BEACON Researchers at Work: The KBS GK-12 program: Graduate training in science communication through K-12 classroom engagement

This week’s BEACON Researchers at Work blog post is by MSU postdoc Sarah Bodbyl.

It is 6 AM on a Wednesday. Graduate student Di Liang is preparing to head in to the lab to collect data on a set of research plants. He wonders if one set of plants will be showing yellow leaves, a sign of nitrogen depletion, then considers whether or not a student will ask if he can eat the experimental plants again. Wait, what?! Di is not working in a typical MSU research lab–it is a middle school classroom. Di is one of many graduate student fellows that share their research and bring hands-on activities to K-12 classrooms as a part of the W. K. Kellogg Biological Station (KBS) GK-12 program.

GK-12 Fellow Di Liang and students display their hydroponically grown plants. Photo credit: Di Liang

GK-12 Fellow Di Liang and students display their hydroponically grown plants. Photo credit: Di Liang

The Graduate STEM Fellows in K-12 Education (GK-12) Program is a training program for graduate students to develop broad science communication skills and prepare for advanced careers. Specifically, GK-12 fellows learn to place their research in a broader societal and global context, integrate research with teaching, collaborate across disciplines, and more effectively communicate their research to professional, K-12, and public audiences. A unique aspect of the GK-12 program is the partnership with K-12 educators, fostering transformative learning opportunities for students, teachers, and graduate fellows alike. Fellows spend up to 15 hours a week in K-12 classrooms, learning how to effectively convey advanced concepts and their love of science to broad audiences.

The participation and support of the many K-12 educators involved in the GK-12 program stems from a rich history between KBS and local school districts. In 1999, KBS professor Phil Robertson established a partnership with 11 nearby districts as a way to share current KBS research with the community. This collaboration between the teachers, administrators, and students of K-12 classrooms and the graduate students, faculty, and staff of MSU is called the KBS K-12 Partnership for Science Literacy. The partnership continues to grow and there are currently 140 active teachers representing 15 school districts.

Two awards have shaped the GK-12 graduate fellow experience since 2006. The first, Ecological Literacy in the K-12 Classrooms of Rural Michigan, focused on one-to-one graduate student and mentor teacher classroom partnerships. Fellows spent over 5,000 hours in the classroom over the three-year award, testing the KBS GK-12 model and searching for ways to enhance the experience. When applying for a second award, project leaders and partner teachers developed a plan to bring two KBS research strengths, bio-energy and sustainability, directly to the schoolyard. They posed the question, “Can we grow our fuel and have our birds and butterflies, too?” This was the birth of the BioEnergy SusTainability Project plots, or BEST plots. The plots, planted with experimental biofuels, are modeled after large-format experiments established at KBS by the Great Lakes Bioenergy Research Center (GLBRC) and the Long-Term Ecological Research (LTER) program. Since the second award was granted in 2010, 304 research plots have been established at 22 school sites across the K-12 Partnership. GK-12 fellows assist teachers and their students as they use the plots to gain experience with the scientific method: making observations, generating hypotheses, collecting field data, and making claims from evidence.

A BioEnergy SusTainability, or BEST plot, part of the GK-12 schoolyard network. Photo credit: Dani Fegan

A BioEnergy SusTainability, or BEST plot, part of the GK-12 schoolyard network. Photo credit: Dani Fegan

It is a beautiful summer day at KBS and there’s a commotion on the soccer field. Three GK-12 fellows are calling out instructions to a pack of K-12 teachers as they compete to find cryptic green twist-ties lurking in the grass. The fellows have designed this game to illustrate how biological competition for resources can affect population trends; the teachers provide critical feedback. Will the game engage students? How and what will students learn from the exercise? Fellows learn the art of pedagogy by working with experienced teachers, not only in the classroom, but also at professional development workshops held at KBS multiple times per year. Fellows have also found that their mentor teachers help them discover specific aspects of their research that are relevant and inspiring to others–a useful skill for grant-writing and applying for professional careers! 

