Undergraduate Diversity at Evolution 2017

This post is written by Hollie Heape and MSU postdoc Alexa Warwick 

Fig. 1. UDE 2017 workshop and discussion panel

As an undergraduate research assistant through BEACON at Michigan State University, I was afforded the opportunity to study the efficacy of a travel award program to increase diversity in evolutionary science. In order to share some preliminary results of this study I spent five days at the annual Evolution Conference in Portland, Oregon, coincidentally my hometown. Here I attended both talks and poster presentations on a myriad of topics ranging from computational evolutionary biology methods all the way to queen ant aggression.

The conference began with a special undergraduate professional development workshop where undergraduate students gained insight and advice on various evolutionary biology career pathways (Fig. 1). I was fortunate enough to speak one-on-one with the presenters and gain a deeper understanding of their research. Each undergraduate student could also opt to be paired with two specialized mentors in the field the student showed an interest. Through this pairing, the students were able to create a personal connection with their mentor by spending time getting to know each other throughout the five days of the conference.

Fig. 2. Hollie presenting her poster at Evolution 2017

On the fourth evening of the conference, I presented a poster (Fig. 2) of my research in which I evaluated the efficacy of the Undergraduate Diversity at Evolution (UDE) Conference Travel Award program. This program has been running almost every year* since 2001 with the goal of increasing diversity in the evolutionary sciences (Fig. 3). This travel award solicits applicants around February each year and awards are made in late March or early April to undergraduates specifically chosen to diversify the field (see more at beacon-center.org/ude). In order to collect data from program alumni, an online survey was created and then sent to all applicants and awardees of the program since 2001. A total of 427 requests were sent out to undergrad awardees, applicants, and attendees, including emails to some current and/or past student advisors, as needed. So far we have received 150 completed responses**, which included 92 awardees (36% of the total) and 58 non-awardees (Fig. 4). As might be expected, most responses (84%) were from the most recent conference years (2010–2016). Some preliminary results are summarized below, or you can view the presented poster here.

Fig. 3. UDE 2017 travel awardees and some of their mentors

Most respondents are currently in academia, and the majority are still students. More females than males responded, although this proportion was representative of the applicant pool. Of the awardees who responded, almost half (43%) self-reported their ethnicity/race as white. This result raises a possible concern as the main focus of the travel award program is to increase the diversity within evolutionary sciences. However, this value was lower than the percentage of white non-awardees who responded (55%). Because ethnicity/race is not requested as part of the application we cannot determine what the expected response proportion would be. In addition, ethnic/racial diversity is not the only factor of diversity that is considered during the selection process, so this result does not necessarily indicate an issue.

Fig. 4. Summary of UDE alumni survey responses to date

When comparing the responses regarding receipt of awards in evolutionary science, 40% of UDE awardees had at least one other award whereas only 12% of non-awardees did. Although awardees reported more often than non-awardees that the field of evolution was very important their current position, the average ranking of importance was not significantly different. Of the respondents who attended at least one Evolution meeting, 88% made at least one new contact and 72% reported following up with at least one of these contacts within six months. Finally, 88% of awardees said they would not have been able to attend the conference without the UDE travel award. When asked what the impact of their participation was on their career success or path, the top two categories in terms of number of responses were: (1) networking with students and professionals and (2) reinforcing their career path in science and/or going to graduate school. For many it was also their first time attending/presenting at a scientific conference. Two example responses:

“The experience was transformative. I really connected with my mentor and he introduced me to lots of different scientists, helping me feel really engaged with the Evolution community. I also found presenting a poster at Evolution very empowering and I received validation early on that I am competitive enough to be a research scientist. It actually inspired me to pursue a PhD in Evolution.”

“My participation at UDE really helped understand the importance of studying Biology from an evolutionary perspective. In fact, it solidified my commitment to the field regardless of the profession I end up choosing.”

Even those who did not continue in the field still found it impactful in making decisions on their future careers, such as learning they didn’t want to continue in academia or reinforcing their goal in pursuing medicine. Approximately seven responses indicated little to no impact for a variety of reasons, and three said it was moderately impactful but they had already been accepted into a Ph.D. program. I will continue to analyze these data, along with my mentor, Dr. Alexa Warwick, in preparation for publication.

For me, my favorite part of the conference was the last night at the Oregon Zoo for the “super social.” During this event, I caught up with my fellow undergraduate friends and was even able to network while enjoying the beautiful backdrop of the zoo animals. The few days at Evolution 2017 were some of both the fast-paced, non-stop, and rewarding days of my undergraduate career. I vastly expanded my knowledge of evolutionary biology, while also gaining life long friends.

In terms of impact on my future career, I am currently heading into my third year at Michigan State with a major in Animal Science with hopes to attend Veterinary School in the near future, specializing in zoo animals. This research project was the first of my undergraduate career, and Evolution 2017 was the first professional conference at which I attended and presented. The networking opportunities and contacts I made at this conference far exceeded my expectations. Although not directly focusing on the veterinary profession, this conference allowed me the opportunity to talk to professionals who get the opportunity working to study species they love, which is something with which I can relate. My end professional goal is to work on rehabilitating species that are facing extinction in the wild, thus connecting my loves for veterinary medicine and ecology/evolution.

