CLICK HERE TO READ ON IGB WEBSITE Animals often use vocalizations to warn of nearby danger to others. While this information is generally intended for members of the same species, other species can eavesdrop on the warnings to use the information for their own benefit. Sentinels are animals that have warning calls so widely understood by others that those other species will form groups with them, relying on the sentinels to provide warnings for danger. For example, the family Paridae, which are a group of birds that consist of chickadees, tits, and titmice, are known as sentinels because their alarm call for danger, which fittingly sounds like “chick-a-dee-dee-dee,” is understood by most other bird species in their mixed-species flocks. “Many animals form mixed-species groups, and the thought is that this is an anti-predator behavior,” said Henry Pollock, Executive Director of the Southern Plains Land Trust. “There is safety in numbers, and there is a benefit to surrounding yourself with a more diverse set of eyes and ears. However, you have to be able to understand the information that the others around you give to make use of it.”
Sentinel calls are so readily understood as a signal for danger that researchers wondered whether species that have never heard the call would still get the message. After a recent study found that birds in the Neotropics were responsive to unfamiliar chickadee alarm calls from North America, researchers at the University of Illinois Urbana-Champaign wanted to expand on this. The team sought to test if bird communities across three different continents could understand calls for danger from a sentinel they had never encountered before – the dusky-throated antshrike. Antshrikes are birds widely distributed across Central and South America that often act as sentinels in their mixed-species flocks. The study was spearheaded by Pollock and Jonah Dominguez, a graduate student in the Program in Ecology, Evolution, and Conservation, who conducted the experiments along with researchers in the lab of Mark Hauber (GNDP), a former professor of ecology, evolution, and behavior at the University of Illinois Urbana-Champaign, and collaborators from Serbia and China. The researchers presented playbacks of warning calls of the dusky-throated antshrike, along with warning calls of a local Paridae sentinel and controls, to flocks of wintering birds in North America, Europe, and Asia, and measured their behavioral responses. The researchers predicted that birds on each continent would respond most strongly to the playback of their local sentinel since they were already familiar with the calls. However, the team was surprised to find that flocks were also highly responsive to the unfamiliar antshrike’s warning calls. “We expected to see some kind of response to the novel antshrike’s calls, but predicted that birds wouldn’t respond as strongly to it as their own local sentinel’s calls,” said Dominguez. “However, we were surprised to find no statistical difference in how birds responded to the local versus foreign sentinel’s alarm call. Birds were responding to the unfamiliar antshrike’s call as if it was a bird they’ve known their whole lives.” Flocks of birds across all three continents responded equally as strongly to the unfamiliar antshrike’s warning calls as they did to familiar, local sentinel’s warning calls. The researchers say this finding suggests there is something to sentinel calls that makes them so universally recognizable. For messages that contain important information, such as a warning call for danger, evolution likely converges on similar sounding calls that help get across the message as quickly as possible, according to the researchers. “It’s possible that these calls are more readily recognized across species because they have a central theme – essentially something about them that is unique and conserved despite millions of years in evolutionary history,” explained Dominguez. “There is research in other animals on specific amplitudes and frequencies of sound that cause innate responses, even in animals that are unfamiliar with those sounds. Our study can help researchers figure out what those acoustic elements might be for birds.” “What’s amazing is that our findings are consistent across three different continents with completely different bird communities, which suggests there is some signal encoded within these sentinel alarm calls that cause birds to respond to them, independent of previous experience with that signaler,” explained Pollock. “This really highlights that signal recognition is not always something that has to be learned through environmental experience.” The team says the study opens the door to many future research directions to take. Testing birds with the calls of other sentinels and getting more granular in terms of the behavioral responses recorded are potential next steps, according to the researchers. Dominguez also plans to try to standardize what is categorized as a sentinel species across the literature, since it is currently not well established. “Sentinel species are not very well defined, as the term is used nebulously for any animals that engage in mixed-species foraging and signaling,” said Dominguez. “There’s lots of birds that we don’t typically think of as sentinels being classified as them in the literature, and others that probably are sentinels that are being overlooked. I want to figure out if there’s a common thread between them, and whether the term should be used on the species level or more on a flock level.” The study, which is published in Biology Letters, was funded by NSF, Illinois, the Ministry of Education, Science, and Technological Development of Serbia, and the Basic Scientific Research Projects of Liaoning Provincial Department of Education grant. The paper can be found at: https://doi.org/10.1098/rsbl.2023.0332
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CLICK HERE TO READ ON IGB WEBSITE Did you ever collect something from nature as a kid, preserving it to recall cherished memories later in time? Capturing the beauty and wonder of the natural world through foraged finds is the mission of Cris Hughes (GSP), a local artist and Clinical Associate Professor of Anthropology at the University of Illinois Urbana-Champaign. Hughes’ art showcases 3D botanical compositions created from dried specimens of plants and insects foraged from nature. Using traditional pinning display techniques to arrange the specimens, she creates intricate and detailed collages, which she refers to as “natural portraits,” as part of her Secret Gardens CU art collection. “When foraging, you really have to take your time and pay attention to what’s around you,” said Hughes. “I've seen how natural it is for kids to spot small things, and how unnatural it seems to be for adults to take the time to do such. In my art I try to encourage people to focus on the little things. People will often look at it, see some tiny details, then come back and look at it again to find more. I try to invoke that childlike sense of wonder and close attention to the world around you.”
