BEACON Researchers at Work: Life by the Lake

This week’s BEACON Researchers at Work blog post is by College of Charleston junior Kola George. Kola was an BEACON Undergraduate Research Apprentice (URA) at MSU Kellogg Biological Station in summer 2015, with Jeff Conner as his mentor.

Kola_friendsThis summer, I was fortunate to participate in research under the direction of Dr. Jeff Conner concerning evolutionary trait loss. Along with my research, I had many great experiences all of which contributed to an amazing summer filled with science, new experiences, and new friends. Growing up in a rural area, I was always outside playing in the woods or embracing what nature has to offer. Because of this, I was excited to spend time taking advantage of the breathtaking landscape of the Kellogg Biological Station.

Kola_labFor my research project I tested whether the number of short stamens in the model plant Arabidopsis thaliana, which is a highly-selfing plant, impacts the number of seeds produced. A previous study by Dr. Anne Royer showed that A. thaliana appear to be losing their short stamens and she suggested the short stames had lost most, or all, of their function. To examine this idea, I was able to work with 10 populations from across Europe from Belgium, Germany, France, Czech Republic, Spain, Sweden and Italy. We grew 2 plants from each population and I counted the stamens daily without harming the flowers, and marked each flower individually. After two weeks, I counted all the seeds in the fruits that were produced on each plant. Data from our experiment suggested that short stamen number did not affect seed set, and thus the short stamens do appear to have lost their function!

KBS Gull LakeIn addition to an engaging research project, there were many other things going on at the Biological Station, all of which made this a great summer. I camped on the shores of Lake Michigan, hiked the dunes at Sleeping Bear National Dunes National Lakeshore, and spent an entire day exploring the Field Museum in the city of Chicago. Living at KBS on the shores of Gull Lake the whole summer was also an amazing thing in itself. Throughout the summer I got to get to know a lot of cool people and played hours of soccer, basketball, and volleyball to unwind from a long day in the lab. There were days that I felt homesick, but the constant energy that came from Gull Lake and my friends at KBS made it so I could never have a bad day at KBS! From the many experiences I’ve had at KBS, one of my favorites has to be ending most of my days watching the sunset at the dock on Gull Lake. It never failed that every time I watched the sun set it was more of a sight to see than the time before. This summer has provided me with life-long friends, professional development, a great research experience, appreciation of nature and the desire to know more about the world that surrounds us.


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BEACON Researchers at Work: Murphy’s Law

This week’s BEACON Researchers at Work blog post is by MSU sophomore Krista Nicholson. Krista was an BEACON Undergraduate Research Apprentice (URA) at MSU Kellogg Biological Station in summer 2015, with mentors Susan Magnoli & Dr. Jen Lau.

My partridge peas in the greenhouse stubbornly not blooming.

My partridge peas in the greenhouse stubbornly not blooming.

Murphy’s Law states that what can go wrong will, and there may be no better field of science to apply this to than evolutionary ecology. I started my Undergraduate Research Apprenticeship (URA) at Kellogg Biological Station with the illusion that every experiment would work, and that I would always get satisfying results. I didn’t know any better, every lab I’d ever done in school had turned out pretty much exactly like the directions said they would. I soon found out that natural systems don’t like to follow directions.

My main task as a URA was to help my mentor Susan Magnoli with her experiments this summer. She studies how genetic diversity may be beneficial in prairie restorations, so we worked in a handful of prairies close to KBS. For the first half of the summer we set up plots in two of those prairies, cleared them of debris, planted thousands of partridge pea plants from six source populations, and watered all of them. Then all of our plants were eaten by grasshoppers and voles.

Lauren and Aaron my busy helper bees.

Lauren and Aaron, my busy helper bees.

After the devastating blow dealt to us by the voles and grasshoppers, all we could really do was use the remaining plants in the greenhouse to set up a few smaller experiments. Susan gave me a number of those plants to use in my own pollinator experiment. Time passed, my plants got bigger, and soon it was the last few weeks of my internship. Despite getting big and healthy, most of my plants never blossomed.

