Story written by Dan Silvia, Communications Manager

Two Bellevue University undergraduate science students have joined the elite ranks of published student researchers. Shawn Freed and Sydney Robertson, both senior Biology students, each received an author credit on “Draft Whole-Genome Sequence of Green Sulfur Photosynthetic Bacterium Chlorobaculum sp. Strain 24CR, Isolated from the Carmel River.” Freed also received an author credit on “Whole-Genome Sequence of the Novel Rubrobacter taiwanensis Strain Yellowstone, Isolated from Yellowstone National Park.”

“It is very rare that undergraduates get published in a scientific peer-reviewed journal, especially as the lead author,” said Dr. John Kyndt, who co-authored the papers with his students. “Even at larger research universities it is rather unusual that undergraduate students get a first author publication during their undergraduate studies. We are able to give students this opportunity because of our smaller class sizes, close professor involvement, and a deliberate focus to integrate more real life research.”

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The science department celebrated the article publications with a pizza party on Tuesday, March 26. Among those in attendance were Dr. Mary Hawkins, University President; Dr. Mary Dobransky, Dean of the College of Science and Technology; Dr. John Kyndt, Dr. Tyler Moore, and Dr. Scott Pinkerton, science faculty; and Johnny Farnen, Science Lab Assistant, as well as the authors themselves.

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Bellevue University Professors Dr. John Kyndt and Dr. Tyler Moore were each recently awarded $5,000 grants by Nebraska’s Established Program to Stimulate Competitive Research (EPSCoR). The grants were among eight awarded by the organization.

The grants are designed to increase undergraduate research opportunities at Nebraska’s smaller colleges and universities, Nebraska EPSCoR offers funding up to $5,000 per project for collaborations in science, technology, engineering and math (STEM) areas. Faculty and students involved in the selected proposals report their project results to Nebraska EPSCoR and often present their research in scientific publications and at conferences.

The title of the awarded grants are:

Tyler-Moore

ERK as a negative regulator of IRF3 and the antiviral response.

Dr. Moore

 

 

Bellevue University Labs

Devising molecular tools for genetic manipulation of Galdieria sulphuraria, a microalga optimized for biofuel production from waste sources.

Dr. Kyndt

 

If you are interested learning more about one of these projects, or joining as a researcher yourself, feel free to come talk to us.

 

Are you interested in biology or computer science, or maybe both, and are not sure what future career you are planning for? You should definitely consider the field of genomics as a potential career path.

The field of genomics has rapidly changed and applications have exploded in the last decade. Genomics is changing everything: from the way we develop new drugs and treat disease, how we make our food, how forensics solves crimes, to how you diagnose your health.

Illumina, a leading company in next-generation genome sequencing and analysis, has put together a series of short videos on possible careers in the growing field of genomics. Ever considered being a genetic councilor, an artificial intelligence bioengineer, a clinical lab manager, or bioinformaticist?

These videos are absolutely worth watching if you want to learn more about what these careers look like on a daily basis. Each of the videos also includes educational requirements and average starting salaries.

Want to be a gene detective? Consider Genetic Counselor:

Interested in cracking the code of artificial intelligence? Consider AI Engineer:

Want to join the Biological Revolution? Consider Bioinformatics:

Are you a lab nerd that wants to work with real patient samples and help solve disease problem? Consider Clinical Lab manager:

From the clinical lab to patient counseling, currently all of these require at least a basic knowledge of genome sequencing and genome data analysis. Basically every science research project these days, whether it is on human, animal, environmental or microbial subjects, uses some form of genomic data. More information about Illumina and fascinating genomic discoveries made by next generation sequencing can be found here.

If you are interested in a career in genome sequencing and genome data analysis, a biology undergraduate degree is a great place to start. At our BU Science Labs we have many classes teaching you genomics, and always have research projects where you can get your hands wet on sequencing genomes yourself, using Illumina sequencing of course. If you’re interested, come talk to us!

Swimming with sharks – is there anything scarier?

It’s old hat for Taylor Fluellen, a Bellevue University biology student, who completed a two-month research program at the Bimini Shark Lab this past fall. The lab is part of the Bimini Biological Field Station, located on the island of South Bimini, Bahamas.

Even with that experience, Fluellen did have one encounter that made her heart skip a beat or two. She was out on a cloudy September day catching stingrays when a dorsal fin broke the water’s surface. Comfortable in the relative safety of her small boat, she was excited to see what she thought was a lemon shark. It was a tiger shark, a fish with a much more dangerous reputation than its more docile cousin, the lemon.