Throughout the years, Hughes has consistently incorporated a collaborative element into her art, as the specimens featured in her works are often donated by individuals from various locations. This summer, she took this collaborative aspect of her art to a new level by conceiving a project that required a community-wide effort. Hughes, in collaboration with Julia Pollack, IGB’s Creative Program Manager and curator of the Art of Science program, and Wendy Dorman, a graduate student in the department of natural resources and environmental sciences, envisioned the project “Capturing CU in a Collaborative Collage: A Natural Portrait from Foraged Finds.” The project aimed to foster community involvement and appreciation for local flora and fauna through the creation of a massive collage composed of donated foraged objects from all around Champaign-Urbana. Their proposal received the Urbana Arts and Culture Program grant for 2023. This summer, Champaign-Urbana community members were encouraged to collect natural objects from their backyards, gardens, personal collections, or during foraging events organized by the local parks district and contribute them to the project. Over 100 species of flora and fauna were donated, including flowers, plants, insects, mushrooms, and more. Hughes says that the diversity of donated items highlights how everyone appreciates nature in their unique way. “I remember when we did the Farmer’s Market drop-offs, that I would leave out everything people had donated so everyone could see the diversity of items,” said Hughes. “And someone came up and asked ‘did somebody seriously donate a fly?’, and if I was actually planning on including it in my art. I think it’s amazing that somebody in the community connected with this insect that to someone else is totally polarizing. This piece mashes together people’s preferences and emphasizes how we all appreciate different things in nature, and I think that's a really beautiful thing.” The massive collage, titled “Reflection”, was unveiled on September 23rd as part of an art show at the Anita Purves Nature Center. The piece stands over 3 feet tall, and required nearly 50 hours to construct. Everything within the collage was collected during the summer of 2023 to capture that specific moment in time, save for a single butterfly from a special collection donated to Hughes by local residents a few years earlier. “From afar, the piece appears as this striking floral arrangement, but as you get closer you realize how breathtaking the detail of it is,” Pollack remarked. “You notice a bee perched on a flower, eggshells with insects crawling around them, a cicada hiding behind a flower stem. The more you look the more you discover. It’s a beautiful and mysterious experience that everyone should go see.” As part of the exhibit, visitors can engage with a ‘StoryMap’ that accompanies the piece. Dorman created the map using ArcGIS, highlighting 46 locations where some of the foraged specimens in ‘Reflection’ were found, along with stories from those who found them. “‘Reflection’ brings all of these amazing little intricate details together into a single statement, and then the StoryMap explodes it back into its pieces, highlighting the individual stories of the people that contributed to it,” explained Dorman. “The StoryMap emphasizes how the Urbana-Champaign community is profoundly connected to and cares a lot about the natural beauty around us. It’s a snapshot of a moment in this relationship between humans and nature, and I think that relationship runs deep.” The art exhibit also features selected Art of Science images of seeds and leaves created by Pollack. The Art of Science is an IGB program that seeks to merge science and art. Pollack, who has served as the Art of Science curator since 2018, collaborates with researchers at the IGB to enhance their microscopic images and highlight the beauty and significance of their scientific work. Additionally, microscopic images of flowers, pollen, and beetles taken by the 2023 Pollen Power middle-school campers are on display at the nature center. Pollen Power is a weeklong summer camp hosted by the IGB, aimed at introducing middle schoolers to plant biology while providing strong female mentorship, especially to underrepresented groups in STEM. As a final tribute to the communal nature of the piece, every visitor to the opening ceremony was entered into a raffle to select one lucky winner who would take home ‘Reflection’ after its debut at the nature center. ‘Reflection,’ along with the StoryMap, works from the Art of Science, and images from the Pollen Power campers, are on display at the Anita Purves Nature Center. CLICK HERE TO READ ON IGB WEBSITE
Women have made significant contributions in STEM, and have become increasingly prevalent in the STEM community. However, their online visibility, particularly regarding their accomplishments and contributions to science, remains disproportionately low due to factors such as inherent bias. Wikipedia is a free online encyclopedia, and the 5th most visited website in the world. In recent years it has emerged as a powerhouse of trusted information, largely due to the collaborative nature behind article creation and management on the platform. However, less than 20% of Wikipedia’s pages feature women. To address this disparity, Wikipedia edit-a-thon events have gained traction in universities across the world. These events provide scheduled times for groups to come together and create or edit Wikipedia pages for women and other underrepresented groups. This fall, the Carl R. Woese Institute for Genomic Biology hosted the first event in a series of Wikipedia edit-a-thons, with the inaugural event taking place last week. This initiative is spearheaded by the IGB DEI Task Force, a group dedicated to creating new programs and initiatives meant to increase