Category Archives: Microbiology

Special Series Covid-19: Finding Clarity and Calm During a Global Pandemic

Amidst the challenges of a global pandemic, the Inspiration Dissemination podcast will strive to be an avenue of human connection and inspiration during a more isolated time. This week, we sit down with Joaquin Rodriquez for the first podcast of a special series covering the COVID-10 outbreak and its impact on the research and lives of our OSU community.

Joaquin Rodriguez; Undergraduate student and researcher in the Barbar lab at Oregon State University.

Joaquin is an undergraduate (soon to be graduate) researcher in the Barbar lab at OSU studying how viruses hijack their hosts. Joaquin’s research allows him to view the coronavirus from a biological perspective that yields him clarity and patience.

Although his studies and research are conducted at Oregon State University, Joaquin calls Lima, Peru home. During an unprecedented time where students are leaving campus to be home with their families, travel restrictions render Joaquin unable to leave Corvallis. Despite the challenges Joaquin faces, he emanates a sense of calm and understanding of the coronavirus and shares with us his experience.

Joaquin explains how misinformation is easy to spread and clear answers are hard to discern during times of fear and uncertainty. Even for those that may have the scientific literacy to understand what a virus is, there can be a great difficulty in comprehending just how a virus works within our bodies. In simplified terms, a virus can be thought of as a piece of genetic material (usually RNA) encapsulated by a protein. Debate on whether or not a virus can even be considered a living thing stems from the fact that viruses themselves do not code for the biological machinery needed for replication, but rather use their host as a means to thrive and reproduce. Upon entering the body, the coronavirus binds to respiratory cells at sites called receptors. Receptors are like doors that only viruses have the keys to, and once binded, they are able to enter the cell and replicate before finally causing the respiratory cell to die. This particular coronavirus eventually causes the disease COVID-19.

Simplified Viral Structure– By domdomegg [CC BY 4.0 (https://creativecommons.org/licenses/by/4.0)], from Wikimedia Commons

The death of respiratory cells as the virus multiplies is inarguably harmful to the body, however, the symptoms we experience from COVID-19 are actually an expression of our immune system response rather than the virus itself. This in part explains why some of those infected by the virus appear to be minimally impacted, while others may develop flu-like symptoms or pneumonia. In fact, the range and lack of predictability of symptoms contribute to the high rate of transmission and success of the virus.

There are many evolutionary trade-offs involved in the overall success of a virus. Aggressive replication within a host may cause the virus to be too deadly and thus lower transmissibility between hosts; the virus is unlikely to become widespread.  For this reason, the deadly virus causing Ebola is not likely to become a global pandemic, whereas the new coronavirus is impacting countries around the world. 

Viral success and transmissibility also relies on mutation rate. At first glance it may seem intuitive that a high rate of mutation would be evolutionarily advantageous. Afterall, a small mutation in the genome of the coronavirus lended its ability to jump hosts from bat to human. However, not all mutations are advantageous. Mutations are random, and the potential of a mutation to be detrimental to the virus’s ability to infect and replicate is high. A high mutation rate is a risk to the success of a virus, but a low mutation rate would yield a stagnation allowing for hosts to more easily adapt immunity. 

Joaquin explains that the coronavirus is successful because it has a relatively low mutation rate compared to other RNA viruses, as well as a high transmissibility owing to a relatively low rate of host death, varying host symptoms, and the utilization of airborne avenues of transmission. He tells us that through a global research effort we are continuously learning about the biology of the coronavirus and using this knowledge to explore treatment options and vaccines. 

While many research labs around the world, including Joaquin’s lab at OSU, are shifting their efforts to contribute to the study of the coronavirus, many researcher’s work has been put on hold. Joaquin now finds himself with extra time to connect with family in Lima or take trips to the coast where he finds comfort surfing. He urges us to stay informed, mindful, and calm, and to find that thing that brings up happiness as we all experience an unusual time united in our isolation.

If you are interested in hearing the full interview with Joaquin, want to keep up with new episodes and our special Covid-19 series, or want to check out past interviews, you can find us on iTunes under Inspiration Dissemination.

A blade of seagrass is a powerful thing

Even though seagrasses occupy less than 0.2% of the world’s oceans, they account for more than 10% of all carbon trapped in the sea. In a world and time where we are producing more carbon than we should be and can manage, making sure that seagrasses are healthy and abundant is extremely pertinent. Winni Wang is one such seagrass scientist working to understand the biology of seagrasses and what threatens them.

Winni is a 5th year PhD candidate in the Department of Microbiology working with Dr. Ryan Mueller. Winni specializes in studying the microbiome of different plants, which for her PhD happens to be seagrasses. The microbiome is the community of microorganisms in a particular environment, and therefore it is found on all living things. By studying the microbiome on different seagrasses, Winni hopes to determine how anthropogenic (human-induced) stressors affect seagrass plants as a whole through changes in the microbiome.

