CLICK HERE TO READ ON IGB'S WEBSITE The brains of all higher order animals are filled with a diverse array of neuron types, with specific shapes and functions. Yet, when these brains form during embryonic development, there is initially only a small pool of cell types to work with. So how do neurons diversify over the embryo’s development? Researchers know that neural stem cells called neuroblasts divide multiple times to sequentially produce neurons of specialized function, but the mechanisms of this process, and how the timing varies for different genes and neuron types, is still not fully understood. In a new paper published in eLife, Alokananda Ray, a Ph.D candidate during the time of the study and now graduated, and Xin Li (GNDP), an assistant professor of cell and developmental biology at the University of Illinois Urbana-Champaign, shed light on the process in the optic medulla of Drosophila melanogaster, the fruit fly. As neuroblasts divide and differentiate, they express transcription factors which ultimately direct the daughter cells on what kind of neuron to be. Because they are expressed in a particular way depending on when they split, these transcription factors, called temporal transcription factors, act as a marker that tells researchers what stage the neuroblast is at, and allows them to piece together the order of events in this neurogenesis cascade. The researchers focused on two different TTFs in the fruit fly brain, called eyeless and sloppy-paired, to better understand how differences in the expression of TTFs that lead to different neuron fates. “Nervous systems diversify from a small pool of neural stem cells to the great diversity of neurons we see in adult brains of higher ordered animals,” said Ray. “We really wanted to understand the molecular mechanisms that drive the transition of these neuroblasts from expressing one temporal transcription factor to the next transcription factor, which ultimately determines what type of neurons these progenies will become.” The researchers used genetics and a number of techniques including reporter assays, antibody staining and microscopy to measure the expression pattern of genes within the optic medulla of fruit fly brains during development. Typically, the regions of the DNA that are considered to be “important” are the sequences that contain genes. However, through these experiments, the researchers discovered that two non-coding regions near the sloppy-paired genes were essential to making sure the sloppy-paired TTFs expressed at the right time and amount. Researchers then removed these non-coding DNA regions, called enhancers, using the gene-editing technique CRISPR to see how the brain of the flies were affected, and found that flies with deleted enhancers showed a complete absence of expression of the sloppy-paired TTF in medulla neuroblasts. “On the outside, we don't see morphological changes from removing sloppy-paired enhancers, but neurons generated in the sloppy-paired stage will be missing from the brain, and I think the neurons generated in later stages will also be lost.” said Li. The second major finding in the paper was that a mechanism called Notch-signaling works together with the preceding TTFs to activate the expression of the next TTFs in question. The researchers determined that not only is Notch-signaling important for regulating TTF expression, but the way it regulates is dependent on where in the neurogenesis cascade the cells are at. In other words, once a certain number of a specific neuron type have been made, Notch-signaling regulates the transition such that the neuroblasts start differentiating into a different neuron type. “One TTF is required to activate the next TTF, but that alone is not sufficient to cause the transition,” explained Li. “After each cell cycle, Notch-signaling will further activate the next TTF until a certain level is reached, at which point it will repress the previous TTF, then the transition to the next TTF stage will happen. Basically, this mechanism couples the temporal patterning in these neural stem cells with the generation of the appropriate number of neurons at each temporal stage.” Though TTFs vary between animals, Notch-signaling is highly conserved, meaning that understanding the molecular mechanisms that regulate neuron differentiation in the fly can potentially translate across other higher-order animals. The findings in this study illuminate some of the mechanisms underlying neuron diversity in the brain, but the researchers said there is more to be explored. “Identifying the molecular determinants, or enhancers, that are required for the transition to take place from eyeless to sloppy-paired gives us ideas for how other transitions may also be regulated,” Ray explained. “We're going to try to identify other enhancers that previous TTFs bind to activate the expression of subsequent factors.” The paper, titled “A Notch-dependent transcriptional mechanism controls expression of temporal patterning factors in Drosophila medulla” is published in eLife (https://doi.org/10.7554/eLife.75879), and was supported by the National Eye Institute.
