NCAT Research Excellence Award

Posted on April 2, 2018 by hageyt

We are very excited to congratulate Dr. Joe Graves and the entire BEACON team at NCAT for receiving this year’s Research Excellence Award for Interdisciplinary Team. Every spring, NCAT celebrates outstanding accomplishments and efforts of faculty innovators, mentors and dynamic leaders with a Celebration of Faculty Excellence in Research and Teaching Banquet. The Interdisciplinary Team award honors research teams that break down the traditional boundaries of academic disciplines.

Back row (L—R) Keara Coffield (G), Dr. Misty Thomas, Dr. Joe Graves, Kimberly Hunter (UG), Dr. Jude Akamu Ewunkem, Sada Boyd (G). Front Row: Danielle Williams (G), Dr. Jessica Han, Anuolowapo Odelade (G), Adero Campbell (G); Janelle Robinson (G).

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Art and Science, Science and Art: Science outreach to young artists

Posted on April 2, 2018 by hageyt

This post is by MSU grad student Cybil Nicole “Nikki” Cavalieri

Figure 1: Leonardo da Vinci Antonym of a women; Ernst Haeckel Thalamorpha Plate; Young REACH artist with a Terror Bird

“I am not good at science, I am more artistic.”

“I have decided to drop biology, I am changing my degree to packaging I want to work in a field that lets me be creative.”

“I can’t draw the shape of this skull I am not an artist.”

These are things undergraduate students at Michigan State have told me. Science and art have not always existed in the polarized state we think they do. They have always been connected. In fact, the similarities between artists and scientists far outweigh the stereotypical differences. Neither fear the unknown. They welcome it.

Art communicates scientific research. Art is how we visualize our data. Every scatterplot, phylogeny, and manuscript are art. They might not be judged on their beauty, emotion and uniqueness, but they are still art. Collaborations between artists and scientists can be fruitful. Artists can serve as partners in the communication of scientific research. They can help us visualize data in new ways. They can help us make our results easier to understand and present them more compellingly. Also, they can help us reach a larger and different audience with our scientific message. Not only can art help visualize data, art is data. Researches have examined paintings from the Tate and National Gallery in London (1500 – 2000 BCE) of sunsets as a proxy for information about the aerosol optical depth after major volcanic eruptions. Historically science has produced the materials (pigments, canvas, photographic emulsion etc.) and methods of art. Modern collaborations are more than just better paint. Modern artists use materials from the realm of science such as bacteria, robotics, and computer languages to express their visions. Scientists and artists have even teamed up to explore how art affects the human brain.

Figure 2a: Nikki Cavalieri shows artists pygmy hippo skull.

Figure 2b: Nikki Cavalieri explains the evolution of morphology in primates.

 

 

 

 

 

 

 

 

Figure 3: Kasey Pham botanical artist drawing squash.

In recent years there has been a push to change STEM (Science Teaching Education and Mathematics) to STEAM (STEAM plus an A for art) to ensure that creativity is not left out of education. A group of MSU scientists have been spending one afternoon each month communing with teen artists at a fantastic local (Lansing) community arts center called REACH!. Our goal is to connect MSU students and staff who seek to bridge science and art with junior high and high school artists. Through activities at REACH, we aim to link art and science in as many ways as possible. In one of our earlier visits, I brought museum specimens (Figure 2) for the REACH kids to sketch, emphasizing the link between biological form and function. Later, I helped them develop chimeras incorporating morphologies of plants and animals, endowed with adaptations befitting a randomly chosen (‘wheel of fortune’ style) environment. During another visit, Kasey Pham (Figure 3) brought a live chameleon and tarantula for students to draw. This gave them a chance to focus on the dynamics of animal movement, and the intricacies of the integument – how light catches hairs, scales, and colors. As a talented artist who is also a plant scientist, Kasey spent one afternoon teaching teens about the chemistry of henna tattooing and then left the kids (and us) with favorite animals stained on our arms.