Funding for this project was provided by a BEACON budget request.


*The Undergraduate Diversity at Evolution (UDE) Program will NOT be held as part of the Evolution 2018 meetings because it is a joint international meeting in Montpellier, France: http://evolutionmontpellier2018.org/. However, the program WILL continue in 2019 in Providence, RI, June 21-25. The application will be available by February 2019 at beacon-center.org/ude.

**If you were an undergraduate who applied for or received funding through the UDE program between 2001–2014, we would still welcome your feedback! Please email Dr. Alexa Warwick (awarwick@nullmsu.edu) to receive a link for the survey (plus a $10 Amazon gift card as a thank you for your completed responses!).

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BEACON’s Paul Turner honored at Yale University

This post is written by MSU postdoc Zachary Blount.

Photo of Paul TurnerIn July, BEACON Faculty Affiliate Paul E. Turner was named as Yale University’s first Elihu Professor of Ecology and Evolutionary Biology. Named in honor of the school’s namesake, Elihu Yale, a philanthropist who provided critical support during its early years, the Elihu Professorships are highly prestigious and rarely granted.

It is hard to imagine anyone who could possibly deserve this honor as much as Paul. He stands as one of the leading stars of the experimental evolution community, and has been an excellent mentor to numerous among the rising generation that will carry the field forward. He has won a litany of prestigious fellowships, awards, and grants. In collaboration with his mentees and colleagues, he has made enormous contributions to science with his work using microbial and phage model systems. Some glimmering of his impact may be seen in the list of several dozen high impact papers that bear his name. Much of this work has been on fundamental evolutionary questions ranging from the origins of diversity, to pleiotropy, to epistasis, to the evolution of sex, to robustness and evolvability. He has also pursued extremely important, medically relevant research. Perhaps most importantly, he has been working to apply the insight he has gained over the years of fundamental work to the resurrection and development of phage therapy into what may well become a critical medical tool in this age of rampant antibiotic resistance. Indeed, this work has already saved at least one life. Over and above the research and mentoring, he has provided great service to the community, serving in administrative posts at Yale, as editor for a number of journals, on committees for the National Science Foundation and American Society for Microbiology, as organizer of conferences, including one of the best Gordon Research Conferences I ever attended, and even as a US delegate to global science workshops. Moreover, he has been tireless in his outreach to the community, and in his efforts to further diversity in science. As a researcher and as a citizen scientist, he is a model of what we should aspire to.

All those accomplishments might go to a lesser man’s head, but there is no worry of that with Paul, because his quality as a scientist is matched by his quality as a human being. He is remarkably humble, genuine, kind, approachable, and humane, without a single shred of pretense. This is perhaps most clear at conferences, where he is always a center of calm and good cheer, the brilliant fellow who is always smiling. It is certainly no surprise that his students and colleagues speak of him with genuine love and affection. As I recall, the first time I ever heard a story about Paul, it ended, “Paul’s the coolest.” That pretty well sums it up.

Go to http://turnerlab.yale.edu/ for more information about Paul Turner’s work!

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Africa’s next top animal intelligence model

This post is written by MSU grad student Lily Johnson-Ulrich

Spotted hyenas are found in just about every habitat in sub-Saharan Africa including human-disturbed areas and fully urbanized ones (i.e., cities) (Yirga Abay, Bauer, Gebrihiwot, & Deckers, 2010). While most large carnivores in Africa are decreasing in number, spotted hyenas are thriving. One reason for this inconsistency may be their high degree of behavioral flexibility; they’re dietary generalists eating everything and anything from termites to elephants (Holekamp & Dloniak, 2010). Spotted hyenas also exhibit social complexity and social cognition that are similar to the cercopithicine primates (a group that includes baboons and vervet monkeys) (Holekamp, Sakai, & Lundrigan, 2007). Living in novel or urban environments and complex sociality are factors that are thought to drive the evolution of large brains and intelligence in primates. This makes the spotted hyena an ideal model organism for confirming the relationship between these factors and cognitive abilities outside of primates.

I’m a graduate student in Dr. Kay Holekamp’s lab at MSU where Dr. Holekamp has been studying the lives of spotted hyenas for almost thirty years. This long-term data set provides a unique pool of information on hyena relationships that goes back several generations. I’m interested in looking at how social and environmental conditions may affect cognition in wild spotted hyenas in order to understand the adaptive function of intelligence in a natural system.

One of the things that we think makes humans unique is our large brains and intelligence (think human culture, innovation, science, and technology!). However, large brains are metabolically expensive and we’re still not sure just what the adaptive pay-off for extreme intelligence was in our ancestral environment. In today’s modern world, we no longer experience the same selective forces or live in the same habitat that we did when our large brains were evolving so it’s difficult to retrace the steps that led us to where we are today. I think it’s important to try and understand the adaptive function of intelligence because it can help us understand how to foster intelligent behavior such as creativity and innovation in today’s society. One way to try and understand both how our large brains evolved and how intelligence is adaptive is to take a look at its function in wild extant populations of other species that may share evolutionary pressures with ancestral humans, like spotted hyenas. In other words, we can try to understand the origins of intelligence by studying it in other species.