dialogues and create change internally towards a more inclusive environment. Julia Pollack, former Co-chair of the DEITF, says the idea came about during a discussion with fellow DEITF members Ananya Sen, Claudia Lutz, and Erin Louer. The group was inspired by the story of Jess Wade, a British physicist at Imperial College in London, who has written more than 1800 Wikipedia pages for female and minority scientists underrepresented on the platform. Wanting to build upon Wade’s efforts, the group decided to host their own edit-a-thon series at the IGB. “Learning about Jess’ work got us so pumped, seeing how she is directly impacting the representation of women online through her creation of Wikipedia pages,” Pollack recalled. “When Ananya reached out to her, Jess was so inspiring and kind, and took the time to meet with us, answer our questions, and really help direct our vision for this edit-a-thon.” The first event in the series featured a seminar by guest speaker Mackenzie Lemieux, a fourth-year medical student at the Washington University School of Medicine. Lemieux, who has authored over 100 Wikipedia biographies of women in STEM, has led numerous workshops across the country on how to effectively write and edit women’s pages on Wikipedia. She also conducts research exploring gender and racial bias on the platform. “Wikipedia is a really unique and awesome website that’s volunteer driven, and provides knowledge for free to anyone with access to the internet,” said Lemieux. “Teaching people how to create and edit for Wikipedia removes the black box, and puts the opportunity to contribute to our worldwide database of knowledge into people’s hands.” Lemieux discussed the current issues of bias not only on Wikipedia but in STEM in general. Gender biases manifest at a remarkably young age. Studies have shown that when children are asked to draw a scientist, they typically draw an older, white male figure. However, when children are exposed to a counter-stereotypic environment, such as a diverse lab of researchers from various backgrounds, their drawings became more representative. This highlights the importance of representation, which extends to online platforms. “There are so many women that are incredible scientists, and their contributions are very important to STEM history, yet their accomplishments can easily be lost due to bias,” said Lemieux. “Wikipedia has the power to improve women's visibility in STEM, and rewrite history so that its accurate about women's contributions.” During her seminar, Lemieux delved into the reasons behind why the number of women’s pages on Wikipedia is lacking. First, Wikipedia moderators, who decide which articles to retain or delete, are predominantly white, male, and from North America and Europe, leading to inherent bias in determining notability. Second, notability criteria on Wikipedia are highly subjective, with the main rule being the need for a substantial number of independent online sources to confirm a person's contributions. The work of women and people of color is less likely to be featured online, compounding the issue, according to Lemieux. Efforts by groups like Women in Red, who advocate for women's pages, and edit-a-thon events, which mobilize people to create pages for deserving women, have contributed to increasing the number of pages dedicated to women on Wikipedia. The DEITF hopes the IGB Wikipedia edit-a-thon event series will contribute to the improvement of women’s visibility online. “The more you write, the more you see the tangible impact of your pages ─ the number of views, the amount of people building upon and improving your pages,” said Lemieux. “It’s so inspiring because you think about how that page didn’t exist before you wrote it, and now people are reading and referencing it every day.” The edit-a-thon series will span multiple sessions in the coming months, providing participants with ample opportunities to collaborate and create new pages. Librarians from the ACES FUNK library will be on hand to assist newcomers in creating Wikipedia pages, and provide suggestions for women to write about. “There will be people at these events to assist with the process, and if you can’t make it to the edit-a-thon, there’s a lot of online tools to teach people how to edit for Wikipedia,” explained Lemieux. “The first step is just making an account. I know it can be intimidating to write a page that could be seen by everyone worldwide, but that visibility is what makes writing these pages so important.” The next guest speaker in the series will be Jamie Flood, a master's student in Library and Information Science. Register for the remaining Wikipedia edit-a-thon events at go.igb.illinois.edu/Wikipedia CLICKS HERE TO READ ON IGB WEBSITE Technological advancements in genomics have led to major developments in the areas of medicine, energy, and agriculture, that are impacting society at large. Due to the pace of these developments, many professional sectors of society lack the tools and genomics knowledge necessary to understand how this new research may affect them. The Genomics for Professionals program, otherwise known as Genomics forTM, was created by the outreach team at the IGB to help different sectors of society gain a better understanding of basic concepts in biology and advancements in genomics as a whole. The program involves a series of workshops that provide a space for participants to ask questions and have discussions with scientists regarding the impact genomics may have on their sector’s line of work. Workshops may focus on different topics relevant to the job, or allow participants to conduct hands-on genomic activities to better grasp the science behind it. The program has already featured several workshops catered to a diverse set of sectors, including judges, lawyers, clinicians, journalists, police officers, and more.