Figure 4: Young artists examines a human skull, it is important to note there was a concurrent costume party.

Figure 5: Kasey Pham shares her artist notebook with students.

Figure 6: Artist drawing goliath frog, pygmy hippo and Dinocrocuta skull

 

Figure 7: Kasey Pham gives Eben Gering a henna tattoo.

Figure 8: Artist showing off their sweet henna tattoos.

Figure 9: Artist showing off their sweet henna tattoos.

The world is a much poorer place when we separate things that should be together. It is important that developing artists and scientists see that science and art are not opposed. Through this program and programs like it hopefully future students will understand it is not art or science it is art and science.

 

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Evolution is the New Deep Learning

Posted on March 21, 2018 by hageyt
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Using music, beer, and pop-culture to communicate science. Zombie Brains: Microbial Mind Control

Posted on March 19, 2018 by hageyt

This post is by former UT Austin graduate student Rayna Harris.

I recently gave a talk at The North Door for Nerd Nite Austin. This is a monthly event with an audience of 250 partially inebriated nerds, including about a dozen colleagues and friends. I put a lot of effort into making it fun and relatable, so I thought I would share some of the details about how and why I gave what I think is my best talk ever.

You can view the video here and view my slides are here.

Science and sign language

I knew I would have a sign language interpreter with me on stage, so I tried to minimize jargon and define the scientific words I used. I recorded myself practicing my talk and critiqued the video playback about six times. I focused on reducing my use of filler words “um” and “like”. I specifically asked the interpreter to create a sign for “microbiome”  because I knew I would use it more than a dozen times.

On stage with a sign language translator and a ‘Tom Waits does David Attenborough’ impersonator. Instagram photos available

Incorporating live performance and YouTube videos

I wanted to show this BBC David Attenborough video, but I was worried that people would be bored or that the sound quality would be bad, so I decided to play the video on silent and add my own sound. I invited my friend Joseph Palmer to narrate it using his amazing impersonation Tom Waits. With the help of the sound engineer, I cued a clip of Tom Waits Oily Night song to provide an eerie backdrop. Joseph’s performance received much applause and laughter. It was awesome!

Watch this 30-second video clip on Twitter of the Tom Waits-narrated footage of an infected insect being evicted from the social colony.

The 3 main themes of my talk

I decided that I would cover three main topics during my talk: parasitic mind control in insects, the link between the gut microbiome and the brain in humans, and the potential for parasitic mind control in humans. I opened with a definition of the word “microbiome” because I thought that was the best hook and it allowed me to engage the hearing-impaired viewers with a brand new sign. But, then, I launched into the 3 parts in the ordered described. This collage of images provides a good overview of my talk.

These are all the images I used in my talk to illustrate beautiful biological phenomena and link it to current social phenomena.

First, I describe deadly host-pathogen relations in the jungle using photos from photos from Alex Wild and the Tom-Waits narrated video from the BBC. I describe research from Carolyn Elya, Michael Eisen, and colleagues on a fungal pathogen that manipulates Drosophila melanogaster in the lab. I take a moment to highlight other awesome neuroscience and molecular -development research in flies.

Then, I transition to talking about the dynamics of human microbiomes, with much of my inspiration coming from a book by Ed Yong on the multitudes of microscopic organisms living in our body. I got a lot of questions during the Q&A about how diet and disease affect and are affected by our microbiomes.

Finally, I talked about the possibility of microscopic organisms influencing social behaviors such as kissing, hand holding, breastfeeding, and more. The examples I used are inspired by basic research and by personal experience. I kept my language very casual to keep the audience engaged, and I got a lot of laughs and applause during this part of the talk. I hope they go away knowing what “horizontal gene transfer” is.

Similarities between host-parasite relationships and sexual harassment

I wanted to have something in the talk that made it timely, so I decided to make an analogy between host-parasite relationship and current social movements related to sexual harassment and discrimination. I was very worried that this tangent on sexual harassment might not go over well, but I felt compelled to utilize my moment in the spotlight with a microphone to discuss an important social issue that affects many women in science.