By this point I was losing hope of collecting my own data. There didn’t seem to be any flowering partridge peas that I could use! Mark Hammond, the lab tech for the Lau lab, heard of my plight and came to my rescue. He offered the use of some partridge peas in heating rings at the Long-Term Ecological Research site as long as I helped him collect some data he needed. I was elated, finally a chance for me to do my own science! I decided to examine the impact of ants and rhizobia on pollinator visitation in partridge peas grown 3ºC above ambient temperatures. My mentor and I were at the site by 9 am with our comfy lounge chairs and a coffee and set ourselves up to watch the pollinators stream in. Almost none came.

A bumblebee pollinating a partridge pea.

A bumblebee pollinating a partridge pea.

Again I was nearly ready to give up. I had my plants, they were blooming, but I couldn’t force the pollinators to visit! Then one of the people working in the rings earlier in the morning mentioned to my mentor that he saw pollinators around 8 am, and that if we got there earlier we might see more. Susan and I got up bright and early the next morning, I brought an even bigger cup of coffee, and we set up around 7:30 am. Lo and behold, there were dozens of pollinators! We had difficulty even keeping track of all of them. I was ecstatic, and every day for the next week after we had collected a new set of data I would go back to my room and excitedly input it into excel.

Soon the symposium was approaching, and Susan and I (mostly Susan) analyzed the data. A lot of coding in R and some graphs later, I had my results; the manipulated variables had no direct effect on pollinator visitation. The only significance we found was that plants with more flowers attracted more pollinators, and that plants with rhizobia had more flowers. This wasn’t a direct effect, and because of this I was disappointed. How was I supposed to make a poster and present on an experiment without strong results?

It was then I realized something. Real research isn’t perfect. I had been told all summer that most experiments fail, but I didn’t realize that applied to me as well. It would have been more surprising if I had found something significant actually! In fact, my observations and results inspired me to come up with a new experiment that I hope to conduct next summer. It finally hit me that if I wanted to do research and be a good scientist I would have to be okay with frequent failure. All most people see is the final product, the glossy paper published in some eminent journal. But real science is about getting your hands (and everything else) dirty, it’s about getting up early, staying out late, failing, redesigning your experiment and failing again, it’s about overcoming obstacles and finding novel solutions, and most of all it is about never giving up. I also realized then that I wouldn’t have it any other way.

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BEACON Researchers at Work: EDAMAME!

This week’s BEACON Researchers at Work blog post is by MSU faculty member Ashley Shade.

We received overwhelmingly positive feedback from our Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop last year, which was partially supported by BEACON and MSU’s iCER. It was immediately obvious that EDAMAME was addressing an urgent unmet need in the scientific community. The data from our course evaluation (thank you, BEACON, for facilitating our interactions with STEM ED, LLC to evaluate our workshop!) showed that EDAMAME learners had achieved our overarching goals of increased confidence and competence in microbial sequencing data analysis. In short, we seemed to be doing a lot right and having a positive impact on our learners’ abilities to own their microbial sequencing analyses. We were ecstatic.

EDAMAME Group photo credit: Tom Rayner, @tomonlocation

EDAMAME Group photo credit: Tom Rayner, @tomonlocation

This year, we had double the number of applicants from last year, and many of them were so exceptional that distinguishing among them for the purposes of admissions was challenging. We have reached out to recruit a broader applicant pool than last year, and I see the benefits of our efforts reflected in the diversity of backgrounds and academic interests represented among our EDAMAME learners this year. We also had a portion of our applicant pool from governmental organizations like the USGS and EPA, and also from not-for-profit organizations, which reflects a need beyond academia for the flavor of training that we provide. In retrospect, the high level of interest from many different universities, institutions and agencies makes sense: microbes are the functional foundations for all ecosystems, from human bodies to soils to deep-sea vents. Why shouldn’t there be wide interest in learning how to observe and analyze Earth’s ubiquitous but functionally elusive microbial communities?

