You don’t look your age: pruning young forests to mimic old-growth forest

“I’m always looking at the age of the forest, looking for fish, assessing the light levels. Once you’ve studied it, you can’t ignore it.” Allison Swartz, a PhD student in the Forest Ecosystems and Society program in the College of Forestry at Oregon State, is in the midst of a multi-year study on forest stream ecosystems. “My work focuses on canopy structure—how the forest age and structure influences life in streams,” says Allison. “People are always shocked at how many organisms live in such a small section of stream. So much life in there, but you don’t realize it when you’re walking nearby on the trail.”

Three scientists holding large nets stand in a rocky forest stream. One wears a backpack with cable coming out of it.
No, that’s not a Ghostbuster backpack! Here, Allison is using an electrofishing device that stuns fish just long enough for them to be scooped up, measured, and released. From left to right: Allison Swartz, Cedar Mackaness, Alvaro Cortes. Photo credit: Dana Warren

Following a timber harvest, there is a big increase in the amount of light reaching the forest floor. The increase in light also results in an increase in stream temperatures. Fish such as salmon and trout, which prefer cold water, are very sensitive to temperature changes. Since these fish are commercially and recreationally important, Oregon’s water quality regulations include strict requirements for maintaining stream temperatures. As a result, buffer areas of uncut forest are left around streams during timber harvests. These buffer areas, like much of the forests in the Pacific Northwest, and in the United States in general, can be characterized as being in a state of regeneration. Dense, regenerating stands of trees from 20-90 years old, are sometimes called second-growth forest. These forests tend to let less light through than an old growth forest does. Allison’s work focuses on how life in streams responds to differences in forest growth stage.

A Pacific giant salamander – a top-level stream predator and common resident of Oregon’s forest streams. Photo credit Allison Swartz.

The definition of the term old-growth forest depends on which expert you ask, and there is even less agreement on the concept of second-growth forest. Nevertheless, broadly speaking an old-growth forest has a wide range of tree species, ages, and sizes, including both living and dead trees, and a complex canopy structure. Openings in the canopy from fallen trees allow a greater variety of plant species to be established, some of which can only take root under gaps in the canopy but which can persist after the gap in the canopy is filled with new trees. The tightly-packed canopy limits the amount of light that can reach the forest floor, including the surface of the streams that Allison studies.

Forest stream near Yellowbottom Recreation Area, Oregon. Credit: Daniel Watkins

Allison’s research project is focused on six streams in the MacKenzie river basin, which includes private land owned by the Weyerhaeuser company, parts of the Willamette National Forest, and federal land. At some of these sites, after an initial survey, gaps were cut into the forest canopy to mimic light availability in an old growth forest. Sites with cut canopies were paired with uncut areas along the same stream. The daily ebb-and-flow of aquatic species is monitored by measuring the oxygen content of the water. The aquatic and terrestrial ecosystems have mainly been studied separately, she explained, but the linkages between these systems are complex. Measurements of vertebrate species are carried out using electrofishing techniques. “We do vertebrate surveys which infludes a few species of fish and Pacific giant salamanders. We measure and weight them and then return them to the stream,” Allison explained.

Measuring cutthroat trout. Photo credit Allison Swartz.

Over the last few years, Allison has spent three months of the summer living and working at one of her research sites, the HJ Andrews Experimental Forest. “We didn’t have much in terms of internet the first few years, so you connect with people and with the environment more,” Allison said. 

Allison never expected to be in a college of forestry. Her background is in hydrology, and she spent some time working for the United States Geological Survey before beginning graduate work. She has enjoyed being part of a research area with such direct policy and management impacts. “We all use wood, all the time, for everything. So we can’t deny that we need this as a resource,” says Allison. “It’s great that we’re looking at ways to manage this the best we can—to make a balance for everybody.”

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!

Over sixty years digging and we’re still finding new ‘dirt’ on HJ Andrews

One kilometer. Or roughly ten football fields. That’s the extent of the area over which Karla Jarecke, a Ph.D. candidate in the College of Forestry’s Department of Forest, Ecosystems & Society can feasibly navigate her way through the trail-less HJ Andrews Experimental forest to collect the data she needs in a typical day of field work. Imagining a football field is perhaps not the best way to appreciate this feat, nor envision the complex topography that makes up this coniferous forest on the western flanks of the Cascade mountains, roughly 50 miles East of Eugene. But these characteristics are precisely what have made this forest valuable to scientists since 1948 and continue to make it the ideal place for Karla’s research.

