Historic $12.7 million gift to BEACON Center, MSU College of Engineering

John R. Koza, who is considered the "father of genetic programming," has donated $12.7 million to the Michigan State University College of Engineering -- the college's largest individual gift.

John R. Koza, who is considered the “father of genetic programming,” has donated $12.7 million to the Michigan State University College of Engineering — the college’s largest individual gift.

The Michigan State University College of Engineering has received its largest individual gift in the history of the college.

A $10.7 million bequest from a California entrepreneur joins a previous cash gift of $2 million, bringing his total giving to $12.7 million to support the college and the BEACON Center for the Study of Evolution in Action, one of the National Science Foundation’s Science and Technology Centers.

The commitment is from computer scientist John R. Koza, who is considered the “father of genetic programming.”

The $10.7 million bequest will fund two endowed faculty positions to attract eminent scholars for the development of computational tools inspired by nature. New endowments also will advance genetic programming and evolutionary computation through endowed prizes, fellowships and programs to attract top graduate students and an increasingly strong pool of faculty members, said engineering Dean Leo Kempel.

“The creation of two new faculty endowments joining a third endowed chair, as well as endowed prizes and graduate student support, is unprecedented in the College of Engineering,” Kempel said. “We are very grateful to Dr. Koza for the advances our faculty will achieve and the students we will serve as a result of this extraordinary gift.

“With this gift,” Kempel continued, “and the previous investment by the National Science Foundation in the BEACON Center, Michigan State University will be the leading institution for transformational research and education in this important field of scholarship.”

Koza said he is delighted to make the investment in the BEACON Center and the College of Engineering and believes they are the best place to carry forward his life’s work.

“The mix of private support, NSF support, and backing from MSU, under the guidance of my good friend and colleague, Erik Goodman, means the BEACON Center and its ground breaking work will continue for many years to come,” Koza said. “My personal connections to BEACON, MSU and the partner institutions have been very gratifying and I look forward to what we can do together.”

MSU President Lou Anna K. Simon said the gift will create a hub of expertise and excellence in a demanding and promising field.

“John Koza’s continued generosity will empower us to build on his pioneering work. We are thankful for his vision and investment in the research and learning being done at Michigan State, which will resonate far into the future.”

Koza’s $2 million cash gift was received in 2014 and created the John R. Koza Endowed Chair in Genetic Programming. In August 2016, MSU welcomed renowned specialist in genetic programming and evolutionary computation Wolfgang Banzhaf as the Koza endowed chair.

Koza is a computer scientist and pioneer in the use of genetic programming, or GP. For much of his career, he was a consulting professor at Stanford University, teaching classes about evolutionary computation and genetic programming while conducting his research in that field.

“His ideas have helped to push back the horizon of what we believe computers can do now and in the future,” said Erik Goodman, director of the BEACON Center for the Study of Evolution in Action. The BEACON Center unites those who study natural evolutionary processes with computer scientists and engineers to solve real-world problems.

Goodman, who has been friends with Koza since they were graduate students in the 1960s and 1970s, called Koza a brilliant computer scientist.

“John Koza is frequently called the father of GP. His publication of four gigantic books introducing genetic programming to the world, beginning in 1992, helped to earn him this accolade,” Goodman explained. “In his books, he introduces the concepts of automated programming of computers by evolutionary processes.”

Goodman said Koza’s early work also included organizing a series of international conferences on Genetic Programming, which he and Goodman helped later to merge into a broader conference series on evolutionary computation, the Genetic and Evolutionary Computation Conferences.

“All of us owe some of our inspiration to the successes achieved by Koza,” Goodman added. “In the end, there may be few of us whose lives are not touched in some way or another by John Koza’s work.”

Endowed funds allow the university to provide continual support to specific programs and projects. The gift’s principal is invested and a portion of the annual earnings is used for annual program support.

The gifts support Empower Extraordinary, the $1.5 billion campaign for MSU that launched publicly in October 2014. To date, the College of Engineering has raised more than $76 million of its $80 million campaign goal.

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Dr. Judi Brown Clarke as a 2016 Sequoyah Fellow

This post is written by BEACON postdoc Wendy Smythe

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Judi Brown Clarke (center) with her two sponsors Drs. Kenneth Poff and Holly Schaffer

On November 12th, Drs. Kenneth Poff and Holly Schaffer nominated BEACON Diversity Director, Dr. Judi Brown Clarke as a 2016 Sequoyah Fellow at the 2016 American Indian Science and Engineering Society (AISES) National Conference in Minneapolis, Minnesota. Judi will formally be inducted next September at the 2017 AISES Conference in Denver, Colorado.

The Fellowship is name in honor of Sequoyah, the great Cherokee Indian who perfected the Cherokee alphabet and syllabary in 1821, resulting in the Cherokee Nation becoming literate in less than one year.  In this spirit, AISES Sequoyah Fellows are recognized for their commitment to the mission of “excellence in STEM” and to the entire American Indian community. They bring honor to AISES by engaging in leadership, mentorship, and other acts of service that support the students and professionals in the AISES family.

