  That first day, Dr. Hunter discussed what the goals for the summer were. She primarily wanted to finish getting the DNA sequences for all the specimens we had. Specifically, there were three genes that we were trying to isolate from each brittle star specimen. She had almost all of the ribosomal sequences, but she was still missing many of the mitochondrial COI gene sequences.  Initially, this task seemed very simple; however, I was very mistaken.

For the first 5 or 6 days, Dr. Hunter walked me through the different lab procedures such as PCR (polymerase chain reaction) and gel electrophoresis. She planned to teach me how to do DNA purification and DNA extraction as well, but Ethan (Dr. Hunter’s son) made his appearance a few days early. After Dr. Hunter went into labor, I attempted to isolate the mitochondrial gene in several species on my own. Amidst many failed attempts, I was able to isolate the COI gene for one species. While Dr. Hunter was gone, I did learn a lot of procedures from other researchers like Dr. Brokaw (he researches plants) and his student researcher, Tina Johnson. However, I was very excited when Dr. Hunter came back.

As the summer continued I felt like I was not making much progress with the COI gene. I tried a variety of modifications in an attempt to isolate COI, but nothing was working. About three weeks before the end of the summer, Dr. Hunter decided to set the COI gene aside and instead focus on the ribosomal genes, 16S and 18S. After this decision, my new mission was to help Jessica Bryan and Bailey Gaspard, two other members of the team, finish sequencing the 16S and 18S DNA genes for all the species we had left.  During the last two weeks I spent over 90 hours in the lab doing combinations of PCRs, gels, and purifications. By the end of those two weeks, Jessica, Bailey, and I had just about isolated and purified the DNA for all the species we had obtained. All that remained was the sequencing.

Lydia-Brown

Last summer was definitely an amazing experience. I loved going to lab each day and challenging myself with each new adventure the lab held for me. I am also incredibly thankful for the friendships I made this summer! Though I learned a lot through researching, the most significant lesson I learned is that sometimes you have to sort through a lot of failed attempts to find what you are looking for.

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Students spend the summer researching

Posted on September 5, 2013 by Amber

As originally posted in “The Optimist” on September 5, 2013:

By Maggie Marshall
Posted on September 5, 2013

Over 50 students from at least 12 departments conducted research across the country this summer.

Research was supported in part by grants and conducted from New York to California, covering subjects such as wildlife on the Dyess Air Force Base, the effect of having too much choice and the role of technology in higher education.

Undergraduate research projects are overseen by a faculty member and are thus often related to the interests of that professor.

Tanner

“I worked with Dr. Joshua Brokaw,” said Tanner Hamilton, junior biology major from Fort Worth. “Prior to the project, I had him as a professor freshman year but didn’t know him on a personal level. Now I do and can talk to him comfortably one-on-one, first name basis.”

Dr. Jennifer Shewmaker, associate professor of psychology worked with Caitlyn Spain, junior marketing major from Denton, over the summer and is continuing research into this semester.

“We’re looking at children’s responses to gendered product packaging,” Shewmaker said. “We’re studying something called stereotype threat… the idea that we all have parts of our identity that we’re aware that other people are going to make judgments about us because of.”

This kind of hands-on research is a special experience, said Shewmaker.

“From the very beginning, she’s a part of what I’m doing and that is so rare, to get to do that.”

Much of the undergraduate research is done during the summer, but it often continues into the school year.

“We’re still working on ours,” Shewmaker said.

Students often benefit from having a faculty mentor. The wisdom and knowledge that is shared between professor and student is one rarely seen during the regular school year.

“He has been very helpful and willing to teach and instruct me,” Hamilton said.

Research reinforces classroom knowledge and ultimately leads to a better understanding of the topic.

“This is super hands-on for her,” Shewmaker said, “so she’s gaining so many valuable experiences.”

These hands-on experiences differ quite a bit from a typical lecture-based class.

“My project is a biology major specific one, specifically genetic variance in a specific genera of South American rodent,” said Hamilton. “There is no classroom involved. It’s strictly a laboratory setting with a few hours a week of active work in the lab performing experiments and interpreting data… it really helps in the application of concepts and classroom knowledge.”

From beginning to end, students are involved in these research projects. They help choose what to research, gather data, conduct tests and see every aspect of the project through to the end.

“I think it’s a huge opportunity because, for example, Caitlyn, she’s involved in every aspect, every phase of my research,” said Shewmaker.

Hamilton said undergraduate research made him commit to learning about the subject he was researching.