Experimental watersheds like the HJ Andrews forest were established initially to understand how clear-cutting influenced forest drainage and other ecosystem processes such as regrowth of plants and change in nutrients in soils and streams. This was during the time when timber-take was increasing and we still had little understanding of its ecosystem effects. Karla’s work is also forward-thinking, but less on the lines of what will happen to drainage when trees are removed and more focused on understanding the availability of water for trees to use now and in the future. She wants to know what influence topography has on plant water availability in mountainous landscapes.

Meter deep soil pits at Karla’s field site.

Back to bushwhacking. The answer to Karla’s research question lies beneath the uneven forest floor. Specifically, in the soil. Soil is the stuff made up of weathered rock, decomposing organic material and lots of life but it is also the medium through which much of the water within a forest drainage moves. Across her study area, Karla has 54 sites where she collects data from sensors that measure soil moisture at two different depths. These steel rods send electrical currents into the ground, which depending on how quickly they travel can tell her how much water is present in the soil. She also keeps track of sensors that measure atmospheric conditions, like temperature and air humidity. This information builds on the incredible sixty-year data set that has been collected on soil moisture within HJ Andrews, but with a new perspective.

Digging soil pits on steep slopes occasionally required stacking logs at the base of a tarp to prevent the soil from sliding down the hill.
Photo credit: Lina DiGregorio

Karla explains that there have been long-standing assumptions surrounding elevation gradients and their control on water availability in a forest system. This understanding has led to modeling tools currently used to extrapolate soil moisture across a landscape. But so far, her data show huge variability on surprisingly small scales that cannot be explained by gradient alone. This indicates that there are other controls on the spatial availability of soil moisture in such mountainous terrain.

“We’re finding that model doesn’t work really well in places where soil properties are complicated and topography is variable. And that’s just the first part of my research.”

The next phase of Karla’s work seeks to evaluate tree stress in the forest and determine if there are any connections between this and the variability she is finding in soil moisture across spatial scales. True to the complex nature of the landscape, this work is complicated! But to Karla, it’s important. Growing up in the mid-west, Karla came to know water as “green” and when she moved West, first to fulfill an internship in Colorado and then to pursue her graduate work here in the Pacific Northwest, she was (and still is) amazed by the abundance of clean, clear rivers and streams. And it’s something she doesn’t ever want to take for granted.

Karla and her sister Stephani snowshoeing on Tumalo Mountain in the Cascade Range of central Oregon.

To find out more about Karla’s research and her journey from farming in Italy to studying soil, tune in on Sunday, October 27th at 7 PM on KBVR 88.7 FM, live stream the show at http://www.orangemedianetwork.com/kbvr_fm/, or download our podcast on iTunes.

Monkeying around in the lab to find a good egg

In vitro fertilization (IVF) treatment is a procedure in which a woman’s mature eggs are removed via surgery, combined with sperm in a petri dish in a lab, and then the fertilized egg is placed in the uterus to continue growing into an embryo. Unfortunately, IVF is not covered by all insurance companies and is successful less than 50% of the time. Consequently, undergoing IVF can be a significant burden financially, physically, and emotionally for those who seek out this procedure.

What makes a “good” fertilizable egg? In this week’s special episode, we’re joined by Sweta Ravisankar, a 5th year PhD candidate in the Cell and Developmental Biology program at OHSU (Oregon Health & Science University), who is trying to answer this question in hopes that being able to screen for the “more likely to succeed” eggs, will lower the economic, financial, and physical hurtles of IVF.

Sweta works at the at Oregon National Primate Research Center, OHSU within the division of Reproductive and Developmental Sciences OHSU. She is a graduate student mentored jointly by Dr Shawn Chavez and Dr. Jon D. Hennebold.

The Hennebold lab studies reproduction before the egg is fertilized. This stage involves studying the female reproductive system, the oocyte (egg) itself, and the development of the follicle (region that holds the immature eggs) before ovulation (dropping of immature egg into the ovary). In contrast, the Chavez lab looks at what happens after fertilization such as chromosome abnormalities and how these abnormalities effect embryo development. This joint mentorship allows Sweta to study a more complete story of development.

Screenshot from a video of development from 1C stage to a blastocyst stage. Complex human being development can be traced back to these 120-150 cells implanting in the uterus.
Sweta is always excited to share her science!

Looking at reproduction from these two perspectives allows Sweta to correlate the environment the egg exists in with how the embryo develops. For example, what is the impact of a western style diet (high in fat) on the biochemistry and development of follicles and embryos long term? How does polycystic ovarian morphology (POM) mimicked by prolonged exposure to high fat diet and high testosterone levels in females impact reproductive success at the biomolecular level?

Will work when needed: in the lab on a weekend with a cast on my foot (visible on the left leg).