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BEACON attends the 2016 AISES National Conference

This post is written by BEACON postdoc Wendy Smythe

BEACON co-sponsored Alaska Native (Haida) pre-college students who presented research projects, two summer interns, presented research talks, and volunteered as undergraduate and graduate research judges.

Left to Right: intern Lauren Smythe, Judi Brown Clarke, Wendy F. Smythe, Alexa Warwick, intern Sarah Peele

Postdoctoral Fellows Wendy F. Smythe presented the research talk “Traditional Ecological Knowledge Coupled with STEM” and Alexa Warwick presented the research talk “Treefrog tales: incorporating evolutionary biology in research, conservation, and education”.

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Sarah Peele (left) and Lauren Smythe (right)

Summer interns Lauren Smythe and Sarah Peele presented their research projects at the National Conference. Lauren was mentored by Chandara Jack, Ph.D. presented the poster “Influence of Rhizobia and Herbivory on Rapid Evolution and Invasive Plants”. Sarah mentored by Wendy F. Smythe, Ph.D. presented the poster “What the HEK-Haida Ecological Knowledge Coupled with STEM”. Lauren and Sarah are both Alaska Native students, from the Kaigani Haida community of Hydaburg, Alaska.

Back row, left to right: Judi Brown Clarke, Traesea Miramontez, Sonia Ibarra, Wendy F. Smythe, Joe Hilliare, Lauren Smythe. Front row, left to right: Stasha Sanderson, Nevaeh Peele, Sarah Peele, Lillian Borromeo, Alexa Warwick

Back row, left to right: Judi Brown Clarke, Traesea Miramontez, Sonia Ibarra, Wendy F. Smythe, Joe Hilliare, Lauren Smythe. Front row, left to right: Stasha Sanderson, Nevaeh Peele, Sarah Peele, Lillian Borromeo, Alexa Warwick

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Mormyrids might be Pokémon: Can we see ‘evolution’ within a single individual?

This post is written by MSU grad student Savvas Constantinou

Savvas Constantinou preparing to inject single cell Brienomyrus brachyistius embryos.

I’m Savvas Constantinou and I am a second year PhD student studying Integrative Biology (IBIO) & Ecology, Evolutionary Biology, and Behavior (EEBB) in the Natural Science department at Michigan State University. I came to grad school to study Evolutionary Developmental biology; specifically what interests me is understanding how gene regulatory networks are modified over evolutionary time to generate new species and novel structures. I am probing this question using Mormyrids, a species-rich group of weakly electric fish. Mormyrids generate low levels of electricity (less than 1 volt) from their electric organ, and then sense this electric field on their skin with specialized cells; by monitoring distortions of their electric field these fish can locate and discriminate objects in their environment and communicate with their own species and discriminate other species.

Development of the larval and adult electric organs and the accompanying electric organ discharges in Brienomyrus brachyistius. A. Top to bottom. The larval electric organ differentiates from skeletal muscle in the body but is restricted from a region of the tail called the caudal peduncle. As the fish metamorphoses into an adult, the adult electric organ develops and discharges simultaneously with the larval electric organ. Eventually the larval electric organ is lost and the adult electric organ fully matures and develops penetrations. B. Top to bottom: The electric organ discharges from a larval fish (note the simplicity), from a fish discharging from both a nearly degenerated larval electric organ (arrow, note small relative amplitude) and a non-mature adult electric organ, and from an adult, fully mature fish (arrowhead note small head negative peak). Figure modified from Denzoit et al. 1978. The larval electric organ of the weakly electric fish Pollimyrus (Marcusenius) isidori (Mormyridae, Teleostei). Journal of Neurocytology 7: 165-81.

The electric organ actually develops twice within the lifetime of a single individual. In the species I work with, Brienomyrus brachyistius, they develop a larval electric organ about a week after hatching. The electric signature of the larval electric discharge is very simple. During metamorphosis from fry into an adult, the fish begin to develop their adult electric organ in a different location from the larval electric organ. The electric signature from the adult organ is more specialized and complex than the larval organ and begins discharging while the larval organ is still active. Eventually the larval organ is completely lost and the adult organ becomes more complex through a specific change in anatomy (see figure for clarity).

What excited me so much about this system was the idea of being able to “see evolution” within the lifetime of an individual. The function of the larval electric organ has yet to be experimentally determined: it is a costly structure as they discharge upwards of 100X a minute and it is like a homing beacon for electroreceptive predators. The adult organ is responsible for the more complex signals; variation in these signals have thought to been a driving force in speciation of mormyrids. So why do mormyrids waste the energy to even build the larval electric organ? I believe it has to do with evolutionary constraints.