“It is also preparing me for next level after college because you have to hold yourself accountable. I would suggest it to anyone with any interest just to see what it’s like and to help with the comprehension of material.”

Experiences like that of Hamilton and Spain are not often found at other universities.

“It sets our graduates apart because a lot of students who go to larger universities aren’t going to get hands-on, one-on-one mentoring with a faculty member,” Shewmaker said. “It’s something at ACU that’s really special.”

Such extensive research cannot remain a secret, however. Every year, students who participated in research get to show off their hard work at the Undergraduate Research Festival.

The festival is held to celebrate and recognize the students who participated in research that year. Applicants must be current undergraduates or recent graduates from a local college. Presentations can be in the form of a paper or a poster presentation and students must fill out an application and meet certain standards to be accepted.

“I’ve been a part of the Undergraduate Research Festival since we started it,” said Shewmaker, “and it has just grown and it’s really, really fun.”

The next Undergraduate Research Festival is scheduled for April 1, 2014 and will feature students who conducted research April 2013 – April 2014.

Students interested in ACU Undergraduate Research can visit blogs.acu.edu/undergradresearch/ and click on Get Involved!

The festival brings people together from all disciples across the university from the sciences to literature.

“That’s what being a university is all about,” Shewmaker said. “It’s about learning and growing together.”

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SNP Haplotyping

Posted on August 3, 2013 by Tina Johnson

For the majority of the summer (save for my two week adventure), I have been continuing my research with M. monoensis in the lab. Much of our prior research focused on identifying a DNA barcode, a region that can be utilized to identify an unknown specimen. So recently, we established the ndhF-rpl32 region as a DNA barcode to differentiate between M. monoensis and its relatives: a SNP (single-nucleotide polymorphism) exists within the region. Mentzelia monoensis has the “G” allele and others (such as M. montana and M. albicaulis) have the “T” allele.

With the barcode, then, identification becomes less difficult–you just need to examine the specimen’s sequenced DNA. Sequencing, however, is expensive. Often, we pay upwards of $6 for each sample’s sequence. Individually, this figure seems insignificant (I mean we pay $50 for our gel combs, right?). But given 100 or so samples, that $6 easily becomes $600. This can hamper small labs with limited funds and, in turn, our efforts to establish the true distribution of M. monoensis. Thus, using our understanding of the SNP, we decided to investigate more cost-effective methods of identification. We found one method, known as SNP haplotyping, particularly promising. This approach primarily utilizes allele-specific PCR and gel electrophoresis, which are both cost-effective procedures.

In order to begin our work with SNP haplotyping, we first needed to design primers–they would be the key to the project’s success. The process itself requires three primers total: a common reverse primer and two forward allele-specific primers. The common primer didn’t require much alteration; we just made sure it worked well with our sequence. However, the allele-specific primers required a few additions. Specifically, we added destabilizing mismatches within five bases of the 3’ ends, which facilitated primer specificity and, thus, identification.  Additionally, we had to attach 5’ tails to our primers. The lengths of said tails differed by about 10 base pairs, which allowed us to distinguish the different species on a gel. This was definitely one of the more difficult aspects of the project, especially as Dr. Brokaw and I both had limited experience with primer design. We suddenly had to consider GC content (for the Tm), primer dimers (when the primers bind to each other), and hairpin loops (when the DNA folds back on itself) among other things. Though with the help of Dr. Huddleston (she’s awesome!), we were able to design a common primer and 7 (yes, 7) potential primer pairs. Why 7? Well, often (as I now understand) primers tend to be a mixed bag. Sometimes they work and sometimes…not so much.

Once we received our primers, we began testing them using DNA from a few samples of M. montana, M. monoensis, and M. albicaulis. We ran many PCRs and many gels. With those PCRs and gels came many failures and disappointments. We soon discovered that most, if not all, of our primers behaved inconsistently. Some primer pairs didn’t even amplify at all! And don’t even get me started about our negative controls. In fact, until about two weeks ago, we weren’t quite sure if this project would have a “successful” result. But, lo and behold, we found hope in primer pair 3 after testing a few of the primer pairs again. The M. monoensis samples (whose AS primers had shorter tails) traveled noticeably further than the M. albicaulis or M. montana samples. So, what was so special about primer pair 3? Well…we’re not quite sure. But primer pair 3, interestingly enough, was the only pair to have 2 strong mismatches (ie a purine replacing a pyrimidine, etc.). All the other pairs had combinations of weak (ie a pyrimidine replacing a pyrimidine, etc.) and strong mismatches. In the future, it would be interesting to design primer pairs with only strong mismatches–perhaps more of our primers would work? But quite honestly, I am thrilled that primer pair 3 even cooperated at all.