Figure 1. A hyena interacting with the multi-access box used to test innovative problem-solving. The box has four doors that a hyena may manipulate to retrieve bait from the interior.

For my graduate research I am testing two specific cognitive abilities that are related to intelligence, innovation (Figure 1) and inhibitory control (Figure 2), in three populations of wild spotted hyenas, one urban, one disturbed, and one protected. Innovation is the ability to solve a novel problem or solve a familiar problem in a novel way and. It has a strong relationship with brain size, behavioral flexibility, and also the ability to survive in novel environments across many animal taxa (e.g. Cognitive Buffer Hypothesis (Sol, 2009)). Cities are becoming more widespread and urbanization creates dramatic changes across a landscape, posing evolutionarily novel problems for animals to cope with. Spotted hyenas are among the few species that are actually able to thrive in urban environments and I suspect this may be related to their innovative abilities. To test this idea, I’m studying the innovative abilities of fully urbanized hyenas and comparing them to the abilities of hyenas in a fully protected national reserve and to those of an intermediate population. The intermediate population also resides inside a national reserve but the population’s boundaries overlap the border of the reserve and a growing human town where the impacts of tourism and cattle grazing are increasing.

Figure 2. A hyena successfully detours to the side of the transparent cylinder during an inhibitory control test.

Inhibitory control is the cognitive ability to resist a prepotent, but ultimately incorrect, response. In humans, strong inhibitory control in childhood is related to later life success (Meldrum, Petkovsek, Boutwell, & Young, 2017). Inhibitory control is thought to be important to other cognitive abilities like innovation, because it allows individuals to “stop and think” prior to making a decision (Hauser, 2003). In the social world of spotted hyenas, each group member is part of a linear hierarchy, or “pecking order” that determines access to food. An alpha female and her children are at the top, followed by other females, and then the males are at the bottom. Adult male hyenas fall at the bottom of this hierarchy because male hyenas will leave their natal clan when they reach sexual maturity and join a new clan in search of mating opportunities while female hyenas remain in the clan they were born in (and benefit from the support of their mother and sisters). Male hyenas, on the other hand, when they join a new clan don’t have the support of family members they had in their natal clan and they begin their new lives at the very bottom of the social hierarchy along with other immigrant males. At the bottom of the hierarchy individuals must inhibit all aggression towards higher ranking clan members or risk strong retaliation (Kruuk, 1972). Since all male hyenas are “doomed” to live their adult lives as the lowest ranking members of a clan we suspect that they will possess better inhibitory control than female hyenas. If so, it would support the idea that many advanced cognitive abilities evolved in challenging social contexts, an idea known as the Social Intelligence Hypothesis (Dunbar, 1998).

In sum, I hope to examine if individual hyenas with better inhibitory control are also more innovative and if these two cognitive abilities are related to the environment hyenas live in or if they are related to social factors such as group size, sex, and rank. Ultimately, I plan on relating variation in both innovation and inhibitory control to heritability and fitness. If variation in innovation and inhibitory control is heritable and related to annual reproductive success this would suggest that evolutionary selection is currently acting on cognitive abilities in spotted hyenas. I hope that my research can shed light on where and why intelligence is adaptive, which in turn can give us clues about where and why human intelligence might have evolved. I also hope to highlight the fact that many animals, even distantly related ones, share many of the same cognitive abilities with humans. Increasingly, it looks like the difference between human and non-human animal minds is one of degree, not kind.

Dunbar, R. I. M. (1998). The social brain hypothesis. Evolutionary Anthropology: Issues, News, and Reviews, 6(5), 178–190. http://doi.org/10.1002/(SICI)1520-6505(1998)6:5<178::AID-EVAN5>3.3.CO;2-P

Hauser, M. D. (2003). To innovate or not to innovate? That is the question. In S. M. Reader & K. N. Laland (Eds.), Animal Innovation. Oxford University Press.

Holekamp, K. E., & Dloniak, S. M. (2010). Intraspecific Variation in the Behavioral Ecology of a Tropical Carnivore, the Spotted Hyena. In Behavioral ecology of tropical animals (1st ed., Vol. Volume 42, pp. 189–229). Elsevier. http://doi.org/http://dx.doi.org/10.1016/S0065-3454(10)42006-9

Holekamp, K. E., Sakai, S., & Lundrigan, B. (2007). The spotted hyena (Crocuta crocuta) as a model system for study of the evolution of intelligence. Journal of Mammalogy, 88(3), 545–554.

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

Meldrum, R. C., Petkovsek, M. A., Boutwell, B. B., & Young, J. T. N. (2017). Reassessing the relationship between general intelligence and self-control in childhood. Intelligence, 60, 1–9. http://doi.org/10.1016/j.intell.2016.10.005

Sol, D. (2009). The cognitive-buffer hypothesis for the evolution of large brains. Cognitive Ecology Ii, 111–134.