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One of the Carl R. Woese Institute for Genomic Biology’s main goals is fostering partnerships between departments across campus to encourage more trans-disciplinary research. Initiatives provide an avenue for this goal, bringing researchers across departments, study systems, and disciplines together and encouraging collaborative research. Here we highlight the initiatives that the IGB has been involved with during the 15 years since its inception. CompGen Initiative Genomics data contains billions of data points that require a lot of expertise and computing power to analyze. The CompGen Initiative, established in 2014, was created to alleviate this issue, combining the strengths of genomics research at IGB with the high-performance technology and computational abilities of computer scientists. The initiative created collaborations between biologists and computer scientists across campus to be able to analyze large sets of genomic data. The initiative was awarded funding from both NSF and NIH to create new instruments for genomic data storage and analysis, along with a community database of genomic data from studies. This database, the Knowledge Network, serves as resource of prior knowledge of genes and networks embedded in an analysis platform called KnowEnG, that is used for genomic information management and integration of that information. By combining genomic findings across multitudes of studies, and using new algorithms and models to analyze this pool of data, researchers can improve accuracy and scalability of their findings leading to new discoveries on how genomics inform life and evolutionary processes. Throughout the years, teams utilizing the KnowEnG platform have been able to explore causes of disease and potential new treatments, expedite the sequencing of genomic data from humans, and increase our understanding of how genomic variations influence the traits we see across several species. In addition, KnowEnG also worked as an educational tool for both classrooms and corporations to manage genomic data and explore connections between genes and phenotypic traits. Personalized Nutrition Initiative Nutrition has a large impact on human health and wellness, but nutritional needs can vary by individual, making diet recommendations that could improve quality of life less accurate. The Personalized Nutrition Initiative was established in 2020 to facilitate transdisciplinary collaborations across campus to research individualized nutrition, and create a source for information on how nutrition impacts health and disease. The initiative’s research spans across multiple model organisms and biological disciplines, providing insights on how nutritional needs vary on a wide scale. The goal of the program is to be able to provide tailored recommendations on nutrition that take into account not only a patient’s history and phenotype, but their genetics, microbiome, and metabolome as well. Researchers in the initiative are looking at the impact of these measures on propensity for disease, cognition and learning, physical well-being, and more. The Initiative also brings together engineers and computer scientists with biologists to improve analytics for measuring nutritional impacts on health. The Personalized Nutrition Initiative hosts seminars on the research being conducted both at the campus and beyond, and also features a newsletter with the latest information on research, government/organization press releases, news from nutritional wellness groups, and more. The initiative has hosted Personalized Nutrition Innovation Day multiple times, a seminar where researchers can present new data from their nutritional studies. Microbial Systems Initiative Despite their small size, microbes make up a large portion of biomass on earth, second only to plants, and they can exist nearly everywhere, from the inside of our guts to the bottom of the ocean. Yet, with how populous and diverse microbes are, there is so much still unknown about them. The Microbial System Initiative was established in 2018 to bring together microbial researchers across campus and create an integrative, collaborative community. By connecting researchers from over 50 campus units, the initiative aims to evoke more interdisciplinary projects, provide avenues for support and training, and ultimately increase our understanding of microbes through impactful research. MSI hosts a variety of seminars, symposiums, and collaboration-building events meant to spark new questions and connections within microbial research in the community. One of the priorities for the initiative is training a diverse set of next-generation researchers. As such, there are numerous workshops and training sessions provided to give skills to trainees, along with a new recruitment program meant to help new hires find success in the program. Thus far, MSI has led to new methods for detection of microbial diseases in humans, including COVID-19, novel treatments for disease, and a better understanding of how microbiomes influence behavior and health. READ ON IGB'S WEBSITE Honey bee workers collect pollen and nectar from a variety of flowering plants to use as a food source. Honey bees typically forage from up to 1-2 miles away from the hive, though sometimes they travel even further, including up to 10 miles away. However, much of the modern landscape consists of agricultural fields, which limits the foraging options for honey bees in these areas. Furthermore, when crops decline at summer’s end, honey bee populations in corn-soy heavy areas experience massive losses, posing the question of how agricultural landscapes impact the type of food the honey bees bring in, and if this food then affects the queen’s production of eggs. Adam Dolezal (IGOH), an assistant professor of entomology at University of Illinois Urbana-Champaign, and Ashley St. Clair, a postdoctoral researcher in Dolezal’s lab, explored these questions in a new paper published in Frontiers in Sustainable