Author Archives: delventk

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.

Robots! A Story of Engineering and Biology

Meet Nathan Justus, a Robotics Engineer at Oregon State University.

“I never thought I’d end up in graduate school funded by grape lobbyists,” says Nathan Justus, a robotics engineer at OSU, “but here we are!”

Imagine you reach down into a bag of grapes only to notice a black widow spider crawling through the grape stems. These small spiders have an unusually potent venom containing a neurotoxin that is harmful to large vertebrates (aka humans!). Although there haven’t been any deaths from black widows transmitted through grape production to date, you can imagine why the 800 people that find black widows in their grapes every year get quite the scare. Not surprisingly, the grape industry is looking for a sustainable way to solve this problem. After all, the use of pesticides and fumigants is harmful for humans and the environment, and black widow spiders are actually beneficial to the grape-growing ecosystem. Nathan is part of a team that is using robotics as a creative tool to tackle this issue, and by taking this interdisciplinary approach, the development of a promising solution is underway.

Generally, Nathan studies the robotics of biological motion. It turns out that when a black widow spider enters the web of another, the two spiders pluck at the web to communicate and ultimately determine who gets to stay and who has to leave. Nathan’s lab is partnered with arachnologists and researchers at the USDA who found that when you record the spiders plucking and play it back to them, sometimes the spiders would leave the webs. Part of what Nathan worked on for his Master’s project was a new method to measure the frequency of the web vibrations in order to fine tune and develop a method for implementing this spider evacuation plan.

The status quo method of measuring such vibrations has been to use a fancy laser, which catches shifts in wavelength in order to deduce the frequency of vibration. Although this method works great for flat surfaces, it is understandably a challenge to use a laser on a moving spider or web. Enter video vibrometry: the new method that Nathan has been working towards developing. Simply put, this method involves pointing a video camera at a target, in this case, the black widow web, and then a little bit of “math magic” will yield the vibration frequency. This piece of technology works towards the greater goal of the project; to allow spiders to live comfortably in their homes as grapes grow, but leave when the time comes to harvest. Happy farmers, (relatively) happy spiders.

Luckily, Nathan is not leaving OSU as a researcher any time soon. He will be beginning his PhD in Robotics with Dr. Joe Davidson working to solve an entirely different puzzle. The overarching project goal is the development of autonomous robots that can navigate and interact with the underwater environment. This has many practical applications; just to name one, there is the extensive feat of keeping up with the frequent maintenance needed for our global telecommunications infrastructure, which, of course, is underwater. Maybe we want robots that will be able to work on ship hull examinations and repair, or perhaps we are envisioning a fleet of scientific robots that can explore shipwrecks or the ocean floor. Currently we have robots for the underwater environment, however, most are either human operated and thus attached to a tether, or must be within 10 meters of controls. Creating a robot that can break free of these limitations and navigate through the noise of currents and frictions, all while receiving feedback from the environment, is incredibly complex. Nathan’s PhD work will move the state of research on underwater robotics closer to autonomy.

Nathan was on the winning team for the NASA RASCAL Robotics Ops Competition. His team received $10,000 of funding to build a rover. Their rover was inspired by the Russian style Marsicon and was roughly 1m by 1m upon completion.

Nathan didn’t always know that he would end up working on underwater robots. He grew up dreaming of being an aerospace engineer, and went to the University of Oklahoma for just that. In his undergrad, he joined a team that got funded 10,000 to join a national competition to build a rover for NASA, and even won. After graduating, he joined NASA and worked in mission controls for the International Space Station. Nathan was part of the communications teams that worked in real time, 24-hours a day to keep the communication channels at NASA up and running. Legend has it that he has even gone rock climbing with astronauts.

Impressed? Me too. Intrigued? Tune into the live interview with Nathan this Sunday, December 8^that 7:00pm on 88.7 KBVR Corvallis or stream it live!

Tsunami Surfing and the Giant Snot

Sam Harry’s research is filled with bizarre scientific instruments and massive contraptions in an effort to bring large natural events into the laboratory setting.

Sam Harry, second year PhD candidate in Civil Engineering

“There’s only a couple like it in the world, so it’s pretty unique”. Unique may be an understatement when describing what may be the largest centrifuge in North America. A centrifuge is a machine with a rapidly rotating container that can spin at unfathomable speeds and in doing so applies centrifugal force (sort of like gravitational force) to whatever is inside. This massive scientific instrument– with a diameter of roughly 18 feet– was centerpiece to Sam’s Master’s work studying how tsunamis affect boulder transport, and the project drew him in to continue studying the impact of tsunamis on rivers for his PhD.

But before we jump ahead, let’s talk about what a giant centrifuge has to do with tsunamis. Scientists studying tsunamis are faced with the challenge of scale; laboratory simulations of tsunamis in traditional water-wave-tank facilities are often difficult and inaccurate because of the sheer size and power of real tsunamis. By conducting experiments within the centrifuge, Sam and his research group were able to control body force within the centrifuge environment and thus reduce the mismatch in fluid flow conditions between the simulated experiment and real-life tsunamis.

When tsunamis occur they cause significant damage to coastal infrastructure and the surrounding natural environment. Tsunamis hit the coast with a force that can move large boulders– so large, in fact, that they aren’t moved any other way. Researchers can actually date back to when a boulder moved by analysing the surrounding sediments, and thus, can back calculate how long ago that particular tsunami hit. However, studying the movement of massive boulders, like tsunamis, is not easily carried out in the lab. So, Sam used a wave maker within, of course, the massive centrifuge to study the movement of boulders when they are hit with some big waves.

Sam’s work space. The Green dye added to the water within the glass tank is what gives this tank it’s name: The Giant Snot

As Sam was completing his Master’s an opportunity opened up for him to continue the work that he loves through a PhD program in civil engineering with OSU’s wave lab. Now Sam conducts his research using the “glass tank”, which, as the name alludes to, is a glass tank roughly the size of a commercial kitty pool that is used to contain the water and artificial waves the lab generates for their research. There are actually three glass tanks of varying sizes. The largest tank, which is larger than a football field, is used for more “practical applications”. Sam gives us the example of a recent study in which researchers built artificial sand dunes inside of the tank, let vegetation establish, and then hit the dunes with waves to study how tsunamis impact that environment. (Legend has it that the largest tank was actually surfed in by one of the researchers!)

Sam’s smaller glass tank, though, is really meant for making precision measurements to better study waves. He uses lasers to measure flow velocity and depth of water to build mathematically difficult, complex models. Essentially, his models are intended to be the benchmarks for numerical simulations. Sam, now into his second year of his PhD, will be using these models in his research to study the interaction between tsunamis and rivers, with the goal of understanding the movement and impact of tsunamis as they propagate upstream.

To learn more about tsunamis, boulders, rivers, and all of the interesting methods Sam’s lab uses to study waves, tune into KBVR 88.7 FM on Sunday, November 3rd at 7pm or live stream the show at http://www.orangemedianetwork.com/kbvr_fm/. If you can’t join us live, download the episode from the “Inspiration Dissemination” podcast on iTunes!