Primer Pair 3
Order (from left to right): 1. M. monoensis 547 , M. monoensis control, 2. M. monoensis 554, M. montana control, 3. M. monoensis 556, M. monoensis control, 4. M. monoensis 557, M. montana control, 5. M. monoensis 558, M. monoensis control, 6. M. monoensis 559, M. montana control, 7. M. monoensis 560 (didn’t amplify), M. monoensis control, negative control (with faint band)

 

Along the way, we made some important discoveries about some of our materials and methods. Early on we made the switch from using TAE buffer to TBE buffer, as some suggested TBE worked well with smaller products (ours are around 200 base pairs) and produces better band resolution. Next, we transitioned to MetaPhor agarose because it can distinguish small PCR products and improve the clarity of the gel. Despite the extra expense, it seems to be working better than the standard agarose (for our purposes at least). Our most important change, by far, was our transition from SYBR-Green to ethidium bromide (SYBR-Green is people!).  Not only that, but now we stain our gels after they’ve run (another change: gels now run in the refrigerator). It is a bit scary handling a carcinogen, but ethidium bromide has facilitated the project. Also, we have been tinkering with the voltage and length of our gels. Initially, we tried smaller (about 40 V) voltages, hoping this would allow us to best distinguish between small distances. However, we now realize that “if the voltage is too low, then the mobility is reduced and band broadening will occur due to diffusion.” So now we’re trying to run our gels at higher voltages (90-120 V) for longer increments of time (3-4 hours). We haven’t quite exactly pinpointed these conditions, but as we continue on with this project we hope to discover the “ideal” setting.

I’m so glad I have been able to continue my research with Dr. Brokaw this summer. I feel like I’m finally getting comfortable around the lab–with the equipment, methods, and the people even. It was nice to be able to focus solely on research, which gave me a more realistic picture of grad school and the research field as a whole. This summer I encountered difficulties and made mistakes, but I also found successes and became more confident in my own abilities. It seems bittersweet to think that my summer work is coming to a close, but I am definitely excited to move forward with this project during the semester (preview of coming attractions: we will use primer pair 3 to identify many samples)!

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A Continued Experience of a Lifetime

Posted on July 17, 2013 by Tina Johnson

Part Two: Fieldwork (With Some Additional Adventures)

 So, back to our adventure! After leaving the Evolution Conference on Tuesday evening, we returned to our campsite to prepare for the proceeding days. Accordingly, the next morning we said goodbye to Snowbird and began our 10-hour journey across Utah and Nevada to Mono County, California (home of M. monoensis).  Nevada was a bit barer than some of our other locales. However, as we progressed further west, we encountered some interesting landmarks—such as the Sierra Nevada. By about 10 or 11 p.m. Wednesday night, we arrived at the Twin Lakes campsite in Mammoth Lakes, California. As you could imagine, it was a bit challenging setting up our tents at night. But luckily for us, Dr. Brokaw and Christian are camping experts; our tents were set up in no time! I cannot say the same of myself (to say the least), but I did manage to provide moral support (in a manner of speaking).

Thursday through Saturday we focused primarily on fieldwork: collecting soil and plant samples throughout the Mono County area. So the next day our fieldwork adventures began!  But first, after eating breakfast, we had to move to another campsite to extend our stay (as we planned to leave on Sunday or Monday). This delayed our fieldwork by a few hours or so, but we still began before noon. So, we took off in our station wagon in search of M. monoensis. Honestly, I wasn’t quite sure what fieldwork would entail. I knew what kinds of environments M. monoensis preferred to live in (disturbed sites with pumice soil), but I wasn’t quite sure how we would differentiate between species or even collect the plants themselves. Furthermore, where we would go looking for them? Luckily, Christian and I were with someone who had a lot experience collecting Mentzelia. As far finding the species was concerned, we used a GPS to return to locations that previously hosted the plants. While this wasn’t a foolproof method (especially as conditions were drier this year), we did manage to collect quite a number of samples this way. Once we arrived at a location, we parked the car and retrieved our supplies—which included brown paper bags (for soil collection), a shovel, a marker, and a plant press. Armed with supplies, we went out in search of our species. Often instead of M. monoensis, we would encounter M. albicaulis or M. congesta. But Dr. Brokaw taught Christian and I ways to better differentiate between the species. M. congesta, for instance, has distinct white bracts. Furthermore, M. monoensis has a subtle coloration difference (particularly in its leaves) compared to other species. Once we identified a plant to collect, we removed it (roots and all) from the soil. Next, we enclosed it in newspaper and preserved it in our plant press. Finally, we collected soil samples for every location. When collecting, we were often met with disappointment and did not encounter any of our plants. However, we still collected soil samples from these locations as samples were previously collected there. I soon came to realize that these disappointments were inherent to fieldwork. We never knew for certain where any specimen might be, for better or worse.