Being at the Oregon National Primate Center, Sweta’s model organism is the “Rhesus macaque” monkey. These monkeys have a genome ~97.5% similar to humans, meaning that the work she does is very relevant and translatable to humans. Working with the monkeys also means that her research is variable depending on the day. The monkeys will sometimes undergo treatments similar to those done in human IVF (in vitro fertilization) clinics, including surgeries to collect eggs for further research. After harvesting these eggs, they can be fertilized and the cells’ growth, division, and development can be monitored in a plate. When these experiments are not taking place, Sweta conducts various molecular biology experiments.

Sweta has become a true Pacific northwestener: hiking in rain with her husband through the Washington Park, Portland, OR. 

          

In India, Sweta completed her Bachelor’s degree at Dr. D. Y. Patil university in biotechnology and her first Master’s at SRM Institute of Science and Technology. During this time, Sweta happened to have several of family and friends undergoing IVF treatments and also worked in a fertility clinic for a time, bringing her attention to scientific needs within this field. Sweta then completed a second Master’s in Biological Sciences with a fellowship from the California Institute for Regenerative Medicine, and fell in love with fertility-related research during an internship at Stanford where she worked on embryo development. Her passion for this field of research led her to OHSU.

In addition to a being an accomplished researcher, Sweta is also an accomplished Indian Classical Dancer! She teaches bharatanatyam dance classes out of her home and travels around the US to perform. Long term, she hopes to continue research and also run a dance company.

Sweta will be presenting a piece on “depression” to work towards mental health awareness October 25th through 27th. The piece will be in Bharatanatyam and presented as a part of the 12th residency performance at N.E.W. 

Sweta writes her own blog posts about her journey through grad school which can be found here: 

  1. https://blogs.ohsu.edu/studentspeak/2017/09/11/it-is-possible-to-make-sad-not-even-seasonal/
  2. https://blogs.ohsu.edu/studentspeak/2018/07/24/phd-is-more-than-your-research/
  3. https://blogs.ohsu.edu/studentspeak/2019/04/18/never-give-up-there-is-a-bright-day-out-there-drudnischay/

To hear more about Sweta’s graduate work, personal struggles, and classical Indian dance moves, tune in on Sunday, October 20th at 7 PM on KBVR 88.7 FM, live stream the show at http://www.orangemedianetwork.com/kbvr_fm/, or download our podcast on iTunes!

Giving therapy-resistant cancer cells a taste of their own medicine

The use of chemotherapy to fight various forms of cancer in the human body has been a successful method for decades, but what happens when it fails? This question strikes a personal note for Martin Pearce, a Ph.D. candidate in the Department of Environmental and Molecular Toxicology at Oregon state University. Prior to his graduate work, both of his grandmothers were diagnosed with breast cancer. One successfully went through treatment and although the other initially responded well to chemotherapy, years later the cancer cells reappeared and there was no other treatment available.

Martin in the lab, running one of many Western Blots.

The academic system in the United Kingdom, from where Martin hails, encourages undergraduate students to take what is termed a “placement year” between their second and third years to gain practical experience. At the time of his grandmother’s returning prognosis, Martin was in the second year of his studies at University of the West of England Bristol which had a connection with East Carolina University in the States. Although deviating somewhat from his initial advanced level courses in business, the opportunity to work full time in a biomedical sciences lab at a university renowned for its medical research provided just the right place for Martin to spend the following year.

Martin’s time in North Carolina was not only practical but a reminder of his experience with biology in secondary school. His teacher was a doctor and she encouraged him to pursue a career in a biomedical field. While biology wasn’t his easiest subject, Martin was inspired by his mentor and enjoyed the challenge. Today, he is fully committed to this challenge as a key member in Dr. Siva Kolluri’s Cancer Biology lab group at Oregon State University researching new strategies to target the cancer cells that continue to grow after treatment with chemotherapeutic agents.

Current members of Dr. Siva Kolluri’s Cancer Biology Laboratory group.

Their work involves screening tens of thousands of compounds against such resistant cancer cells that express a particular group of proteins called the Bcl-2 family of proteins. The lab has discovered a novel compound that binds specifically to the Bcl-2 family of proteins that are consistently expressed in therapy-resistant cancer cells and cause them to change shape. One of the fundamental principles of cell and molecular biology is the relationship between structure and function. Change the structure of a molecule and its function within a cell can completely transform. In the case of the Bcl-2 family of proteins, this literally means life or death for the cell.

Protected within the typical expression of a Bcl-2 protein is a region Martin describes as a “death domain”; if this domain is exposed, it induces cell death. Cell death or ‘apoptosis’ is a naturally occurring process in biology. Without apoptosis in the early stages of human development, we would all have webbed fingers! Martin and his team have discovered a compound capable of binding to a Bcl-2 protein, causing it to unfold and expose its death domain. Thus, the protein transforms from one that protects the resistant cancer cell into one that kills it.  

