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].
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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!” |