If you’re like me and you love marine megafauna, then when thinking about seagrass beds you most likely are picturing a big manatee slowly grazing on seagrass in tropical, warm waters. Well, then you might be surprised to know that seagrasses don’t only occur in warm, tropical waters. In fact, there are over 60 species of seagrass worldwide and they occur in all kinds of habitats and climates. As a matter of fact, there is a species of seagrass right off of our coast here in Oregon, in Yaquina Bay, which is one of Winni’s study sites for her thesis research.

Eelgrass at Yaquina Bay.
Winni with the experimental tanks at HMSC.

Her work in Yaquina Bay relates to understanding how seagrasses are affected by eutrophication. Eutrophication occurs when an excessive amount of nutrients enters an aquatic environment, often due to land run-off, which in extreme cases can lead to severe oxygen depletion in those habitats resulting in death of plant and animal life. Winni hypothesized that with increased nutrients in a seagrass habitat, the microbiome of the seagrass would change in a way that would have an effect on the overall plant. In order to test this hypothesis, Winni had to carry out controlled lab experiments but not without collecting her test species first. She collected over 200 seagrass individuals as well as buckets of mud from Yaquina Bay, which she took back to Hatfield Marine Science Center where she set up tanks for her experiment. The tanks housed seagrasses and the collected mud. Half of the tanks included added fertilizer to test the effects of nutrient addition, and the other half were left as controls. Over the course of the experiment, Winni tracked plant growth metrics and nitrogen concentrations of the tanks, as well as collecting root and leaf samples to look at the microbiomes on both of those parts of the seagrass. 

The mud buckets.

Winni found that the fertilizer affected the roots in such a way that it changed the microbiome community found there. This change resulted in enrichment for microbes that could cycle sulfur, which could potentially have quite detrimental effects on seagrasses. This is because seagrasses grow in anoxic, or oxygen-low, environments where sulfur is found in its reduced form, hydrogen sulfide. Usually, in environments without excessive nutrient input, seagrasses are able to deal with sulfide, which is typically toxic to plants and animals. However, with increased nutrients, the seagrasses may become overwhelmed by the amount of sulfur in the water as it gets converted into hydrogen sulfide. At certain thresholds, the sulfide ends up becoming toxic to seagrasses. Thus, Winni’s research shows that excessive fertilization to seagrass environments, potentially from land run-off, could have detrimental impacts on seagrasses.

Another chapter of her PhD takes Winni half way across the world to the Mediterranean. Well, it is not so much that it takes Winni to the Mediterranean, it is more that the Mediterranean comes to her! Through her advisor, Winni was able to obtain seagrass samples from the Mediterranean. What makes these samples unique is that they were taken from a site near a naturally occurring underwater volcano. You may be wondering how this is relevant to Winni’s research since she is trying to figure out how human-induced stressors impact seagrasses. Well, the underwater volcano spews carbon dioxide into the water, which makes the water more acidic. This phenomenon is essentially a natural experiment because it mimics the effects of human-induced ocean acidification, which is becoming a problem around the world’s oceans. The results are still underway but they will help fill some of the knowledge gaps concerning the effects of ocean acidification on organisms.

This blog started by emphasizing how important seagrasses are in sequestering carbon, however it is not the only thing that makes these small, unassuming plants so vital to our lives and the lives of many other organisms. Coastal waters with seagrass beds have been found to contain relatively less human pathogens than areas without seagrasses. This is because seagrasses filter the water and are able to remove a lot of pathogens. Furthermore, they are important in preventing coastal erosion and often make coastlines more resilient to storms. Not only are they also important habitats to some beloved marine megafauna (manatees, sharks, turtles) but they are also important for many smaller, but equally ecologically and economically important, species. For example, in Oregon, seagrass beds may actually be helping mitigate ocean acidification which is having a negative impact on oysters as it affects the strength of their shells. 

Winni’s life, both at Oregon State and before her arrival here, has not been all about seagrass science though. To hear more about her background and some of the struggles and lessons that she has had during her tenure here, tune in on Sunday, March 8 at 7 PM on KBVR Corvallis 88.7 FM or stream live. To follow Winni and her research, be sure to follow her on Twitter @ramenmicrobiome. Something that we weren’t able to cover on the blog but covered on the show, is that Winni is one of the founders of the Women of Color Caucus (WoCC) at OSU. Read about the origin story of WoCC here, follow their Instagram and Twitter pages and join their listserv here.

The bacteria living inside us and what they have to say about autism

Trillions of bacterial cells are living within us and they’re controlling your brain activity.

