With the recent growth in Natural Science courses and rapid development of the sustainability outdoor lab, the time was ripe to expand on the biology instructors for the science department.

Dr. Sarah Gaughan has a Ph.D. in Natural Resources (from UNL) and a background in aquatic ecology, fishes and genome sequencing. Her research has been focused on applying novel techniques to facilitate conservation of native species. She also focuses on population management and finding new ways to control invasive species.

Sarah Gaughan

Dr. Sarah Gaughan and Justin Haas with Nebraska Game and Parks doing Pallid Sturgeon gut microbiome research.

This provides a perfect fit for the growing science program and at the same time expands the experience and knowledge of the overall science faculty at BU. Having someone with a diverse ecology background will not only be beneficial for the outdoor lab projects, but also opens up the possibility for students that have an interest in environmental biology and ecology research projects or careers.

Dr. Gaughan will be teaching a variety of natural science courses for the general education but will also be available to mentor students in various research projects in the Biology or Sustainability program throughout the year.

To find out more about Dr. Gaughan’s research projects please check out our Faculty and Staff page, or feel free to contact her directly (sgaughan@bellevue.edu) if you have any environmental or ecology questions or project suggestions.

Welcome to the science team Sarah!

During the entire month of May the BU Library has their display around the theme of Sustainability and featuring the development of the new Sustainability Learning lab.

Sustainability on Display at BU

While the library is practicing social distancing, the library is open and provides a great opportunity to refresh your knowledge on native gardens, greenhouses, biofuels and solar and wind energy. Besides a large selection of books on these topics, the display also highlights some tips on how to set up a native garden and provides some more background on the use of algal ponds for biofuels. You might even come away with some ideas and inspiration to set up some renewable energy yourself or start some small-scale sustainable farming at home!


The main inspiration for this display comes from the new outdoor Sustainability Learning lab that is currently being constructed behind the Joe Dennis Learning Center. This lab will be a 7000 square foot indoor/outdoor educational and research area, consisting of a greenhouse (1,600 square foot), algae pond, wind and solar energy generating stations, and a native plants garden. The lab will give students a unique hands-on opportunity to study various aspects of biology, environmental science and sustainability. The garden of native Nebraska plants was already started last October and some blooms are already sprouting up! (check out our @scienceondisplay on Instagram for updates). This is just the beginning of a three year innovative project. Most of the construction will be occurring in the Summer and Fall of 2020 when the greenhouse is built.  In the second phase, the algae pond and the solar and wind generation stations will be installed.


If you can’t make it to the BU Library but still would like more information and resources on the various aspects of sustainability and on the outdoor learning lab, you can also visit the virtual Library Libguide page, where you can find lots of links to library books and ebooks on native plant gardens, net-zero greenhouses (including an interesting historical overview), and renewable energy from solar, wind or biofuels.

Both the library display and Libguide were created and are maintained by Margie McCandless, Reference Support Specialist at the Freeman Lozier Library at Bellevue University.

The COVID-19 pandemic has disrupted everyday lives globally and many scientific research labs have halted or shifted their research efforts. Student research at Bellevue University has also been impacted by this, and students are only allowed to continue working in the labs under restricted circumstances, following social distancing and with additional PPE requirements in place.

Fabiola Aviles

Senior Biology student Fabiola Aviles inspecting her bacterial cultures.

On the other hand, this change has allowed for some students to finish writing up and publish some of the interesting research projects that they had been working on. Many of them have been doing genome sequencing projects, that started in the months before the COVID-19 pandemic, and are now taking time to complete the analysis of the data. This doesn’t require as much, or any, wet lab benchwork and can often be done from their own computer thanks to bioinformatic platforms like BaseSpace (by Illumina) or PATRIC (by Argonne National Labs).

Fabiola Aviles in the SRD Lab

Fabiola Aviles collected water samples from Puerto Rico for metagenomics earlier this year.

Fabiola Aviles, one of our senior Biology majors, recently published her first article in Microbiology Resource Announcements (MRA) entitled: Draft Genome Sequences of Thiorhodococcus mannitoliphagus and Thiorhodococcus minor, Purple Sulfur Photosynthetic Bacteria in the Gammaproteobacterial Family Chromatiaceae.

Fabiola is also continuing her thesis work where she is sequencing metagenomes from water samples collected in her home state of Puerto Rico. She hopes to finish that study by the end of the spring term.

Dayana in the lab

Dayana Montano Salama a junior in the BU biology program recently co-authored two publications.

