Science on Display | Bellevue University 
For scientists, sequencing a genome is truly cause for celebration.
Which is exactly why Bellevue University Science Lab faculty and students gathered recently at a pizza party to mark an important Lab milestone – sequencing 50 genomes from all around the world.
According to Dr. John Kyndt, Associate Professor in the College of Science and Technology, sequencing a genome is an important step toward decoding an organism, which is the ultimate goal. As he describes it, that journey of understanding is serious business, to be sure, but it is also a fun process of discovery for both veteran scientists and the undergraduate microbiology students at Bellevue University.
BU students enjoying the 50th Genome Pizza party
“Sequencing genomes is key to advancing science,” explains Dr. Kyndt. Every living organism includes genomes, which are composed of the organism’s DNA. And whether they belong to human DNA, bacteria, viruses or other simple forms of life, he adds, sequenced genomes provide a roadmap that help scientists find genes and better understand how the genes work together to direct an organism’s growth and development.
Dr. Tyler Moore and BU Biology Alumni reunited at the 50th genome celebration.
As one of the most technologically advanced small labs in Nebraska, Bellevue University’s Science Lab allows students to get directly involved in genome sequencing projects. “Students are at the center of our open access, innovative environment” said Dr. Mary Dobransky, Dean of the College of Science and Technology. Ten genome sequences from organism samples have been published in academic journals and “more are on the way,” says Dr. Kyndt.
“With administration support – and some pizza – we are able to get amazing results in our student-driven research projects.” – Dr. John Kyndt, Assistant Professor, Bellevue University
Because of their important foundational role, scientists around the world study and sequence genomes. Perhaps the most high profile genome study is the Human Genome Project, a 13-year effort to identify all of the 20,000-plus genes in human DNA that was completed early, in 2003, largely due to technological automation.
Technology has accelerated Bellevue University’s efforts, too. Thanks to a partnership with Illumina, a global leader in Next Generation, or high-throughput, genomics, Bellevue University undergraduate students have learned how to use cutting-edge genomic sequencing software – all the way from how to extract DNA from a sample to how to run the samples through the Illumina MiniSeq system.
Dr. John Kyndt and Louise McConnell (Illumina Executive Account Manager) discuss future student sequencing projects.
Amiera Rayyan, who completed her Bachelor of Science in Biology at Bellevue University in 2018, was among the first to use the MiniSeq system and as a result received lead author credit on two research papers published in academic journals. Sydney Robertson, another biology graduate who also has earned lead author credit on multiple published academic research papers, says, “The experience I had was more than just helpful in the classroom. I was able to collaborate with the professors and other institutions, really learning how to communicate effectively.”
As the success experienced by students like Amiera and Sydney and the genome sequencing continues in the University’s Science Lab, Dr. Kyndt says the impact – on science and on students – should never be underestimated. “It is very rare that undergraduates get published in a scientific, peer-reviewed journal, especially as the lead author,” he notes. “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.”
Story written by Cris Hay-Merchant, Director of Strategic Communications at Bellevue University.
Illumina is a global leader in genomics and Next Generation sequencing. Illumina’s innovative sequencing and array technologies are fueling groundbreaking advancements in life science research, translational and consumer genomics, and molecular diagnostics.
This past November, Bellevue University was invited to take part in an Illumina project to beta test their new Microsoft 10 compatible sequencing software. Seven students from the Microbiology, Biology Investigation 205, and Independent Study courses were trained in the entire process, covering DNA extraction, library preparation and Next-Gen Illumina sequencing during this project.
Students showing off their Illumina swag after successfully completing their DNA sequencing library preps. From left to right: Maddy Vasquez, Morgan Leatherman, Jameson Smith, Nina Patel, Daun Kim, Fabiola Aviles, and Dayana Montano Salama.
‘I enjoyed the experience and it was great to be able to learn this in an environment where we can try things out and even sometimes fail, but in the end I appreciate getting more hands-on knowledge of the whole sequencing process’ says Fabiola Aviles, a senior Biology major at BU.