The GK-12 model of pairing graduate student researchers with K-12 educators is a unique opportunity to create interdisciplinary educational and scientific products.

Together, GK-12 Fellows and teachers have designed over 110 freely available lessons addressing topics in ecology, evolution, and sustainability. These lessons meet the guidelines of the Michigan Core Curriculum, High School Science Content Expectations, and Next Generation Science Standards (NGSS) and are available to the public on the GK-12 website “Lessons” page. Four GK-12 Fellows have published their lessons in peer reviewed teaching journals.

Beyond shared goals of graduate student training, science education, and public outreach, BEACON has direct connections to the GK-12 program. Current BEACON members Elizabeth Schultheis (GK-12 fellow 2010-11 and 2012-13) and Melissa Kjelvik (2008-09; 2010-11) collaborated with their partner teachers to create Data Nuggets: worksheet and graphing activities designed to give students practice interpreting quantitative information and making claims based on evidence. The Data Nugget project is now sponsored by BEACON and the Nuggets are undergoing testing, revision, and implementation in classrooms across the nation.

Greeted by cheers, applause, and fist-pumps, GK-12 Fellow Amanda walks into the classroom to spend another day honing her science communication skills with high school biology students. Feedback on the GK-12 program’s impact on the fellows, teachers, and K-12 students has been overwhelmingly positive. Fellows and their advisors report that fellows are more confident, competent, and comfortable placing their research in broader societal and global contexts, and explaining it effectively to professional peers, college students and non-technical audiences. Teacher partners report enhanced professional development; fellows provide them with a variety of real research experiences that help them understand what science is all about. Teachers explain that their students are given the opportunity to work with practicing scientists who differ from the conventional ‘scientist’ stereotypes. The program has shifted classroom emphasis from teaching to the standardized tests to training students to think more like scientists – being able to make arguments based on evidence, reflect on their thinking process, and integrate knowledge across subjects, predicting outcomes based on things that they know. The graduate students serve as role models by communicating, not only the excitement of engaging in research that addresses national needs, but also the pleasure of learning.

The GK-12 project is currently in its final year. The current set of nine GK-12 Fellows is hard at work in the classrooms, learning to share their research, being relatable role models for students, and inspiring the next generation of STEM students. To continue supporting the K-12 partnership in bringing KBS research to the classrooms, the Graduate School will fund two additional fellowships over the following two years. However, the KBS K-12 partnership is looking for new project and faculty sponsors to continue training MSU students and K-12 teachers in science communication, education, and outreach. If you are interested in joining the partnership, please contact coordinators Sarah Bodbyl (bodbyl@msu.edu) and Kara Haas (karahaas@kbs.msu.edu) and check out the GK-12 website at http://kbsgk12project.kbs.msu.edu/

The 2014-2015 GK-12 fellows, partner teachers, and support staff.

The 2014-2015 GK-12 fellows, partner teachers, and support staff.

Posted in BEACON Researchers at Work | Tagged , , , | Comments Off

BEACON Researchers at Work: A Developing Science Teacher – Research, Theory, and Application

This week’s BEACON Researchers at Work blog post is by MSU undergraduate Lazarius Miller.

LazariusTeaching has been a dream of mine since I was a small child. I am a native of Detroit Michigan as well as a proud alumnus of Detroit Public Schools. I am interested in teaching science in urban school systems, which has a very diverse student population as well as resemble the education system that I came from. My hope is to develop curriculum that is focused on evolutionary science, so that diverse learners have the opportunity to understand more about themselves and the world in which they live, like I have been able to do.