Earlier this year, Dayana Montano Salama, who is a junior in our Biology program, was the lead author on a publication entitled: Genome Sequence of the Acidophilic Nonsulfur Purple Photosynthetic Alphaproteobacterium Rhodovastum atsumiense, a Divergent Member of the Acetobacteraceae Family

And just last week, a second paper where Dayana is co-author was also accepted for publication in the journal MRA. This second paper, ‘Genome sequence of the alphaproteobacterium, Blastochloris sulfoviridis DSM 729, which requires reduced sulfur as growth supplement and contains bacteriochlorophyll b’, will be available online in a few weeks.

Although our traditional pizza and cake party to celebrate these achievements will have to wait until later, it is great to see that our students are adaptable in these challenging times and continuously committed to their projects and studies.

We all know how challenging the current COVID-19 pandemic is, and hopefully everyone is doing their part in social distancing and working online. However, imagine if your job is taking you directly in contact with coronavirus patients, makes you work overtime hours with not being able to go to the grocery store until around closing hours, all while you are still taking your college classes online.

Erica Morillo

Erica Morillo is a BU Microbiology student working at Albany Medical Center in NY.

That is exactly what is happening to Erica Morillo, who is currently taking Microbiology at Bellevue University, while working at Albany Medical Center hospital in New York. She normally works in the cath lab, but early on in the pandemic they increased that workload because they knew patients would not be able to come in for non-emergency cardiac treatments. Now they have the staff spread out in different departments and working with coronavirus patients where needed.  They are still doing critical cardiac procedures, but once those are done they focus on assisting in caring for COVID patients being transferred from NYC to their hospital.

And it is insane right now, I work 10hr shifts, 4 days a week plus call. We still have been carrying out emergent cardiac procedures, but have to gown up and wear additional PPE like N-95 masks, goggles and face shields” says Erica.

“Our hospital has in place a system to protect ourselves as we care for these patients, but we have had to reuse our PPE materials which undergo a decontamination process.” 

Erica performing a cardiac structural procedure of a COVID-19 patient.

Through all this, Erica is trying to keep up with the microbiology course assignments and is using a laboratory kit at home to complete the labs from Hands on Labs. In a way this turned out to be a well-suited time to take a microbiology course where students learn all about working under sterile conditions and details about the growth and lifecycle of infectious microorganisms.

As if all of that wasn’t enough, currently Erica’s father is being treated for COVID-19 infection and has been battling with high fever and reduced lung capacity for the past two weeks. He is in NYC in the Bronx, NY. “So that has been stressful as well as convincing my family about protecting themselves and not going anywhere unnecessary” Erica states.

Erica and her father, whom is currently suffering from COVID-19.

It is amazing to hear the stories of our students and their dedications and we are proud of how everyone is contributing in unprecedented ways to slow down the spread of COVID-19, while applying their course materials in real life. We wish Erica and her family the best of luck and are grateful to have her at the forefront of battling this pandemic!

During this growing pandemic, many organizations and companies are doing their part in preventing and limiting the spread of the coronavirus. This often takes significant changes and adaptations to the company production lines and strategies. Valero, a global energy company with several ethanol and renewable energy plants, started producing hand sanitizer at their Hartley, Iowa ethanol plant earlier this week.

Beth Young testing the proof of the ethanol produced for hand sanitizer production at the Hartley Valero plant.

One of Bellevue University’s students, Beth Young, who is a senior in the Sustainability Management program, is employed at Valero and has been involved firsthand in this transition. “While it’s been kind of fun to make this transition, it has also been extra long days”, Beth says. 

That doesn’t mean that she is forgetting her studies and materials she is learning in the program. Beth is current in SUST 430 Leadership in Sustainability, where there is an emphasis on sustainable quality leadership development, and she commented: “I was teaching and implementing Kaizen and other lessons from 5S to our plant manager while him and I were setting up an area to label and ship from.” Flexibility and continuous innovation are part of the leadership lessons and Beth’s example is a true testimonial of the real learning for real life approach. 

The hand sanitizer that they produce will be distributed to ethanol plants and refineries and to health care organizations and first responders to make sure they have what they need to win this fight.

For more information check out the Valero Facebook page:

For more information on how hand sanitizer (and specifically the alcohol) works against bacteria and viruses by denaturing their proteins, you can check out the CDC page:


Wonder if this social distancing is worth it and how the COVID-19 spread work? Here is a short video explaining coronaviruses, the differences with the flu, and what you can do to slow down the spread of it:

Credit to Kurzgesagt, 2020.