The most basal member of the Mormyroidea is Gymnarchus niloticus, a weakly electric fish that has an electric organ similar to the Mormyrid larval electric organ in location and discharge complexity. I think that the ancestor to these groups had an electric organ that was like the larval electric organ of Mormyrids. The Gymnarchus lineage survived with some changes to the electric organ whereas the ancestral Mormyrid developed this second, more specialized electric organ that allowed for their rapid species diversification. I want to investigate what gene regulatory networks are at play to induce development of the adult electric organ. Is this different from the genes involved in differentiation of the larval electric organ? By probing these questions, I hope to test the idea that mormyrids have a strict developmental trajectory that requires formation of the larval electric organ before the adult electric organ can develop.

To further understand evolution and speciation in this group, I also plan to investigate the genes involved in the anatomical change that occurs during the final maturation of the adult electric organ. Through this final maturation the adult electric discharge becomes more complex, a feature implicated as a force driving sexual selection. After Mormyrids evolved the anatomical change to increase signal complexity, multiple species and groups have lost the ability, again suggesting its importance in speciation. To me, understanding what genes drive this process and how they are tweaked in their timing and spatial distribution of their expression to give rise to the amazing signal diversity of Mormyrids is fascinating.

I have been spending most of my time in my PhD developing the “toolbox” of techniques that will help me to answer the questions I am interested in. I have been optimizing laboratory breeding and fry rearing in B. brachyistius to allow me to study these developmental questions. I am a molecular biologist at heart, and have begun to test gene function using the gene modification technique CRISPR. CRISPR is a way in which nearly any region of the genome can be targeted for change: either to modify the DNA and disturb gene function or to direct addition of other genes (like Green Fluorescent Protein). I intend to use RNA-sequencing of larval and adult electric organs at various time points to determine what genes may be responsible for their development. My grand plan is to be able to silence genes involved in larval electric organ development, and then to see if an adult electric organ can still be produced when the larval organ has not.

Eventually I want to compare the gene circuitry regulating the development of electric organs among many species of Mormyrids as well as to those of Gymnarchus. By comparing changes in expression levels, timing, and location, I hope to bring insight into a potential genetic mechanism involved in allowing Mormyrids to speciate so successfully and rapidly. Stay tuned for future “shocking” information on Mormyrid electric organ development!

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Love is in the air (or maybe it’s just bacteria)

This post is written by BEACON managing director Danielle Whittaker

Danielle Whittaker holding a black and white warbler at Mountain Lake Biological Station, Virginia

When we fall in love with someone else, is it because they are our soul mates… or is it because we like the way their microbes smell? We think a lot about the importance of physical appearance and the content of what we say. But when it comes to attraction, we may have less control over our preferences than we think.

Just like humans, birds are thought to rely on sight and sound as their primary senses, yet smell turns out to play an important role in choosing a mate. For the last decade, I have been studying how birds use odors as indicators of a potential mate’s suitability. Dark-eyed juncos (Junco hyemalis) are songbirds found throughout North America that spend the summer breeding in habitats with cooler temperatures, especially in the mountains or far north in Canada. Like most birds, they produce preen oil from their uropygial gland, located above the base of the tail. This oil, which they rub into their feathers while preening, is a source of odor that transmits information about an individual’s species, sex, breeding condition, and hormone levels. This odor also relates to individual reproductive success: males that smell more “male-like” have more offspring, as do females that smell more “female-like,” suggesting that these compounds are also communicating information about reproductive health or ability.

The preen gland is located above the base of the tail

Recently, my collaborator Kevin Theis (former MSU postdoc, now assistant professor at Wayne State) and I have been studying the source of these odors. While at MSU, Kevin studied the bacteria in hyena scent pouches. These bacteria produce the odors that hyenas use to communicate with each other. He suggested to me that symbiotic bacteria in the preen gland could also be responsible for producing junco odors. We decided to test this hypothesis by sampling the bacteria in and around the preen gland, and determining whether any of the bacteria present were capable of producing these compounds. We found that the preen gland is home to a very rich and diverse microbial community. Even better, using the Microbial Volatile Organic Compound database, we discovered that many of these junco bacteria are known odor producers. Two genera in particular, Burkholderia and Pseudomonas, are capable of producing over half of the compounds in junco chemical signals – and these two bacteria were very common and abundant in our samples.

Scanning electron microscope image of bacteria in a junco preen oil sample

Our next step was to test whether removing these bacteria actually changed the juncos’ smell. I injected a broad-spectrum antibiotic into captive juncos’ preen glands, and sampled them before and after treatment. Compared to control birds that were injected with only saline, birds receiving antibiotics had significantly lower levels of three volatile compounds – 2-tridecanone, 2-tetradecanone, and 2-pentadecanone. These three compounds are the same ones that are correlated with reproductive success, suggesting that symbiotic bacteria could be responsible for a chemical signal that’s important in junco mate choice. We are now in the process of sequencing the bacterial swabs from the birds in this study, to examine which bacteria were killed by the antibiotics and to identify candidates responsible for producing the compounds.