Grace Deitzler is a 2nd year PhD student in microbiology working in Dr. Maude David’s lab on the gut-microbiome and its relation to autism spectrum disorder.

The gut-microbiome is the total population of bacteria living within our digestive tract. These bacteria are critical for digestive health, but also for our immune system and mental health. For example, we harbor bacteria capable of digesting plant fibres we otherwise could not digest. And if you’ve been told that probiotics are good for you, that’s because probiotics can change the gut microbiome in a positive way, allowing for increased bacterial diversity associate with improved health. These bacteria communicate with each other through chemical signaling but also communicate with us. Tryptophan, for example, is an amino acid produced through bacteria metabolism and is a precursor for serotonin, a brain-signaling chemical which causes feelings of happiness.

When the gut communicates with the brain, we call this, the “gut-brain axis”. Grace’s work narrows in on the gut-brain axis and more specifically, how one bacterial species in particular impacts autism spectrum disorder. To further complicate things, the gut-microbiome helps to regulate estrogen levels, and we also know that autism is a disorder found primarily in biological males. Which leads Grace to one of her biggest questions: are the bacteria involved in endocrine system regulation in women, also that responsible for this variation we see. Grace uses a mouse model to elucidate underlying mechanisms at play.

Step one is to feed the mice bacteria that have been found in elevated amounts in people with autism spectrum disorder than in neurotypical peers. These bacteria will colonize in the gut, and mice will go through several behavioral tests to determine if they are exhibiting more behaviors associated with autism. Grace performs three types of tests with the mice: one to test inclination to form repetitive behaviors, one to test anxiety, and one to test social behaviors. One test is a marble-burying test, in which a mouse more inclined to form repetitive behaviors will bury more marbles.

After behavioral testing is complete, the mice are sacrificed and different regions of the gut are taken to look for presence of bacterium. Tissues taken from the mice are used to look for transcriptional markers. The transcriptome is collected for both the mouse and the bacteria present, or the sum total of all genes that are read and converted to RNA. RNA are able to be isolated and sequenced using distinctive markers such as a “poly-A tail”. After this data is collected, Grace can finally move to the computational side of her work which involves combining biological and biochemical data with her behavioral studies.

In addition to her work on autism spectrum disorder, Grace also has a side project working in a honey bee lab, looking at the gut microbiome of honey bees in response to probiotics on the market for beekeepers. But Grace is one very busy bee herself because in addition to her lab work, she’s also involved with an art-science club called “seminarium”. The club is filled with scientists interested in art and artists interested in science. Grace is a painter primarily but is also working on ink illustration. The focus of this group is that art and science are complimentary, not at odds. The group has produced some collaborative projects, including a performance for a lab studying a parasite that effects salmon. The group put together a collage of interpretations of the parasites and had a performance in which one member played piano while someone else drew the parasite live.

Grace moved to Oregon from St. Louis Missouri. She completed her undergraduate degree in biological sciences with minors in chemistry and psychology at a small engineering college, Missouri University of Science and Technology, where she was a radio DJ! Grace first became involved in research during a summer internship in a microbiology lab at Washington University. There she studied the vaginal microbiome and how it effects pregnancy outcomes. Grace went back to this lab for the next couple summers and produced 4 publications! Ultimately, Grace graduated college early after they offered her a full time research position where she worked for a year and a half as a research tech. Through this experience, Grace came to realize that medical school was not her path, canceled her scheduled MCAT and signed up for GRE. Grace looked for schools in the PNW because she knew she wanted to live there, got an interview at OSU, loved it, and here we are!

Join us at 7 pm on Sunday, August 11th, 2019, to hear more about Grace’s research and her journey to OSU. Stream the show live on KBVR Corvallis 88.7FM or check out the episode as a podcast after a few weeks.

When Fungus is Puzzling: A Glimpse into Natural Products Research

Ninety years ago, a fungal natural product was discovered that rocked the world of medicine: penicillin. Penicillin is still used today, but in the past ninety years, drug and chemical resistance have become a hot topic of concern not only in medicine, but also in agriculture. We are in desperate need of new chemical motifs for use in a wide range of biological applications. One way to find these new compounds is through natural products chemistry. Over 50% of drugs approved in the last ~30 years have been impacted by natural products research, being directly sourced from natural products or inspired by them.

Picture a flask full of microbe juice containing a complex mixture of hundreds or thousands of chemical compounds. Most of these chemicals are not useful to humans – in fact, useful compounds are exceedingly rare. Discovering new natural products, identifying their function, and isolating them from a complex mixture of other chemicals is like solving a puzzle. Donovon Adpressa, a 5th year PhD candidate in Chemistry working in the Sandra Loesgen lab, fortunately loves to solve puzzles.

Nuclear Magnetic Resonance (NMR): an instrument used to elucidate the structure of compounds.