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“We followed it for a bit, but then lost it and decided to go back to catching stingrays,” she said. “Later, I’m just sitting there in the cold water. It’s cloudy and it’s all very quiet. It felt just like one of those shark movies.”

On the whole, Fluellen describes her experience as “pretty spectacular” rather than pretty scary.

“I saw just about everything I wanted to see in terms of ocean life. My favorite thing to do was trawling. You drive really fast in a boat with a casting line out. Hopefully, you catch some fish. I’ve fished before, but only in a pond. It was deep sea fishing. It was just so much fun.”

A 2011 graduate of Bellevue East High School, Fluellen first became interested in sharks and other ocean creatures while watching “Shark Week” on the Discovery Channel as a kid.

Shark“It was always a fascination. When I was 7, I wanted to be a trainer at Sea World — it’s always been ocean-related,” Fluellen said. “Sharks happened a little later, but they’re an all-consuming passion now. I love them. I think they’re fascinating.”

The daughter of a retired Navy veteran, Fluellen felt studying at her local school was the way to go after experiencing the moves typical of a military career.

“I knew I wanted to stay local for school. I just wanted a few more years with my family,” she said of her decision to attend Bellevue University. “It’s been super convenient. I can see the ASB (Administrative Services Building) from my bedroom window.”

Fluellen was on campus before the science labs were remodeled in the fall of 2016 and even had a hand in some early prep work for the redesign.

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“I actually witnessed the whole process. We helped clean out the old labs. I got to keep some old posters which was kind of cool,” she said. “The new labs are beautiful. It’s like walking into the Starship Enterprise.”

Fluellen is closing fast on completing her degree. Following graduation she has her sights set on a return to the ocean.

“I would love to work in Bimini again if there is an opening,” she said. “I’m looking at other organizations, zoos, and aquariums. There’s a lot of options.”

Story written by Dan Silvia, Communications Manager.

Whether it’s milk, dark or white chocolate this unique food has always been associated with pleasure, but can chemistry tell us why? Our craving for chocolate may arise from its chemical nature like the sugar, fat, caffeine, and other compounds. Furthermore, our desire may be driven by the sensory properties of chocolate, which include aroma, sweetness, and texture.

On Valentine’s Day, the American Chemical Society is hosting a webinar on the chemistry of chocolate and desire. We will have a watch party with free Belgian Chocolate and hot cocoa at our BU Science Labs (LCN555). Please join us around 12:45 pm to satisfy your brain cells with chemical knowledge and chocolate cravings! The presentation starts at 1 pm.

Michael Tunick, Assistant Clinical Professor of Culinary Arts & Food Science at Drexel University will explain the science of chocolate desire and why chemistry may be responsible for our craving.

What You Will Learn:

  • The components that give chocolate its characteristic flavor and aroma
  • Why people crave chocolate
  • Is chocolate an aphrodisiac?

Thu, Feb 14, 2019 1:00 PM – 2:00 PM CST; LCN 555chocolate desire acsacs banner

Dr. Tyler Moore and Bellevue University alum Jennifer Mather recently published a paper on their research into how viruses can avoid being eliminated by the immune system in order to persist in their hosts. The paper is published in mBio, an open access journal within the American Society of Microbiology, and can be viewed here: https://mbio.asm.org/content/10/1/e02578-18. The work was accomplished in collaboration with Dr. Kim Hasenkrug of the National Institutes of Health (NIH) and Dr. Ulf Dittmer of the Institute for Virology at the University of Duisberg-Essen in Germany. Jennifer, a Bellevue University Biology undergraduate at the time, spent the summer learning new techniques and conducting experiments alongside her faculty mentor, Dr. Moore, in the NIH Laboratory for Persistent Viral Diseases at the Rocky Mountain Laboratories in Hamilton, Montana. If you are interested in learning more about undergraduate research opportunities at Bellevue University, check out the Student Research page. If you are not yet a student, go to https://www.bellevue.edu/ and apply!

Here is description of the paper, including why we thought this was an interesting problem, how we approached solving the problem, and what we learned from our experiments that could be used to solve additional problems.

T cells kill cells that are infected by viruses

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We have known for a while that special immune cells called T cells have the ability to kill cells infected with viruses. Because viruses need healthy cells to live in and reproduce, killing these cells prevents the virus from spreading. In order to make sure our T cells only kill infected cells, special cells called Antigen Presenting Cells (or APCs) train the T cells what to kill. It is kind of like showing a picture to a search party.

What happens when APCs are infected by viruses?