At EDAMAME, we strive to provide the best learning materials and instruction that we can, and there is always room for improvement! For #edamame2015, we’ve refined our learning objectives (listed at the bottom of this post) and backwards-designed tutorials to meet those objectives. We’ve also spent more time on topics we glossed over last year like starting, using, and transferring files to an Amazon EC2 instance, which we hope will help learners who do not have access to a high performance computing cluster to know how to access the computing resources needed to execute analysis of our ever-larger sequencing datasets. After feedback for “MORE TIME” from last year’s EDAMAME learners, we expanded to 10 days so that we can spend more time with the more complex material. We also scheduled time for independent study with instructors available to give learners the opportunity to analyze their own datasets with our support. We additionally organized our tutorials in a GitHub wiki (with a CC-BY license) so that folks outside of the course can more easily find and use our materials. Help yourself!

TAs: Siobhan, Jackson, Paul, Sang-Hoon, and Jin

TAs: Siobhan, Jackson, Paul, Sang-Hoon, and Jin

And, this year, with almost a full year behind me on the tenure-track at Michigan State University, I also was able to bring with me my own new team of students and post-docs to serve as teaching assistants for the course. They bring contagious enthusiasm, patience, and experience to the course (they took EDAMAME in its inaugural year in 2014, even before joining my team). At every break, we collect “minute cards” (borrowed form Software Carpentry best practices) to receive immediate feedback from learners on what is going well and what needs to be addressed. With this feedback, our learners “spoke” loudly: our TAs were just amazing. I am so lucky to be supported by these stellar young scientists, including: Siobhan Cusack, Dr. Sang-Hoon Lee, and Jackson Sorensen from my group; Paul Wilburn from Elena Litchman’s group at Kellogg Biological Station; Dr. Jinlyung Choi from Adina Howe’s group at Iowa; and Aaron Garoutte from Jim Tiedje’s group at MSU.

We also recruited a celebrity line-up of local microbial ecology geniuses as guest speakers, including MSU’s Jim Tiedje, Matt Scholz, as well as RDP’s Jim Cole and Qiong Wang; KBS’s Sarah Evans and adjunct Ariane Peralta (East Carolina University); University of Michigan’s Vince Young, Vincent Denef, and members of the Schloss research team; Indiana University’s Jay Lennon; and the University of Notre Dame’s Stuart Jones.

Within a week and a half, our learners dive in to an array of computational and bioinformatics topics. We covered navigating the shell, cloud computing, remote sessions for running long jobs, within-sample and comparative diversity, merging paired end MiSeq reads and QIIME and mother for microbial amplicon analysis, shotgun metagenome analysis (assessing quality, digital normalization, assembly, annotation), R for ecological statistics, RDP tools and their new exciting targeted gene assembler Xander, using high performance computing resources, and accessing public databases. During breaks, there was volleyball and campfires and the backdrop of the summery Kellogg Biological Station on Gull Lake.

We were thankful and excited to be awarded transition funds from BEACON’s internal small grants competition to support our workshop this year until we found external funding. We couldn’t have continued the workshop without BEACON’s interim support. And… an announcement! I am pleased to share that the National Institutes of Health have taken an interest in EDAMAME, and we just have been awarded EDAMAME support for an additional three years! So, EDAMAME onward!

Thank you, again, BEACON for supporting EDAMAME!

Ashley Shade @ashley17061

Assistant Professor, Microbiology and Molecular Genetics

Newbie BEACON member – since 2014!

EDAMAME 2015 Learning Goals

  1. Increase computing literacy
  2. Develop proficiency in cloud computing
  3. Analyze microbial amplicon sequences
  4. Analyze microbial shotgun metagenome sequences
  5. Apply ecological statistics to analyze and interpret microbial sequencing data
  6. Access resources provided by public sequence databases


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BEACON Researchers at Work: Bases vs Bytes- Bioinformaticians to the Rescue

This week’s BEACON Researchers at Work blog post is by University of Texas at Austin Research Scientist Dhivya Arasappan.