Donovon’s thesis research involves isolating novel compounds from fungi. Novel compounds are identified using a combination of separation and analytical chemistry techniques. Experimentally, fungi can be manipulated into producing compounds they wouldn’t normally produce by altering what they’re fed. Fungi exposed to different treatments are split into groups and compared, to assess what kind of differences are occurring. By knocking out certain genes and analyzing their expression, it’s possible to determine how the compound was made. Once a new structure has been identified and isolated, Donovon moves on to another puzzle: does the structure have bioactivity, and in what setting would it be useful?

Donovon’s interest in chemistry sparked in community college. While planning to study Anthropology, he took a required chemistry course. Not only did he ace it, but he loved the material. The class featured a one-week lecture on organic chemistry and he thought, ‘I’m going to be an organic chemist.’ However, there were no research opportunities at the community college level, and he knew he would need research experience to continue in chemistry.

At Eastern Washington University, Donovon delved into undergraduate research, and got to work on a few different projects combining elements of medicinal and materials chemistry. While still an undergrad, Donovon had the opportunity to present his research at OSU, which provided an opportunity to meet faculty and see Corvallis. It all felt right and fell into place here at OSU.

As a lover of nature and hiking in the pacific northwest, Donovon has always had a soft spot for mycology. It was serendipitous that he ended up in a natural products lab doing exactly what interested him. Donovon’s next step is to work in the pharmaceutical industry, where he will get to solve puzzles for a living!

Tune in at 7pm on Sunday, March 18th to hear more about Donovon’s research and journey through graduate school. Not a local listener? Stream the show live.

Hungry, Hungry Microbes!

Today ocean acidification is one of the most significant threats to marine biodiversity in recorded human history. Caused primarily by excess carbon dioxide in the atmosphere, the decreasing pH of the world’s oceans is projected to reach a level at which a majority of coral reefs will die off by 2050. This would have global impacts on marine life; when it comes to maintaining total worldwide biodiversity, coral reefs are the most diverse and valuable ecosystems on the planet.

Unfortunately, there is reason to believe that ocean acidification might proceed at levels even faster than those predicted. Large resevoirs methane hydrates locked away in deep sea ice deposits under the ocean floor appear to be melting and releasing methane into the ocean and surrounding sediments due to the increasing temperature of the world’s oceans. If this process accelerates as waters continue to warm, then the gas escaping into the ocean and air might accelerate ocean acidification and other aspects of global climate change. That is, unless something– or someone– can stop it.

The area of the seafloor Scott studies lies several hundred to a few thousand meters below the surface–much too deep (and cold!) to dive down. Scott gets on a ship and works with a team of experienced technicians who use a crane to lift a device called a gravity corer off the ship deck and into the water, lowering it until it reaches the bottom, capturing and retrieving sediment.

The area of the seafloor Scott studies lies several hundred to a few thousand meters below the surface–much too deep (and cold!) to dive down. Scott gets on a ship and works with a team of experienced technicians who use a crane to lift a device called a gravity corer off the ship deck and into the water, lowering it until it reaches the bottom, capturing and retrieving sediment.

This is where methanotrophs and Scott Klasek come in. A 3rd year PhD student in Microbiology at Oregon State University, Scott works with his advisor in CEOAS Rick Colwell and with Marta Torres to study the single celled creatures that live in the deep sea floor and consume excess methane. Because of their importance in the carbon cycle, and their potential value in mitigating the negative effects of deep sea methane hydrate melting, these methanotrophs have become a valuable subject of study in the fight to manage the changes in our environment occurring that have been associated with anthropogenic climate change.

 

Here Scott is opening a pressure reactor to sample the sediment inside. Sediment cores retrieved form the ocean floor can be used for microbial DNA extraction and other geochemical measurements. Scott places sediment samples in these reactors and incubates them at the pressure and temperature they were collected at, adding different amounts of methane to them to see how the microbial communities and methane consumption change over weeks and months.

Here Scott is opening a pressure reactor to sample the sediment inside. Sediment cores retrieved form the ocean floor can be used for microbial DNA extraction and other geochemical measurements. Scott places sediment samples in these reactors and incubates them at the pressure and temperature they were collected at, adding different amounts of methane to them to see how the microbial communities and methane consumption change over weeks and months.

Most people don’t wake up one morning as a kid and say to themselves, “You know what I want to be when I grow up? Someone who studies methanotrophs and the threat of warming arctic waters.” Scott Klasek is no exception, in fact, he went into his undergraduate career at University of Wisconsin, Madison expecting to pursue an academic career path in pre med. To learn all about Scott’s research, and the twists and turns that led him to it, tune in this Sunday, April 10th, at 7pm to 88.7 KBVR FM or stream the show live!