I practiced this segment of my talk a lot, and I posted a short video of my last practice session here. What I said on stage was a little different than during that last practice session, but I kept the analogy between infected ants being evicted from colonies to women fearing job loss if they showed evidence of being harassed.

To my surprise, this portion of my talk drew even more applause than my friend’s impersonation of Tom Waits! However, this time people weren’t clapping and cheering because it was funny or novel; I think they were signaling to me that the could relate to what I was saying and that they were glad I had the courage to talk about it on stage.

The Q&A session

The Q&A lasted for what felt like 15 minutes. I made sure to repeat every single question from the audience in my own words before responding, which I think is something I will try to do in the future. Most of the questions were of a biomedical nature that I felt I didn’t have the expertise to answer, so I tried to say “I don’t know for sure, but here is what I think…” when responding.

I did get one fun question and I responded with some research from the Lenski Lab. The audience member asked something along the lines of whether or not we should fear gut colonization by ancient bacteria that have been trapped in glaciers but are now being brought back to life. I responded by saying Lenski had done a lot of experiments competing older generation and newer generations of bacteria against each other and the most recently evolved bacterial almost always performed than the ancient ones. I didn’t give him a citation, but this paper on sustained fitness is what I think backs up my response.

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Feral chickens are a-changing: updates on the rapid evolution of Kauai's hybrid Gallus gallus

Posted on March 8, 2018 by hageyt

This post is by MSU research associate Eben Gering.

The author, a collaborator (Kayleigh Chalkowski), and an especially ‘domestic-like’ feral chicken in the Florida Keys

After an hour of trying to trap chickens at Hanalei Beach Park, we had only caught odd looks from locals. Finally, one bold rooster approached our buried net, cautiously tapped the spring-loaded frame, and gave an ear-splitting crow. The whole flock disappeared into the bushes, and I won a high-stakes wager with Kathyrn Fiedler, a local collaborator. “Fine,” she grumbled “they’re not so stupid after all.”

We will contemplate feral chickens’ tenacity and intelligence a bit further on. Meanwhile, if you’re curious what these animals were doing on a beach immortalized by Peter, Paul and Mary1, join the crowd. In an earlier blog entry, I described how DNA sequencing of Kauai chickens and fossils helped unravel their fascinating origins. Like the Hanalei locals, it turns out, these birds are exceptionally diverse. They are descended from both Red Junglefowl, brought to Hawaii by ancient Polynesians, and domestic chickens that arrived later, with western explorers and farmers. Recent hybridization between these ‘wild type’ and domestic chickens produced the highly variable, extremely successful, and ‘not-so-stupid’ flocks that occupy Kauai today2.

Understanding how populations came to be where they are is the central goal of biogeographical research, and it serves many purposes. Distributions of living organisms led Charles Darwin and Alfred Russel Wallace to a theory of evolution supported by countless comparative and experimental studies. Among them are studies of bacterial evolution led by Michigan State colleague Richard Lenski, who also co-founded BEACON to “illuminate and harness the power of evolution in action to advance science and technology and benefit society”.

Feral chickens inhabit most of Kauai’s scenic and variable habitats. This image from Kōkeʻe State Park highlights the mixture of wild (forest) and artificial (asphalt) elements feral chickens navigate on a daily basis.

In support of this mission, biogeographical analyses can help predict where invasive or endangered species might one day thrive.  It is not always clear though, whether and how we should apply this powerful insight. Consider the case of Kauai and its neighboring (Hawaiian) islands. There are both cultural and environmental reasons for conserving the archipelago’s heritage species, which arrived many centuries ago with Polynesian colonists. Today, these animals and plants serve a variety of useful purposes, and they are embedded in the Hawaiian ecosystem and culture. On the other hand, these non-native species also have negative impacts on native wildlife and local residents. Feral pigs, for example, are wreaking havoc on Hawaiian forests and farms. They also create breeding grounds for non-native mosquitoes, which spread human and wildlife diseases.