This year saw the start of the Genomics for Faith program, a new series of workshops that focus on bringing scientists and faith communities together to discuss meaningful, and sometimes controversial, topics in genomics. The goal for this particular series is to promote a dialogue between scientists and faith communities about genomic technologies, to gain a shared understanding for how these may intertwine within their lives and faiths. The first installation of the program took place in May 2023 at the Channing-Murray Foundation, where a crowd gathered to discuss perspectives on “what constitutes life?” and consequently, “what is death?” The second workshop in the series occurred on September 7th, 2023 at the Baháʼí Center in Urbana, where a new topic was posed to participants – gene editing. Gene editing is the process by which a targeted part of an organism’s DNA is added, removed, or altered. After a brief introduction on gene editing by Dan Urban, IGB Senior Outreach Activities Coordinator and one of the organizers of the program, participants were broken into discussion groups based on three major taxa – microbes, plants, and animals. Within each group were scientific representatives whose research focused on the group’s specific taxa. “Our goal was to delve into a topic that is important, but that some members of the general public may find more controversial – editing the very foundational building blocks of a living creature,” said Urban. The groups were prompted with discussion questions such as “when is it ok to edit a genome?” “are there organisms that gene editing is more acceptable in and why?” and “how do we reach a consensus on when and how to use a new technology, like gene editing?” These discussions prompted further ethical considerations, such as whether gene edits that could occur naturally (making plants grow bigger fruits, for example) were seen as more acceptable among the population than edits that could not occur naturally in nature (placing the human gene for producing insulin inside of bacteria). This also led to a fruitful discussion on weighing the risk of a new technology versus the reward of using it to save lives. Afterwards, participants were given a chance to ask a panel of scientists any questions they had. The panel addressed misconceptions and fears of the technology being misused, and detailed how they were each training the students in their labs to utilize gene editing tools in a safe and ethical way. Many panel members gave examples of beneficial uses of gene editing in their own line of research, including but not limited to: the production of medicines via gene-edited microbes, gene therapies to fix otherwise terminal diseases, the creation of animal models to research cures for cancer, and the alteration of plants to produce more food and energy. Participants inquired about areas of concern for scientists in the field, which led to conversations surrounding current regulations, containment of altered microbes/plants, and ensuring that the technology is not weaponized in any way. According to the post-event survey, most participants walked away with a better understanding of gene editing, and its uses and limitations. Many participants thought the dialogue was positive, and that they were now more informed about the technology. After the first workshop, which featured a whole-room question and answer session with a panel of experts, participants indicated that they wanted smaller, more intimate group conversations. For the second workshop, this smaller group format was implemented. “The new discussion format allowed for extra time for close-knit discussions among smaller groups, which led to some great conversations between the scientists and community faith leaders,” said Urban. “I think participants got a better sense of how deeply scientists consider the safety implications and ethical questions that come with this technology.” More Genomics for Faith workshops are being planned for the future. Any comments on past workshops or suggestions for new workshop topics, please contact Claudia Lutz, IGB Outreach Manager, at [email protected]. CLICK HERE TO READ ON IGB WEBSITE The human genome consists of roughly 20,000 genes. Most of those genes contain instructions for making proteins, which work to build, repair, and regulate everything in our bodies. The genes are separated into distinct domains, and between those domains are boundary regions of DNA, which help to separate genes and ensure there isn’t crosstalk resulting in expression (genes turned on) or silencing (genes turned off) between the genes. Unfortunately, disruptions within boundary regions can still occur, leading to gene misexpression and disease in humans. Some boundary regions contain barrier elements that can help block gene misexpression or shield against gene silencing, but the latter is far less studied due to the difficulty of identifying elements with such activity. In a recent study by the lab of Huimin Zhao (BSD leader/CABBI/MMG/), Steven L. Miller Chair of Chemical and Biomolecular Engineering at the University of Illinois Urbana-Champaign, the researchers describe a new technology, called SHIELD, which can effectively screen for barrier DNA elements that protect genes from being silenced.
“Barrier DNA elements work to stop repressive heterochromatin spreading, which is one of the ways that genes become silenced,” explained Meng Zhang, a former graduate student in Zhao’s lab and first author on the study. “A gene that is flanked by these protective barrier DNA elements will still be able to express, even within highly repressed regions of the chromosome. These elements essentially function as a counter to the silencing effect.” Following this principle, the team decided to use a highly repressive area of the genome as the stage for their experiment – the Lamina-associated Domain. Often dubbed the “gene-silencing hub of mammalian genomes,” the LAD provides an ideal environment to screen for DNA elements that may contain barrier activity. Genes placed inside this region normally would be unable to express due to the LAD’s repressive nature. But if DNA elements with barrier activity are placed alongside the gene, then the gene should still be able to express. Zhao refers to this as a “stress test” for the barrier element’s “anti-silencing” capabilities. The researchers used a fluorescent protein as their reporter, so that cells where the gene was able to express would glow and could be easily identified. The gene encoding the fluorescent protein was placed in the LAD of cells alongside candidates for barrier DNA elements, and the cells were then screened for fluorescence. The SHIELD technology was able to quickly screen 1000 candidate elements at once, and using flow cytometry to sort cells with the highest fluorescence expression, the team was able to identify 8 candidates that showed potent barrier activity. The researchers found that three of these elements performed equally or better than the barrier element currently used in medicine and research. “Barrier DNA elements have not been well characterized before in the human genome compared to other non-coding elements like promoters or enhancers,” said Zhang. “This is partly because there wasn’t a technology available to readily evaluate activity of these DNA elements and screen for barrier activity. The barrier element widely used right now was initially discovered in 1993 and has been in use since then. Our technology will now allow us to identify new barrier elements in a quick and efficient manner, thus expanding the toolbox of such elements for synthetic biologists.” Newly identified barrier elements have many potential therapeutic applications. For example, scientists typically use a viral vector to deliver therapeutic genes to patient cells lacking the working gene, but sometimes the therapeutic genes become silenced by the host cell. Barrier elements could be used to protect the therapeutic cargo from being silenced. Zhao says the applications for the new technology extend beyond just therapeutics. “Our findings have many therapy applications, but they also are important for fundamental studies in the field of biology, particularly for those studying genetic circuits,” said Zhao. “Identifying these barrier elements will give them better tools to work with for their research. Furthermore, the knowledge gained from such screening can help us understand what types of DNA sequences contribute to the establishment of chromatin boundaries in the genome.” Zhao also hopes other researchers will use the tool to discover more barrier elements and expand the library, not only in mammals, but in other eukaryotes such as other animals, plants, and fungi, as well using a similar strategy. The study is published in Nature Communications and was supported by the NIH. The paper can be found at https://doi.org/10.1038/s41467-023-41468-3 CLICK HERE TO READ ON IGB WEBSITE Technological advancements in genomics have led to major developments in the areas of medicine, energy, and agriculture, that are impacting society at large. Due to the pace of these developments, many professional sectors of society lack the tools and genomics knowledge necessary to understand how this new research may affect them. The Genomics for Professionals program, otherwise known as Genomics forTM, was created by the outreach team at the IGB to help different sectors of society gain a better understanding of basic concepts in biology and advancements in genomics as a whole. The program involves a series of workshops that provide a space for participants to ask questions and have discussions with scientists regarding the impact genomics may have on their sector’s line of work. Workshops may focus on different topics relevant to the job, or allow participants to conduct hands-on genomic activities to better grasp the science behind it. The program has already featured several workshops catered to a diverse set of sectors, including judges, lawyers, clinicians, journalists, police officers, and more.