Female junco incubating eggs at Mountain Lake Biological Station, Virginia

We are also now studying how these symbiotic microbes are transmitted between individuals. We have found that nestling juncos have bacterial communities very similar to their mothers, and less similar to their fathers. This pattern makes sense because it’s only mothers that sit on the nest and keep the nestlings warm as they are growing, and microbes are shared through physical contact. We also found that the adult male and female pairs were more similar to each other than they were to other adults of the same sex – again, physical contact is the likely explanation. Our next steps are to examine more closely the effects of social behavior on individual microbial communities, and whether an individual’s odor reflects their social patterns.

So the next time you find someone attractive, stop for a moment and wonder why. Is it the way their blue eyes sparkle when they say something witty? Or could it be the scent of bacteria… maybe even bacteria they got from somebody else?

For more information:

Whittaker, D. J., N. M. Gerlach, S. P. Slowinski, K. P. Corcoran, A. D. Winters, H. A. Soini, M. V. Novotny, E. D. Ketterson, and K. R. Theis. 2016. Social environment has a primary influence on the microbial and odor profiles of a chemically signaling songbird. Frontiers in Ecology and Evolution 4:90.

Whittaker, D. J. and K. R. Theis. 2016. Bacterial communities associated with junco preen glands: ramifications for chemical signaling. In Chemical Signals in Vertebrates 13, eds. Bruce A. Schulte, Thomas E. Goodwin, and Michael H. Ferkin. New York: Springer International Publishing, pp. 105-117.

Whittaker, D. J., S. P. Slowinski, K. A. Rosvall, N. M. Gerlach, H. A. Soini, M. V. Novotny, E. D. Ketterson, and K. R. Theis. 2016. It’s what’s on the inside that counts… or is it? Microbial vs. physiological mediation of sexually selected chemical signals in a songbird. Oral presentation at Evolution 2016.

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Better Together: Of Hyenas and Men

This post is written by MSU grad student Zachary M. Laubach

“A guy needs somebody―to be near him. A guy goes nuts if he ain’t got nobody. Don’t make no difference who the guy is, long’s he’s with you. I tell ya, I tell ya a guy gets too lonely an’ he gets sick.”

– John Steinbeck, Of Mice and Men

Myself and Philomon, the head chef and camp manager of the Serena Hyena Camp. During my time in Kenya, I came to see Philomon as a source of social support and dear friend.

The notion that our social environment is important to our health and well-being is not new. There are profound and heartbreaking historical illustrations of how social interactions (or lack thereof) shape behavior and physiology. For example, adults who once resided in Romanian Orphanages, notorious for their depraved lodging conditions and neglect, exhibit severe psychoses and debilitating mental disease 1,2. Likewise, famous primate studies from the 50’s and 60’s demonstrated the importance of maternal touch and interactions with peers to healthy psychosocial development 3,4. However, despite the flurry of convincing correlative results linking the early social environment to future stress-related disease, the underlying molecular mechanisms remained poorly understood until the mid 2000s when Drs. Michael Meaney and Mose Szyf showed that DNA methylation (a stable epigenetic mechanism that alters gene expression without changing the nucleotide sequence) is both responsive to social stimuli and has a direct effect on stress phenotype. These scientists found that offspring born to mothers who did not engage in licking and grooming behaviors had higher methylation of the glucocorticoid receptor gene, which resulted in an inability to respond to elevated stress hormones. The elegant part of this study was that cross-fostering (e.g., switching the rat pups at birth between high licking and grooming and low licking and grooming moms) revealed that the effects of DNA methylation were not due to genetics, but rather, a direct effect of maternal care during the first few postnatal weeks 5.

My PhD research extends current knowledge of the relationships among the social environment, DNA methylation, and biological condition using data from Dr. Kay Holekamp’s population of wild spotted hyenas in the Masai Mara of East Africa, Kenya. You might ask, ‘Why spotted hyenas?’

A snapshot of Bart, a dedicated mom still nursing her nearly full-grown cubs. This photo highlights the extent to which hyena moms care for their young, even when they are rapidly catching up in size!