What about the feral chickens? Local attitudes towards these charismatic and often noisy neighbors are as variable as the chickens themselves. Kathryn, who still owes me a cocktail, is concerned they may transmit bacterial pathogens to local crops. However, as many farmers already know, chickens can also provide ecosystem services like pest control and soil improvement.

For better or worse, feral chickens’ ecological impacts have not been well studied –  this is something my collaborators and I are currently exploring. For now, let me give one fairly simple observation: it’s a pity that so many well-intentioned humans feed feral animals haphazardly. This only boosts populations to higher densities than local resources can support. In Hawaii and elsewhere, I have seen humanitarian efforts backfire, causing both unnecessary animal suffering and environmental degradation. So, if you are moved to help feral animals – please coordinate your efforts with local animal control and wildlife authorities. Thanks!

Getting back to our research update: Dr. Fielder may have lost our bet, but her research is succeeding. Her findings from Kauai will soon help guide intelligent management of feral populations, both in and beyond Kauai. But let’s get back to the apparent intelligence of the Kauai chickens themselves, and some basic questions about its recent evolution. Steven Gould, a celebrated author and evolutionary thinker, once asked what would happen if we could restart earth’s history and watch life evolve again. Would it take similar paths to produce life as we know it? Research from the Lenski lab has given us some clues. If evolution is replicated under carefully controlled conditions, adaptation to novel environments is indeed repeatable… if, and only if, a population crosses a stochastic (randomly attained) threshold of ”background’ evolutionary change.

It turns out evolution is also somewhat repeatable outside of the laboratory. For instance, studies of Caribbean lizards by Jonathan Losos’ group show that animals often evolve predictable forms and ways of life when they colonize similar ecosystems. Surprisingly, these evolutionary changes can occur very quickly – in just a handful of generations or less. If you’re interested in learning more, have a look at Dr. Losos’ new book, about the paradoxical predictability and capriciousness of evolution3.

By studying feral animals, my collaborators and I ask a related, but different question from Steven Gould: what happens when we reverse domestication (a human-directed evolutionary process)? Can evolution in natural environments undo behaviors, or other traits, instilled by centuries of selective breeding? Can we predict such changes, and use them to build better livestock, or protect wild populations? Feral animals abound nearly everywhere humans do, yet neither Lenski’s lab studies, nor Losos’ lizards can tell us precisely how these human-altered organisms will evolve in a human-altered landscape. This is one reason for my fascination with Kauai’s feral chickens. Now that we know where they came from, we can better understand how they are evolving.

DNA sequencing revealed that Kauai chickens are hybrid descendants of wild Red Junglefowl and domesticated breeds. It also suggested Kauai hens might inherit a gene from the Red Junglefowl that enhances their ability to raise their young in the wild. This hen’s offspring showcase the Kauai population’s impressive diversity, which was enhanced by hybridization between domesticated and wild populations.

To learn how chickens have adapted to feral environments, several European collaborators and I are now searching their genomes for signatures of recent, rapid evolution. Analyses by Martin Johnsson, a former graduate student in Dominic Wright’s lab (Linköping University, Sweden) found that genes controlling chicken reproduction and behavior are evolving quickly in the Kauai population4. We have also made progress in identifying the sources of the favored variants (i.e. versions) of the quickly-evolving genes. Care to bet where the winners came from?

You might have guessed that the Red Junglefowl gene variants would outperform the domesticated alternatives. After all, Red Junglefowl thrive in wild Asian jungles without any human help. This prediction is partially accurate: certain ‘wild-type’ (Red Junglefowl) gene variants are, indeed, over-represented in the Kauai population. And included among the genes that follow this pattern is one that critically affects brain development and maternal care behavior. Why is the domesticated chicken’s version of this gene disadvantaged in feral hybrids? We predict experiments will show this reflects their comparative inability to hatch and nurture young in the wild. Perhaps ‘wild-type’ (Red Junglefowl) versions of this gene also help hybrids build brains that can respond to dangers of the wild, such as nosy biologists’ traps. Together with Dominic Wright and Rie Henrickson, we will soon begin testing these ideas, and learn how feral brains and behaviors evolve.