When I was younger, my mom jokingly told me that I had been a monkey previously. She pointed to my tailbone and told me that I use to have a tail and that it fell off one day. I figured my mom was just joking, but it did pique an interest in how could I have been a monkey. When in middle and high school, I was told that evolution was not true and that I should not believe in something like that. I never thought much of evolution in high school, because we did not get a chance to talk about it in my biology class. My interest was piqued again during my freshman year at Michigan State University. The summer after my freshman year was completed, I worked with Dr. Louise Mead in the BEACON Center for the Study of Evolution in Action on a project entitled “Does Religion and Education Background affect Student Perceptions of Evolution.” This project had opened my eyes to teaching and learning that I did not truly understand. The project looked at how religion affected student perceptions of evolution using education background as another measuring factor, influenced a student’s desire to pursue a science career. As an aspiring middle/high school science teacher, this topic was important because the ages 13-17 seem to be very influential ages where individuality and independence start to develop. This age also seems like a time in which students begin to show rebellious behavior towards their guardians, but the beliefs that have been instilled in them have not had a chance to modify completely.

The original sample of students surveyed was invitees of a summer enrichment camp for high school achievers. The group of 29 students was from different grades, hometowns, school locations and types, as well as had taken a difference in science course difficulty. Racial background was not included in the study, but I did read a whitepaper by Dr. Joseph Graves, Dr. Louise Mead, and Dr. Judi Brown Clarke on African Americans in Evolutionary Science. The paper talked about how many people of color, primarily African Americans, are extremely religious, possibly due to the reliance of “God” during slavery, and any deviation from religion would not be received well. 

My original hypothesis was that the students would have a high religiosity and their attitude towards evolution would be negative. That was not the result. The students generally had a more positive attitude toward religion and studying science. I tried to figure out why the results turned out the way they did and then I remembered that these students were invited for their academic performance in science and math in high school, so they were probably more accepting of scientific phenomenon than non-science students. I wanted to test another group of students and compare results, but I also started to get interested in curriculum and if all students were getting equal access to proper scientific instruction and materials. 

The next summer, Summer 2014, I studied and researched at the Kellogg Biological Station in Hickory Corners, MI. There I took an ecology lecture and lab course that was more practical and applied. One of our assignments was to write a blog post about an ecological or biological concept that we found interesting. I immediately thought about my research project the previous summer and decided that I would talk about that. The initial article did not work out because it was focused too much on the social side of the study, but I wanted to find a way to explain evolution to someone who had professed disbelief. I instantly recalled a conversation with my aunt who happens to be a minister in a Baptist church. I used the concept of sin to explain to her how evolution works. I explained that sin would continue to grow and develop until an outside stimulus threatens the survival of sin. Our conversation was a bit longer, but she told me that she understood evolution better than she did before. I decided to write about something that many people would relate to and I chose to talk about the evolution of iPhones. In this article, I created an iPhone phylogeny that detailed some of the major changes in appearance (phenotype) and operating systems (genotype). At the time the newest iPhones out were the iPhone 5c and 5s. I also stated in the article that based on the phylogeny, we would have an iPhone 6c and 6s.

In December 2014, I got the opportunity to go back to my high school to speak with the AP Biology students about evolution, mainly trying to interest them in science. These students in this class were freshmen when I was a senior in high school; so some of them were familiar with me, which probably made the reception a bit easier to see familiar faces. My initial thoughts about this visit was that it was going to be tough because my school is primarily students of color and their ties to their religious beliefs would be strong and some may not entertain the thought of the evolution. As the day got closer to my presentation, I decided to develop a website that the students could access on their phones to take 3 short surveys, as well as a short presentation on evolution. I also provided my blog post on the evolution if iPhones for them to read over, hopefully to open their minds to the process of evolution before I stated talking about dichotomies and relatedness of unfamiliar organism.

As the hour started, I was excited to share my experiences and hope to spark an interest in other future scientists. Before I was introduced, I heard two students talking about me. One young man suggested I was a former student; another disagreed with him. Another girl waived to me and said that she remembered me. I introduced myself and started the presentation. Everything was going well, I had the students take the pre-survey then I explained a couple of results from my research project, and finally I distributed the articles. I had the students read them before the phylogeny presentation. Some students had questions during the presentation that seemed to be thought out and not just disagreement. I observed the students faces across the classroom. Some were engaged, others were disengaged, and I could not tell about the others. The dialogue at the end of the presentation consisted of students expressing that they were conflicted, some were interested, and others were silent.