Yirga Abay, G., Bauer, H., Gebrihiwot, K., & Deckers, J. (2010). Peri-urban spotted hyena (Crocuta crocuta) in Northern Ethiopia: diet, economic impact, and abundance. European Journal of Wildlife Research, 57(4), 759–765. http://doi.org/10.1007/s10344-010-0484-8

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Getting a Head with Ptychodera flava Larval Regeneration

This post is written by UW grad student Shawn Luttrell

Figure 1. Deuterostome phylogeny. Humans are vertebrates, to the right. Hemichordates are a sister group to the well known echinoderms.

One of the great marvels in biology is the ability to regenerate a fully functional nervous system after damage from disease or injury. Scientists have studied this remarkable process for decades, but it is still largely a mystery how some animals accomplish this incredible feat. Humans have limited regenerative abilities, particularly in the central nervous system (CNS; Chernoff et al., 2002; Poss, 2010; Stocum, 2006). Some peripheral neurons can regenerate to a certain degree however, damage to the brain or spinal cord usually results in permanent, catastrophic impediments that are not corrected though regenerative mechanisms (Yannas IV, 2001). Animal models that are capable of extensive and complete nervous system regeneration are needed to effectively make strides in understanding the molecular mechanisms underlying this trait. Moreover, models that are closely related to humans will likely provide greater insight to achieving extensive mammalian CNS regeneration as many of the same genes, gene networks, and developmental programs are shared between the deuterostomes (Figure 1; Davidson and Erwin, 2006; Swalla, 2006).

Figure 2. Ptychodera flava, a hemichordate, from Honolulu, Hawaii.

I am a fifth year graduate student in the Swalla lab in the Biology Department at the University of Washington and I am defending my Ph.D. at the end of this month. I have focused my dissertation research on CNS regeneration in the solitary hemichordate, Ptychodera flava. This animal is also known as an acorn worm and is closely related to echinoderms, like sea stars and sea urchins. Hemichordates are strictly marine animals and all acorn worms have a tripartite body plan with anterior proboscis that is used for digging and burrowing in the sand and mud, a middle collar region, a ventral mouth between the proboscis and collar, and a long posterior trunk (Figure 2). Hemichordates are in the same group of animals as chordates, including humans, and as such, share numerous developmental and morphological features (Figure 1). Most notably for my research, P. flava has a hollow, dorsal neural tube in the collar region that our lab has shown develops in a very similar fashion to the chordate neural tube (Luttrell et al., 2012). In humans, the neural tube becomes the brain and spinal cord. More impressive is the fact that P. flava can regenerate its neural tube after complete ablation. In fact, they can regenerate all of their body structures (Figure 3; Humphreys et al., 2010; Luttrell et al., 2016; Rychel and Swalla, 2008).

Figure 3. Regenerating Ptychodera flava. A) The open wound of the cut site on day zero of regeneration. B) Day 1 of regeneration showing the wound has healed. C) Day 7 of regeneration showing the proboscis and partial collar. D) Day 14 of regeneration showing complete proboscis and collar regeneration.

The first two chapters of my dissertation are published on chordate evolution and hemichordate regeneration (Luttrell and Swalla, 2014; Luttrell et al., 2016). We detailed the regeneration transcriptome for anterior regeneration in adult P. flava worms. This showed all of the genes that are turned on or off controlling the regeneration process. Now we know nearly a thousand genes involved with hemichordate regeneration and we are investigating which of these genes are actually required for regeneration and which genes play a support role. The second chapter also details the internal regeneration morphology, so we know when structures and organs regenerate in hemichordates and from what tissues they are derived. We compared this temporal and spatial regeneration data to early development and found there are differences between the way certain structures regenerate and the way they are originally made when P. flava larvae metamorphose into adult worms.

Figure 4. Ptychodera flava Krohn stage larva. an = anus; ao = apical organ; cb = ciliary bands; g = gut; mo = mouth; tt = telotroch.

Ptychodera flava begins life as a planktonic, feeding, tornaria larva that can remain in the water column for up to three hundred days (Figure 4; Hadfield, 1978). It had not been determined, however, at what point during development the regeneration program is activated. It may have been that regeneration is initiated after the animal undergoes metamorphosis from a planktonic larva into a juvenile worm or it may be that the regeneration program becomes active at some point before metamorphosis. The final chapter of my dissertation investigates these questions, and I have shown that P. flava larvae are also able to extensively regenerate. This is important because functional studies aimed at uncovering the genetic and molecular mechanisms controlling the regeneration process may, in certain cases, be more tractable in the larvae due to their small size, transparency, and relatively simple body plan and tissues compared to adults acorn worms. Even though P. flava larvae do not possess a neural tube pre-metamorphosis, the regeneration program is likely the same for both larvae and adults. This final chapter of my dissertation is now complete and will soon be submitted for publication. Many of these studies benefited from BEACON funding. In particular, BEACON funded the last two quarters of my graduate studies, which allowed me to gather most of the data for this chapter and finalize my dissertation. I will start Postdoctoral studies at ISCRM (The Institute of Stem Cell and Regenerative Medicine in Seattle in August, continuing to study regeneration and evolution in action! Thank you BEACON!!