In other compartments of feral chicken genomes, evolution is taking a very different path. For example, evolution has favored the domesticated version of a gene cluster affecting bone growth, comb mass, and egg production in Kauai chickens. We think this may reflect the domesticated chicken’s ability to outgrow and out-reproduce Red Junglefowl, a legacy of selective breeding for streamlined poultry production. For an educational activity exploring this idea (using data you can gather from tourist photos), have a look at our Data Nugget activity.

In this entry, I have focused on what genomic data tell us about the role of hybridization in Kauai chickens’ recent adaptive evolution. Ultimately, though, experimental studies are still needed to truly understand the environmental and social challenges that drive observed genomic changes. Fortunately, with practice and stealth, our trapping abilities have vastly improved. Unfortunately, we still get strange looks when we put them to use. Our understanding of feral chicken behavior and adaptation are also evolving quickly. Stay tuned for the next update, if you’d like to know more.

1 https://en.wikipedia.org/wiki/Puff,_the_Magic_Dragon

2 Gering E, Johnsson M, Willis P, Getty T, & Wright, D (2015). Mixed‐ancestry and admixture in Kauai’s feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs. Molecular ecology.

3 Losos, J. B. (2017). Improbable destinies: Fate, chance, and the future of evolution. Riverhead Books.

4 Johnsson, M, Gering E, Willis P, Lopez S, Van Dorp L, Hellenthal G, Henriksen R, Friberg U, Wright D (2016). Feralisation targets different genomic loci to domestication in the chicken. Nature Communications 7: 12950.

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Can birdsong signal immune gene quality?

Posted on February 25, 2018 by hageyt

This post is by MSU postdoc Joel Slade. 

Joel recording bird song in 2014.

“BEEP! BEEP! BEEP!” – I wake up to the dreaded sound of my alarm clock at 3:45 am in my cabin. Even though it’s mid-April at the Queen’s University Biological Station in Elgin Ontario, the chilly air still penetrates my bones as I rapidly put on my warm field gear and grab my flashlight to meet the field team. In the back of our field vehicle are two parabolic microphones, and kits to collect blood, take body measurements, and band our study species, the song sparrow (Melospiza melodia). This relatively plain looking songbird has been the main model species for the MacDougall-Shackleton lab in the biology department at Western University in London, Ontario (where I completed my PhD). However, where this bird is lacking in coloration, it makes up for in melodic beauty. Male song sparrows are one of the first songbird species to arrive to their breeding ground at our field site around late March/early April to stake out their territory. When you arrive early in the morning all you can hear are males defending their territory and trying to attract females that are slowly arriving. However, not all males are of equal acoustic quality, and this may be determined by a family of genes called the major histocompatibility complex (hereafter, MHC).

Listen to one of Joel’s recorded song sparrows Photo Credit: Tosha Kelly.

In jawed vertebrates, MHC genes produce cell-surface proteins that recognize pathogen-derived antigens, which are presented to T cells to initiate an adaptive immune response. What’s fascinating about MHC is its incredible genetic diversity. The MHC is one of the most polymorphic gene families in existence, whereby many species contain multiple alleles. For example, in my PhD study species, the song sparrow, we characterized up to 26 MHC alleles per individual, and 517 different alleles across the population. It is posited that pathogen-mediated balancing selection is responsible for this immense diversity at MHC in many animals. For example, risk of disease by multiple pathogens should favor heterozygosity at MHC loci. Likewise, antagonistic coevolution (host-pathogen arms races) should generate new MHC alleles. So, there is no doubt that expressing a wide-variety of MHC molecules should confer fitness benefits, but could being too diverse be a bad thing?