Friday and Saturday continued in a similar vein. We collected more samples—some in secluded destinations and others near crowded highways—and recorded our findings. But we did break from our scheduled routine for some recreational activities. On Friday, for instance, we had dinner at the Whoa Nellie Deli, a famous restaurant (it has its own Wikipedia page, so that tells you something!) located inside a Mobil gas station near Yosemite National Park. Now typically gas stations do not serve gourmet fare (unless you consider Subway “gourmet”), but this restaurant did, in fact, do just that. Dr. Brokaw and Christian took a break from their usual Spam sandwiches and ordered lobster tacquitos (three taquitos served on a bed of Brazilian black beans topped with tomatillo salsa and fresh salad), while I chose a veggie burger (of the Portobello Mushroom variety). While I’m no food critic by any means, the food was truly exceptional and all of us were satisfied. Our adventures for the day weren’t quite finished yet, for later that evening we collected wood and built a campfire—the quintessential camping experience, right? Again, I can’t say my efforts were truly instrumental in the campfire building process, but I digress. Saturday, too, brought with it more adventures. After completing our fieldwork, we decided to try hiking around the area. Again, I wasn’t quite sure what to expect. But let’s just say I liked the idea of hiking more than the actual hiking experience itself. Naturally, I am bit uncoordinated so our journey (particularly downhill) was a bit of challenge for me. But even so, it was really amazing to see the area from a bird’s-eye view; hiking gave me a new appreciation for it even.

hiking

Come Sunday we decided to spend the day in Yosemite National Park. We left at a decent time, so we entered the park about mid-morning—which left us with plenty of time to explore the area. We first stopped by the Visitor Center, which gave us (Christian and me, as Dr. Brokaw had been to Yosemite before) a feel for the park. Leaving the Visitor Center, we were excited to see the amazing natural wonders, such as El Capitan and Half Dome. But—and this is where things get a little interesting—God had other plans in store for us. As we were driving through Yosemite (about 15 minutes after leaving the Visitor Center), our car started to malfunction. I should preface this by mentioning a couple of things. Throughout the trip, we had been charging a few of our accessories through the car: namely, Dr. Brokaw’s laptop and our portable refrigerator. Save for some minor difficulties, this charging system was working pretty well. In hindsight, yes, we probably could have seen it coming, but at the time our issues didn’t seem that serious. But, as evidenced, they were serious. Back to the car troubles: our car surged forward and back cyclically, our power windows stopped working, and our radio/clock completely shut off (among many other things that I don’t quite remember). As we made our way through Yosemite, other drivers were giving us weird looks and drivers behind us were frustrated. Luckily, we found a place to pull over. However, we quickly discovered that the car wouldn’t turn on and that we had to little to no cell phone service. We were stranded in Yosemite.

As we needed our car towed, we realized we were going to have to hitchhike to a payphone. So, we made a sign out of cardboard (“CAR TROUBLE. NEED RIDE.”) and waited for help. Approximately 45 seconds later, a nice couple from Denton, Texas pulled over and assisted us. They drove us 4 miles up the road to the nearest payphone; they were even nice enough to stay with us and wait. After being dropped off back at the car by the friendly Texans, we made the best of our situation and had a makeshift picnic. In all honesty, it wasn’t a bad place to be stranded—we certainly had a nice view. About 2-3 hours later, a tow truck arrived and drove us back to the Goodyear at Mammoth Lakes. Conveniently for us, Mammoth Lakes provided a free bus service; there was even a stop at our campsite! So, we hopped on a bus and headed to an affluent area known as the Village to catch a bus to our campsite. Not so conveniently for us, however, was the fact that the bus to our campsite stopped running after 5 p.m. So, we found ourselves stranded again. Luckily, Dr. Brokaw found us a nice place to stay for the night (the Alpenhof Lodge) and we “camped” in our hotel rooms for the night. Like I said, not a bad place to be stranded.

