Tag Archives: research

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!

A bird’s eye view: hindsight and foresight from long term bird surveys

The Hermit Warbler is a songbird that lives its life in two areas of the world. It spends its breeding season (late May-early July) in the coniferous forests of the Pacific Northwest (PNW) and migrates to Central America for the winter. Due to the long journey from the Central America to the PNW, it is dependent on food resources being available throughout its journey and when it arrives to breed. The environmental conditions across its range are tightly linked to habitat resources, and unfavorable climatic conditions, such as those becoming less frequent due to climate change, can negatively affect bird populations. Changes in bird populations are not always easy to notice, especially with small songbirds that live high in tree canopies. Studying birds for one or a few years may not be enough to signal the change in their well-being.

A Hermit Warbler singing on a lichen-covered branch in the forest canopy. Male Hermit Warblers will defend their territories ferociously against other males during the breeding season. H.J. Andrews Experimental Forest, May 2017.

Fortunately, long term data sets are becoming more available thanks to long term study programs. For example, the Willamette National Forest in Oregon is home to H. J. Andrews Experimental Forest (the Andrews). Designated by the USDA Forest Service Pacific Northwest Research Station, the Andrews forest hosts many forest research projects and has been monitored since 1948. In 1980, it was became one of the National Science Foundation’s Long Term Ecological Research sites ensuring that it will remain a resource for scientists for years to come. Bird surveys at the Andrews began 11 years ago, and researchers at Oregon State University are beginning to draw connections between changing climate and bird communities in relation to the forest’s structure and compositions.

H.J. Andrews Experimental Forest, where long-term bird study is launched in 2009 by Drs. Matt Betts and Sarah Frey. The forest sits on the moist foothills of western Cascades in Willamette National Forest.

One of these researchers, Hankyu Kim PhD student in the Department of Forest Ecosystems and Society, is using this data to study the Hermit Warbler and other bird species at the Andrews. Hankyu is interested in how and why bird communities are changing over time. With 11 years of bird observations and extensive temperature data, he is attempting to estimate how population of birds persist in the forests. To begin approximating how current climate effects birds, we need to have an idea about bird communities in the past. Past conditions can help us explore how birds might respond to future climate scenarios. Without the effort of many researchers before him to monitor birds, his investigation would be impossible.

Bird surveys are conducted via point counts. Researchers stand at a point count station for 10 minutes and count all bird species they see and hear. Listen to a hermit warbler and some other background birdsongs recorded at H.J Andrews in June 2017.

Hankyu realized the importance of long-term data after reviewing the 45-years of wintering waterbird surveys collected by the Birdwatching Club at Seoul National University, Korea during his time as an undergrad. The group took annual trips to the major Rivers and Coastal Areas, and in just a couple decades the members of the club had recorded declines and disappearances of some species that were once common and widespread. This finding inspired Hankyu to pursue graduate school to study unnoticed or uncharismatic species that are in danger of decline. Every species plays a critical role in the ecosystem, even if that role has not yet been discovered.

Tune in on Sunday May, 19 at 7 pm to hear more about Hankyu Kim’s research with birds. Not a local listener? Stream the show live or catch up when the podcast episode is released.

Want more about the Hermit Warblers in Oregon? Check out this video of Oregon Field Guide featuring Hankyu and some of his colleagues from Oregon State University.

Hankyu’s episode on Apple Podcasts

Infection Interruption: Identifying Compounds that Disrupt HIV

Know the enemy

Comparing microbial extracts with Dr. Sandra Loesgen.

The Human Immunodeficiency Virus, or HIV, is the virus that leads to Acquired Immunodeficiency Syndrome (AIDS). Most of our listeners have likely heard about HIV/AIDS because it has been reported in the news since the 1980s, but our listeners might not be familiar with the virus’s biology and treatments that target the virus.

  • HIV follows an infection cycle with these main stages:
    • Attachment – the virus binds to a host cell
    • Fusion – the viral wall fuses with the membrane of the host cell and genetic material from the virus enters the host cell
    • Reverse transcription – RNA from the virus is converted into DNA via viral enzymes
    • Integration – viral DNA joins the genome of the host cell
    • Reproduction – the viral DNA hijacks the host cell activity to produce more viruses and the cycle continues
  • Drug treatments target different stages in the HIV infection cycle to slow down infection
  • However, HIV has adapted to allow mistakes to occur during the reverse transcription stage such that spontaneous mutations change the virus within the host individual, and the virus becomes tolerant to drug treatments over time.