Example of Breast cancer cells that are resistant to chemotherapeutic agent Taxol, that are responsive to compound Bcl-2 Functional Converter (BFC). Blue dots are cancer cell colonies.

Demonstrating the effectiveness of this pathway at the cellular level is remarkable, but Martin explains even the years it has taken to reach this stage are just the beginning of a very long process until it can be used to treat people with cancer. Beyond discovery, through the work of his Ph.D. Martin has realized other critical steps in developing effective cancer treatments that occur outside of the lab. For example, once a compound has been identified that successfully binds to a target protein, medical researchers must work with a patent attorney to protect their work and generate funding. Without patent protection, new drugs can’t be developed.

The dedication to ‘translational research’ or science that is specifically designed to be applied in improving health outcomes is what drew Martin to work with Dr. Kolluri in the first place and continues to inspire his plans for the future. Drawing back to his early interest in business, after finishing his Ph.D., Martin intends to explore a career as a patent attorney.

“This way I can be involved in the most exciting part of the process for me and be a part of people being at the edge of achieving what I was initially inspired in this career to achieve.“

Lifelong Bristol City F.C. supporters, Martin and his dad at Ashton Gate Stadium.

To hear more about Martin’s graduate work and insights into translational research, tune in on Sunday, October 13th at 7 PM on KBVR 88.7 FM, live stream the show at http://www.orangemedianetwork.com/kbvr_fm/, or download our podcast on iTunes!

What ties the Panama Canal, squeaky swing sets, and the Smithsonian together? Birds of course!

Have you ever wondered why you see birds in some places and not in others? Or why you see a certain species in one place and not in a different one? Birds have wings enabling them to fly so surely we should see them everywhere and anywhere because their destination options are technically limitless. However, this isn’t actually the case. Different bird species are in fact limited to where they can and/or want to go and so the question of why do we see certain birds in certain areas is a real research question that Jenna Curtis has been trying to get to the bottom of for her PhD research.

Jenna is a 4th year PhD candidate working with Dr. Doug Robinson in the Department of Fisheries & Wildlife. Jenna studies bird communities to figure out which species occur within those communities, and where and why they occur there. To dial in on these big ecological questions, Jenna focuses on tropical birds along the Panama Canal (PC). PC is a unique area to study because there is a large man-made feature (the canal) mandating what the rest of the landscape looks and behaves like. Additionally, it’s short, only about 50 miles long, however, it is bookended by two very large cities, Panama City (which has a population over 1 million people) and Colón. Despite the indisputable presence and impact of humans in this area, PC is still flanked by wide swaths of pristine rainforest that occur between these two large cities as well as many other types of habitat.

Barro Colorado Island can be seen in the centre of the Panama Canal.

A portion of Jenna’s PhD research focuses on the bird communities found on an island in the PC called Barro Colorado Island (BCI), which is the island smack-dab in the middle of the canal. To put Jenna’s research into context, we need to dive a little deeper into the history of the PC. When it was constructed by the USA (1904-1914), huge areas of land were flooded. In this process, some hills on the landscape did not become completely submerged and so areas that used to be hilltops became islands in the canal. BCI is one such island and it is the biggest one of them in the PC. In the 1920s, the Smithsonian acquired administrative rights for BCI from the US government and started to manage the island as a research station. This long-term management of the island is what makes BCI so unique to study as we have studies dating back to 1923 from the island but it has also been managed by the Smithsonian since 1946 so that significant development of infrastructure and urbanization never occurred here.

Large cargo vessels pass next to BCI on their transit of the Panama Canal

Now back to Jenna. Over time, researchers on the island noticed that fewer bird species were occurring on the island. There are now less species on the island than would be expected based on the amount of available habitat. Therefore, Jenna’s first thesis chapter looks at which bird species went extinct on BCI after the construction of PC and why these losses occurred. She found that small, ground-dwelling, insectivore species were the group to disappear first. Jenna determined that this group was lost because BCI has started to “dry out”, ecologically speaking, since the construction of PC. This is because after the PC was built, the rainforest on BCI was subjected to more exposure from the sun and wind, and over time BCI’s rainforest has no longer been able to retain as much moisture as it used to. Therefore, many of the bird species that like shady, cool, wet areas weren’t able to persist once the rainforest started becoming more dry and consequently disappeared from BCI.