In reflection of my visit, I realized that if I had a little bit more time with the students I would be able to gage how interested they were as well as I would be able to answer underlying questions about evolution. This visit proved to be very important for me because I was able to use the knowledge I gained working with BEACON and a couple of classroom management skills from my Teacher Education classes at MSU, to talk with a group of high school students about a subject that I had not had an opportunity to learn about in my high school classroom. Education in the present is comprised of so many more components than I realized before and it is essential to meet students where they are and provide them with the skills to reach the next level.

For more information about Lazarius’ work, you can contact him at mill2321 at msu dot edu.

Posted in BEACON Researchers at Work | Tagged , , , | Comments Off

BEACON Researchers at Work: Outreach in the lion’s den – An evolutionary biologist at a creationist conference

This week’s BEACON Researchers at Work blog post is by MSU graduate student Carina Baskett. 

CarinaImagine that you are a construction worker, and one day a group of people set up a tent outside the house you are building. In this tent, people give impassioned lectures about how the fundamental physics of construction are wrong, how there is no evidence that nails actually hold wooden beams together, and how there is a direct connection between houses and Hitler (he lived in a house). How would you feel? What would you do?

This was the dilemma that Michigan State University biologists faced when we learned that a conference about young-Earth creationism was going to be held on campus November 1st last year. 

Personally—and I want to emphasize that this is my opinion, not necessarily representative of the diversity of opinions among the students and faculty at MSU—I felt upset that an anti-science, anti-fact conference would be held in the same building where I watch weekly seminars about ecology and evolutionary biology, on the campus of an institution supposedly devoted to discovering fundamental truths about the world. But the facilities were reserved through a student organization, so there was nothing to be done about blocking the event from taking place.

What to do, then? My fellow grad student Dan Brickley and I were dead set on responding in some way to the Creation Summit. We organized a couple of meetings with other students and faculty to discuss how best to respond. One idea was to ignore it completely, advice that we seriously considered but decided not to follow (see several reasons here). There were some confrontational ideas, such as staging a protest of the existence of the moon to mock the idea that evolution is debatable. But after much discussion over list-servs and other email threads, on Facebook, and in meetings, a few of us decided that the best course of action would be to channel outrage into outreach.

Outreach is a broad goal. Specifically, we aimed to engage in conversations with conference attendees to (1) give scientists a friendly face and to share our passion about science and research, (2) learn about misconceptions about science and evolution, and (3) dispel some of those misconceptions. However, we also wanted to avoid confrontation, which some of us feared would alienate attendees, and avoid direct debate about the evidence for evolution, which would give the impression that evolution is scientifically debatable.

We had grand ideas about educational displays, but there was not enough time to marshal the resources or obtain a university permit to set up a table. So I made a flyer that pictured two evangelical scientists (Francis Collins and Jennifer Wiseman) and text about how many Christians see no conflict between faith and evolution. On the back, there was a list of resources related to compatibility of Christianity and science, and introductory resources about evolution. I don’t know anything about the philosophical or theological arguments for how faith and evolution are compatible, but I thought that conference attendees would be more likely to ponder that message than a message about how they were wrong and we were right about evolution.

After all this planning and anticipation, I was nervous when the day of the conference arrived, but it was a bit underwhelming. There were less than 100 attendees, a third or less under age 30, plus 25 scientists, many who came just to watch and learn what creationists were saying, and others who came to engage (handing out flyers and/or having conversations with attendees). Dan, a campus minister named Brenda Kronemeijer-Heyink, and I handed out about 80 flyers.

I talked with a couple of attendees, including one who seemed to be a conference organizer. Dan and I talked with him for about an hour. I felt that we were able to convey the message that scientists are humans with no hidden anti-religion agenda, a sense of excitement about science and evolution, and to educate (to some small degree) about how science works.