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We know that some viruses can actually infect APCs. In some cases, this makes the APCs less able to instruct T cells. Without proper instructions, T cells do not become fully activated and can’t kill infected cells. We thought this might be why some potentially acute viruses become persistent. We study a particular mouse virus known as Friend virus (named after Charlotte Friend, who discovered it). We can use this virus as a model to learn more about virus infections and the immune system in general. This particular virus infects many types of cells, including APCs. However, the immune system doesn’t fully eliminate the virus, causing a chronic infection. We were particularly interested in the fact that a particular type of APC, known as “B cells”–these are the cells that make antibodies, are one of the main types cells infected during the chronic infection.

Are APCs more or less activated when they are infected with Friend virus?

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Friend virus infects many types of cells, but one of them is a type of APC known as B cells. We were curious if there was a difference in activation between B cells infected with Friend virus compared to B cells from an infected mouse that didn’t actually have the virus growing inside of them. In order to test this, we used a technique known as FACS. This allows us to identify which cells are infected with a virus and analyze them separately from cells that are not infected.

We infected a mouse with Friend virus. Then, we analyzed all the B cells by FACS. We compared the B cells that had virus growing inside of them to B cells that came from an infected mouse but were not infected with a virus. We were surprised to find that the B cells infected with the virus were actually much more activated than uninfected B cells. This suggests that Friend virus infection of B cells didn’t impair their function as APCs.

Are Friend virus-infected B cells better at activating antiviral T cells?

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We know that B cells can be APCs. We also know T cells need APCs to become activated and proliferate. Our new data show that infected B cells are more activated than uninfected B cells. Because of these data, we wondered if infected B cells would be better at activating T cells. To test this question, we infected mice with Friend virus and purified out infected B cells from uninfected B cells using FACS. We then could use these cells as APCs to activate T cells. To make sure the T cells were given the same chance to be activated in both conditions, we used T cells that only recognize a special protein from eggs known as ovalbumin (“OVA”). We gave both groups of APCs OVA and tested how well each could activate the T cells. Even though both APCs had OVA (think of it as the search party picture to show the T cells), the infected B cells were much better at activating the T cells. This means infected B cells more activated (like we showed in Fig. 1), but they are also better at activating antiviral T cells.

Regulatory T cells inhibit antiviral T cell responses

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One thing that is interesting about Friend Virus is that it induces a type of cell known as a Regulatory T cell (or Treg). Tregs are important because they make sure our immune system doesn’t cause too much damage to our tissues. However, when Tregs are induced during Friend virus infection, they prevent T cells from being fully activated. This is a major factor contributing to the persistence of Friend virus.

We can specifically deplete Regulatory T cells using special mice

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We were interested in how Tregs contribute to the activation and function of APCs during Friend virus infection. In order to test this, we had to use a mouse system where we can specifically get rid of the Tregs in a mouse. We are lucky that Tregs are the only cells that turn on a particular protein known as FOXP3. A group of scientists already developed mice that have the receptor for diphtheria toxin on every cell that turns on FOXP3. Mice don’t normally have the receptor for diphtheria toxin. With these mice, we can inject diphtheria toxin to kill Tregs without harming the other cells or the mouse.

Does depleting Regulatory T cells make the APCs better at activating T cells?

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In order to see if Tregs change the function of APCs, we specifically depleted Tregs in mice infected with Friend virus. Then, we purified out virus-infected APCs from mice with Tregs (left) or mice with Tregs depleted (right). We found more activation in the T cells that were cultured with APCs from Treg-depleted mice. This suggests that suppressing APC function is one way Tregs are preventing T cell activation during Friend virus.

Final Conclusions

  • When Friend virus infects B cell APCs they become more activated and more able to activate antiviral T cells
  • Regulatory T cells (Tregs) prevent APCs from becoming activated and reduce their ability to activate T cells
  • From an evolutionary standpoint, sometimes getting rid of a virus isn’t as important as protecting our tissues
  • If we want better immune-based clinical therapies, we need to have a better understanding of how the immune system balances getting rid of things that could cause disease while also not damaging our own bodies

Remaining Questions

  • Some viruses infect APCs and make them less able to activate T cells–what is happening in Friend virus that is causing the immune system to respond differently?
  • If Friend-virus infected B cells are better at activating T cells, and T cells kill virus-infected cells, why are B cells the main cells infected during chronic Friend virus infection?

The Bellevue University Science Lab was awarded funding from the Greener Towns Program to complete public landscape improvements on their campus. This is one of 14 projects in the state to receive funding aimed at improving green infrastructure for pollinator habitat, managing storm water or accomplishing other economic, environmental, aesthetic and social goals.