stranded

After eating a nice complementary breakfast, the next morning we took the bus to the Goodyear. But we were met with more disappointment, as we would have to wait another day for the mechanics to look at our car. But we made the best our situation and headed to the library (our new favorite hangout), continuing to exploit Mammoth Lakes’ free services. After reconnecting with civilization (thank you, Wi-Fi), we headed back to our campsite for the remainder of the day. Come Tuesday, we started to fall into a “routine,” so to speak. We headed on the buses to the Goodyear, followed by the library, and then back to the Goodyear again. Fortunately, the mechanics were able to look at our car. And we happily discovered that our stay in Mammoth Lakes would (if all things went as planned) be coming to a close the next day at noon. Though, as Dr. Brokaw put it, we were cautiously optimistic.

On Wednesday, we packed up most of our supplies and headed back to the now-familiar Goodyear. We waited, finding ways to entertain ourselves until our car was ready to pick up (such as reading magazines intended for private jet owners and whatnot). Thankfully, they were able to fix our car (the alternator was blown, if you were curious) and, by 1 p.m. or so, we drove it back to the campsite to pack up the remainder of our supplies. We were now able to leave Mammoth Lakes, California and head back to Abilene, Texas—it would just take us an additional 21 hours of driving to get there. Luckily, we weren’t too off schedule (we originally planned to return on the 4th), however Christian did have to reschedule his flight. Anyway, we had a long drive ahead of us. Again, we traveled through Nevada; however this time we went through Las Vegas and briefly visited the Hoover Dam (both very cool). I wish I could say I stayed awake throughout the entirety of our drive (like Dr. Brokaw), but alas I failed. Though a couple of hours after I fell asleep we stopped at a rest stop in Arizona for a few hours, which was beneficial for us all. After our stop, we continued our journey through the rest of Arizona, New Mexico, and finally Texas. We ended our journey in Abilene on the evening of the 4th of July.

Again, I would like to offer a few words of reflection before I put this blog post to a close. First, I want to thank Dr. Brokaw for this entire experience; I am so grateful that I was able to grow academically and spiritually as a part of this trip. It is nice to know that Christian and I have an academic mentor to guide us throughout the rest of our time at ACU. Furthermore, I think this experience allowed me to more fully appreciate my teachers—both past and present—which I am glad that I realize early on in my academic life. Additionally, after this experience, I am more aware of how I perceive myself in relation to others, which is another vital personal realization. Finally, I am glad I was able to actually experience fieldwork and interact with the plant I’ve been studying for these past 7 months. In a way, it was cathartic to visit the Mono Lake area—a place that before had only existed in articles and the like. Now, more than ever, I feel connected to what I’m studying in the lab. To reiterate my title, it was an experience of a lifetime.

 

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An Experience of a Lifetime

Posted on July 11, 2013 by Tina Johnson

This summer I decided to continue my M. monoensis research with Dr. Brokaw (Assistant Professor of Biology at ACU), hoping to further develop my research experiences in and outside of the lab. As far as lab experiences are concerned, I have learned so much this summer alone, and I am so grateful for the opportunities afforded to me thus far. But I will expand on those experiences more in another blog post. This blog post, however, will focus on my research experiences outside of the lab: specifically, a two-week research expedition with Christian Hofsommer (a fellow research student) and Dr. Brokaw. The first half of our trip centered on the Evolution Conference in Snowbird, Utah and the latter half focused on fieldwork we conducted in Mono County, California—two widely different, yet vital experiences.  Unbeknownst to me at the time, this journey would shape the very way I perceive myself, others, and ultimately science itself.  But let me back up a bit and set the scene.

 

Part One: The Evolution Conference

Three weeks ago, on the morning of June 20th, 2013 (at 7 a.m. to be precise), I arrived at the parking lot of the Foster Science Building to begin my expedition. Honestly, I wasn’t quite sure what to expect—I’d certainly never been to a scientific conference before (let alone presented at one). Not to mention my camping experiences, or lack thereof, enhanced my apprehension (but more on that later). My anxieties aside, I was looking forward to exploring the field of evolution and actually performing fieldwork (as my experiences thus far had been limited to strictly the lab setting). But back to the expedition: a little after 7 a.m. Christian and Dr. Brokaw arrived and our journey began.