Juvenile male song sparrows experience a critical learning period during their first year of development. Within this critical period, males will listen to the songs of local males and create their own song types. After a year, males are no longer capable of learning new songs. Therefore, their condition in early life is critical for them to increase their song repertoire size. Males range from singing as little as five song types and as much as 12 song types. Females are more likely to choose males with more song types, as it is considered an honest signal of quality. Since MHC diversity is critical for the adaptive immune health of vertebrates, I postulated that MHC diversity of male song sparrows is related to their song repertoire size. I predicted that males with high diversity could fight off more pathogens while learning songs in early life, and therefore would be able to invest more energy into song learning instead of immune defense.

Figure 1: Relationship between song repertoire size and the number of MHC alleles in male song sparrows. (#MHC t = 2.20, p =0.036; #MHC2 t = -2.26. p =0.031)

When I compared song repertoire size to MHC diversity, I found that MHC diversity is related to song diversity, but in a direction that I did not anticipate. It was males with intermediate MHC diversity that sang the most amount of songs, rather than males that were maximally-diverse at MHC. This created a non-linear (quadratic) trend whereby males with low and high MHC diversity sang the least amount of song types (Figure 1). What may explain this trend?

Apparently maximal MHC diversity may be bad for your health. Two main hypotheses exist to explain this phenomenon: (1) too many MHC alleles may cause autoimmune disorders whereby MHC proteins start recognizing self-antigens as non-self antigens, and (2) too many MHC alleles expressed may cause a dilution effect whereby the most important MHC alleles required to recognize a pathogen are not in high abundance, and therefore you may not be able to recognize the invading pathogen. My study is not the first to discover an intermediate MHC diversity advantage. In fact, in three-spined sticklebacks (Gasterosteus aculeatus), individuals with intermediate MHC diversity had the lowest parasite loads than those that had low or high levels of MHC alleles (Wegner et al. 2003). My study may therefore reflect a balance between pathogen-mediated selection and selection against maximal MHC diversity, which is critical for song learning in these sparrows.

At BEACON, I am bringing my expertise on avian immune genes by working with Dr. Danielle Whittaker and Dr. Kevin Theis. We are exploring how host immune genotype can shape their microbiome, and thus shape the semiochemicals produced by commensal bacteria.

This blog post is based on Slade et al.’s (2017) study in Biology Letters.

Reference:

Wegner KM, Kalbe M, Kurtz J, Reusch TBH, Milinski M. 2003 Parasite selection for immunogenetic optimality. Science 301, 1343.

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BEACON collaboration to study amphibian-associated skin bacteria

Posted on February 21, 2018 by hageyt

This post is by MSU grad student Patric Vaelli

Rough-skinned newt (Taricha granulosa) along the edge of a pond near Moscow, ID.

Animal bodies are inhabited by diverse communities of microorganisms that we collectively call the microbiome. These communities consist of bacteria, fungi, and viruses, all of which can affect the physiology, behavior, and even the evolution of their animal hosts. In our research, we seek to understand what roles the skin microbiome of amphibians, specifically newts and salamanders, play in the production of specialized toxins that protect the animal host from predators.

We set out to address this question through a BEACON-supported collaboration between the Eisthen lab at Michigan State University and the Foster lab at the University of Idaho. The Eisthen lab has been working on the sensory biology and behavior of a poisonous salamander called the rough-skinned newt (Taricha granulosa) for a number of years, while the Foster lab specializes in the preparation, sequencing, and analysis of bacterial DNA. Details of the project can be found in an earlier BEACON blog post.

BEACON graduate student Patric Vaelli, with a rough-skinned newt (Taricha granulosa)

In September of 2016, I boarded a plane from Detroit to Moscow, ID, where I began a five week “mini-sabbatical” at the University of Idaho. As part of this trip, I would learn how to extract and prepare bacterial DNA for high-throughput sequencing. This was the easy part – the more challenging endeavor was to begin developing the computational and statistical skills necessary for reconstructing and interpreting the newt microbiome from the short pieces of DNA sequence generated by high-throughput sequencing. Last but not least, there were also wild populations of rough-skinned newts near Moscow! How lucky could we be?