This year saw the start of the Genomics for Faith program, a new series of workshops that focus on bringing scientists and faith communities together to discuss meaningful, and sometimes controversial, topics in genomics. The goal for this particular series is to promote a dialogue between scientists and faith communities about genomic technologies, to gain a shared understanding for how these may intertwine within their lives and faiths. The first installation of the program took place in May 2023 at the Channing-Murray Foundation, where a crowd gathered to discuss perspectives on “what constitutes life?” and consequently, “what is death?” The second workshop in the series occurred on September 7th, 2023 at the Baháʼí Center in Urbana, where a new topic was posed to participants – gene editing. Gene editing is the process by which a targeted part of an organism’s DNA is added, removed, or altered. After a brief introduction on gene editing by Dan Urban, IGB Senior Outreach Activities Coordinator and one of the organizers of the program, participants were broken into discussion groups based on three major taxa – microbes, plants, and animals. Within each group were scientific representatives whose research focused on the group’s specific taxa. “Our goal was to delve into a topic that is important, but that some members of the general public may find more controversial – editing the very foundational building blocks of a living creature,” said Urban. The groups were prompted with discussion questions such as “when is it ok to edit a genome?” “are there organisms that gene editing is more acceptable in and why?” and “how do we reach a consensus on when and how to use a new technology, like gene editing?” These discussions prompted further ethical considerations, such as whether gene edits that could occur naturally (making plants grow bigger fruits, for example) were seen as more acceptable among the population than edits that could not occur naturally in nature (placing the human gene for producing insulin inside of bacteria). This also led to a fruitful discussion on weighing the risk of a new technology versus the reward of using it to save lives. Afterwards, participants were given a chance to ask a panel of scientists any questions they had. The panel addressed misconceptions and fears of the technology being misused, and detailed how they were each training the students in their labs to utilize gene editing tools in a safe and ethical way. Many panel members gave examples of beneficial uses of gene editing in their own line of research, including but not limited to: the production of medicines via gene-edited microbes, gene therapies to fix otherwise terminal diseases, the creation of animal models to research cures for cancer, and the alteration of plants to produce more food and energy. Participants inquired about areas of concern for scientists in the field, which led to conversations surrounding current regulations, containment of altered microbes/plants, and ensuring that the technology is not weaponized in any way. According to the post-event survey, most participants walked away with a better understanding of gene editing, and its uses and limitations. Many participants thought the dialogue was positive, and that they were now more informed about the technology. After the first workshop, which featured a whole-room question and answer session with a panel of experts, participants indicated that they wanted smaller, more intimate group conversations. For the second workshop, this smaller group format was implemented. “The new discussion format allowed for extra time for close-knit discussions among smaller groups, which led to some great conversations between the scientists and community faith leaders,” said Urban. “I think participants got a better sense of how deeply scientists consider the safety implications and ethical questions that come with this technology.” More Genomics for Faith workshops are being planned for the future. Any comments on past workshops or suggestions for new workshop topics, please contact Claudia Lutz, IGB Outreach Manager, at [email protected]. CLICK HERE TO READ ON IGB WEBSITE Using mathematical models to explain plant community structures If you have any preconceived notions of what a mathematician is supposed to sound like, perhaps based on representation from the media, a chat with Kenny Jops will have you thinking otherwise. Witty conversation, unfeigned curiosity, and deadpan humor are the trademarks of Jops, a graduate candidate in the Evolution, Ecology, and Behavior program at University of Illinois Urbana-Champaign, who currently studies the math underlying plant communities. Jops grew up on the northwest side of Chicago, near a large forest preserve along the city’s edge. This is where he says he made his first, perhaps unconventional, connection with nature.