However, it was harder than I’d anticipated to walk the fine line between answering questions about science and getting drawn into an unproductive discussion of creationist talking points. We had brainstormed in advance about how to strategically avoid debates, such as saying, “That’s not my expertise, please see these resources,” but it wasn’t always possible to shut down that line of conversation.

We were successfully able to avoid confrontations (e.g., shouting). There was fear among some MSU scientists that attending the conference would inevitably cause dramatic conflict and lead to bad press, but I think we proved that civil outreach is entirely possible. Maybe in the Internet age we have forgotten that it’s much easier to avoid nastiness in face-to-face conversations than online. Despite the fact that we were there in opposition to the creationist message of the conference, and that we represented the scientific establishment that creationists view as oppressive, people were friendly and gracious.

I learned so much from this experience. I wanted to humanize scientists, but I had not realized that humanization is a two-sided coin. Just like me, creationists are doing their best to understand how this crazy world works and what our place in it is. They have come to radically different conclusions from me, and I do not agree with their methods that ignore reason and evidence, but we both share a concern about the future of our society. Now creationists are not faceless enemies to me, and I hope that the ones I talked with feel the same about scientists.

I also really enjoyed the communal aspect of the experience. It was exciting to talk and brainstorm with so many people about what to do in response to the conference. I was incredibly grateful and humbled to receive the advice and support of people who are much more experienced than me with evolution outreach and education, like Josh Rosenau, Bjørn Østman, Erik Hanschen, Emily Weigel, and Louise Mead.

At the end of the conference, I needed a shower to wash off the nervous sweat, and I have to say that it was a lot of effort for just a few good conversations with attendees. However, I would definitely do it again. There are very few avenues for civilized dialogue between evolutionary biologists and creationists, so we need to take advantage of these opportunities when they arise.

Speaking of which, if a creationist conference is coming to your town (University of Texas at Arlington, it’s coming your way at the end of April!), please get in touch. I’d be happy to share more about my experience.

For more information about Carina’s work, you can contact her at baskettc at msu dot edu.

Posted in BEACON Researchers at Work, Education | Tagged , , , | Comments Off

BEACON Researchers at Work: Evolving ways to switch genes on and off

This week’s BEACON Researchers at Work blog post is by MSU graduate student Kurtulus Kok.

“In considering the Origin of Species, it is quite conceivable that a naturalist…might come to the conclusion that each species…had descended, like varieties, from other species. Nevertheless, such a conclusion, even if well founded, would be unsatisfactory, until it could be shown how the innumerable species inhabiting this world have been modified, so as to acquire that perfection of structure and coadaptation which most justly excites our admiration.” – Charles Darwin, Origin of Species, 1859 

KurtulusAt least since the appearance of Darwin’s seminal work, biologists have speculated on the sources of biological variation, and many current studies have pointed to the importance of variation in gene expression as a foundational principle. Exactly what changes at a molecular level is a topic of lively interest, with important ramifications for human health. My studies of the Hairy protein, a transcriptional repressor from the fruit fly Drosophila, have revealed new concepts on the consequence of “random” events affecting genomic interactions by transcription factors. These insights prompt us to reconsider mechanisms for the evolution of gene regulatory networks (GRNs).

Figure 1. Evolution of cis regulatory interactions through changes in DNA elements. (A) A transcriptional regulator normally regulating gene X may be recruited to an additional target gene Y by acquisition of a new binding site. (B) Interposing a new genetic link by such a modification can reconfigure a gene regulatory network (GRN).

Figure 1. Evolution of cis regulatory interactions through changes in DNA elements. (A) A transcriptional regulator normally regulating gene X may be recruited to an additional target gene Y by acquisition of a new binding site. (B) Interposing a new genetic link by such a modification can reconfigure a gene regulatory network (GRN).