Faulty Machinery

Due to the highly mutable nature of HIV, a constant supply of new drug treatments are necessary to fend off resistance and treat infection. Our guest this week on Inspiration Dissemination, Ross Overacker a PhD candidate in Organic Chemistry, is screening a library of natural and synthetic compounds for their antiviral activity and effectiveness at disrupting HIV. Ross works in a Natural Products Lab under the direction of Dr. Sandra Loesgen. There, Ross and his lab mates (some of whom were on the show recently [1] [2]) test libraries of compounds they have extracted from fungi and bacteria for a range of therapeutic applications. Ross is currently completing his analysis of a synthetic compound that shows promise for interrupting the HIV infection cycle.

“Uncle Ross” giving a tour of the lab stopping to show off the liquid nitrogen.

Working in Lab with liquid nitrogen.

 

 

 

 

 

 

 

Havin’ a blast

Chemistry Club at Washington State University (WSU) initially turned Ross onto chemistry. The club participated in education outreach by presenting chemistry demonstrations at local high schools and club events. Ross and other students would demonstrate exciting chemistry demos such as filling hydrogen balloons with salt compounds resulting in colorful explosions piquing the interest of students and community members alike. Ross originally made a name in

Collecting Winter Chanterelles in the Pacific Northwest.

WSU’s chemistry club, eventually becoming the president, by showing off a “flaming snowball” and tossing it from hand to hand—don’t worry he will explain this on air. For Ross, chemistry is a complicated puzzle that once you work out, all of the pieces fall into place. After a few undergraduate research projects, Ross decided that he wanted to continue research by pursing a PhD in Organic Chemistry at Oregon State University.

 

 

Tune in this Sunday October 7th at 7 PM to hear from Ross about his research and path to graduate school. Not a local listener? Stream the show live or catch this episode on our podcast.

Crabby and Stressed Out: Ocean Acidification and the Dungeness Crab

One of the many consequences associated with climate change is ocean acidification. This process occurs when high atmospheric carbon dioxide dissolves into the ocean lowering ocean pH. Concern about ocean acidification has increased recently with the majority of scientific publications about ocean acidification being released in the last 5 years. Despite this uptick in attention, much is still unknown about the effects of ocean acidification on marine organisms.

Close-up of a Dungeness crab megalopae

Our guest this week, Hannah Gossner, a second year Master’s student in the Marine Resource Management Program, is investigating the physiological effects of ocean acidification on Dungeness crab (Metacarcinus magister) with the help of advisor Francis Chan. Most folks in Oregon recognize the Dungeness crab as a critter than ends up on their plate. Dungeness crab harvest is a multimillion dollar industry because of its culinary use, but Dungeness crab also play an important role in the ocean ecosystem. Due to their prevalence and life cycle, they are important both as scavengers and as a food source to other animals.

Hannah pulling seawater samples from a CTD Carrousel on the R/V Oceanus off the coast of Oregon

To study the effect of ocean acidification on Dungeness crab, Hannah simulates a variety of ocean conditions in sealed chamber where she can control oxygen and carbon dioxide levels. Then by measuring the respiration of an individual crab she can better understand the organism’s stress response to a range of oxygen and carbon dioxide ratios. Hannah hopes that her work will provide a template for measuring the tolerance of other animals to changes in ocean chemistry. She is also interested in the interplay between science, management, and policy, and plans to share her results with local managers and decision makers.

Hannah working the night shift on the R/V Oceanus

Growing up in Connecticut, Hannah spent a lot of time on the water in her dad’s boat, and developed an interest in marine science. Hannah majored in Marine Science at Boston University where she participated in a research project which used stable isotope analysis to monitor changes in food webs involving ctenophores and forage fish. Hannah also did a SEA Semester (not to be confused with a Semester at Sea) where she worked on a boat and studied sustainability in Polynesian island cultures and ecosystems.  Hannah knew early on that she wanted to go to graduate school, and after a brief adventure monitoring coral reefs off the coast of Africa, she secured her current position at Oregon State.

Tune in Sunday June, 17 at 7 pm PST to learn more about Hannah’s research and journey to graduate school. Not a local listener? Stream the show live or catch the episode on our podcast.

Hannah enjoying her favorite past time, diving!

A Space for Me

Minerva presenting at the Radical Imaginations Conference on the panel ” Feminist Radical Imaginations: Marches and Revolutions” with Andrea Haverkamp, Carolina Melchor, Maria Lenzi Miori, Minerva Zayas, and Nasim Basiri

Everyone handles their personal growth differently, and for many finding an identity category can lead to feelings of comfort and an opportunity to find community. However, for folks who identify with more than one category or find identity in LGBTQ+ categories may find difficulty navigating their identity in spaces that have been shaped by the heteronormative majority. Moreover, for people of color, retaining identity in their culture might add another layer of complexity to navigating the path to their goals. Our guest this week, Minerva Zayas a Master’s student in Women, Gender, and Sexuality Studies, is interested in how folks who identify as LatinX and LGBTQ+ navigate the intersection of these identities, especially in university spaces. In particular, Minerva is asking how LatinX, LGBTQ+ individuals engage in a system that has historically catered to white heteronormative college students. Minerva, speaking from personal experience, expects that University life offers little tailored support systems for folks of color who identify as ‘other,’ but that a university campus might offer opportunities to build a support systems that other institutions might lack: the opportunity to participate in a campus cultural/lifestyle community and engage in activism.