“My friends and I would often ride our bikes up there and hit each other with sticks we found,” Jops joked. “You know, the stuff that boys do when they're unsupervised in a forest. That was my first connection to plants and trees, because the trees provided me the opportunity to hit my friends with sticks.” In addition to playing in the forest, he said his mother also kindled his early interest towards nature. “My mom is this awesome, second-wave feminist, hippie weirdo,” Jops said. “When they stopped providing bins for recycling in our neighborhood, she drove me out to this nature reserve where they have a whole recycling program. We would throw glass bottles into shipping crates and sort our recycling, and that experience got me thinking more about the environment and being eco-conscious.” Growing up, Jops also had a profound love for math, which he says came naturally to him. He participated in Mathletes throughout school and excelled in his math classes. While attending Northwestern University for his bachelor’s degree, he double majored in math and environmental science. “I thought it was the perfect way to apply math,” Jops explained. “There are really cool mathematical problems in biology that you don't get in other fields. And I appreciate that with biology, you have to step back every once in a while and think about what's actually happening in nature, and whether your math is applying correctly to reality.” An analysis class with Jared Wunsch, a mathematics professor at Northwestern, cemented his love for math. Jops says though the class was difficult, it gave him the tools to be successful in his current work. He recalls spending hours a week with his friend trying to solve some of the homework problems. “We would just completely dissociate from the world trying to solve these absurdly hard problems,” Jops said. “Those challenges really got me going, and now I can say that I don't need to learn any more analysis math for the rest of my life because of Wunsch.” When he finished college, Jops joined a law firm as a contract consultant, but quickly grew to dislike it. “Right out of undergrad I went into contract law, with my thought being ‘Well, I gotta make money, and this is what normal people do. Science and math is fun, but it’s time to get a big boy job.’ But that kind of work culture is not for me. I couldn’t take the thought of 50 more years of standing around the watercooler being asked how my weekend was.” Jops decided to quit his job and enroll into graduate school, with the goal of eventually becoming a professor. He reached out to undergraduate mentors to discuss options for him, and they connected him with James O’Dwyer (CAIM), an associate professor of plant biology at University of Illinois. Jops is now a 5th year PhD candidate in O’Dwyer’s lab, studying the mathematical properties behind the processes that allow diverse communities of flora to live together. Jops creates mathematical models and theories that work to explain the biodiversity found in an ecosystem, and how varying plant life histories function within the community. “Let’s say you have a fast-growing weed that produces tons of offspring, and a slow-growing tree that’s robust but takes years to mature,” Jops explained. “Despite having different strategies, they manage to live together, and they end up having the same long-term growth rate in the community. As a mathematician, I ask what makes this possible.” Jops uses large databases of real-world data to create his mathematical models. First, he creates theoretical plants with varying properties based on what is seen in the wild. Then he uses an algorithm to test how the theoretical plants would fair in the real-world communities based on the real-world data. By changing out and testing different properties, he can create models explaining how these factors influence the diversity of plant communities. “One of the really fun parts of my job is taking biological reality and trying to figure out what lines of code, equations, and probability distributions would make the model look real,” Jops said. “Basically, I throw the kitchen sink at things until I’ve used so much of the school’s computing resources that I feel bad and decide to go home, only to get an epiphany as soon as I’m there. Then I jump back on my laptop and try reworking the model again.” His most recent paper was published in Nature. The study looks at niche partitioning of plant species, essentially the selective roles that plants evolve to fit into that allows them to share resources. Jops is also currently working on other projects involving new areas of interest, such as spatial modeling, population genetics, and the influence of external factors on community stability. Jops says he enjoys graduate school, and work-life balance that the flexibility of his field allows for. “I enjoy history-themed podcasts and books, as well as video games, and going out and doing ‘normal human’ social activities,” Jops said. “It sounds shocking but mathematicians do have hobbies. I actually think I have a good work-life balance. Since my most important tool is my computer, that allows me to work in the office, at home, or even while traveling. I’m not on the normal field season schedule of a biologist which is nice, so my work schedule is flexible.” He says this makes it easier to travel to Chicago to see his friends and family, and to Europe to visit his girlfriend Hannah Scharf, former PhD candidate in the EEB program, now a postdoctoral researcher working with Great Tits at Ludwig Maximilian University of Munich, in Germany. “I want to give a shout out to Hannah!” Jops said, “She’s a great researcher with a cool position and cool system. And because of my flexibility I can pop away to Europe to see her and still work while I’m there, which is awesome!” New Team Science Leadership Program aims to form new collaborations among mid-career faculty8/31/2023 CLICK HERE TO READ ON IGB WEBSITE The Team Science Leadership Program is a new program being offered by the Carl R. Woese Institute for Genomic Biology, consisting of a series of workshops that bring together faculty from all over campus. The workshops are tailored to mid-career faculty, and focus on leadership training, communication skills, networking, and community building. The ultimate goal of the program is to empower faculty to develop new research ideas and collaborations, particularly between disciplines that might otherwise never have the opportunity to interact. “Nationwide there is increasing interest in focusing on the professional development of mid-career faculty, and this program addresses this need for our faculty from the unique perspective of multi-disciplinary team science, which is the IGB’s calling card,” said IGB Director Gene Robinson.