For up to date stats on COVID-19 cases and mortality rates in the US and Canada, we recommend the following link:


And of course check out the CDC website for current information and tips on what to do during this pandemic:


Keep calm, social distance yourself and wash your hands!

How do Coronavirus tests work?

COVID-19, caused by the novel coronavirus, has captured the attention of scientists, healthcare professionals, and concerned citizens. One way to improve public health efforts to slow COVID-19 spread is to know who is infected. If you have been glued to all the updates, you may have heard that the test uses “RT-PCR.” If you are not a biologist (or not a biologist with a molecular biology background), you may have heard that acronym and relegated it to the parts of your brain where you shoved the memorized list of all the counties in your home state (sorry Mrs. Lorenzen and all the residents of Boyd County, Nebraska). But today, that is ALL ABOUT TO CHANGE! You are going to understand the test for this novel coronavirus (that just so happens to be a widely used technique in biological research).

***[In order to teach you this method efficiently, we are going to use some analogies. These analogies are mostly analogous, but in real life your enzymes do not have eyes. In my lesson, all of your enzymes have eyes…you are just going to have to live with it.]***

Cast of characters:

Mr. Ribosome: Reads RNA, writes proteins

Ms. DNA Polymerase: Reads DNA, writes DNA copy

RNA-Dependent RNA Polymerase: Reads RNA, writes RNA copy

Mr. Reverse Transcriptase: Reads RNA, writes DNA 

Let’s say your DNA is a list of things your cells need to make (it kind of is) and Mr. Ribosome is the thing in charge of making all those things. Unfortunately, the list (the DNA), is written in Spanish and Mr. Ribosome can only speak English. What will we do???


Let me introduce you to Ms. RNA Polymerase (in blue). Ms. RNA polymerase is quite talented, because she can read Spanish (your DNA) and write it as English (RNA). So Ms. RNA Polymerase reads “Manzana, Naranja, Fresa” and writes “Apple, Orange, Strawberry.”

Now that the list is in English (RNA), Mr. Ribosome can read it. When he reads the list, he generates the fruit (proteins) on the list. Simply put, this is how our DNA dictates the functions of our cells.


You may be asking yourself how this is relevant to COVID-19 detection tests. Don’t worry, we are getting there. But first, we have to explain a technique called Polymerase Chain Reaction (PCR).

In PCR, we have a new character: Ms. DNA Polymerase. Ms. DNA Polymerase can read DNA and write a copy of that DNA. So, if we have a list of “Manzana, Naranja, Fresa”, Ms. DNA Polymerase will create many many many copies of that exact list in a [you guessed it] chain reaction. Why is PCR useful? If there is too little DNA to detect with our instruments, we can amplify it into millions of exact copies. This means we can see if the DNA we are interested in is present in a sample (all you crime scene show watchers probably recognize this as a technique to identify the source of a blood stain or hair follicle).


Ah, but we have now arrived at a problem. Coronaviruses don’t encode their information in the same way humans do. See the life cycle of coronavirus below:

Coronavirus Replication

The virus attaches to its receptor and enters the cell. Then, the virus releases its genetic information. But instead of using DNA (Spanish) as the genetic language, coronaviruses use RNA (English). Because their “list” is in English, Mr. Ribosome can immediately read it and turn it into virus proteins (represented by the fruit). One of the virus proteins (the tomato) is an RNA-Dependent RNA Polymerase–this means it reads RNA (English) and copies it into more RNA. Finally, the virus gathers its RNA and proteins into a package and leaves to go infect more cells.

At no point in the virus life cycle does it ever use DNA (Spanish) as its language.

There are some benefits to using RNA as your language, but discussing them is not the point of this lesson. Instead, let’s focus on the problem this poses for diagnosis.

If we want to see if someone is infected with COVID-19, we might want to swab their nose and throat and do PCR to see if we can amplify virus genes. But remember: in our analogy, DNA is Spanish and RNA is English. Ms. DNA Polymerase, the crucial enzyme in PCR, can only read DNA (Spanish) and make DNA copies (Spanish). This means we can’t amplify viral RNA with PCR! Oh no!


This is where we introduce the “RT” part of RT-PCR, and the final character in our story. Our last enzyme is Mr. Reverse Transcriptase, who has a unique skill: he can read RNA (English) and copy it over as DNA (Spanish). This creates a DNA version of the viral RNA. When we have that DNA version of the viral RNA, Ms. DNA Polymerase can make many many copies (enough copies to detect with our equipment).