One of the most important processes in biology is regulation of precise temporal and spatial use of genetic information to establish the physiological state of multicellular organisms. Proteins called transcription factors (TFs) bind to the genome and regulate the use of genetic information for embryonic development, cellular differentiation and cell fate in response to endogenous and exogenous signals. In other words, what cells are doing, how tissues work, and how organisms survive are dependent on transcriptional regulation. Therefore, understanding the mechanisms in transcription can inform and teach us about what happens when something goes wrong, which may result in diseases. TFs have to regulate gene expression at the right place at the right time (Figure 1A). In eukaryotes, this task is achieved by networks of very complex and combinatorial interactions between DNA binding proteins, co-regulators, and the matrix of DNA and histone proteins termed chromatin. Transcriptional networks represent an important evolutionary target for the development of morphological innovations. Molecular studies have demonstrated that the acquisition or loss of binding sites on DNA drive significant changes in gene expression that initiate critical evolutionary transitions (Figure 1B). Significantly, although relatively subtle changes have been linked to such important evolutionary innovations, it appears that sometimes gene expression is functionally conserved, even as there are major changes in the structure of transcription control regions. Thus, only some rearrangements of gene control elements alter output enough to meaningfully affect biological processes.

Figure 2. Patterning of the early Drosophila embryo is driven by spatially distinct expression patterns of transcriptional activators and repressors, including Hairy, which is expressed in transverse stripes.

Figure 2. Patterning of the early Drosophila embryo is driven by spatially distinct expression patterns of transcriptional activators and repressors, including Hairy, which is expressed in transverse stripes.

I am using an excellent model system, the fruit fly Drosophila melanogaster, for the study of transcriptional networks. Since it is subject to easy manipulations, a wide range of genetic and molecular approaches have been applied to characterize regulatory interactions for several decades. Understanding the fly regulatory circuitry will help reveal similar phenomena in other animal systems, since they use closely related genes in conserved genetic pathways. In the Drosophila embryo, localized transcriptional repressors provide essential patterning information that establishes the primary anterior-posterior and dorsal-ventral axes of the organism (Figure 2). The Hairy repressor, a founding member of the Hairy/Enhancer of Split (HES) transcription factors, plays essential and conserved roles in animal development, including segmental gene patterning in the early embryo and specification of neuronal differentiation. Disruption of HES signaling is a prominent aspect of leukemia, lung and prostate cancers. Thus, elucidation of molecular mechanisms of Hairy activity could shed light on a number of important gene circuits that are prominently represented in key developmental pathways. I carried out genome-wide analysis of dynamic transformations in gene expression, chromatin modifications and transcriptional machinery to get insight into direct molecular interactions of Hairy on genome systematically.

Figure 3. Chromatin marks for an “active” histone modification are lost in large blocks after expression of the Hairy transcriptional repressor. Only a small fraction of these Hairy-mediated events are associated with transcriptional regulation, however.

Figure 3. Chromatin marks for an “active” histone modification are lost in large blocks after expression of the Hairy transcriptional repressor. Only a small fraction of these Hairy-mediated events are associated with transcriptional regulation, however.

My work revealed that Hairy removes chromatin marks associated with activators in large blocks of chromatin, at hundreds of loci throughout the genome (Figure 3). Hairy may therefore work through a dynamic competition with activators, undoing their positive effects on the chromatin states that would be necessary for RNA polymerase to engage genes to transcribe them. At the genome-wide level, an unexpected aspect of Hairy activity was observed on chromatin that may provide a pervasive and accessible entry point for evolution of novel gene regulatory switches. Metazoan TFs usually interact with thousands of regions in the genome, but only small subsets of these interactions are associated with changes in gene expression. In general, the overall view from other studies is that the majority of the interactions between TFs and genome may be non-functional, and are not important for activity of GRNs. My work demonstrates that Hairy interacts dynamically with many parts of the genome; some genes are impacted but most are not. This finding let us to propose the so-called “shotgun model” for this apparent off-target activity of TFs on chromatin modifications; many pellets are fired, but few are expected to reach the duck flying overhead. Yet the Hairy molecules that don’t “hit the target” still appear to be quite active, biochemically, inducing chromatin modifications that are similar to those seen on transcriptionally controlled loci. Hairy may be relatively nonselective about where it can attract chromatin modifying agents across the genome.