Food Systems. Their study involved two components. The first involved placing honey bee colonies across differing agricultural vs wildflower prairie landscapes, and measuring the species and amount of pollen collected, as well as the number of eggs laid by the queen. The researchers found that the quantity of pollen didn’t vary based on crop vs prairie location, but that the species of pollen did, the main difference being that honey bees near prairie collected more evening primrose pollen than honey bees near crop fields. Additionally, queens from colonies placed closer to prairie laid more eggs than those near crop fields, particularly in late summer, when crop availability decreases. St. Clair explained that this result did vary a bit year by year, because field experiments with honey bees have so many variables to account for. “It's very complicated in the field to tease apart these differences. I mean, it could be corn, pesticides, the randomness in the colonies…It could be all kinds of interactions,” said St. Clair. “We wanted to see if we could replicate those findings in the lab because it would mean that pollen nutrition was actually an indicator of that reduced queen egg laying we see in August, and not some other environmental factor.” For the second part of the study, the researchers used small microcolony honey bee boxes to test the question of nutritional impacts on egg laying in a controlled laboratory setting, the first study replicate a field experiment in this way. The cage is made of two clear pieces that snap together around an injection-molded 264-well honeycomb plate for the bees to store food and for the queen to lay eggs in. At the bottom, there's a trough that food can be put into for worker bees to collect, but that the queen can’t access. The cages were originally designed by IGB Director Gene Robinson’s (GNDP) lab, to be used for automated beekeeping. However, St. Clair and Dolezal discovered they were an excellent way to house multiple colonies together in a laboratory setting, with each colony holding about 60-100 honey bees. The colonies were fed one of three treatment diets that mimicked the dietary mixtures found in the field component of the study: crop mixture, prairie mixture, or 100% evening primrose, which was added to see if its nutritional value was the reason the honey bees favored it as a pollen source in the field. The researchers then counted the number of eggs the queen of each colony had laid every day.
In line with what was found in the field, queens laid more eggs under the prairie diet compared to those under the crop or primrose diet. The results from both the field and lab components of the study suggest that honey bee colonies do better when given a diverse diet, as would be found in a field of prairie flowers, compared to a less diverse diet of crops. “The results indicate that it's the quality of the pollen that matters more than the quantity that they're bringing in,” St. Clair said. “There are specific pollens, like evening primrose, that when mixed in can be more nutritious overall. However, in the lab, primrose did not provide enough nutrition by itself to change the queen's fecundity. So, the take home here is that the honey bees need a diverse diet.” So, what can farmers and/or beekeepers do to help honey bees through the shortage of food in August? The researchers explained that prairie strips, which are already being implemented by farmers for other reasons, come with the added benefit of helping the honey bees. By placing strips of native prairie plants around water ways and farm edges, farmers reduce erosion and water loss on their farms, and also provide an additional food source for honey bees. And with laboratory studies like this, researchers can give better suggestions on what types of prairie plants to provide on the strips. “This is a new way of thinking about what we're measuring in these colonies,” said Dolezal. “Being able to see that when you have this or that on your landscape, your queens are more productive, is really valuable.” The team plans to use the microcolony cage system for the next research steps, which will focus on pesticide exposure and interactions with pollen on queen fecundity. Pesticides present a large problem for bees in general, but the specific effects of pesticides can be hard to study in such variable field settings. Dolezal explained that this laboratory microcolony system provides an excellent controlled setting to continue exploring these questions in the future. “There's a lot you can do with this system, and coming from someone who has been doing work in the field, this is like magic,” Dolezal said. “This laboratory system will allow us to conduct manipulative experiments and look very finely at what's going on in the honey bee colonies.” This work, titled “Access to prairie pollen affects honey bee queen fecundity in the field and lab”, was supported by the USDA and the Eastern Apicultural Society. https://doi.org/10.3389/fsufs.2022.908667 READ ON IGB'S WEBSITE Students at the University of Illinois Urbana-Champaign once again hosted “Owl Night,” a public outreach event where people of all ages can learn about owl behavior and ecology, and if they’re lucky, see an owl up close. Owl Night takes place on two separate nights: November 1st at Kennekuk County Park, and November 8th at Homer Lake. At Owl Night, participants can learn about owls through a series of hands-on activities, including dissection of owl pellets, examination of owl feathers under a microscope, tracking owls by hand using radiotelemetry, and more! The event is created and run by the students of NRES 285: Owl Migration & Education, a class designed not only to teach students about owl biology, but also give them skills in science communication and outreach. The class—currently in its second year—is co-instructed by Joy O’Keefe, an assistant professor and extension specialist of natural resources & environmental sciences, and Michael Ward, a professor of NRES as well.