Chernoff EA, Sato K, Corn A, Karcavich RE. (2002). Spinal cord regeneration: intrinsic properties and emerging mechanisms. Semin Cell Dev Biol. 13(5): 361-368.

Davidson EH, Erwin DH. (2006). Gene regulatory networks and the evolution of animal body plans. Science. 311: 796-800.

Hadfield MG. (1978). Growth and metamorphosis of planktonic larvae of Ptychodera flava (Hemichordata: Enteropneusta). In: Chia FS, Rice ME, editors. Settlement and metamorphosis of marine invertebrate larvae. New York: Elsevier. p 247–254.

Humphreys, T., Sasaki, A., Uenishi, G., Taparra, K., Arimoto, A,. Tagawa, K. (2010). Regeneration in the hemichordate Ptychodera flava. Zoolog Sci. 27(2), 91-95.

Luttrell S, Konikoff C, Byrne A, Bengtsson B, Swalla B. (2012) Ptychoderid hemichordate neurulation without a notochord. Integr Comp Biol. 52(6): 829-34.

Luttrell SM, Gotting K, Ross E, Alvarado AS, Swalla BJ. (2016). Head regeneration in hemichordates is not a strict recapitulation of development. Dev Dynamics 245: 1159-1175.

Luttrell SM and Swalla BJ. (2014). Genomic and Evolutionary Insights into Chordate Origins. In “Principles of Developmental Genetics”, 2nd edition. Sally Moody, ed. (Elsevier, San Diego.) pp. 116-126.

Poss KD. (2010). Advances in understanding tissue regenerative capacity and mechanisms in animals. Nat Rev Genet 11: 710–722.

Rychel, A.L. and Swalla, B.J. (2008). Anterior regeneration in the hemichordate Ptychodera flava. Dev. Dyn. 237(11), 3222-3232.

Stocum D. (2006). Regenerative Biology and Medicine. London: Academic Press.

Swalla BJ. (2006). Building divergent body plans with similar genetic pathways. Heredity 97: 235-243.

Yannas IV (2001) Tissue and organ regeneration in adults. Springer-Verlag New York, Inc. pp. 138–185.

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Science Communication Strategies

This post is written by UT postdoc Tessa Solomon-Lane

Science communication strategies often focus on communicating to other researchers within your field or to the general public. Interdisciplinary conversations require a mix of communication skills to bridge the gaps in domain knowledge and overcome the jargon. At the University of Texas at Austin, we just wrapped up a 3-week collaborative and interdisciplinary Pop-Up Institute called Seeing the Tree and the Forest: Understanding Individual and Population Variation in Biology, Medicine, and Society. Pop-Up Institutes are a novel framework for collaboration being funded for the first time this year by UT’s Vice President for Research. Designed to be longer than a conference and less permanent than a research center, these Institutes bring diverse experts together, into the same physical space, to work. In our Institute alone, we had researchers from multiple fields of biology, statistics, nutrition, medicine, public health, anthropology, sociology, ethics, and physics.

Our Pop-Up Institute tackled the causes and consequences of individual and population variation. Individuals differ in a variety of ways, from their genetics to their lifetime health. Understanding the underlying causes of this variation across individuals and populations is critical to the success of both the individual and the population within which they live. However, the directionality of cause and consequence is complex, and the pertinent factors that underlie why individuals are the way that they are crosses traditional research boundaries. Two additional Pop-Up Institutes were funded this year. The first brought together social scientists to study Discrimination and Population Health Disparities. The second focused on Building a Digital Humanities Ecosystem for Innovative Research in the Liberal Arts.

One of the highlights of our Institute was talking to each other—faculty, administration, staff, postdocs, and graduate students, together—about our research and discovering shared interests, approaches, and future goals. However, communicating with each other wasn’t always easy. Here are some approaches we used to build bridges across disciplines.

First, we introduced ourselves. This seems simple, but how often do we take the time to learn who is in the room, especially if there’s a large group? But the time invested here will be worthwhile. Not only does it start the getting-to-know-you process, knowing the areas of expertise represented facilitates collaboration.

Second, we participated in a number of activities together that required communication but had their own end goals, other than research collaboration. For example, many BEACONites will be familiar with the Post-It note exercise where an overarching question is posed to the group and each participant answers on a Post-It note. All of the Post-Its get placed on a wall, and participants work together to organize the answers into categories. This organizational process is a great motivator for conversation!

Third, we explicitly tackled the differences in vocabulary and domain knowledge by building a common glossary. We started with a list of important words that participants used when discussing their own research, prioritizing those that prompted the most questions and interest, such as health, variation, mechanism, learning, achievement, personality, and development. The resulting discussions were fascinating and highlighted areas of overlap and gaps to be addressed among disciplines.

Finally, the importance of time cannot be overstated. While one-time workshops can be very productive, building relationships and developing ideas takes time. For the Pop-Up Institute, the goal was to work together in the same physical space, but technology can facilitate additional formats, such as video conferencing and collaborative digital workspaces.