Another chapter of Jenna’s thesis considers on a broader scale what drives bird communities to be how they are along the entire PC, and what Jenna found was that urbanization is the number one factor that affects the structure and occurrence of bird communities there. The thing that makes Jenna’s research and findings even more impactful is that we have very little information on what happens to bird communities in tropical climates under urbanization pressure. This phenomenon is well-studied in temperate climates, however a gap exists in the tropics, which Jenna’s work is aiming to fill (or at least a portion of it). In temperate cities, urban forests tend to look the same and accommodate the same bird communities. For example, urban forest A in Corvallis will have pigeons, house sparrows, and starlings, and this community of birds will also be found in urban forest B, C, D, etc. Interestingly, Jenna’s research revealed that this trend was not the case in Panama. She found that bird communities within forest patches that were surrounded by urban areas were significantly different to one another. She believes that this finding is driven by the habitat that each area may provide to the birds. 

Jenna has loved birds her entire life. To prove to you just how much she loves birds, on her bike ride to the pre-interview with us, she stopped on the road to smash walnuts for crows to eat. Surprisingly though, Jenna didn’t start to follow her passion for birds as a career until her senior year of her undergraduate degree. The realization occurred while she was in London to study abroad for her interior design program at George Washington University in D.C. where on every walk to school in the morning she would excitedly be pointing out European bird species to her friends and classmates, while they all excitedly talked about interior design. It was seeing this passion among her peers for interior design that made her realize that interior design wasn’t the passion she should be pursuing (in fact, she realized it wasn’t a passion at all), but that birds were the thing that excited her the most. After completely changing her degree track, picking up an honor’s thesis project in collaboration with the Smithsonian National Zoo on Kori bustard’s behavior, an internship at the Klamath Bird Observatory after graduating, Jenna started her Master’s degree here at OSU with her current PhD advisor, Doug Robinson in 2012. Now in her final term of her PhD, Jenna hopes to go into non-profit work, something at the intersection of bird research and conservation, and public relations and citizen science. But until then, Jenna will be sitting in her office (which houses a large collection of bird memorabilia including a few taxidermized birds) and working towards tying all her research together into a thesis.

To hear more about Jenna’s research, tune in on Sunday, October 6th at 7 PM on KBVR 88.7 FM, live stream the show at http://www.orangemedianetwork.com/kbvr_fm/, or download our podcast on iTunes!

Proteins run the show (except when they unfold and cause cataracts)

Your eye lenses host one of the highest concentrated proteins in your entire body. The protein under investigation is called crystallin and the investigator is called Heather Forsythe.

Heather is a 4th year PhD candidate working with Dr. Elisar Barbar in the Department of Biochemistry and Biophysics. The Barbar lab conducts work in structural biology and biophysics. Specifically, they are trying to understand molecular processes that dictate protein networks involving disordered proteins and disordered protein regions. To do this work, the lab uses a technique called nuclear magnetic resonance (NMR). NMR is essentially the same technology as an MRI, the big difference being the scale at which these two technologies measure. MRIs are for big things (like a human body) whereas NMR instruments are for tiny things (like the bonds between amino acids which are the building blocks of proteins). Heather employed OSU’s NMR facility (which has an 800 megahertz magnet and is on the higher end of the NMR magnetic field strength range) to investigate what the eye lens protein crystallin has to do with cataracts.

Your eye completely forms before birth, and the lens of the eye that helps us see is made of a protein called crystallin. This protein is essential to the structure and function of the eye, but it cannot be regenerated by the body so whatever you have at birth is all you will ever have. However, in the eye lens of someone affected by cataracts, the crystallin proteins become unfolded and then aggregate together. They stack on top of each other in a way that they are not supposed to. A person with cataracts will suffer from blurry vision, almost like you’re looking through a frosty or fogged-up window. While the surgery to fix cataracts (which basically takes out the old lens and puts in a new, artificial one) is pretty straight-forward and not very invasive, it isn’t easily accessible or affordable to a lot of people all over the world. Cataracts is attributed to causing ~50% of blindness worldwide, likely due to the fact that not everyone is able to take advantage of the simple surgery to fix it. Therefore, understanding the molecular, atomic basis of how cataracts happens could result in more accessible treatments (say a type of eye drop) for it worldwide.

This is where Heather comes in. There are different types of crystallin proteins and Heather zeroed in on one of them – gamma-S. Gamma-S is one of the most highly conserved proteins (meaning it hasn’t changed much over a long time) among all mammals, which tells us that it’s super important for it to remain just the way it is. Gamma-S makes up the eye lens by stacking on top of itself, making a brick wall of sorts ensuring that the eye lens retains its structure. However, research prior to Heather’s found that with increased age there is an increase in a modification called deamidation, which occurs in the unstructured loops of the gamma-S protein. Deamidation is a pretty minor change and is common in proteins all over the body, however in the eye lens if too much of it happens it no longer is a minor issue since it starts to disrupt the structure and protein-protein interactions of the eye lens. Heather’s collaborators at Oregon Health Sciences University found that there are two sites on the gamma-S protein (sites 14 and 76) where these deamidation events increase the most in cataracts-stricken eyes. It’s been known for a while that this deamidation is associated with cataracts however we never knew why it is associated with cataract formation because the changes caused by this modification were seemingly minor. This is how the Barbar Lab, and Heather specifically, became connected to this work since they specialize in studying unstructured proteins and protein regions, such as the loops present in gamma-S.