Two sequencing runs were performed after upgrading the MiniSeq system. The second run was performed using a pooled library exclusively prepared by Bellevue University students and faculty. Both sequencing runs were successfully completed, and feedback shared with the Illumina team.
“We truly appreciate the continuous engagement of Dr. John Kyndt and his team during beta testing. Illumina is delighted to empower genomic research of the next generation biologists at BU” says Violet Chu, Senior Product Manager and lead of the Illumina Beta testing team
Dr. John Kyndt who was the lead BU Faculty for this project states that “This was a unique opportunity for both the BU Faculty and students to work closely with a major global company on an innovative sequencing project. We were able to provide Illumina with valuable customer feedback while students had an exclusive chance to learn a new technology and connect with industry leaders in the field of genomics.”
Are you a BU Biology student interested in doing some research or learning Next Gen sequencing yourself? Contact one of the professors at the BU Science labs and we’ll be happy to get you involved!
Last October the Bellevue University Science Labs were honored with an AIA Central States Region Distinguished Award in the Interiors Category.
This prestigious regional award was presented at the regional American Institute of Architect (AIA) 2019 Design Award Ceremony in St Louis. Mike Hamilton (HDR) and Dr. John Kyndt and Diego Kyndt were present to accept the award.
Mike Hamilton (HDR), John Kyndt (BU) and Diego Kyndt accepting the AIA award.
The BU Science Labs were designed by HDR in close collaboration with the science faculty at BU and were intended to have ‘Science on Display’ and combine a teaching, research and collaboration space.
Shortly after establishing the new lab spaces, the BU Faculty also collaborated with HDR Research on a study, led by Francesqca Jimenez, to understand how the space impacts student learning and the overall vision of science education at BU. Earlier this year, the Environmental Design Research Association (EDRA) awarded this research project a ‘Certificate of Research Excellence’ (CORE). A paper describing the outcomes from this study is forthcoming.
It is great to see that these lab spaces are being recognized not only locally, but also on a regional scale, and rewarding to see how this space impacts the life of the instructors, visitors, and current and prospective students.
Sydney Robertson, a recent graduate of the Bachelor of Science in Biology program, recently has had two papers accepted for publication.
Robertson’s paper “Whole-genome sequence of a novel Elioraea species, isolated from a Yellowstone National Park hot spring”, has been published in Microbiology Resources Announcements (MRA), and the paper “Whole-Genome Sequences of the Purple Nonsulfur Photosynthetic Bacteria Rhodobacter capsulatus SP108 and SL Reveal a Need for Reclassification of the Genus” will be published in an upcoming issue of Microbiology, Immunology and Pathology Journal (MIP).
Sydney Robertson showing off her Illumina swag after completing several successful runs and publishing four genome papers.
“It’s a very accomplished feeling doing something outside your comfort zone. I have now a whole new skill set I didn’t even think was possible” Robertson mentioned.
Robertson is the lead author on both papers and collaborated with Dr. Terry Meyer from the University of Arizona and Dr. Robert Ramaley from UNMC.
“The experience I had was more than just helpful in the classroom. I was able to collaborate with the professors and other institutions, really learning how to communicate effectively”, she commented. Robertson had previously also published another paper in collaboration with fellow student Shawn Freed. These papers were made possible because of the in-house Illumina Next Generation sequencing that can be done at the BU Science Labs, and the Wilson Enhancement Fund for Applied Research at BU.
“The commitment that Sydney has shown for this sequencing project has really paid off. Her enthusiasm and positive attitude kept her engaged and has allowed her to complete these publications even after she graduated earlier this year,” said Dr. John Kyndt, a Professor in the College or Science and Technology and Sydney’s mentor on these projects. “It’s great to see this kind of drive for scientific discovery in our students. I am sure these publications will help her with her future applications to graduate schools or programs.”
Are you a BU Biology student interested in doing some research or learning Next Gen sequencing yourself? Contact one of the professors at the BU Science labs and we’ll be happy to get you involved!
On a vacation trip to New Mexico this summer Dr. Kyndt sampled some water from Dripping Springs in the Organ Mountains to look at the bacterial composition in this pristine natural area.