James O’Dwyer, an associate professor of plant biology and the Director of Graduate Studies, was the driving force behind the program’s creation. O’Dwyer explained that after the COVID-19 pandemic, many faculty, especially those new to the university or that recently received tenure, were eager to renew pre-pandemic connections and build new ones with other departments and IGB themes. The TSLP was formed to bring people together and connect faculty from different disciplines across the campus. “This program builds on what the IGB does best—team science at a large scale—to develop new skillsets among our mid-career faculty,” said O’Dwyer. “We hope that the program will help build community and enhance the leadership skillsets among our faculty, forming the next generation of leaders in team science at the IGB and Illinois.” O’Dwyer organized a few preliminary TSLP workshops along with Robinson in Spring 2023 to gauge interest and collect feedback from participants. After a successful trial run, the TSLP was established as a certificate program for the IGB, which will begin workshop sessions Fall 2023. The workshops will be led by experts who will discuss different aspects of team science, including how to create a healthy and productive team, crafting proposals that highlight a team’s strengths, and building effective teamwork skills. Experts include experienced faculty on campus, alongside program officers from federal agencies, private foundations, and other professions working in team science. The format of the workshops will vary based on the topic, but usually workshops will involve smaller group discussions followed by larger conversations between the whole group, said O’Dwyer. At the end of the year-long program, participants will receive a certificate. The program already has 15 participants registered for this year’s cohort. “James has done an outstanding job of assembling a program of topics and experts that participants should find to be very educational and engaging,” said Robinson. “We look forward to learning about their experiences as we seek to make this program available for the long-term.” The program is open to IGB affiliated faculty that are either associate professors or recently promoted full professors. The first workshop of the year will be held on September 22 at noon in 612 IGB. For more information about the upcoming program, visit https://www.igb.illinois.edu/team-science-leadership-program CLICK HERE TO READ ON IGB WEBSITE Researchers are realizing that animal communication is more complicated than previously thought, and that the information animals share in their vocalizations can be complex. For example, some animals produce calls that warn of specific dangers in the environment, such as a predator, and these calls can even contain information about the type of predator (e.g. flying vs ground predator). These calls are known as referential calls. “Referential calls are a type of symbolic signal that is considered by some to be an evolutionary precursor of more complex communication systems, including human language,” said Mark Hauber (GNDP), a professor of evolution, ecology, and behavior at the University of Illinois Urbana-Champaign.
It is still not completely clear whether and how animals learn referential calls, though evidence suggests animals need experience with the threat being referenced in order to connect the call to it. In a new study published in Behavioral Ecology and Sociobiology, researchers tested this using a population of birds that have been living apart from a specific threat for over 300,000 years. In North America, yellow warblers produce referential “seet” calls which warn of nearby brown-headed cowbirds. Cowbirds are brood parasites, meaning that instead of making a nest and raising their own young, they leave their eggs in other species’ nests, forcing those hosts to care for the cowbird. When yellow warblers spot a nearby cowbird during the breeding season, they produce seet calls to warn each other about the threat and increase their vigilance around their nests. Yellow warblers also seet call in response to seet calls from others to pass on the warning. While this behavior is common in temperate North America, where yellow warbler and cowbird breeding overlaps, seet calls are more rarely produced by warblers in northern Canada and Alaska, where cowbirds do not breed. This suggests that experience with cowbirds may be necessary for yellow warblers to produce and respond to referential seet calls. Researchers at Illinois, along with collaborators from Western Michigan University and Australia’s Flinder’s University, decided to test this hypothesis using a yellow warbler population in the Galápagos Islands, where the population has been breeding apart from cowbirds for over 300,000 years. “We were very interested in how experience plays a role in ability to seet call,” said Shelby Lawson, a previous graduate student in the Hauber lab, now a postdoctoral science writer fellow at the IGB and first author on the paper. “We already know that experienced, older yellow warblers produce more seet calls in response to cowbirds, and are more responsive to seets than younger birds. But what about warblers from a population that has never experienced brood parasitism? We wondered if they would be able to recognize the seet call as a warning call for danger.” “The Galápagos population has been isolated from brood-parasitic cowbirds for hundreds of thousands of years,” explained Janice Enos, a former postdoctoral researcher in the Hauber lab, now an avian biologist at the Illinois Natural History Survey. “Because of that, it’s the best candidate population to ask about the propensity of warblers to seet call based on the presence of cowbirds, because every other yellow warbler population has had some experience with cowbirds. This is the only one that presumably hasn’t.” The researchers first found breeding pairs of yellow warblers on the islands of Santa Cruz and Floreana in the Galápagos. Then they presented playbacks of cowbird calls, seet calls, and controls that had been recorded in North America, along with playbacks of local Galápagos predators, to the pairs. The researchers measured and compared the aggression and vocalizations the warblers made in response to the playbacks, predicting that the birds would be most aggressive towards the threats they had experience with, and less towards the sounds that were novel. They found that the Galápagos yellow warblers were indeed much more aggressive towards playbacks of a local nest predator compared to cowbird and seet call playbacks, of which responses to were comparable to the controls. This response is unlike yellow warblers in North America, which are highly aggressive towards playbacks signaling nearby cowbirds, said Lawson. Surprisingly, Galápagos yellow warblers never once produced a seet call in response to the cowbird and seet call playbacks. The researchers say this was unexpected, as yellow warblers in northern Canada and Alaska that have been breeding apart from cowbirds for about 6000 years still occasionally produce seet calls when tested. “Other allopatric (meaning apart) yellow warbler populations still occasionally produce seet calls when shown cowbird models, albeit rarely, so the fact that the Galápagos yellow warbler never produced any seet calls was surprising to see,” explained Lawson. “The warblers did not seem to recognize the cowbird threat at all. One female warbler even fell asleep on her nest while a nearby speaker played cowbird calls!” The team