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Exploring Genetic Design Space with Phylosemantics

This post is written by UW grad student Bryan Bartley 

Synthetic biology is a fascinating, interdisciplinary field at the intersection of biology and engineering. Synthetic biologists envision that life can be re-programmed by rewriting the genetic code of organisms. A variety of biotechnologies for synthesizing, assembling, and editing DNA now make this possible. Of course, this idea has many profound and serious implications, one of many reasons why it is such an interesting field to work in.

Many people are uncomfortable with the idea of tinkering with the genetic code. My scientific and personal convictions lead me to believe that if humanity wants to live in harmony with nature, then we must learn to speak the language of life.

The language of life is written mostly in terms of A, C, T, or G, which, as you perhaps learned in biology, stand for the four molecular bases of the genetic code. These bases are strung together into long sequences of DNA by means of a polymeric backbone. It’s a bit of an oversimplification to describe DNA as genetic code, because frankly there is still a lot we don’t understand. However, every organism on earth, to our knowledge, uses DNA to encode living processes inside their cells. Human beings are related to the rest of the animal kingdom and in fact to all living organisms. The story is written in our DNA.

If you ever have the opportunity to take courses in biology or biochemistry, then you might just learn the basics of decoding DNA. However, unlocking the mysteries of the genetic code has taken decades, and continues to be a scientific challenge full of surprising discoveries. The approach I discuss in this week’s BEACON blog, called phylosemantics, is a technique for interpreting the genetic code that might be useful in some special cases.

Phylosemantics is a computational algorithm I developed as part of my PhD research in synthetic biology. It is a combination of methods called phylogenetics, which is commonly used in evolutionary biology, and semantic clustering, an idea with roots in artificial intelligence. Tree diagrams are used by all of these methods to classify information into families or groups with similar characteristics. There’s a good chance you have seen a phylogenetic tree before, and just don’t remember! In case you have forgotten what they look like, evogeneao.com has a nice interactive tree-of-life. Phylogenetics uses similarities in DNA sequence to group related sequences together. In contrast, phylosemantics makes a semantic comparison between different components of DNA.

For example, consider the Cox combinatorial promoter library1, which consists of 288 variant genetic promoters. Each individual promoter is composed of three genetic operators arranged sequentially in distal, medial, and proximal positions (Fig. 1). The boundary between positions are defined by the -35 and -10 sigma70 RNA polymerase binding sites. Promoter variants were derived by varying operator types at each position (repressor, neutral, or activator). Operator sites may also be varied by substituting operators derived from different species. For example G and H variants represent operators specific to LacI and TetR repressor proteins, respectively, while activator variants J and K represent AraC and LuxR binding sites. Thus, it is possible for two operators to be semantically equivalent, even while they differ in terms of their DNA sequence.

The phylosemantic tree (Fig. 2) diagrams 12 variant promoters from the Cox library. This tree systematically groups the promoter variants into 3 families based on similar configurations. The length of branches of the tree correspond to semantic distance between variant designs. If the adjacent branches have no length, then adjacent promoters have the same configuration. Tabulated next to each variant are levels of gene expression corresponding to each variant promoter. The advantage of graphing these data with a phylosemantic tree is that some patterns in gene expression become more apparent.

The first family of variants (FJK, IDD, FDB, and HEB) are clustered by my algorithm because they all have a repressor operator distally. These promoters exhibit high gene expression, despite the presence of a repression operator. In other words, repression in this family of promoters appears to fail. In contrast, the middle cluster contains similar promoters DGB and AFI with a medial repressor operator. Promoters with a medial repressor operator exhibit very low gene expression consistent with repression. This makes sense from a biophysical perspective—a repressor bound in medial position will sterically hinder RNA polymerase binding.. A design pattern may thus be stated that repressor operators in medial position exhibit a pronounced repression effect while repressor operators in distal position appear ineffective. The point of the phylosemantic tree is to systematically organize the different genetic architectures and find patterns in their behavior.

This brief explanation of phylosemantics barely scratches the surface, but I hope some readers will at least find it intriguing. Phylosemantics encompasses a number of related approaches that might apply in different scenarios. For example, different formulae for calculating semantic distance can produce trees that are more useful for one type of analysis versus another. Another choice with interesting implications is whether to construct a rooted versus unrooted tree. Scenarios in which phylosemantics might be useful include:

  • Phylosemantic classification might be useful for comparing different genetic architectures in natural biological variants
  • Phylosemantics can be used to discover genetic design rules for synthetic biology
  • Phylosemantic classification might be used to systematically classify permutations of genes in different orientations.
  • Phylosemantics could enable biodesign automation efforts by helping synthetic biologists plan rational assembly strategies starting from the given DNA templates.

If you found this discussion interesting, I will be presenting this topic at the BEACON Congress and the International Workshop for Biodesign Automation in Pittsburgh, PA in August. I’m very interested in connecting with collaborators in industry or academia who are interested in applying phylosemantic approaches to a case study. Thanks for reading my post today!


[1] R. S. Cox et al., “Programming gene expression with combinatorial promoters,” Mol. Syst. Biol., vol. 3, no. 1, p. 145, 2007.