An example of an “1H(x-axis) 15N(y-axis) HSQC” spectra, aka, the fingerprint of a protein. This spectra is of WT gamma-S crystallin.

These deamidation changes are mimicked in the lab by creating two different mutants of the gamma-S protein’s DNA. Heather then compared the two mutants with the normal DNA by putting them through a series of experiments using the trusty NMR. The NMR is basically a large magnet that can make use of the magnetic fields around an atom’s nucleus to determine protein structure and motions. When Heather puts a protein sample into the NMR, the spins of the atomic nuclei will either align with or against the magnetic field of the NMR’s magnet. The NMR spits out spectra, which look like a square with lots of polka dots. This is essentially the fingerprint of the protein, unique to each one and extremely replicable. Heather can analyze this protein fingerprint since the different polka dots represent different amino acids in the gamma-s protein. Heather can compare spectra of the two mutants to the spectra of the normal protein to see whether any of the dots have moved, which would signal a change in the position of the amino acids.

After running experiments which measure protein motions at various timescales, from days to picoseconds, Heather discovered significant changes in protein dynamics when either site 14 or 76 was deamidated, however at different timescales. What this discovery means is that if both of these mutations are associated with cataracts and they are changing the same regions of the gamma-S protein, then these regions are likely central to changes resulting in cataracts. Therefore, research could be directed to target these regions to perhaps come up with solution to prevent and/or solve cataracts in a non-surgical way. The results of Heather’s study were recently published in Biochemistry.

Heather with her dog Piper.

Heather is from Arkansas where she completed her high school and undergraduate education. Living in a single-parent, non-academic home at this time, it took Heather a long time to figure out how to navigate the scientific and college-application scene, as well as even coming to the realization that science was something she was good at and could pursue. Despite receiving scholarships for college, she still had to work multiple jobs while in high school and college to have enough money for car-payments and gas to get to extra-curricular activities and volunteer jobs in the science field; things critical for graduate school applications. As a result, Heather is a strong advocate for inclusivity, striving to make things like science and college in general more accessible to low-income and diverse students. Heather’s decision to leave Arkansas and come to the PNW was inspired by advice she received from her undergraduate advisor who told her “not to go anywhere where you wouldn’t want to live. You will learn to love research, whatever it ends up being, but if you live in an environment that you don’t find fulfilling, then you are going to suffocate.”. Following this advice has lead Heather to where she is now – the senior in her lab where she has become a mentor to undergraduates, makes Twitter-famous Tik Tok videos (see below), goes on adventures with her dog Piper, and publishes cutting edge structural biology research.

Heather and her undergraduate mentee performing The Git Up in the lab.

To learn more you can check out the Barbar Lab website and Twitter page.

To hear more about Heather’s research, tune in on Sunday, September 29th at 7 PM on KBVR 88.7 FM, live stream the show at http://www.orangemedianetwork.com/kbvr_fm/, or download our podcast on iTunes!

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.

Language is a barrier to diversity and inclusion in natural resources research

Language usage in natural resources research

As a 3rd year Master’s student in the Department of Forest Ecosystems & Society, Jasmine Brown is investigating diversity and inclusion in the field of natural resources. Her research has consisted of examining how language usage reinforces barriers to inclusion. For example, the usage of terms such as ‘women or minorities’ fails to capture identities that exist at the intersection of both categories. Efforts to include members of marginalized groups still fall short, as current language usage does not include people whose identities intersect multiple categories. As a Black woman working in forestry, Jasmine’s understanding and lived experience of the forestry profession is acutely different from the typical experience of a White male. Through her research, Jasmine is examining what it means to be a Black woman in forestry. Although the demographics of who is contributing to natural resources research is slowly changing, language usage in the field has remained somewhat static. Conventional language used in natural resources is not connected to the historical trauma associated with forest spaces and requires change moving forward.

Jasmine attending the Society of American Foresters 2018 National Convention in Portland as a part of their Diversity Scholars Program.