Bioinformatics is an interdisciplinary field in which computer algorithms and statistical methods are applied to answer biological questions. It is a field that is often talked about as the next biggest thing; it is a field I knew nothing about when I started college. As it happens with many things in life, I never planned on becoming a bioinformatician, but I’m happy that I did. After completing my undergraduate studies in Computer Science, I was underwhelmed by the standard career opportunities that were available to me. I was interested in applying computer algorithms towards a greater goal. This is when I learned about the field of bioinformatics and I chose to to do my graduate work in it. Now after 7 years as a bioinformatician, I can say that the challenges in the field are more interesting and the demand greater than ever. With the advent of next generation sequencing, our ability to generate biological data is rapidly outpacing our ability to store and make sense of it. This has made bioinformatics crucial both in research and industry settings.

rhazyaplant_bob1At the University of Texas at Austin, I work at the Center for Computational Biology and Bioinformatics (CCBB) as part of the bioinformatics consulting group. At its core, what I do as a bioinformatician is parse through large amounts of data to identify patterns that may be biologically meaningful. A large and often most exciting aspect of my job is collaborating with labs to guide experimental design and perform computational analysis of their high throughput data sets. For the last two years, I’ve worked with Dr. Bob Jansen’s lab to sequence, assemble and annotate a medicinally important desert plant known as Rhazya stricta. This plant grows abundantly in arid environments in the Middle East and India and belongs to the Apocynaceae family and Gentianales order. Like others in the Gentianales order, Rhazya is a producer of monoterpenoid indole alkaloids. These compounds are of great interest because several have antibacterial activity and some have found use as anticancer agents. We assembled and annotated the nuclear genome of Rhazya stricta in order to better understand the pathways related to the generation of these compounds. For the de novo assembly of the genome, we generated data from multiple sequencing platforms. Each sequencing platform comes with inherent strengths and weaknesses. Some, like PacBio, produce very long reads which are conducive to whole genome assembly, but are low in yield and high in error. Other platforms, like the Illumina HiSeq, produce a high yield of high quality reads, but the reads are short in length. By using a complementary set of data from multiple platforms, we were able to generate a high quality genome assembly. Bioinformatically, it is a challenge to find a genome assembler that is well equipped to handle data from multiple platforms. These challenges are compounded by the fact that each platform has different error rates and is prone to different types of sequencing errors. We used an iterative assembly method by pipelining multiple assembly, gap filling and scaffolding tools in sequence to generate a high quality draft genome in a reasonable amount of time. By annotating this genome, we’ve been able to elucidate some of the metabolic pathways in the plant.

RHAplant_bob2Along with our collaboration and research efforts, another important facet of the consulting group is training. We provide numerous educational opportunities for researchers from within UT and outside to learn bioinformatics skills. These skills become especially vital when the researchers are bombarded with their own large-scale data sets and need to parse something meaningful out of them. I have had an opportunity to teach and train many graduate students, post-docs and professors in the last 2 years and it has been a very rewarding experience. As part of our Big Data in Biology Summer School program, I teach an Introduction to RNA-Seq course that allows students to get hands-on skills in analyzing RNA-Seq data sets. Apart from this longer course, I also teach 3-hour short courses during the fall and spring semesters on topics related to data analysis. We also strive to develop the bioinformatics community within the University and on that front, I run a monthly meeting of bioinformaticians called byte club. A play on the movie title Fight Club, byte club, offers a place for people doing bioinformatics and people interested in bioinformatics to listen to an interesting talk, communicate with each other and hopefully resolve issues that they may be facing.

classroomAnother exciting avenue for bioinformatics training that is opening up at UT is a new stream as part of the freshman research initiative called ‘Big data in Biology’. The Freshman Research Initiative (FRI) provides first-year students the opportunity to participate in real research with UT faculty and staff. It has been a very successful program for the last 10 years and this spring, FRI is introducing three new technology streams that focus specifically on improving undergraduates’ industry relevant technological skills. I will be the technology educator responsible for the Big Data in Biology stream and I’m very excited about the prospect of designing a curriculum and research projects to impart undergraduates with skills in large-scale data analysis.