Minerva presenting at Corvallis Poetics Open Mic Night on the poem, “My worst NightMare” at Interzone Inc.

Minerva participating in a creative photo session in downtown Corvallis, OR.

For her Master’s, Minerva will conduct interviews with LatinX, LGBTQ+ students and ask questions than run the gamut of identity in sexuality, culture, community, and activism. She hopes to highlight their experiences and examine themes that arise. In addition to her research, Minerva, a poet herself, plans to extend her project in a creative way, ideally through a podcast. After completing her Master’s, Minerva hopes to complete a PhD and has considered becoming a counselor for Spanish-speaking folks. This aim coincides with her mission to bring voice to folks who share identity with her in LatinX culture. Minerva ultimately wants institutions, academia and beyond, to be more inclusive and cognizant of minority identities, but she realizes that change comes from within. By pursuing her aspirations for a PhD and engaging in academia, she hopes that others who share her identity will be drawn to academia so that a system that has been shaped by the majority identity can grow to support all.

Tune in to KBVR Corvallis 88.7 FM this Sunday May, 20 at 7 pm to hear more about Minerva’s research and personal journey to graduate school. Listeners, local and otherwise, can stream the live interview at kbvr.com/listen or find the podcast of Minerva’s episode next week on Apple Podcasts.

 

The Grape Depression: Powdery Mildew in Willamette Valley Vineyards

Brent at the Foliar Pathology Lab research vineyard where the small plot field trials in his project were conducted.

Viticulture is the science, production, and study of grapes, and when growing grapes for wine both quantity and quality matter. One challenge facing farmers in the Willamette Valley is a plant pathogen: grape powdery mildew. This pathogen can live in a field year-round and emerges to infect grape leaves, flowers and fruits annually. Grape plants infected with powdery mildew suffer low berry yields and mildew may affect the taste of wine. In the Willamette Valley, where vineyards abundant, grape powdery mildew is a big problem. Brent Warneke, a Master’s student in the department of Botany and Plant Pathology, is studying the effect of fungicide application timing on the reduction in severity of powdery mildew on grapes, and he is our guest on Inspiration Dissemination this week.

Moldy Grapes

A grape bunch severely infected with powdery mildew. Note the berry cracking, powdery appearance, and poor color accumulation.

Brent works at the USDA Horticultural Crops Research Lab with Walt Mahaffee, and his research tests the effect of fungicide application timing on grape powdery mildew control. Timing fungicide applications is especially crucial during the one to three-week window of grapevine flowering. Optimal fungicide application timing can slow the mildew epidemic allowing grape berries to mature and become less susceptible to powdery mildew. Across the Willamette Valley, fungicide application to grapes is a well-known prevention solution for powdery mildew, but less is known about the best fungicide to use and when to spray plants during berry development. The findings of his research are now being validated at a larger scale in commercial vineyards. In the lab, Brent is also studying the mobility of fungicide “through the grapevine,” from tissue to tissue through the air and xylem, and Brent is helping with a project to identify strains of mildew resistant to commonly used fungicides.

 

The Grape State of Colorado 

Brent with a harvest of varnish conk (Ganoderma oregonense), Lobster mushroom (Hypomyces lactifluorum).

Brent hails from Colorado where he spent his early years outside gardening, snowboarding, and hiking. During undergrad at Colorado State University (CSU), Brent majored in Horticulture and held research positions at the Center for Agricultural Resources Research and the Bioenergy Lab. Among his many projects during undergrad, Brent completed a senior thesis project, under the direction of Dr. Courtney Jahn, developing a LAMP-PCR to diagnose Canada thistle rust on infected plants that were not displaying symptoms.

Wine Not?

While at CSU, Brent also began studying viticulture. He liked the challenge and complexity of growing grapes for wine. Brent chose to pursue graduate school at Oregon State because his current program blends plant pathology with viticulture. He’s happy with his decision because Oregon is similar to Colorado for outdoor recreation, not to mention its world class Pinot Noir!

Hear more from Brent this Sunday September, 10 at 7PM on KBVR Corvallis, 88.7FM! Not a local listener? Not sweat! Stream the show live.

Brent on top of South Sister (10,363 ft). Middle and north sister can be seen in the immediate background. In the far background the small peak to the left without snow is Mount Washington , then Mount Jefferson behind north sister and Mount Hood in the background to the right of North Sister.