The first day we drove approximately 10 hours to Colorado Springs, staying with my family for the night. The next morning we got off to another early start and headed through the mountains of Colorado to Snowbird. As we traveled, it was amazing to observe an unfamiliar part of the natural world—especially compared to Abilene! On the western edge of Colorado, even, our fieldwork began a little early; we were able to collect some samples of M. thompsonii, a species in the same genus as M. monoensis. After an eventful drive, we arrived at the Snowbird Conference Center in time for the Opening Reception of the Evolution Conference. In a way, it was surreal seeing hundreds of students and professors congregating together for the sake of evolution. Following the reception, we headed to the Steven Jay Gould Award Lecture, which this year was awarded to Judith G. Scotchmoor (behind the website “Understanding Evolution”). Personally, I really enjoyed her presentation, especially her discussion of education and evolution. It also helped me to further realize that science is more than just memorizing facts or taking tests: it’s a process of discovery and exploration (among many other things). Off to a good start, we discussed that night’s lecture and headed back to our hotel.1

The next day we got off to another early start (there were many of these) to attend a series of presentations on macroevolution. These were a little less accessible to Christian and me given our knowledge (or lack thereof), but they were still generally interesting nonetheless. We even got to listen to a presentation by one of Dr. Brokaw’s colleagues from Washington State University. After these, we treaded into more familiar territory with behavior and social evolution presentations; we heard talks ranging from sexual selection on eye color to bold-shy exploratory behavior. Following lunch, we headed to a symposium on the “Tree of Life,” specifically a talk pertaining to microbes by Laura Katz from Smith College. One of the major sticking points was that researchers now suspect that the eukaryotes are just one of the lineages within the Archaea. This could potentially shift us from a three-domain system to a two-domain system! So it was definitely an exciting moment for all of us at the conference. We continued the day listening to more talks from the symposium and returned to microbial biology with a talk from the Society for the Study of Evolution (SSE) President Richard Lenski.

Come Sunday we decided to stick with one symposium for the entire day, which was a very different—yet rewarding—experience. This particular symposium dealt with the study of evolution with other, unconventional fields—such as economics, agriculture, and robotics. One of my personal favorite was a talk on “The History and Evolution of Infectious Disease” by Betty Smocovitis from the University of Florida. I could sense her passion for her field(s); it was truly fascinating learning how infectious diseases shaped other elements of human culture and development. Her talk ignited an excitement and passion within me even! As the day continued, we listened to more talks in the symposium (in between breaks and lunch). We even attended a fairly popular talk by Joan Roughgarden, a population geneticist (who apparently wrote one of Dr. Brokaw’s textbooks), on “Evolution and Human Sexuality.” Needless to say, it was a really interesting presentation. At the end of the symposium there was a discussion panel featuring all of the day’s speakers, which drifted into a discussion of evolution and religion. As a Christian, this was particularly pertinent to me. And after it was all over, I came to further realize that Christians aren’t a monolithic body—there are Christians that (like myself) affirm macroevolution and others that don’t. And that’s just one of thousands of differences. I think it’s important to be reminded of that sometimes. We rounded off the day by attending a talk by the President of the American Society of Naturalists (ASN), which I enjoyed. We also ran into some more of Dr. Brokaw’s friends from grad school—they were awesome to meet and very encouraging! Sunday was definitely one of my favorite days of the conference.

Monday: the second to last day of the conference and also presentation day. Dr. Brokaw had a talk at 10:30 on “The Evolution of Horizontal Gene Transfer in Aeromonas,” while Christian and I had a poster session from 7-9 p.m. So it goes without saying that we all had a very exciting day! Before attending Dr. Brokaw’s presentation, Christian and I listened a few interesting talks about education and evolution. It was definitely beneficial to be exposed to an educator’s take on the matter, especially coming from a student’s perspective. After our “warm up,” Christian and I sat in on Dr. Brokaw’s presentation—which I truly enjoyed. Granted, a lot of the information went over my head (and not just in this presentation) but it was really valuable to listen to a presentation from someone I already knew; it made the process seem more real somehow. Following Dr. Brokaw’s presentation, Christian and I viewed a few other talks (including another by a colleague from Washington State) before heading out for our “recess.” During this time we set up our campsite for the night and explored the area a bit more. Before we knew it, it was time for Christian and I to present our poster. It was scary initially, but once we got into the “swing of things” I genuinely began to enjoy the experience. The people who came to our poster were generally very encouraging and curious about ACU; quite a few even thought we were grad students! All in all, it was a very good experience for me. I realize that as I present more presenting itself will become easier, routine even.23

The final day of the conference came and went in a blur. After our first night of camping, we decided to head into the conference a bit later. Much like Sunday, we spent most of the day at one symposium hosted by the SSE President: “Everything You Wanted to Know About Evolution But Never Thought to Ask.” Again, this symposium featured an array of different topics and speakers, from evolutionary medicine to ancient proteins. While not my favorite set of talks, I did generally enjoy the symposium. We ended the day with a German dinner at the “Super Social,” where we socialized and what not. All in all, it was nice end to a busy five days.