“The class teaches students about basic biology and ecology of birds, wildlife research techniques, and outreach tactics that you can use to engage the public,” said O’Keefe. “The students learn the components of putting together a big outreach event and deciding what activities they want to run. We encourage them to think about what they really want the public to take away from the event.” Besides hosting the two public owl nights, students also gather weekly at the Kennekuk Education Center to assist with research on the migration and behavior of Northern Saw-whet owls, which are the smallest species of owl in Illinois. The research is led by Mike Avara, lab manager and field coordinator for Ward’s lab. The research team uses mist nets, which are thin and indiscernible nets stretching 12 meters in length, to safely capture the owls. Owls are then aged, sexed, banded, and tagged with a radio transmitter that utilizes a local tower telemetry system to constantly take spatial data on the owls after release. The project’s original goal was to see if owls use Kennekuk Park as a stopover point during migration. But Avara says that since then, the project’s scope has grown, with new questions arising about the factors affecting movement of owls during migration and potential territorial responses to playbacks. “First we wanted a systematic way to test for the presence or absence of owls,” said Avara. “Then last year that evolved into more questions about the activity of the owls. Are they staying for extended periods of time, like the entire winter? Or are they migrating further south? This year we’re looking at migratory connectivity, so when and where the owls go, how far they're moving around, and how weather might be impacting that.” Because the scale of research has grown, so has the need for extra hands and experienced banders to train the students. Mac Chamberlain, a 2nd year graduate student in the lab of Mark Hauber (GNDP), a professor of integrative biology, joined the team last year as a field coordinator and educator for both the public Owl Nights and the research nights. Chamberlain previously banded raptors at Cedar Grove Ornithological Station before attending Illinois, and now helps train the students on handling and banding the owls. “I like introducing the students to owl banding because owls are very charismatic birds,” said Chamberlain. “At the first station that I worked at, we always called them ‘killer sky kittens’, because they’re cute and fluffy but have quite dangerous talons. Teaching people about owls can really get them hooked on birds.” Through their owl tracking efforts, the researchers have found that although the owls move all around the park, they do have specific roosting spots they prefer. Interestingly, these spots change occasionally over the season, and this seems to coincide with loss of leaf cover in their roosts. Researchers also found that the owls were most active at dusk and dawn, but still moved around throughout the day. Out of the owls caught, 80% were female, matching patterns seen at other stations, and eliciting new questions about the reason for a female-skewed sex ratio during migration. O’Keefe and Ward plan to keep offering the class each Fall, and hope to have future students learn how to analyze the owl data they collect, and run a social media campaign to advertise the public event and communicate research findings. O’Keefe also hopes to get more historically excluded groups involved in the research and outreach components. Avara says there is much more research to be done with the owls, and that he hopes that both the outreach and research of owls at Kennekuk continue to grow. Erin Wunderlich, a senior undergraduate, says the class merges her interests in environmental science and science communication, and gives hands-on experience that is important for her career ambitions. “This experience has been eye-opening because not only do we learn all these things about owls and outreach, but we actually get to do the public event ourselves and see the results,” said Wunderlich. “It's really amazing.” “Working with the students and the public, watching that interest in birds and science grow in the community…I think is my favorite part.” Chamberlain said. |