What is the significance of this chromatin modification associated with non-functional binding? For the organism, it is another instance of the extravagance of Nature –all of that chromatin modification for naught! As long as it is not particularly onerous metabolically or genetically, however, it may be the price paid for hitting the duck. “Futile cycling” by Hairy may however provide a unique mechanism for creation of new genetic switch elements; most DNA regulatory modules involve the combined action of transcriptional activators and repressors, thus these off-target sites may provide a path for evolution of novel transcriptional connections through addition of new TF binding sites. Where Hairy is busy acting as if it were shutting down a regulatory circuit by chromatin remodeling, small changes in DNA sequence that draw in existing activators may be sufficient to create a novel genetic switch, and a new connection between nodes in a genetic circuit. Thus modification of core elements of gene expression machinery may be an important answer to the question Darwin raised 150 years ago. How influential this particular mechanism may be will be the focus of future molecular work.

For more information about Kurtulus’ work, you can contact him at kokkurtu at msu dot edu. 

Posted in BEACON Researchers at Work | Tagged , , , , , , | Comments Off

BEACON Researchers at Work: Coach, Put me on the bench! A Novice’s Journey into Old-Fashioned Experimental Evolution

This week’s BEACON Researchers at Work blog is by MSU graduate student Jay Bundy.

Jay “on the bench” performing a transfer during a competition experiment.

Jay “on the bench” performing a transfer during a competition experiment.

As a kid I played a lot of basketball. I loved almost everything about the game. But there was one thing I hated: spending time riding the pine. In sports, nothing interesting happens on the bench. The bench is where players who aren’t very good spend most of the game sitting, like a spectator, watching all the action. If they’re lucky, the coach will put them in for a few minutes when the game is out of hand or a star player really needs to take a quick break.

When I came to BEACON last year, I was a research technician while finishing my master’s degree in Anthropology. Perhaps the most profound decision I made was to start working in the lab of Dr. Richard Lenski on his E. coli long-term experimental evolution (LTEE) project. I had never worked in a microbiology lab before. To be honest, I didn’t really know anything about E. coli other than that they were bacteria. As an anthropologist, I studied the evolutionary basis of mating behavior in contemporary human populations. What was I going to learn from a system of experimental evolution using germs?

After reading some of the early microbial and long-term experimental evolution papers, I began to realize that microbes were an awesome way to study evolution! They have really fast generation times, they are super easy to maintain in the lab, and they can be frozen to be revived years later (yes, a real-life time machine). I decided that I wanted to get trained in the methods of the Lenski lab. So I uttered those words that as a former basketball player I never thought I’d say. “Dr. Lenski, will you please put me on the bench?”

Unlike basketball, in evolutionary biology all of the action happens on the bench. The bench is the name for a researcher’s work area in a wet lab. A wet lab is a space with the proper equipment, ventilation, and plumbing to allow researchers to work directly with biological materials, often suspended in liquid solutions (hence the name wet lab). If MTV cribs were to visit science labs instead of celebrity homes, it would be the bench instead of a king-size bed associated with the cliché “this is where the magic happens.” In the Lenski lab, that magic is all about competition experiments. The basic protocol for a three-day competition is as follows:

Day -2: A small population of E. coli from two competitors is put into a flask with bacteria food to promote growth.

Day -1: The E. coli are transferred to new flasks containing a very minimal broth with 25 mg per liter of glucose added (DM25). This is the environment of the actual competition.

Day 0: Both competitors are put together in a common competition flask containing DM25. This marks the beginning of the actual competition.