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STEMprov for improving science communication

This post is written by UT Austin grad student Rayna Harris

Communicating science is important, and there are plenty of ways to improve. Improv is a theatrical technique that can help scientists tell better stories, understand group dynamics, and say yes in the face of the unknown. Former UT graduate student Nichole Bennett has started hosting a STEMprov workshops to help STEM folks improve how they communicate with different audiences. Let me tell you about two of my favorites improv games Nichole taught that can be used to specifically improve science communication.

‘Yes but’ versus ‘Yes and’

Have you ever pitched an idea at a meeting only to have it ripped apart to shreds by your lab mates? I know that even when I have the best intentions, sometimes I’m too quick to point out the flaws in my colleague’s research plan rather than point out the strengths. To illustrate the difference between discouraging and encouraging peer ideas, we played two games. In both games, one person pitches and idea, but the peer’s response either with discouragement or encouragement. Compare these two games or lab meeting scenarios:

Yes but example: It would be awesome to build an automated video tracking system! Yes, but John already tried it and it failed. Yes, but you can’t do that and graduate on time. Yes, but we don’t have the money.

Yes and example: It would be awesome to build an automated video tracking system! Yes, and John could give you some advice. Yes, and this would really enhance your thesis. Yes, and we can apply for a technology grant to support it.

I’d like to have a lab meeting where we brainstorm and only provide positive feedback before we perform a more critical analysis of ideas. Let us know if you’ve ever tried this.

Story Spines

Nichol also taught us how we could use a template or a ‘story spine’ to tell a well-constructed story about our science or career. The format of the story spines is this

Once upon a time ___. Every day, ___. One day ___. Because of that, ___. Because of that, ___. Until finally ___. And, ever since then ___.

I think these are perfectly adaptable for science storying because it isn’t that different from the introduction, results, conclusions format we are used to using, but it is much more compelling. In the story spine, the world exists in a certain way with routines, but then sometime changes and there are consequences. Finally, there is a resolution and now the world is different.

After the workshop, I wrote a very short story spine about my career trajectory here. I encourage you to write a story spine today and tweet it to @BEACON with the hashtag #STEMprov.

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Mapping Antibiotic Resistance in Pseudomonas aeruginosa Biofilms to Develop Better Therapies for Cystic Fibrosis

This post is written by MSU DO-PhD student Michael Maiden

I have always been interested in bacterial resistance. My first science fair project was comparing antibacterial soap versus regular soap in terms of selecting for resistant bacteria with use. In addition, I have also always wanted to be a clinician to both better understand the human body and help those around me. At Michigan State University, I’ve found a program that allows me to continue my research while earning a medical degree at the same time. Currently, I am a 6th year DO-PhD student in the physician scientist training program in Dr. Christopher Water’s biofilm laboratory. Here, I study how Pseudomonas aeruginosa, the most common pathogen in cystic fibrosis, evolves resistance with long-term antibacterial treatment.

P. aeruginosa is the leading cause of death in patients with cystic fibrosis (CF). CF is a debilitating disease that compromises host immunity, most dramatically in the lungs, resulting in life-long chronic bacterial infections. The most important clinical obstacle in CF is treatment failure due to biofilms. Biofilms are a community of sessile cells enmeshed in a self-produced thick gel matrix that leads to thousands of times more resistance to antibacterial therapies, macrophages, and neutrophils. A hallmark of CF is a defective mucociliary transport system that results in dry mucus production and clogged airways, creating an environment that is ideal for colonization by P. aeruginosa. Central to this pathogen’s success is its biofilm mode of growth within the lungs of CF patients, which are essentially impossible to eradicate with current antibacterial therapies, leading to immune complex-mediated chronic inflammation, neutrophilic tissue damage, decreased lung function, and ultimately death. Furthermore, due to their high level of tolerance, cells often re-grow after multiple rounds of therapy becoming even more resistant with time. By early adulthood, P. aeruginosa evolves and establishes a chronic infection recalcitrant to intervention in 80% of patients. Numerous retrospective studies have shown that eradication of P. aeruginosa before its chronic infectious state leads to better clinical outcomes. A key step in accomplishing this goal is enhancing current eradication therapies.

Image shows P. aeruginosa resistant mutants spread on Pseudomonas Isolation Agar plates. Plates were then imaged using a UV-light. Lower right-hand corner is ancestral strain, moving counter clock-wise, you move through time and evolution, gradual loss of fluoresces is seen indicating loss of production of a fluorescent molecule along with the development of resistances to tobramycin and triclosan.

How P. aeruginosa evolves to become more resistant, is what I am most interested in studying. I’ve found that by treating with two specific antimicrobials, tobramycin and triclosan, I can drive P. aeruginosa down certain evolutionary trajectories that render them resistant to one antimicrobial (tobramycin) but sensitive to another (triclosan). In essences, out-smarting the bacteria at their own game. To do this, I serially treated P. aeruginosa biofilms over the course of 6-months with ever increasing concentrations of tobramycin and triclosan. Using this method, the biofilms gradually evolved resistance to the combination therapy and lost the ability to produce a fluorescent molecule shown in figure 1. To date, I have evolved 191 single colony isolates that are ~200x more resistant triclosan and tobramycin combined. Next, whole-genome sequencing will be performed on these evolved resistant mutants to look for genetic mutations that could explain how becoming resistant to one class of antimicrobial renders them sensitive to another.