As a member of the bioinformatics consulting group, I believe I help enable cutting-edge research, both by collaborating with labs on all aspects of their projects and by educating the community on bioinformatics skills. This is very fulfilling and it makes going to work every day a joy.

For more information about Dhivya’s work, you can contact her at darasappan at mail dot utexas dot edu.

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BEACON Researchers at Work: Pacific Land Snail Evolution

This week’s BEACON Researchers at Work blog post is by University of Idaho postdoc Andrew Kraemer. 

Andrew Kraemer“When was the last time this island was searched for snails?” I asked as I picked my way through the loose cobble of lava rock.

“Over 100 years,” Christine replied. “The last time a malacologist searched Santa Fé was during the California Academy of Sciences Galápagos Expedition of 1905-1906.”

A 100-year gap between censuses is only one of the reasons I find myself looking for Galápagos snails (genus Naesiotus) during my postdoc with Dr. Christine Parent. Islands like Santa Fé, it turns out, are not particularly hospitable to snails. These islands are hot, dry, and often go through rapid shifts in climate. As a result, any snails found may be recent colonists from older, larger islands. Similarly, species found on the young volcanoes of the archipelago are also colonists. By comparing these young colonists to species found on older islands, we hope to learn more about the colonization process.

After a long ascent, we finally climb onto the heap of boulders that constitute one of Santa Fé’s small peaks. While much of the island is hot and dry, clouds passing over sometimes drift low enough to bump up against these peaks. As a result, snails are able to eke out a living in the moist grass clumps that grow at the highest points of the island. On our trip to Santa Fé, we find 4 adults and a handful of juvenile snails of Naesiotus cucullinus. A small and tenuous population, but a live population nonetheless.

Through this research I am lucky to explore corners of Galápagos that few are given access to. As a result, we sometimes rediscover species long presumed extinct (e.g. Naesiotus rabidensis) or even find snails that do not correspond to any species previously described.

Pacific land snailOur research requires us to seek out these snails wherever they live, whether that is on a tiny island, the rim of a volcano, or at a construction site. We use a portable spectrometer to measure shell coloration in the field and collect empty shells to measure shell shape back in the lab. Previous research on these species has indicated that shell size and shape are tightly linked to local environment, and our recent work suggests that bird predators may direct the evolution of shell coloration. As for the colonist species, we are finding phenotypic similarities among species found on young volcanoes and among those found on small, relatively inhospitable islands. This could be due to rapid evolution after colonization or a filtering process that determines which species become successful colonists in the first place. We are currently constructing a new phylogeny of all Galápagos Naesiotus snails, living and extinct, that should indicate which scenario is most likely.

Unfortunately, extinction is all too common in Galápagos and other Pacific islands. In particular, land snails like Naesiotus have been hit hard by many recent threats, including rats, invasive snails, habitat destruction, and even direct collection by humans. A reasonable question, then, is which species are we losing? Furthermore, why those species and not others? Another project I am working on will attempt to answer those questions for two snail groups (Galápagos Naesiotus snails and the tree snails of Hawaii), both of which have endured massive declines over the last 100 years. For this project I will visit several museums around the U.S. that have extensive snail shell collections. Using these collections and the records associated with them I will characterize distribution, shell size, shell shape, and shell coloration for each species. At the same time, my host lab (Parent) and a collaborator in Hawaii (the Holland Lab) will be expanding the phylogenies of each snail group using next generation and ancient DNA sequencing techniques. Together, we will find out if the catastrophic declines within these two major radiations are randomly distributed, or if the declines are funneling away the ecological and morphological diversity these groups are known for. The former result would be disturbing, but the latter result would prove ruinous for the evolutionary heritage of these two groups.

The voyage of the Beagle and Darwin’s theory of natural selection ensured Galápagos would forever be a mecca for biologists, the truly astounding species make it a place worth studying, and the shocking recent declines of some of its fauna adds urgency to this work. My hope is that our research will contribute to the important conservation efforts of other scientists in the Pacific.

For more information about Andy’s work, please see his website or email him at: akraemer at uidaho dot edu.

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