When I arrived at the Pullman-Moscow regional airport I was greeted by our friend and collaborator Dr. Janet Williams. She brought me to my new home for the next five weeks: an apartment that I shared with a fellow graduate student from U Idaho. Within two days of arriving in Moscow, I was catching wild newts near a forested park north of town and collecting bacterial samples from every newt I could find. We collected bacterial samples using sterile swabs, from which we later extracted bacterial DNA for sequencing. We also collected small skin biopsies from each animal that would later allow us to measure the amount of toxin in the skin of each newt.

Patric Vaelli and BEACONite Yannik Roell (now at Aarhus University in Denmark) collect bacterial samples from wild newts near Moscow, ID. Bacterial samples will be used for DNA-based analysis of the amphibian skin microbiome. Samples are also collected from the pond and soil for comparison.

For the next 3 weeks, I spent each day carefully extracting bacterial DNA from each swab. This process is extremely sensitive to contamination; bacteria are everywhere, even in many commercially available DNA extraction kits (a problem now referred to as the “Kitome”). Once I had extracted the bacterial DNA, I performed targeted sequencing of the 16S rRNA gene, a “phylogenetic marker” gene present in all bacteria. The sequence of this gene can be used by biologists to identify the species of bacteria within a sample, similar to a species “barcode”. Once we obtained the sequence data, I used a combination of data processing pipelines including dbcAmplicons and mothur to assemble the raw sequence data into the “barcode” sequences that I could then classify into different bacterial groups.

From here, we could ask broader ecological questions about the skin microbiome. What’s the total diversity (alpha diversity) of the microbiome within each animal? How different is the composition or structure of the microbiome across different groups of animals (Beta diversity)? Do these measures correlate with traits in the animal host such as toxicity?

As a BEACON graduate student, I’m extremely grateful for the opportunity to conduct interdisciplinary research at a partner BEACON school. Through this BEACON-supported “mini-sabbatical”, I was able to conduct field work with my model animal in its natural habitat, gain lab experience in preparing bacterial samples for sequencing, and begin to develop computational skills in sequence processing and data analysis. This training is invaluable for my success in future projects. I also had the opportunity to meet and work with a new lab group and live in a new place. I strongly encourage new graduate students to seek out and develop collaborations, especially with your fellow BEACONites!

 

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A Tail of Two Ascidians

Posted on February 19, 2018 by hageyt

This post is written by UW grad student Alexander Fodor

Figure 1. Photographs of the ascidian Molgula occidentalis taken in an isolation tank at the University of Washington’s Friday Harbor Labs. Photo by Alexander Fodor.

Searching through the lower intertidal and subtidal rocky beaches you notice a small strange creature attached to the underside of a rock in a small pool of water. It has a round body and two tubes pointing straight at you. You reach down and touch it, it feels leathery and almost plant like; you squeeze it and it shoots a stream of water right in your face. You have found a sea squirt (also called ascidians or tunicates) (Figure 1). These creatures appear very different from us and you may not even recognize it as an animal, but they are chordates, members of our own phylum that you can easily see in their tadpole larvae (Figure 2L). When it comes time to reproduce they are free spawners, spraying sperm and eggs into the water where the eggs are fertilized by another individual and develop into tadpoles. Ascidian development (Figure 2) is determinant and invariant across all solitary sea squirts where the cellular fate is set up with each division and each cell is always destined to become the same structures; so if you trace the cellular fate of a cell in one solitary ascidian, if you look in a different species, that same cell will become the exact same tissue. As they develop they form a tadpole that looks much like a tiny larval frog, complete with a notochord in the center of the tail and gravity sensing and light sensing structures in the head. They spend anywhere from a few hours to several days as a tailed larva with a notochord, searching for the appropriate substrate, using their light sensing and gravity sensing structures to swim underneath an object (like a dock or rock) and attach their head to the bottom. They then absorb their tail and completely change their anatomy, absorbing all of their larval structures, growing two feeding siphons, and surrounding themselves with a tough tunic, containing cellulose. The cellulose operon, consisting of three genes, was retro-virally spliced into the tunicate ancestor’s genome (Dehal et al. 2002).