says that this finding only leads to more questions to explore. The Galápagos yellow warbler split off from the mainland lineage so long ago that it begs the question of whether yellow warblers had even evolved the seet call prior to the split. According to the researchers, the Galápagos lineage could have split before the warblers developed the ability to seet call, which could explain why they did not respond to the call or produce it during the experiment. The researchers say future directions include testing other yellow warbler populations with varying overlap with cowbirds, in order to tease apart the role experience may play, and to identify when in the warbler’s evolution the seet call evolved. “Projects like these rely on national and international collaborators with different skill sets,” said Hauber. “Our team’s next step is to study the closest mainland relatives of the Galapagos yellow warblers, in Mexico or the Caribbean, which still coexist with parasitic cowbirds.” “This study gives us one of the pieces of the puzzle about the evolution of communication, especially complicated communication like referential calls,” said Enos. “It also brings up questions about whether the seet call is tied to genetic underpinnings, or if it is learned through social aspects that influence use of the call. We can't tease those two apart in this study, but this begins to fill in a little of that gap.” The study was supported by NSF, the Austrian Science Fund, and the Center for Latin American Studies at Illinois. The paper can be found at https://doi.org/10.1007/s00265-023-03372-0 CLICK HERE TO READ ON IGB WEBSITE Scientists are becoming increasingly aware of how the human microbiome, or the collection of microbes the live on and inside of us, has a major connection to health and human physiology. Microbial engineering, which changes the structure of the microbiome through methods such as probiotics, antibiotics, and microbe transplants, has been found to be a useful strategy for improving human health, but the mechanisms underlying this improvement are still unclear and difficult to test. However, a team of researchers hopes that their new study, published in Microbiology Spectrum, will provide a platform that will make mechanistic studies on the microbiome more feasible. The study was conducted by the labs of Yong-Su Jin (BSD/MME/CABBI), a professor of bioengineering, and Michael Miller (MME co-leader/IGOH), a professor of food microbiology, based at University of Illinois Urbana-Champaign, along with first author Jungyeon Kim, a former postdoctoral researcher in Jin’s lab and now assistant professor at Seoul National University in South Korea. The researchers utilize a genetically engineered strain of Saccharomyces boulardii, a species of yeast, as their delivery vehicle, or ‘chassis,’ to deliver bioactive proteins into the gut. The yeast is commonly used as a probiotic, and the researchers say that it’s not only easy to genetically engineer, it also moves quickly through the gut, unlike other options for vehicles. “When we first started this study, many people were using a probiotic E. coli strain as their chassis,” said Kim. “The problem with E. coli is that it’s great at colonizing the gut, and can stay in the system for several months. Even after you have recovered from a disease, the E. coli could still be in the gut producing recombinant proteins, which can trigger immune responses and inflammation. S. boulardii on the other hand leaves the system in just 1-3 days. This feature of yeast makes it easy to control the supply of recombinant proteins.” The goal of the study was to genetically engineer the yeast to produce lysozyme, an antimicrobial protein that mammals naturally produce in milk, tears, saliva, and more. The researchers used CRISPR/Cas9 genome editing to integrate the human gene for lysozyme directly into the yeast genome. The engineered yeast was then fed to mice for 2 weeks, and the microbiome of these mice was compared to mice fed either wild-type unengineered yeast or a saline solution. First, the researchers measured the presence of lysozyme in the gut and fecal matter of the mice fed the engineered yeast, to verify that the yeast was producing and delivering lysozyme into the gut. After verifying this, they measured the gut microbiome and fecal metabolome (the collection of metabolites microbes produce) of the mice across all three treatment groups. While the diversity of the microbiome increased across all groups, the mice fed either type of yeast saw significant increases in the diversity of microbes present in the gut, including increases in the ratio of gram-positive to gram-negative bacteria. The researchers say this is to be expected, due to the probiotic nature of the yeast. When they specifically examined the mice fed the lysozyme-secreting yeast, they found the structure of their gut microbiome and diversity of their fecal metabolome was significantly altered compared to mice fed saline or wild-type yeast. The researchers concluded that the lysozyme secretions by the yeast had indeed impacted the gut microbial community. “We found a dramatic increase in firmicutes, or gram-positive bacteria, compared to gram-negative bacteria in the mice fed S. boulardii,” said Kim. “We investigated whether there were changes to specific strains, and found that probiotic bacteria increased after administration of lysozymes. We also found increases in diversity of microbiome, and decreases in sugar found in blood in the mice given yeast. So, we’re thinking administration of this engineered yeast could be helpful for maintaining a healthy microbiome or preventing growth of pathogens.” “What’s cool is that we show that our engineered S. boulardii is able to produce proteins in the gut that significantly affect the microbiome,” said Miller. “But I think the bigger picture is that lysozyme is just a starting point. We can engineer the yeast to make any bioactive protein that we want, and have them deliver that cargo functionally to the gut.” The researchers say that the activity of the yeast could be improved, as they may not have had enough sugar or nutrients to proliferate fully within the gut. However, for a follow-up study the researchers added a new genetic pathway to the yeast that will allow them to utilize lactose, the sugar found in milk. The lactose can then be fed to the mice alongside the yeast to provide a new fuel source for the newly engineered yeast. The researchers have already found that doing so dramatically increases lysozyme production in the gut. In the future, the researchers are hoping to figure out how to deliver specific quantities of a target protein into the gut to be used in therapeutics. Jin says the ultimate goal of their research would be to utilize engineered yeast in “in-food fermentation,” such that the yeast that’s already in foods people enjoy, like baked goods, milk, and alcohol, would produce additional proteins that help maintain healthy gut microbiomes. “My vision is to use this engineered yeast in food,” said Jin. “We already use yeast for making bread, wine, beer and such. But if we create these fermented foods using engineered microorganisms designed to be helpful for the gut microbiome, we can enjoy the benefits of the engineered microorganism simply through the consumption of food.” The study was funded by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry, and Fisheries, the Ministry of Agriculture, Food, and Rural Affairs, and the USDA. The paper can be found at https://doi.org/10.1128/spectrum.00780-23. |