Before I end this post, I’d like to offer a few reflections on the Evolution Conference. First, it was a very humbling experience. I came to realize that there are a lot of things I don’t know and never will. Not to mention there are a lot of people out there who know more than I do—and there’s nothing I can do to change that. But more importantly, I realized that’s okay. I am not expected to know it all or to be the best. I can succeed just being myself, utilizing what I have been given. Second, I realized that I do not want to study evolution—at least at the graduate level. While I enjoyed the conference a lot, I recognized that evolution is not where my primary interest lies. But that’s not to say I’m not interested in graduate school or research. In fact, the evolution conference opened my eyes to the opportunities that these venues can provide professionally, personally, and even spiritually. As I head further into my academic career, I look forward to exploring these options in greater detail. I am so thankful I had the opportunity to attend this conference with Christian and Dr. Brokaw. In my next blog post I will expand on the second week of our adventure: my experiences with fieldwork, camping, and cars.

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Week 1

Posted on June 18, 2013 by Kathryn Davis

Davis PhotoFirst week back in the CS lab!

I actually started back in the lab on May 29th and, go figure, Baby Huddleston decided he was ready to meet his family! Of course, Dr. Huddleston, who was in labor, was worried about running a gel on a vector she made and asked me to do it for her. That lady. I was more than happy to do it for her! It felt so good to be back in the lab! I really missed it in there. It was so nice because nobody else was in the lab so I shut the doors and played my music loud. I started initial PCRs for my SOE PCR that week. I got 2 out of my 3 of my needed gene combo products done!

So, the official first week back in the lab and there’s a lot of new changes! First, meeting at 8 am (really bad since I’d been waking up at 4pm every other day). Second, I had two new lab partners (since Kristin and Zach left me to be adults and go to dental and medical school. Whatever.).  Third, Dr. H was out being a good mom. And fourth,  I was bestowed the honor of showing the new kids the way around the lab. They’re Madeline, my dear friend who lived across the hall from me freshman year, and Jacob, a freshman sophomore who is actually the sweetest. I am so excited to spend the summer with them.

We’re beginning the summer with SOE (splice overlap extension) PCR . I am so excited because we’ve been talking about doing SOE for over a year and we’re finally here! On our agenda this week we needed to do the initial PCR of their products so we can sew (get it??) them together. We’re replacing our genes with a gentamicin cassette to be used for screening. It’s sort of bizarre teaching people how to get around the lab because it’s second nature to me now. They were asking me how to pipette product into the wells in a gel, and I stood there for a minute just going… uhhhhh. I had to watch myself do my technique so I could articulate it to them. Funny how far I’ve come. I was in their shoes a year ago. Poor guys are stuck with me and not Dr. H!

Once we obtained and confirmed our initial products, they were purified to be used for the second step of SOE PCR: the first SOE reaction. This will bind initial products A and B to each other. Both Madeline and I encountered the same problem: we obtained products AB of the correct size, 1kb, but we also had products that were 500bp, which indicated to me that the pieces of DNA were breaking up into their initial products, A and B, or they weren’t binding together at all and the gel was picking up the original amount of template added to the PCR reaction (thanks Dr. Brokaw).

So, the plan was to change the annealing temperatures and extension times to see if we obtained better results for the next week. Until…

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Wrap up – Sort of

Posted on May 19, 2013 by Samantha

Well, this could be my last blog for this project, or not! Although we have worked a lot on pushing to complete our research it was just not feasible to get all of our samples run before graduation, or the end of our Pursuit Grant time frame, so the work continues. So far I think the thing that has helped us the most was being able to have a lab that I could get into any time, if Emily had the same access to the Gas Chromatograph we probably would be done running all of our samples by this time, but I bet Dr. Brokaw doubts that.