As antimicrobial resistance continues to be a major threat to global health, it is important to develop better strategies that more effectively used our current antimicrobial arsenal. This is especially true for CF, where patients become infected with evolved strains of P. aeruginosa that are essentially impossible to kill with current therapies. For this reason, P. aeruginosa is the leading cause of lethality in these patients and is a major clinical concern. This approach, funded by BEACON, could yield insights into how bacteria evolve resistance and methods for out-smarting bacteria at their own game. As a future clinician-scientist, developing new therapies that could possibly improve clinical outcomes is an exciting opportunity that I am grateful to be a part of this research.

From my fist childhood experiments studying the effects of antimicrobial soap vs regular soap on bacterial selection, to studying how the human pathogen P. aeruginosa evolves resistance to antimicrobial therapies, it is clear that my curiosity for the invisible human foe has persisted. BEACON has, in-part, sustained this interest and allowed me to learn, not just about the human body, but how bacteria are so central to our evolution as a species. Evolution remains a largely un-tapped resource, and I hope this work inspires others to consider it as a tool for learning more about the world around us.


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BEACON goes back to Alaska!

This post is written by MSU postdoc Wendy Smythe.

IMG_7302We have just returned from another amazing trip to Alaska where we visited Ketchikan, and the Haida communities of Hydaburg and Kasaan Alaska located on Prince of Wales Island. The trip is an effort funded through BEACONs Native American/Alaska Native Institute (NAANI) to increase diversity in STEM and to raise cultural awareness for non-native future PIs. During the visit participants taught in the Hydaburg School K-12 classes; teaching evolution of butterfly vision, shipworms, and oceanography, participants took part in harvesting local dietary resources such as spruce tips, tea, seaweed, and sea cucumbers, we were lucky to get to take a cedar weaving class from community member Becky Frank. Visiting scientists learned about the Haida culture and language from community members and conducted interviews on Haida culture, Traditional Ecological Knowledge and how the Haida way of life uses STEM to build canoes and totem poles from large cedar trees, when and how to gather resources, and how to they monitor and protect the land and sea that they are very much a part of. Traditional Knowledge is passed on through oral traditions of story telling grounded in centuries of stewardship to the region. While in Hydaburg our group participated in the 4th Annual Science/Career Fair by presenting hands on demonstrations of our own science for the students and community. Interviews with community members and local scientists were conducted for a series of documentaries featuring Traditional Knowledge coupled with STEM for the creation of culturally relevant curriculum. During our trip we encountered and ran from an angry mother bear, and participated in a spiritual dip into the ocean (which was very cold!). Postdoc Wendy Smythe, is from Hydaburg and hosted the group of BEACON graduate students Klara Scharnagl, Carina Basket, and Aide Macias Munoz, we were accompanied by Christie Poitra from MSUs Native American Institute. On July 28 the documentaries produced during this trip will be shown at the Friday seminar.

Canoe that is being carved in Kasaan Alaska

Spruce tips used to make spruce tip jelly,

sea cucumbers

Harley Bell-Holter discussing the totem pole in Kasaan Alaska

Klara Scharnagl wrapping up an interview at sunset in Hydaburg, Alaska.






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BEACON Research Fellow Dr. Wendy F Smythe receives an AAAS Science & Technology Policy Fellowship

Michigan State University BEACON Research Fellow Dr. Wendy Smythe receives an AAAS Science & Technology Policy Fellowship. Wendy will be working at NSF within the EHR/Division of Research on Learning in Formal and Informal Settings/Innovative Technology Experiences for Students and Teachers/Discovery Research PreK-12.

Fellows demonstrate leadership and excellence in their research careers, in addition to an interest in promoting meaningful dialogue between science and society, learning first-hand about policymaking while contributing their knowledge and analytical skills in federal policy. Fellows serve year-long assignments in the executive, legislative, and judicial branches of the federal government in Washington.

Dr. Smythe received her doctorate in Oceanography/Environmental Science from Oregon Health & Sciences University in 2015 and investigates microbe-mineral interactions from groundwater ecosystems and the evolution of microbial populations in metalliferious springs. She is also a Co-PI on a collaborative NSF GEOGOLD project to increase awareness of diversity in Geoscience. In addition Smythe works to couple STEM with Traditional Ecological Knowledge in an effort to increase representation of Native American/Alaska Natives in STEM disciplines, working with her tribal Haida community in Hydaburg Alaska, a tribal community located on Prince of Wales Island.

The American Association for the Advancement of Science publishes the journals Science, Science Translational Medicine, Science Signaling, and Science Advances, a digital, open-access journal. Science has the largest paid circulation of any peer-reviewed general-science journal in the world. AAAS was founded in 1848 and includes nearly 250 affiliated societies and academies of science, serving 10 million individuals. The nonprofit organization is open to all and fulfills its mission to “advance science and serve society” through initiatives in science policy, international programs, science education, public engagement and more. To learn more about AAAS STPF go to www.aaas.org/page/stpf/become-st-policy-fellow.

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