Organ Mountains, NM
After returning to the labs at Bellevue University, he grew the samples on bacterial agar plates and noticed several bright orange colored colonies on one of the plates. Intrigued by this, he purified the bacteria and isolated its DNA. After genome sequencing, he found out that this species was closely related to species only found before in dead or diseased fish, so it appeared to be a potential fish pathogen. Since Dr. Moore is more of a fish person (he is an experienced fly fisherman) and knows more about cell infections in general, Dr. Kyndt invited him to join in this study. Together they did some more research and comparison with other species in this genus, which resulted in a new collaborative publication:
“Draft whole-genome sequence of a novel Chryseobacterium viscerum strain, isolated from fresh water at Dripping Springs, New Mexico.” was published this week in the journal Microbiology Resource Announcements. The new strain was designated Chryseobacterium viscerum DPS (for Dripping Springs).
Chryseobacterium viscerum strain DPS
Although this was an exciting find, since no one has ever found this species free living in nature, the most exciting part comes now as they are planning a student-led project to test the pathogenicity of this bacterium.
A more comprehensive metagenomic study of the water and soil samples from Dripping Springs, that looks at all the several hundred bacterial species in the samples, has also been submitted for publication in the journal Microbiology Resource Announcements and is currently under review. Undoubtedly these results will lead to further student research projects at Bellevue University.
The past few weeks we had several news reports about new developments at the BU Sciences.
One was the Bellevue Leader article about the discovery of a very unique flatworm species at the BU science labs. The worm is a local species that was discovered during regular field work with our students:
Another piece was a Fox 42 News story on the new Sustainability Outdoor Learning Lab that is being developed, and the NET grant that support part of the project. This was based on a recent talk we gave at Green Bellevue:
https://fox42kptm.com/news/local/bellevue-university-to-create-outdoor-sustainability-lab
With the start of a new academic year approaching quickly, more cool stuff will be happening at the BU Science Labs soon. So keep an eye out for more intriguing stories or research projects, and come and join us if you like to do some research yourself!
Every year, Bellevue University recognizes and awards faculty for their contribution to teaching and service to the university. Peers and students have a chance to nominate the faculty for one of four awards. This year the science department took home two of the awards!
The ‘Excellence in Innovation Award’ recognizes innovation by faculty/staff that has a positive impact on the University and/or student learning, and is described as: “Innovation, for the purposes of this award, is defined as the introduction of a new technique/structure/idea/technology that addresses a specific problem or issue and has a demonstrative positive impact”.
The 2019 Excellence in Innovation was awarded to the science team: Dr. Scott Pinkerton, Dr. Tyler Moore, Dr. John Kyndt and Johnny Farnen.
The ‘Excellence in Teaching Award’ recognizes teachers that demonstrate mastery of:
- High standards of teaching effectiveness.
- Outstanding or innovative teaching techniques.
- Positive reputation for teaching from the perspectives of students, colleagues, and alumni.
- Evidence of sustained commitment to teaching.
- Evidence of high levels of student learning or achievement.
This year’s Excellence in Teaching Award was given to Dr. Dr. Scott Pinkerton, Dr. Tyler Moore, and Dr. John Kyndt.
Drs. Kyndt and Moore accepting the awards from Dean Dobransky at the Annual BU All Campus meeting.
The comments of the awards recipients illustrate their passion for science and continuing commitment teaching and innovation:
“We have made significant changes to the science curriculum, lab spaces and overall science education over the past couple of years and our students are now starting to see the benefits of this. We just do our jobs and have fun doing it, but it’s certainly great to see these efforts being recognized by our peers and the University” – Dr. John Kyndt.
“It is wonderful to be recognized by our peers that we don’t just meet standards…we set them!“—Johnny Farnen.
“I really enjoy having the opportunity to spend time working closely with students, both in the classroom and the research lab. When I see the growth of a student from the beginning to the end of the program, or hear from graduates about how prepared they were for their jobs or subsequent education, that is the real reward.”—Dr. Tyler Moore.
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.”
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.
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:
ERK as a negative regulator of IRF3 and the antiviral response.
Dr. Moore
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!
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