Figure 2. Development of Boltenia villosa up to tadpole larva (L) then metamorphosis (M) though adulthood (N and O). The orange color in the developing embryos (A-N) is caused by myoplasm of cells destined to become muscle cells. Larva photos taken during an Undergraduate Apprenticeship at the University of Washington’s Friday Harbor Labs spring of 2001, adult photo by Alexander Fodor at Friday Harbor Labs.

Molgulids are a special family of sea squirts where the larval tail and notochord has been lost several times in species in the family completely independently of one another. The tailless species all have a similar phenotype where they only have fewer than 40 notochord cells, and they do not converge and extend into a notochord, but rather sit on the side of the embryo in what has been described as a “notoball”. In addition they have lost their gravity and light sensing organs (Figure 3C). These animals typically live in northern waters where there are very strong tidal currents so it is conceivable that animals could still disperse enough even without a swimming tail (Huber et al. 2000). We are uncovering the molecular mechanisms underlying this tail loss by studying two species, Molgula oculata and Molgula occulta, in the Swalla lab at the University of Washington’s Friday Harbor Labs. These two species are sister species, but they have very different looking larvae: M. oculata has a fully functioning tail with a 40 cell notochord inside and gravity and light sensors in the head, but M. occulta is lacking all of the larval structures. The species are still closely enough related that they can be hybridized them in the lab. If the egg of the tailed M. oculata is used, then the resulting larva always has a fully functioning tail and notochord; but if the egg of the tailless M. occulta is used, then some of the time the resulting hybrid has a half tail which is only composed of 20 notochord cells, but it still converges and extends out (Swalla et al. 1990), in addition, the paternal expression of the tyrosinase gene saves the gravity and light sensors (Raccicopi et al. 2017) (Figure 3).

In collaboration with the C. Titus Brown Lab (formally MSU, now UC Davis), our lab has recently sequenced the genomes and transcriptomes of M. oculata, M. occulta, the hybrid made with M. occulta eggs, and M. occidentalis (the outgroup for the Molgula family) (Stolfi et al. 2014). We are currently searching through the genomes and transcriptomes, looking for the molecular mechanisms responsible for this change in morphology. We have identified a number of genes that could be involved in this tail loss, and examining their sequences, and are testing their expression profiles. In the summer of 2018, Dr. Billie Swalla and I are going to go to Roscoff, France where M. oculata and M. occulta live to dissect gravid adults and obtain embryos for transgenic experiments. We will use gene-editing techniques to express tailed M. oculata genes in the tailless M. occulta and the hybrid made with the occulta eggs to see if we can recapitulate the tailed expression. It is very intriguing to think about how evolution can make a small number of changes to a gene network, which can in turn change the expression of a whole structure and the life history of the organism. It is nice to use sea squirts for such experimentation as they are very closely related to the vertebrates so can teach us much about how complex gene networks can be altered, and in turn change complex evolutionary traits. We are grateful for the BEACON funding that we have received for this project and are looking forward to making progress on the project in the coming years.

Figure 3. Pictures and cartoons of the larvae of A. M. oculata C. M. occulta and B. The hybrid made with M. occulta eggs and M. oculata sperm. Adapted from Swalla and Jeffery 1996

Sources:

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Racioppi, C., Valoroso, M. C., Coppola, U., Lowe, E. K., Brown, C. T., Swalla, B. J., Christiaen, L., Stolfi, A., Ristoratore, F. 2017. Evolutionary loss of melanogenesis in the tunicate Molgula occulta. EvoDevo. 8:11

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Stolfi, A., Lowe, E., Racioppi, C., Ristoratore, F., Swalla, B. J., Brown, C. T. and Christiaen, L. (2014) Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians. eLife 2014:3:e03728

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