What do marine ecosystems, worm regeneration, and a soccer-themed video game have in common? On the surface, perhaps nothing, but these are some of the fascinating projects middle schoolers pursued as part of the STEAM TRAIN program this year. The STEAM (Science, Technology, Engineering, Arts, and Mathematics) TRAIN (Transdisciplinary Research Across Institutional Near-peers) program is a collaboration between the Carl R. Woese Institute for Genomic Biology, Franklin STEAM Academy, and Uni High, that encourages middle school students to explore any science or engineering projects that interest them, with no limits other than their own creativity (and feasibility, of course).

STEAM TRAIN is organized by IGB’s Senior Outreach Activities Coordinator Daniel Urban and Franklin’s Magnet Site Coordinator Zanne Newman, and funded by the University of Illinois’ Community Research Partnership Program. The program runs from September to May every year, and has just completed its fourth successful year, engaging over 20 middle school students.

The program provides mentorship across multiple levels, including Uni High students, and graduate students and professors from the IGB. With guidance from their near-peer mentors, middle schoolers learn to formulate hypotheses, refine their research questions, collaborate effectively, and take the lead on their investigations. The program empowers student-driven research, giving middle school students the opportunity to conceive and design their own scientific and engineering projects. Mentors play a crucial role in steering the project design and equipping students with the tools needed to realize their innovative ideas.

Middle schoolers then use these tools to develop their group’s science projects over the course of the year. This year five groups presented the culmination of their projects in May, which delved into a range of disciplines including biology, engineering, and computer science.

Some groups researched the ecology of different animals, with one focusing on habitats, diets, and potential threats to various marine species, and another examining the different locomotions of snakes and the environments those movements are used in. Another group instead explored computer science, coding a Pong-like video game using Python, where two players compete to push a ball into the opposing goal to score points.

One group, fascinated by the regenerative abilities of planaria flatworms due to their stem cells, conducted an experiment in which worms were bisected and observed for regrowth. They found that whether a worm was cut into two or four pieces, all segments regrew into whole, separate individuals within five weeks, noting that previous research has shown that even a 1/200th piece of worm can regenerate.

Another group took an engineering approach, deciding to test the tensile strength of different materials, including wood, plywood, cloth, silk, and various metals. Materials were clamped between tables, and a bucket was hung from them and filled with weight until the material broke or became severely warped. Brass, wood, and silk proved to be among the strongest materials in the tensile test. The group also tested the durability of different materials under a blowtorch (operated by an adult, of course) or when submerged underwater for prolonged periods.

"I am always impressed by the types of questions our students ask,” said Danny Ryerson, IGB’s Outreach Activities Coordinator. "They choose incredibly interesting and challenging topics to research, and the levels of excitement and ingenuity they tackle these problems with are amazing."
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The STEAM TRAIN program exemplifies the power of creativity and mentorship in inspiring the next generation of scientists and engineers, showing that with guidance and resources, young minds can achieve extraordinary things.

CRISPR, (short for “clustered regularly interspaced short palindromic repeats”), is a groundbreaking gene-editing tool that empowers scientists to finely manipulate DNA, whether by inserting, deleting, or swapping genetic materials. This technology harnesses programmable enzymes, acting as molecular scissors, to precisely cut DNA at targeted locations. Among these enzymes, Cas12a stands out for its specificity and accuracy in its genome editing capabilities compared to the more widely used Cas9 enzyme. However, Cas12a's efficiency in making these edits currently falls way short of Cas9.

In a recent study published in Nature Communications, researchers at the University of Illinois Urbana-Champaign unveiled a novel strategy to bolster Cas12a's activity while preserving its accuracy. Led by Huimin Zhao (BSD theme leader/CABBI/CGD/MMG), Steven L. Miller Chair of chemical and biomolecular engineering, the team included graduate students Guanhua Xun and Zhixin Zhu, postdoctoral researcher Jingxia Lu, and automation engineer Nilmani Singh from the Carl R. Woese Institute for Genomic Biology.