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Dr. Tyler Moore applied for the funds and will coordinate the project to be completed in 2019. The Greener Towns program will provide $16,177.50 in funding that will be matched by community efforts. One of the main goals of the project is the completion of a native garden area as part of the larger outdoor sustainability lab which is planned to be constructed later this year.

The Greener Towns and Community as Habitat programs are coordinated by the Nebraska Statewide Arboretum and funded by the Nebraska Environmental Trust, a beneficiary of the Nebraska Lottery.

For more information about this or future funding assistance, go to http://plantnebraska.org/community-landscapes/project-funding/greener-towns.html or contact Rachel Anderson at randerson@unl.edu.

In the summer of 2016 we went through a complete redesign of the science labs at Bellevue University. This was a close collaboration between the global architecture company HDR and the Science Faculty and Administration, that resulted in a remarkable transformation of the science department. Last month the project was recognized with an award at the American Institute of Architects (AIA), Nebraska Excellence in Design program:

http://aiane.org/aia_design_awards/2018-AIANE-design-awards/aiane_awards_18-202.html

One of the key aspects of the project was the integrated research and collaboration, which is something we had set forth as our intention from the initial planning of the redesign. ‘Science on Display’ was kept as a central theme throughout the entire design, which the architects at HDR successfully translated into an inviting and stimulating environment (no scary ivory towers here…).

Since the redesign we have been able to integrate new and relevant research projects into our courses and have noticed a significant increase in number of students spending time in the lab spaces, even outside the required course times. This stimulates the generation of new ideas, which is essential to any science research project, and is a great experience for our students to develop critical, scientific thinking.

According to the Jury of the AIA award, the redesign “revitalized the labs for experimentation and exchange between students and faculty”, and creates a “visual atmosphere of openness and lightness.” If you want to come experience this for yourself, please stop by anytime at our ‘award-winning’ science labs and we’ll be happy to give you a tour, or even get you involved in your own science project!

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At the BU Science Labs we take the ‘real learning for real life’ quite literally, especially when it comes to brewing beer. Every year our Microbiology students learn in depth about fascinating metabolic reactions involved in the process of beer production. Students also have to come up with their own home beer brewing protocol as one of their assignments.

This turns out to be a very educational experience, as you have to understand the microbiology and biochemistry involved in order to write up a comprehensive protocol. In addition you learn some cool terminology like lauter tun, mashing and sparging wort, which makes you feel like knowing a different language and gives you some bragging points at your next party.Nebarska Brewing tour_0677.jpg

As a perfect closure of the fall term, our microbiology students got to tour the Nebraska Brewing Company and were able to see how this process runs in a small local industrial setting. During the tour student received an entertaining overview of the malting, mashing, fermentation and bottling process, and how different types of beers are produced. Of course, as good scientists do, there was some necessary sampling and testing involved during the tour as well!

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By Dr. Tyler Moore

I had the wonderful opportunity to spend two weeks studying in the Gene Regulatory Networks in Development course at the Marine Biology Laboratory (MBL) at Woods Hole, Massachusetts.  The course was led by Dr. Scott Barolo (U Michigan Medical School) and Dr. Isabelle Peter (Cal Tech) with contributions from many additional faculty.

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The course focused on ways to experimentally and computationally analyze and visually represent the regulatory networks that control gene expression (“Gene Regulatory Networks”).  Integrated networks of gene expression control developmental processes ranging from sea urchin endoderm and mesoderm specification, arthropod body segment patterning, development of limbs, determination of organ size, and more. ShhNetwork

In addition to hearing from faculty about their research into gene regulatory networks, I also had the opportunity to do some hands-on learning of computational tools for analyzing and representing gene regulatory networks.  Here is a regulatory network my group put together on sonic hedgehog (Shh) signaling in patterning the posterior versus anterior hand during limb development.  The arrows represent inducers of a gene and the blocks represent inhibitors of a gene.  The colored lines are signals that are present in a particular region and the grey lines are signals that are absent from a particular region.

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Although the class was rather high paced, we did have some down time.  We had the opportunity to tour the MBL rare books collection, which included early editions of Antonie van Leeuwenhoek’s drawings, Newton’s publication describing his new telescope design, early Ernst Haeckel work, and hand-painted illustrations from the Captain Cook voyages.  I even had the opportunity to hold Thomas Hunt Morgan’s Nobel Prize (awarded for his uncovering the role of chromosomes in inheritance).

I was in awe to be surrounded by so many people with vast and diverse experiences, both the faculty and the students.  I’m very grateful to have been a part of this class.  I received more advice and instruction than I can describe in this post, and I am excited to put it to use in our classes and research.

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