And this is how RT-PCR works to determine if someone is infected with COVID-19. Feel free to share this with your friends, family, or students for something new to think about during these times of social distancing.

Follow up questions (for open-ended interactions between teachers/students or family/friends):

  1. There are many diverse strategies of virus replication: some replicate in the nucleus, some outside of the nucleus. Some are made of DNA, others are made of RNA. How might the different location of replication or the different composition of the genes impact virus strategies?
  2. What might be some other uses for RT-PCR besides diagnosis of RNA viruses? If you had the ability to do RT-PCR in your home, what experiments would you want to do? What things would you want to test?
  3. Reverse Transcriptase is an enzyme that scientists discovered in a virus. If a virus had the reverse transcriptase enzyme, what might that tell you about how that particular virus replicates? (HINT: HIV is an example of a virus with reverse transcriptase)
  4. RT-PCR has been used to detect COVID-19 in blood and feces, yet the CDC states that this is not a likely route of transmission. Why do you think this is the case?


Please contact me if you want to discuss this further or if you would like additional materials to help out your classes during this distancing period.

Coronavirus: structure-function

The outbreak of a novel coronavirus, COVID-19, has now become a pandemic threat that has been declared a public health emergency of international concern. Although it is hard to predict the future expansion of the COVID-19 pandemic, disease experts agree that it is still going to spread in most places. For an updated live tracking of COVID-19 cases, check out trackcorona.live For a detailed updated overview of the features, evaluation and treatment of COVID-19, you can check out the NCBI page here.

Transmission electron microscope of SARS-CoV-2

Figure 1: This transmission electron microscope image shows SARS-CoV-2, the virus that causes COVID-19—isolated from a patient in the U.S. The spikes on the outer edge of the virus particles give coronaviruses their name, crown-like. Credit: NIAID-RML

There is certainly a lot of similarity between the current COVID-19 virus and the SARS-CoV virus responsible for the 2003 pandemic. They both belong to the Coronavirideae family and have very similar structures and virus replication cycles. All coronaviruses are positive-stranded RNA viruses with a crown-like shape due to the spike glycoproteins on the surface (Figure 1; coronam is the Latin term for crown). However, when we look in more detail at a structural comparison at the biochemical level, we can see some possibly important differences between COVID-19 and the 2003 SARS-CoV virus.

One essential component of the virus infection is the spike protein. These spike proteins are on the surface of coronaviruses and attach the virus to the human cells during infection. After attachment, it fuses with the host cell membrane and releases its own genome into the host cell. Because the spike protein is on the surface and is essential for infection of the host, it is a key target for potential vaccines and diagnostics. Figure 2 shows a structural overlay of the spike protein from COVID-19 (yellow) and SARS from 2003 in blue. Both of these bind the human angiotensin-converting enzyme 2 (ACE2) receptor, but have distinct differences in their affinity for the receptor. The COVID-19 S protein binds ACE2 with higher affinity than does SARS-CoV, which likely contributes to its higher infection rate.

SARS-COVID-19 SpikeOverlay

Figure 2: Structural overlay of the spike protein S from COVID-19 (yellow) and SARS from 2003 (blue). The protein structures were obtained from PDB and rendered with Pymol by J. Kyndt. PDB Accession numbers: PDB6vsb and PDB6crz.


Another interesting comparison can be done by looking at the protease that cuts the long viral polypeptide into functional pieces (once it is inside the host cell). This protease also clips several proteins in the infected host cell and is certainly a target for therapeutics. There is a very high amino acid sequence identity (96%) between the COVID-19 coronavirus 3CL hydrolase (Mpro) and the SARS-CoV virus main protease. A structural overlay is shown in figure 3 with COVID-19 Mpro in green and SARS-CoV in red. There are 14 amino acid differences which are shown with their side chains in white.


Figure 3: Structural overlay of the main protease MPro from COVID-19 (green) and from SARS (red). Amino acid differences are shown as stick models in white. A known inhibitor of MPro is shown in its binding site in blue. The protein structures were obtained from PDB and rendered with Pymol by J. Kyndt. PDB Accession numbers: PDB6lu7 and PDB1q2w.

Comparisons like these help us understand why this virus is more contagious, but less deadly than SARS, and can eventually give us a potential target for vaccines or therapeutics.