CRISPR relies on programmable editing enzymes called nucleases, sourced from microorganisms like bacteria and viruses, to cut DNA. These enzymes, which include Cas12a and Cas9, are guided to their DNA targets by CRISPR RNA. Cas12a exhibits superior accuracy, displaying fewer off-target effects compared to Cas9, as well as the ability to edit multiple genome locations simultaneously. Yet Cas12a’s high accuracy is a double-edged sword, as it can hinder its genome editing activity.

“The human genome is large, around 3 billion base pairs. But if you just want to hit a specific 20 base pairs, there’s a high chance you won’t hit just that,” explained Singh. “That’s a big hurdle. CRISPR offers lot of potential for drug development, but these won’t make it to clinical trials unless you minimize off-target effects.”

Prior efforts by other researchers to enhance Cas12a's efficiency involved tinkering with the enzyme itself, but the Illinois team took a different approach, focusing on the guide crRNA instead.

The researchers incorporated 2-aminoadenine, also known as base Z, into the structure of the crRNA. This alteration fundamentally transforms the base pairing dynamics through the substitution of base adenine for base Z. The resulting Z – thymine bond is stronger due to the three-hydrogen bonds, increasing the binding efficiency of crRNA to the target DNA. This, in turn, enhances Cas12a's activity while maintaining its specificity, rivaling the efficiency of Cas9 in mammalian cells.

“Our guide RNA engineering is very unique, because we incorporate a natural occurring, non-conical base,” said Zhao. “When we think of DNA we think of the typical ATCG bases, but a few years ago we discovered some organisms have base Z instead of an A in their genome. Ever since then we’ve been building off that discovery, exploring new applications for this.”

The team says this new approach has many implications for therapeutics, cell engineering, and in-vitro diagnostics, as it addresses a significant hurdle in gene editing efficiency. In fact, the team had previously used this strategy to integrate base Z into mRNA used in the COVID-19 vaccine, substantially bolstering antigen-specific immune responses. Xun explained that base Z holds promise for vaccine development due to its ability to decrease immunogenicity, or the bodies incorrect immune response to antibodies, of the vaccine.

“Compared to protein engineering strategies which alter the Cas nuclease, our strategy is very simple,” said Xun, who is first author on the study. “We showed previously that this strategy was effective in creating a Z-based COVID-19 vaccine, and we think it has many more potential uses across both academia and industry.”

“It was surprising to me how such simple engineering could lead to a huge improvement in efficiency,” said Zhu. “Other methods like protein engineering require many rounds of screening, but with our method we can move the process along faster.”

CRISPR technology has countless potential applications, from treating genetic diseases, to creating genetically modified organisms, to advancing biomedical research. Its ease of use, precision, and versatility have made it one of the most powerful tools in modern biotechnology. By extending this strategy to other genome editing tools, the team envisions more efficient targeting of disease-associated genes, fostering new frontiers in precision medicine.
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The study was funded by the NIH and the Steve L. Miller Endowed Chair fund. The paper can be found at https://doi.org/10.1038/s41467-024-48012-x

Decoding decisions of parental stickleback fish
Growing up in upstate New York, Tina Barbasch spent countless hours catching salamanders and frogs in her backyard woods. Although her initial dream was to become a veterinarian, a suggestion from a friend’s mother, who was a biologist, steered her towards a career in research. Reflecting on her upbringing, she credits her father, a mathematics professor at Cornell, for showing her that "research was a real profession that people could have.”

Barbasch pursued her undergraduate studies at Cornell, majoring in Biology. It was there that her interest in behavioral studies blossomed, particularly through working on a project with local spotted salamanders. This passion led her to Boston University, where she earned a PhD in marine ecology and animal behavior under the guidance of Peter Buston. Her doctoral research delved into social behaviors and parental care in clownfish.