How Jasmine gathered the data

At the beginning of her project, Jasmine found that language used in natural resources research is ambiguous. She explains how in medical science, “a kneecap refers to a specific body part, and leaves no room for interpretation. However, in natural resources, the term ‘diversity,’ for example, might have multiple meanings depending on the context. It might refer to habitat diversity, biodiversity, and wildlife diversity in addition to diversity of social identities such as race, ethnicity, and gender”. Despite being excited to learn about how diversity and inclusion is discussed in natural resources, Jasmine struggled to find a comprehensive body of text to base her work on. So she ended up having to compile the sources on her own. While conducting a systematic review, she was able to develop targeted search terms to evaluate existing research about diversity and inclusion of researchers in natural resources. A systematic review is comparable to a literature review, and is a method typically used in medical and social science to collect and evaluate published research using specific criteria. The advantage of a systematic review is that it provides a method to systematically and methodically identify relevant literature.

Jasmine talking about her research while dressed in her forestry uniform at a Science Communication Event

To compile a body of literature for her systematic review, Jasmine looked for signifiers, or markers, of diversity in natural resources, such as ‘underrepresented, women, females, minorities.’ Researchers told Jasmine she would have difficulty locating articles on diversity in natural resources, but Jasmine found over 260 articles! The literature she found is a combination of published sources, including scientific journals, and unpublished sources, including magazines, presentations, conference papers, theses, and technical reports. 

By evaluating the body of literature, she has identified which research methods are most popular for investigating diversity and inclusion in natural resources. Jasmine unearthed program evaluations by practitioners in the field, consisting of a summary of their successful implementation of diversity and inclusion programs. Methods used by practitioners in the field tended to be different than methods employed by scientific researchers. She observed that the scientific methods used by natural resources researchers have changed considerably over time. She also indicated that editorials about diversity and inclusion are abundant. Although authors may be highly educated researchers, the methods used to derive conclusions in editorial pieces are casual and less rigorous than in other standardized science disciplines. 

Jasmine further investigated the institutions where authors were working, and found that the top two categories were government and academia. Then, she investigated what titles were held by the authors. Over time, position titles have become more difficult to classify. Early in the field of forestry, a researcher might be known as, ‘forester.’ Today, however, position titles are more complex and reflect hierarchical changes to the academic system. An academic title might consist of multiple categories, such as, ‘assistant professor of forestry in the department of agriculture.’ 

While authors are adept at identifying barriers to diversification, the application of ideas to increase diversity and inclusion is lagging behind. Much more work is required to improve implementation of ideas that will increase diversity and inclusion in natural resources. 

A plan for action

Jasmine is looking forward to presenting her body of work to the larger community. She intends to present her work at the 35th Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS) Conference. She also intends to publish at least 1 of 2 articles from her thesis. Her dataset of more than 260 articles will be made public after her graduation. Her hope is that other researchers trying to locate published articles about diversity and inclusion in natural resources will be able to access the information she has compiled and won’t need to spend over eight months searching for it themselves. She has recognized that the interest and need for writing about diversity and inclusion is increasing, and hopes to move the field, and the language it is built upon, forward. 

Why did Jasmine want to study this topic?

As a senior undergraduate student studying forestry, Jasmine stepped out of her comfort zone and took several sociology classes about sustainability. These courses served as an illuminating accompaniment to her forestry degree, where she was introduced to forests as living ecosystems. Previously, from a forestry perspective, she was accustomed to thinking about trees in terms of their quantitative measurements and economic benefit to society. It was during this time that she became curious about how language is wielded in the forestry discipline. 

Jasmine has been working with the U.S. Forest Service for close to four years. In this environment, she recognized the importance of having difficult conversations, and it is these conversations that pushed her towards grad school for a Master’s degree. Jasmine chose OSU’s Forestry & Ecosystem because of the flexibility of the program and its relevance to her specific interests concerning the ‘human dimension’ of natural resources. She hoped to pursue research at the intersection of race, gender, and ethnicity, in part, because her identity is a part of everything she does. With this in mind, her Ethnic Studies graduate minor was a perfect fit. Jasmine has assembled an interdisciplinary team with faculty from forestry, wildlife, ethnic studies and a research librarian. She has two advisors: Brenda McComb from Forestry and Dana Sanchez from Fisheries and Wildlife. She pitched her research idea about the use of language in natural resources to her advisors, and they expressed excitement about its novelty and potential for impact. 

Jasmine in front of the Student Experience Center after participating in the 4th Social Justice Tour of Corvallis

Future direction

Jasmine’s realization that her identity as a Black woman has been a barrier does make her feel more invested in and passionate about her research. The feedback and pushback she has received during her Master’s research has informed her desire to continue in academia. Now, she identifies as both a forester and a social scientist. After completing her degree, Jasmine will pursue a PhD in a related discipline, where she will continue to drive change surrounding language usage in natural resources research. Jasmine hopes to continue inspiring youth of color to become natural resource professionals. 