Several aspects of spotted hyena biology make them a powerful and relevant study population for my research interests. First, hyena cubs depend on their mothers for nourishment and protection through 2 years of age, presenting a window of opportunity to quantify a variety of novel measures of mother-offspring interactions. I am collaborating with Julia Greenberg, another PhD student in Dr. Kay Holekamp’s lab, to quantify patterns of maternal care using archived behavioral data. We are interested in the proximity of mothers to their young, time spent nursing, and frequency of grooming. Second, in addition to living in clans, hyenas hang out in cliques within each clan. Our detailed observational data regarding the number of individuals in a clique, the nature of interactions within group-members, and the amount of time spent together can be used to quantify unique aspects of a hyena’s social support system (see a previous post by Julie Turner). This notion that social support is critically important to well-being has been found in both non-human primate and human studies where both mothers and their babies are in better condition when social support is stronger 6–8. Finally, hyena societies follow a strict and well-defined rank system, which is of particular interest to me because it is analogous to socioeconomic status in humans; rank determines access to resources, friends, and mates. Thus, findings regarding the relationship between rank and stress phenotype in hyenas may be relevant to studies of socioeconomic position and health in humans.

A pile of hyena cubs keeping each other company, dozing off after a long bout of play.

Spotted hyenas are wild, gregarious, and perhaps not all that different from other social species (like non-human primates and even humans). Another reason why I am interested in this species is because most epigenetic research to date has taken place in highly controlled rodent and primate populations, limiting generalizability of findings to gregarious animals. Dr. Holekamp’s study population, therefore, represents a unique opportunity to explore how naturally occurring social behaviors correlate with epigenetic mechanisms and stress outcomes in a wild species exhibiting complex sociality. One huge hurdle that I’ve encountered thus far revolves around the task of carrying out epigenetics research in a species whose genome is not yet publically available (NB: the genome of the spotted hyena was sequenced and annotated years ago, but the Beijing Genome Institute has not yet released it). Fortunately, with the help of experts at the University of Michigan and at the University of Minnesota, I was able to sequence the region of interest (the glucocorticoid receptor promoter) using a technique known as multi-species alignment. In brief, I identified a sequence of hyena DNA that is comparable to the established target region in humans and rats. Next, I mapped the sequence to genomes of species in the same order as hyenas (Carnivora) – namely, the cat, dog, and walrus. Then, with a touch of bioinformatics, I sequenced the region in hyena DNA so that we could measure a comparable set of epigenetic marks to those identified in the rodent and primate literature. In addition to gene-specific epigenetic marks, I am also measuring genome-wide methylation content, which can be thought of as a proxy for an individual’s genomic stability and overall condition. Taken together, I hope that the measures of gene-specific and genome-wide epigenetics will shed light on how early social experiences shape adult phenotypes.

Preliminary results and what’s in store. Based on our initial work, which showed strong effects of a hyena mom’s rank on her offspring’s genome-wide DNA methylation, I suspect that inter-individual relationships and social status interact in ways that profoundly affect phenotype. The ways in which social experiences affect biology is relevant not only to health of individual organisms, but also has potential to impact how natural selection shapes phenotypes over time. The latter is of particular interest to me, as it implies that social experiences play a role in evolution. It is my hope that what we learn from animal models like hyenas, primates, and rodents will compel us to step back, and consider that humans are also merely animals whose behaviors, physiology, and health are shaped by social experiences. However, unlike other animals, we are uniquely endowed with the capacity to recognize the impact of our social experiences on our biology and how they may transcend generations. Knowing this should motivate social support, and the impetus to move beyond I-llness to WE-llness 9, especially in a world championed by individualism.

  1. Chugani HT, Behen ME, Muzik O, Juhász C, Nagy F, Chugani DC. Local brain functional activity following early deprivation: a study of postinstitutionalized Romanian orphans. Neuroimage. 2001;14(6):1290-1301. doi:10.1006/nimg.2001.0917.
  2. Kaler S, Freeman BJ. Analysis of environmental deprivation: cognitive and social development in Romanian orphans. J Child Psychol Psychiatry. 1994;35(4):769-781. doi:10.1111/j.1469-7610.1994.tb01220.x.
  3. Harlow HF, Harlow M. Learning to love. Am Sci. 1966;54(3):244-272. http://www.pitzer.edu/academics/faculty/banerjee/psyc109/readings/w1-Learn.PDF. Accessed August 21, 2014.
  4. Harlow HF, Zimmermann RR. The Development of Affectional Responses in Infant Monkeys. Proc Am Philos Soc. 1958;102(5):501-509.
  5. Weaver ICG, Cervoni N, Champagne FA, et al. Epigenetic programming by maternal behavior. Nat Neurosci. 2004;7(8):847-854. doi:10.1038/nn1276.
  6. Campos B, Schetter CD, Abdou CM, Hobel CJ, Glynn LM, Sandman CA. Familialism, social support, and stress: positive implications for pregnant Latinas. Cultur Divers Ethnic Minor Psychol. 2008;14(2):155-162. doi:10.1037/1099-9809.14.2.155.
  7. Silk JB, Beehner JC, Bergman TJ, et al. The benefits of social capital: close social bonds among female baboons enhance offspring survival. Proc R Soc B Biol Sci. 2009;276(June):3099-3104. doi:10.1098/rspb.2009.0681.
  8. Silk JB, Beehner JC, Bergman TJ, et al. Strong and consistent social bonds enhance the longevity of female baboons. Curr Biol. 2010;20(15):1359-1361. doi:10.1016/j.cub.2010.05.067.
  9. From an anonomysous quote.
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Kombucha: More Than Meets the Eye