“Clownfish behavior is fascinating. They live in these social groups, they can undergo sex changes, and the male and female share the duties of parental care,” Barbasch said. “I was originally very behavior-focused, but as time went on, I started thinking about mechanisms, because they really shape how behavioral responses occur, and they can facilitate evolutionary change.”

Now a postdoctoral researcher at the IGB, Barbasch has refined her focus on social decision-making in animals, integrating behavioral work with genetic analyses. Under the mentorship of Allison Bell (GNDP leader), a professor of integrative biology, Barbasch investigates how animals navigate various sources of information to make decisions, particularly in the context of parental care. Her primary study subjects are threespined stickleback fish.

“Sticklebacks are really charismatic study organisms,” explained Barbasch. “The males build nests and provide all of the parental care to the eggs, fanning them and defending them from predators. And they also care for the fry after they hatch. They're doing lots of behaviors all at once, and I wanted to understand the mechanisms in the brain underlying how they respond to these multiple competing demands.”

Barbasch employs a blend of lab and field experiments to explore her questions. Her experiments often involve exposing fish to multiple stimuli simultaneously to observe their choices. This could range from territorial challenges, to mating opportunities, to predation risks. She examines what breeding males prioritize when faced with these multiple challenges, and then analyzes the gene expression in their brains to see how this relates to the observed behaviors.

Thus far, she has found that stickleback males make compromises in response to tradeoffs in different social situations, with individual variations in decision-making strategies. She has also identified a set of genes activated in the brain when males face behavioral tradeoffs.

“I found there’s a ton of individual variation in how they can manage these competing demands,” said Barbasch. “I want to further explore how these genes contribute to individual variation, and if that makes some males better at decision making than others. If this set of genes harbors genetic variation, then it can be a target for selection.”

In her most recent experiment, Barbasch journeyed to Alaska to study how wild sticklebacks juggle tradeoffs between feeding and parental care. Sticklebacks in Alaska exhibit varied foraging niches, with some foraging in shallow water and others in the deeper water of lakes. However, since they all nest within the shallow waters, this prompted questions about their parenting and feeding tradeoffs.

Barbasch presented the wild males with a feeding opportunity near their nests, observed their behavior, and collected them for gene expression and neural activity analysis, which she is currently analyzing. When asked about the challenges of working in Alaska, she noted that swarms of mosquitoes and cold waters were surprisingly not the most daunting aspects.

“When you're snorkeling in Alaska, you need to wear a dry suit to keep you warm,” explained Barbasch. “But it's almost impossible to get all the air out of the suit, and then when you get in the water, you're just this big floating balloon. So, the challenge is not so much swimming, but rather trying to approach these fish as a terrifying human balloon without freaking them out.”

As she aspires to continue her career in academia, Barbasch is currently applying to faculty positions at various universities, though she says she would be open to anything that allows her to “get out there and be with nature and animals.”

Outside of her research, Barbasch enjoys fly fishing, a hobby she picked up during graduate school. “I believe it’s important to have something to turn off your brain, and for me, that’s fly fishing. Artificial lures called flies are used to trick a fish into thinking that it's an insect or something tasty. It’s very appealing to me because every time I catch one I get that satisfaction of knowing that I tricked the fish based off of their ecology.”

Barbasch says the irony of fishing to get a break from researching fish was not lost on her, but did remark that “fly fishing gets me thinking about fish in a very different way. I learn what fish are in different rivers, and what attracts them. Some fish are very picky, and sometimes your fly needs to look like a specific insect that's hatching out at that particular moment.”

Apart from fishing, she loves spending time with her supportive husband, Alex. “It’s nice to have someone outside of academia that you can go home to and get new perspectives from. Someone that can ground you and help you think outside the box,” said Barbasch.

While research can often be a rocky road of trial and error, Barbasch says she navigates this road by embracing the wisdom encapsulated in a quote by Radhakrishnan Pillai that her grandfather often cited.
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“There are three types of people in the world. The first type learns by making mistakes; the second type keeps making mistakes but never learns; and finally, the third is the most intelligent type – they learn from the mistakes of others.”