Test your 3D Stereo viewing skills of the coronavirus (Figure 4) and of the protease Mpro and spike protein S (Figures 5 and 6). Position your eyes about a foot away from the screen, stare at the middle of the image and slowly cross your eyes. A third image will appear in the middle in 3D! Keep trying and move closer or further away from the image and eventually you’ll get it.

Stereoscopic Sars-cov-2 virus

Figure 4: Stereoscopic image of a model of the complete SARS-Cov-2 (COVID-19) virus. Just stare at the red pixel in the center, and allow yourself to go cross-eyed!   Stereo rendering by J. Farnen.


Figure 5: Stereo view of MPro overlay from COVID-19 (green) and SARS (red). Image by J. Kyndt.

SARS SpikeOverlay Stereo

Figure 6: Stereo view of the spike viral protein from COVID-19 (yellow) and SARS (blue). Image by J. Kyndt.

A lot of research is currently ongoing, with many new research and funding opportunities on this topic. For example, the Bill and Melinda Gates foundation recently launched an initiative to speed up the development and access to therapies against COVID-19, this includes a $100 million dollar commitment to the COVID-19 response.

Although there are many scary and worrisome aspects of this current pandemic, in the long run it will eventually lead to a better understanding and valuable scientific lessons to be learned. This is certainly not the last pandemic humankind will experience, afterall we live in a microbial world, but understanding the biochemistry and molecular biology that is underneath these outbreaks might help us to react more efficiently and possibly prevent the fast spread of future viral outbreaks.

Spike COVID-19 spacefill

Space fill model of the COVID-19 Spike protein. Chains A, B and C are colored pink, green and cyan. NAG (N-Acetyl-D-Glucosamine) ligands are colored yellow.                                                            PDB 6vsb rendered in Pymol by J Kyndt.


Story written by Margie McCandless

What is going on in the area of campus just to the north of the Learning Center? You might have noticed that space was cleared, large landscaping pavers installed, and little plants appeared everywhere on the hill. This is actually a garden of native Nebraska plants and just the beginning of a three year innovative project, the Bellevue University Sustainability Learning Lab.

IMG_2982Partially funded by a $200,000 grant from the Nebraska Environmental Trust, the lab will be a bonus to both students, especially biology and sustainability management students, and the community. Commenting on the award, Dr. Dennis Joslin, Executive Director of the Council of Independent Nebraska Colleges Foundation, sums it up by saying, “The Sustainability Learning Lab has tremendous potential to benefit the State of Nebraska by raising awareness and educating future generations of students and citizens about how to conserve, enhance and restore natural environments.”

Sustainability is a word that is tossed about a lot these days, but what exactly does that mean? A commonly quoted definition from the UN World Commission on Environment and Development says, “Sustainable development is development that meets the needs of the present without compromising the ability of future generations to meet their own needs.” It revolves around three fundamental pillars, people, planet, and profit. In a nutshell, that means that it is beneficial to the community, good for the environment, and makes economic sense. Dr. John Kyndt, Associate Professor of Microbiology and Director of Sustainability, notes that our energy resources are finite and some day will be used up if we don’t start finding ways to conserve them. He sees the lab as being a good way to have “science on display” and to involve the community by inviting them to enjoy the space and even plant their own native plants.

When finished, the Lab will be a 7000 square foot indoor outdoor area consisting of a greenhouse, algae pond, wind and solar energy generating stations, and the native plants garden. The lab will give students a unique hands-on opportunity to study renewable energy. Specifically, the new lab will allow students to create biofuels out of pond algae. They will be studying types of algae and best methods to efficiently create biofuel. In the greenhouse, students will study and work with hydroponic methods of plant production, a method of growing plants using mineral nutrient solutions in water rather than soil. This method provides higher yields, better quality crops, uses less water, and nearly eliminates disease, pests, and weeds.

IMG_2353Though it is a three year project, much progress will already be seen in the Spring of 2020 when the 1,600 square foot greenhouse is built. In the second phase, the 1200 square foot algae pond and the solar and wind generation stations will be installed. The third phase will see the construction of a 25-seat outdoor amphitheater classroom.  Though the NET grant provided the initial impetus, this will be matched by the university and its donors. Ground was broken in October and the lab will be officially completed in 2022 though much of it will be in use well before then.

For more information, see these news stories:



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.”

50th Genome ShowStory written by Cris Hay-Merchant, Director of Strategic Communications at Bellevue University.