This post is written by UT Austin undergrad researchers Katelyn Corley, Matthew Hooper, and Zachary Martinez

“What starts here changes the world.” This is the motto that we as students at the University of Texas at Austin have come to embrace and strive towards in our everyday lives. In 2016, we began conducting research at UT Austin. For most of us, this was the first time we conducted research. We also took part in iGEM (international genetically engineered machine), and attended the annual conference in Boston. Our research experiences broadly spanned topics including microbiology, molecular biology, and synthetic biology, but our main work in 2016 focused on studying the microbiome of kombucha, with an ultimate goal of creating a designer beverage by altering the kombucha microbial community.

Example of kombucha “brewed” in a test tube. The large mass at the top is a layer of cellulose, while the mass at the bottom and the stringy “material” throughout the tube are clumps of bacterial and yeast cells.

Example of kombucha “brewed” in a test tube. The large mass at the top is a layer of cellulose, while the mass at the bottom and the stringy “material” throughout the tube are clumps of bacterial and yeast cells.

Kombucha is a popular fermented tea beverage that is home to a variety of microbes, both bacteria and yeast. Many die-hard consumers of kombucha love its acidic qualities and its characteristic vinegar taste, while these same attributes are what often turn others away from the drink. More importantly, kombucha is commonly referred to by its producers as being healthy or “rejuvenating” due to the presence of probiotics that are said to aid in digestion. As undergraduate scientists, we are skeptical of these claims, particularly because no current scientific evidence supports them. To us, kombucha soon became a vast frontier full of gray areas and large unknowns. Is it healthy, and if so, what makes it healthy? If not, could we make it healthy? These questions are what continually drove us forward as both researchers and as members of a community who desire to put something good into the world.

So then what did we learn? Over the course of roughly 6 months, the three of us along with our team, studied the “mysteries of kombucha”. We first identified some of the microbes that are naturally found in the drink. Species of bacteria such as Gluconobacter oxydans and Gluconacetobacter hansenii became commonplace names in our lab as we characterized these organisms and attempted to genetically engineer them for future study. Another major contributor to kombucha that we identified was the yeast, Lachancea fermentati. Interestingly, we found two unique strains of this species in our samples of kombucha with different phenotypes, and both appear to be required for proper kombucha brewing. One grew more quickly, while the other produced higher amounts of CO2. This finding immediately intrigued us. Not only do an array of species of bacteria and yeast coexist in kombucha, but differences in members of the same species appeared to have evolved in the process! Differentiation in the species was a possibility that we had not considered at first. The community of organisms that exists within kombucha appears to have evolved in a way that was much more complex than we had initially imagined. Kombucha was not simply a tea drink that was commercially sold and consumed, but was an exciting example of the world of microbial communities, which possess aspects of evolution and symbiosis that are still not fully understood.

Members of the Austin UTexas 2016 iGEM Team (from left to right): Prachi Shah, Matthew Hooper, Zachary Martinez, Katelyn Corley, Stratton Georgoulis, Alex Alario, Ian Overman

Members of the Austin UTexas 2016 iGEM Team (from left to right): Prachi Shah, Matthew Hooper, Zachary Martinez, Katelyn Corley, Stratton Georgoulis, Alex Alario, Ian Overman

We had the privilege of presenting our research at the 2016 iGEM “Giant Jamboree” in Boston. This research competition is one of the most incredible opportunities offered to both undergraduate and post-graduate students in the field of synthetic biology. We spoke with other students who work in our field and shared many of our successes and difficulties along the way. Additionally, we had the chance to present our research on kombucha to scientists, who gave us feedback and additional suggestions for expanding our project in the future. Our future plans include studying how the microbial community changes during a single brewing cycle as well as how the community might collectively evolve over multiple brewing cycles.

The major take-away from this experience was that, there is still work to be done, but that it is important work. Many of us first saw this project as being fun and approachable, and though we still view our lab work in this way, we have now begun to see how the scope of this project extends into greater, more compelling fields of science. Kombucha offers immense outlets for exploring the limitations of synthetic biology, as well as in exploring the types of evolutionary changes that must occur to enable specialization and the coexistence of microbes. Additionally, if we were to create a “designer” kombucha beverage, we need to consider the potential evolutionary shifts that might occur as we alter the microbial community found within kombucha. The great part about science is that you never know where it will lead you. This project took us from a grocery store shelf holding a bottle of kombucha, to an international conference in Boston, to a situation where we are now beginning to see how our work could shed light on an area of science that is not fully understood. On behalf of the entire Austin UTexas iGEM team, we encourage others to never stop digging deeper into science.