Jasmine’s research has made her realize how important is it to consider previous scientific texts as data. Considering how many articles she’s been able to find, she places value on looking at the big picture. While it may not be easy to try evaluating criteria that have surely changed over time, Jasmine gladly accepts the challenge. As a budding researcher, her Master’s degree has taught her that there is much to be learned from previous trends when it comes to scientific standards and language use regarding diversity and inclusion in natural resources. 

Join us at 7 pm on Sunday, August 4th, 2019, to hear more about Jasmine’s research and her experience as a Master’s student at OSU. Stream the show live on KBVR Corvallis 88.7FM or check out the episode as a podcast after a few weeks.

Are Microplastics the New Fish Food?

Geologists have considered an entirely new geologic era as a result of the impact humans are having on the planet. Some plastic material in our oceans near Hawaii along are hot magma vents and is being cemented together with sand, shells, fishing nets and forming never before existing material — Plastiglomerates. This new rock is a geologic marker providing evidence of our impact that will last centuries. Although rocks seem inert, that same plastic material floating around our oceans is constantly being eaten, purposefully and accidentally, by ocean creatures from as small as plankton to as large as whales and we’re just beginning to understand the ubiquity of microplastics in our oceans and food webs that humans depend on.  

Our guest this evening is Katherine Lasdin, a Masters student in the Fisheries and Wildlife Department, and she has to go through extraordinary steps in her lab to measure the quantity and accumulation of plastics in fish. Her work focuses on the area off the coast of Oregon, where she is collecting black rockfish near Oregon Marine Reserves and far away from those protected areas. These Marine Reserves are “living laboratory” zones that do not allow any fishing or development so that long-term monitoring and research can occur to better understand natural ecosystems. Due to the protected nature of these zones, fish may be able to live longer lives compared to fish who are not accessing this reserve. The paradox is whether fish leading longer lives could also allow them to bioaccumulate more plastics in their system compared to fish outside these reserves. But why would fish be eating plastics in the first place? 

These are the locations of Oregon’s Marine Reserves. The sampling for juveniles and adult black rockfish is occurring at Cape Foulweather which is between the Cascade head and Otter Rock Reserves. PC:
Black rockfish are a common fish off the Oregon coast and due to their abundance it’s a great study species for this research.

Plastic bottles, straws, and fishing equipment all eventually degrade into smaller pieces. Either through photodegradation from the sun rays, by wave action physically ripping holes in bottles, or abrasion with rocks as they churn on our beaches. The bottle that was once your laundry detergent  is now a million tiny fragments, some you can see but many you cannot. And they’re not just in our oceans either. As the plastics degrade into even tinier pieces, they can become small enough that, just like dust off a farm field, these microplastics can become airborne where we breathe them in! Microplastics are as large as 5mm (about the height of a pencil eraser) and they are hoping to find them as small as 45 micrometers (about the width of a human hair). To a juvenile fish their first few meals is critical to their survival and growth, but with such a variety of sizes and colors of plastics floating in the water column it’s often mistaken for food and ingested. In addition to the plastic pieces we can see with our eyes there is a background level of plastics even in the air we breathe that we can’t see, but they could show up in our analytical observations so Katherine has a unique system to keep everything clean. 

In order to quantify the amount of plastics in fish, you have to digest some of the fish guts. PC: Katherine Lasdin

Katherine is co-advised by Dr. Susanne Brander who’s lab studies microplastics in marine ecosystems. In order to keep plastics out of their samples, they need to carefully monitor the air flow in the lab. A HEPA filtration laminar flow hood blows purified air towards samples they’re working with in the lab and pushes that clean air out into the rest of the lab. There is a multi-staged glassware washing procedure requiring multiple ethanol rinses, soap wash, deionized water rinses, a chemical solvents rinse, another ethanol, and a final combustion of the glass in a furnace at 350°C for 12-hours to get rid of any last bit of contamination. And everyday that someone in Dr. Brander’s lab works in the building they know exactly what they’re wearing; not to look cool, but to minimize any polyester clothing and maximize cotton clothing so there is even less daily contamination of plastic fibers. These steps are taken because plastics are everywhere, and Katherine is determined to find out just big the problem may be for Oregon’s fish.  

Katherine Lasdin working in the laminar flow hood that blows purified air towards the samples in Dr. Brander’s lab. PC: Cheyenne Pozar

Be sure to listen to the interview Sunday 7PM, either on the radio 88.7KBVR FM or live-stream, to learn how Katherine is conducting her research off the coast of Oregon to better understand our ocean ecosystems in the age of humans.

Listen to the podcast episode!

On this episode at the 16:00 mark we described how every time you wash clothing you will loose some microfibers; and how a different student was looking at this material under microscopes. That person is Sam Athey, a PhD student at the University of Toronto who also studies microplastics.