Looking back I feel as if we probably could have found our “groove” earlier, but it is what it is….and what it is is this: a chance few undergrad students get. I feel very blessed to have gotten to work on this project. Dr. Brokaw took a chance on me, and later on Emily, letting a couple of Ag girls work on Biology research. Not only were Emily and I lucky to get to work on this project but we were fortunate to get a grant to help us complete the second year of our project. I loved getting a taste of field work in Oklahoma, and my time on this project has helped me to decide that I would like to go on to study ecology either in native plants or in aquatic systems.

Dr. Brokaw has helped Emily and I both grow as students, guiding us through our problems with his ever present “answer a question with a question” style that makes me crazy but also forces me to think- thanks Dr. B…..truly.  We have also learned what it is like to get turned loose and expected to complete lab work in a given time frame, sometimes we met deadlines and sometimes we had to face the music and own up to the fact that we couldn’t get things done in time. Emily and I also got valuable experience presenting our research, which for me proved to be a nerve wracking experience.

So far our work has shown us what we expected to see as far as remaining hydrocarbons in the soil but our plant community composition data has only shown a weak correlation between the amount of remaining hydrocarbons and the plant communities found in those areas. We hope that when we have more samples the correlation will be a bit stronger. More samples- that means finishing the samples we have plus maybe continuing this work in the future, which I would love to see and be kept in the loop on.

I want to say “good luck” to whoever works on our project next, may the chromatograph be with you…I also want to say thanks to Dr. B, again, because who else would have put up with us, and a huge thank you to to the Pursuit Grant folks. Don’t think I forgot you Emily- you rock my socks- or if I’m not wearing socks…you rock my flip flops. I am so glad we get to work together for another month- congrats on graduating- we made it!Samantha & Emily Graduation

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End of the Project

Posted on May 19, 2013 by Kristin Goodwin

Microbiology research is a step-by-step process that continues to build on newly discovered information.  The Huddleston Research Lab was in the beginning stages when I started this past summer.  As a part of the team, Kathryn, Zack, and I picked up where Dr. Huddleston had left off and set up the ACU portion of microbiology research.  Mini goals were set along the way, and several of them were accomplished.  I was able to perform gene sequencing, and determine the gene sequence for the tapY1 gene through Polymerase Chain Reaction and Gel Electrophoresis.  I created primers and successfully amplified Product A, B, and C for use in the Splice Overlap Extension PCR.  When I reached the end of my time in the lab, I was still working on the SOE-PCR, trying to obtain the full sequence of Product ABC.  Summer Research is definitely more manageable and productive than research during the semester.  It is very difficult coordinating schedules and finding the time to run multiple PCR’s and gels.  This was a year of learning to help future researchers collaborate and run experiments on started projects and be able to gauge their time in the research lab.

 

Research has been a wonderful opportunity to deepen my scientific knowledge by performing procedures discussed in the classroom.  This has opened my eyes to understanding more fully the message the textbooks are trying to relay.  I am starting Dental School in July, and research could definitely be a part of my journey there.  By having experience through ACU, I will be even more prepared for this undertaking and have confidence in the skills I have learned to perform the research tasks.  Even if I do not perform research in Dental School, the hand eye coordination I have worked on through pipetting and setting up tiny tubes will be extremely beneficial to my career.  I was surprised at how many times PCRs must be run over and over to obtain the appropriate results.  Also, I became very frustrated with ethidium bromide gels in the end of my research.  An unusual red line decided to interrupt the results I was hoping to obtain.  If only I would have had more time to research this phenomenon, but I left my research in a great spot for the next research assistant to resume.  It was sad turning in my lab notebook, but I feel as though I accomplished quite a bit the past year, and I am excited to see how the tapY1 gene sequence natural transformation research persists in the future.

 

I learned valuable skills through performing research.  I was extremely nervous on my first day in the lab because everything was unfamiliar to me.  After learning the specific techniques and repeating reactions over and over, I slowly built confidence with my ability to execute the research efficiently.  I became very aware that research is full of mistakes, and that it is ok to make them because it is part of the learning experience.  Dr. Huddleston was very patient with me and encouraged me every step of the way!  She was a wonderful mentor, and anyone in the science department at ACU would be lucky to do research with her.  Through experimentation and analyzing the effectiveness of different methods, our research lab deducted the best resources to use for the procedures we were undertaking.  Hopefully, the future researchers will be set with certain protocols and kits to make their research run smoothly.

Kristen Presentation

I had the opportunity to present my research as a poster presentation at ACU’s Undergraduate Research Festival.  I thoroughly enjoyed creating awareness of what the Microbiology lab has been undertaking the past several months.  The effort made this past year established the foundation for research to persist and I am thankful to have been a part of it.

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