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Social networks in spotted hyenas

This post is written by MSU grad student Julie Turner 

I’ve always loved animals. This love isn’t exactly unusual in young children, but my fascination and curiosity about animals has not wavered. Among my earliest memories as a toddler was catching turtles in my backyard because they were slow enough for me to grab. As I got older, I started reading everything I could about animals, starting with lions (like many kids who grew up in the ‘90s, I was enthralled with The Lion King—except in my case, the movie became a recurring theme in my life). While learning more about lions, I realized that I thought their family groups were fascinating! I moved on to reading everything I could about other animals that lived in family groups, which grew into an interest in animals that live in larger groups with complex relationships like bottlenose dolphins and orcas.

When deciding what to do after college, I knew I wanted to study animals with complex social interactions and came across a program that studied spotted hyenas in Kenya. Prior to learning about this program, the most I thought about hyenas was watching The Lion King. I figured that the portrayal of hyenas couldn’t be right—as wonderful as the movie is, it is not renowned for its biological accuracy. I started reading obsessively about a new species and found that hyenas are so cool! They live in groups called clans that consist of multiple families reaching up to 130 members. Like humans they live in fission-fusion societies which means that, though they’re all in the same clan, the individuals they associate with change as hyenas come together or split apart to be alone or join other individuals (Kruuk, 1972). Their societies are as complex as certain baboon species and vervet monkeys, which is rare to see in non-primate species, especially carnivores (Holekamp, Smith, Strelioff, Van Horn, & Watts, 2012). As it turns out, these social traits make hyenas a great animal to study if you’re interested in how lots of individual little interactions like greetings, aggressions, and hanging out go together to form a cooperative social group, otherwise known as sociality in animals. I am studying a small part of sociality, specifically how sociality develops in growing hyena cubs and what that means for them throughout their lives.

Figure 1. PhD candidate, Julie Turner, with a darted hyena in Kenya

Sociality, especially complex sociality, is surprisingly difficult to understand and even to observe. For instance, imagine you’re at work with your officemates or in a class of 100 people. You might have a general idea of who hangs around with whom, but would you know how often everyone associated with everyone else in the group? Could you name each person’s friends? Shelly may be friends with Max, but does Max consider Shelly a friend in return? Is anyone actively avoiding someone else? In studying humans, at least researchers can conduct interviews or give people surveys. So, assuming people are answering truthfully, these challenges are difficult but manageable. Now imagine that you want to be able to address these questions in an animal that doesn’t speak any language you may know or could easily learn (though we have researchers trying to learn how hyenas communicate right now).

One method scientists use to try to tease apart and try to explain complex relationships is using social network analysis (SNA). A social network isn’t just Facebook. A social network is a group of individuals or entities (businesses, classes, etc.) that are connected by relationships or interactions (associating together, being friends, writing papers together, etc.). Individuals are represented by nodes; relationships and interactions are depicted by lines between the nodes called ties.

Figure 2. Random network graph. Blue squares are nodes that represent individuals or other entities. The lines are ties that indicate which nodes are connected by a relationship.

Social network graphs, such as the one just described, help us visualize relationships that may be difficult to see simply by observing. These graphs are especially helpful with animals when we only can use observations of behavior to understand relationships and cannot rely on interviews and surveys.

So, we observe animals over enough time to see many interactions and then build a social network to represent relationships during that time period. Hyenas have the potential to have many different types of relationships. Let’s use this interaction as an example:

Figure 3. A picture of a typical hyena interaction with their names.

Here we have five hyenas in a session together where three individuals are acting aggressively towards another, and GALA is off to the side doing her own thing.

One type of relationship that social network analysis (SNA) can address is relationships that are undirected, also known as binary, like individuals just hanging out with each other. Though all five hyenas here are not necessarily interacting directly, they are all associating together. GALA can’t associate with HEL without HEL also associating with GALA. This association network would be represented as the following graph:

Figure 4. Undirected association network of the illustrative hyena interaction.

Or relationships can be directed, for instance, when one hyena acts aggressively to another, as when HEL, CHLE, and TICA are aggressive to IKA.

Figure 5. Directed aggression network of the illustrative hyena interaction. The direction of the arrow indicates who is being aggressive to whom.

Once relationships are graphed, we analyze aspects of these social relationships statistically through SNA. We can learn things like if one clan of hyenas is bonded by stronger relationships than another, or how one individual’s social role varies from another. I’m using SNA to look at how individual hyenas learn their social role or position in the clan and how that position then affects aspects of their life like their personality or longevity. We already have evidence that cubs “inherit” their mothers’ social network (Ilany & Akcay, 2016), but what does that mean for the cubs’ development? These questions are examples of what we are currently exploring in spotted hyenas. Learning more about the social lives of hyenas helps us to see that hyenas are much more than “nothing but slobbering, mangy, stupid poachers” (I just had to bring it back around to The Lion King).

