The giant phototrophic bacterium Thiospirillum jenense was first discovered in 1838. Its large size (up to 100μm), spiral shape, orange-brown color, and formation of sulfur globules visible under the light microscope, made it an interesting study object for several renowned microbiologists throughout the 20th century.

Thiospirillum jenense

Microscopic image of Thiospirillum jenense.

Although a very intriguing organism, it was proven to be extremely difficult to cultivate in the lab and even to date, no pure culture has been obtained. For a long time, the only source of this bacterium was a pond in former East Germany where it grew April to July, and bacterial cultures had to be smuggled across the then closed borders to West Germany. For more than five decades, the problems in cultivation of Tsp. jenense and later also the missing availability of cultures, have disabled further detailed studies.

Even though the growth and phototactic behavior was studied, nothing was known about the molecular genetics of this intriguing species, not even 16S rRNA sequences, so no complete taxonomic classification could be performed. Up until now.

Illumina-based sequencing was performed at Bellevue University on an enriched sample of Thiospirillum jenense, obtained from Dr. Johannes Imhoff from the GEOMAR Ocean Research Center in Kiel (Germany). Genome sequencing and metagenomic binning analysis now provided the full genome of Thiospirillum jenense which was published just this week in Archives of Microbiology. It showed the unique placement of this species amongst the purple sulfur bacteria and, in addition, potentially resolved some of the genetic reasons behind the challenges of cultivating Tsp. jenense that have been limiting further experiments in the past.

One key component appears to be lack of a high-affinity oxidase (FixNOP), which presumably renders the cells highly sensitive to oxygen damage. In addition, the two sequenced contaminant species, Rhodopseudomonas palustris and a new species Rhodoferax jenense, might help with removal of oxygen in the cultures. These results likely explain the difficulties with obtaining pure cultures of Tsp. jenense as described in the paper, and opens up the doors for new cultivation methods.

Having genomic and genetic data available for Tsp. jenense has widened our understanding of the microbial diversity and will undoubtedly help to further identify similarly unique species in environmental samples, where they play an important role in the sulfur cycle and other nutrient recycling in the environment.

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!

SUST_Display_3

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.

SUST_Display_2

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:

https://www.cdc.gov/infectioncontrol/guidelines/disinfection/disinfection-methods/chemical.html

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:

https://coronavirus.1point3acres.com/

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

https://www.cdc.gov/coronavirus/2019-ncov/index.html

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???

DNA_RNA RT-PCR1


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.

DNA_RNA RT-PCR2


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).

DNA_RNA RT-PCR3


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!

VirusRNA-PCR


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).

RT-PCR


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.

SARSMproOverlayC

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.

SARSMproOverlayStereo

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.