A sample from this flask is immediately spread onto a petri dish containing TA (i.e. tetrazolium arabinose) in gelatin-like form. All competitions take place between an Ara+ strain, which can utilize arabinose and produces pinkish/white colonies and an Ara- strain, which cannot utilize arabinose and produces red colonies. “Plating” on Day 0 allows us to take an initial count of each visually identifiable strain at the beginning of the competition to be compared with the relative counts of each strain at the end of the competition. 

E. coli  “plated” on TA (tetrazolium arabinose) and ready for counting. The pinkish/white colonies grow on arabinose (Ara+) whereas the red ones (Ara-) cannot.

E. coli “plated” on TA (tetrazolium arabinose) and ready for counting. The pinkish/white colonies grow on arabinose (Ara+) whereas the red ones (Ara-) cannot.

Day 1: 24 hours later a small sample from the competition flask is transferred into a fresh flask containing DM25 and the plates from Day 0 are counted.

Day 2: 24 hours later, a small sample is transferred into a fresh flask containing DM25.

Day 3: A small sample from the final competition flask is plated just like Day 0. Comparing the counts between the final day and Day 0 determines the winner. 

Fortunately, after finishing my master’s thesis I was accepted by Dr. Lenski into the PhD program in Zoology at MSU. As a first-year PhD student I have been primarily taking classes. However, Dr. Lenski and I have come up with a research agenda that I recently used to apply for an National Science Foundation graduate research fellowship.

The goal of my research is to answer the question “How do the relative contributions of adaptation, history, and chance change over the course of long-term experimental evolution?”

Experimental design: X is 2,000 generations in E. coli and 20,000 updates in Avida. Following experimental evolution evolved values (i.e. ‘e’) are compared to ancestral values (i.e  ‘a’). Yellow=initial laboratory environment, Blue=experimental environment. b. Hypothetical comparison for ancestral vs. evolved values when evolution is primarily by adaptation, history, and chance.

Experimental design: X is 2,000 generations in E. coli and 20,000 updates in Avida. Following experimental evolution evolved values (i.e. ‘e’) are compared to ancestral values (i.e ‘a’). Yellow=initial laboratory environment, Blue=experimental environment. b. Hypothetical comparison for ancestral vs. evolved values when evolution is primarily by adaptation, history, and chance.

To answer my research question I will be using the competition experiments described above. The long-term evolution experiment was started with a single genotype of E. coli strain B cloned to found 12 populations. These populations have been evolving in DM25 for over 60,000 generations since February of 1988. I will take a single genotype (isolate) from all 12 lines at 2,000, 10,000, and 50,000 generations into the long-term evolution experiment. I will then establish three replicate populations from each line (using clones of the isolate). I will then evolve these 108 populations (12 lines x 3 replicates x 3 time points) for 1,000 generations in maltose. I will be replacing the glucose in DM25 with maltose, an alternative sugar source. Substituting the maltose for glucose will allow me to answer my research question using experimental evolution in a novel environment for these bacteria. Following this initial period of evolution I will compete all 108 populations against their ancestors. Similarities across all 12 replicate lines (such as increased fitness in maltose) reflect the influence of adaptation because all populations are attaining similar results regardless of initial differences between them following 2,000, 10,000, or 50,000 generations of unique history in each lineage. Differences between the 12 replicate populations (such as differences in evolved cell size) reflect the influence of each population’s unique history, since all lineages were originally derived from a single genotype and have evolved in the same environment. Differences between replicate populations (started from clones) within each lineage, reflect the influence of chance events, since differences between replicates will be caused by mutation and genetic drift events unique to each lineage that occur during the experiment (see figure above). Estimating the relative contributions of adaptation, chance, and history at 2,000, 10,000, and 50,000 generations will allow me to determine how the relative effects change over evolutionary time. I will also be performing a similar experiment in Avida, a digital evolution platform maintained by MSU’s digital evolution lab. I am truly honored to be at BEACON, where this type of research is possible. Stay tuned for more.

For more information about Jay’s work, you can contact him at bundyjas at msu dot edu.

Posted in BEACON Researchers at Work | Tagged , , , , , , , | Comments Off