References

Holekamp, K. E., Smith, J. E., Strelioff, C. C., Van Horn, R. C., & Watts, H. E. (2012). Society, demography and genetic structure in the spotted hyena. Molecular Ecology, 21(3), 613–632.

Ilany, A., & Akcay, E. (2016). Social inheritance can explain the structure of animal social networks. Nature Communications, 7, 1–10.

Kruuk, H. (1972). The spotted hyena: a study of predation and social behavior.

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Getting Mixed Signals: Exploring the Evolution of Disjunctive Signaling Games

This post is written by Peter Fetros, an undergraduate computer science research assistant at UI working with James Foster and Bert Baumgaertner

Peter Fetros explaining a section of their research poster presented at an undergraduate research conference

Peter Fetros explaining a section of their research poster presented at an undergraduate research conference

Signals are all around us. Most organisms use signals in order to communicate with one another. They might use them to tell others where the best food is, or possibly to warn them about approaching predators. However not very much is known about the evolution of these signals. How and why some signals are used while others are not, and how organisms decided to use these signals. I’ve always been interested in the ways that things communicate, from tiny organisms who emit chemicals to ward of predators, to humans and the thousands of different ways we choose to communicate information to one another. However, as a Computer Science Student I’m even more interested in finding a way to model these interactions in a meaningful way that will give us insight into how meaningful signals can evolve. Our current research explores how signals evolve over time and what that evolution looks like. We do this by modeling the interaction of “players” in something called a Lewis Signaling-Game.

A Lewis Signaling-Game in its most simple form consists of 2 players, a Signaler and a Receiver. In this game the player, or “agent”, who is designated as the Signaler first observes some world-state. The Signaler then chooses a signal to send to the Receiver based on the world-state it observed. After the Receiver receives the signal from the Signaler, The Receiver then chooses to perform an action based on that signal. If this action is the correct action for the world-state that the Signaler originally observed, they both get a payoff.

An example of this process in nature can be compared to the calls of Vervet monkeys. These monkeys have different vocal calls (signals) for when they see different types of predators, for example leopard, eagles, or snakes. When a Vervet monkey sees a predator (an observation) it will choose the call appropriate for this predator (a signal). It will make the call and then another monkey who cannot see the predator will hear it (Receiver). The monkey who hears the call will then have to decide how to properly avoid this unseen predator (choosing an action). In this example that might be climbing a tree in order to get away from a leopard prowling on the ground, running away from the comparably slow snake, or even hiding in a bush so the eagle can’t reach it. If the Vervet monkey chooses the correct action for the type of predator, it will get a payoff (not being eaten), However if it chooses the wrong action for the type of predator it will not get a payoff (get eaten).

To model these interactions on a large scale we model the Signaling-Game in a programming language called NetLogo. In our models we have a large population of agents that all pick a partner and then play the Signaling-Game. They start out not knowing what signal is correct to use for what world state it observed, as well as what action they should perform when they receive a signal. However, when they do choose the right action based on the world state the observer sees, they get a payoff in the form of an increase in their preference for choosing that signal again (if the player was a Signaler), or choosing that action (if the player was a Receiver) for that specific observation. After each game the agents randomly pick new partners and then play again. Eventually they do this enough so that they all agree on the same meaning for signals. When this happens we call it a signaling System.

There has already been some research into the basic Lewis Signaling Game and Signaling Systems. So what we are currently exploring is how these Signaling Systems evolve when we have observations that are disjunctive. Disjunctive observations are observations that the Signaler can sometimes make in which it doesn’t know the true state of the world. It might be World “A” or World “B”.

An example of this using the Vervet Monkeys might be when a monkey sees a rustling bush and doesn’t know whether it’s a leopard or a snake. Because it doesn’t know which it really is, it must somehow let the other monkeys know that there is a ground predator nearby but it isn’t sure what kind, all it knows is it isn’t an eagle. There are several ways it might do this. It may send a new type of call that means “Leopard or Snake” or it may just guess itself, and make the call for leopard or the call for snake depending on what it decides might be in the bush.

Ternary plot detailing the population preferences for the agents playing as Receivers

Ternary plot detailing the population preferences for the agents playing as Receivers

So far in our simulation we have discovered several different paths the evolution of these Signaling Systems may take. Sometimes the Signalers use a new kind of signal and sometimes they use the old signals while just making a guess at what the world state might be. We plot the results from the simulations on ternary-plots. These plots show the population’s average preference for a particular signal or action based on either the world-state it observed or the signal it received respectively. These graphs allow us to see how a particular preference changed over time at the population level.

If you have any feedback or questions about this research, please contact

Peter Fetros (Fetr0509@vandals.uidaho.edu), James Foster (foster@uidaho.edu), Bert Baumgaertner (bbaum@uidaho.edu) or Kelly Christensen (chri4898@vandals.uidaho.edu).

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