Category Archives: STEM Outreach

Stream ecosystems and a changing climate

Examining the effect of climate change on stream ecosystems

Oak Creek near McDonald Dunn research lab. The salamander and trout in the experiments were collected along this stretch of creek.

As a first year Master’s student in the lab of Ivan Arismendi, Francisco Pickens studies how the changing, warming climate impacts animals inhabiting stream ecosystems. A major component of stream ecosystem health is rainfall. In examining and predicting the effects of climate change on rainfall, it is important to consider not only the amount of rainfall, but also the timing of rainfall. Although a stream may receive a consistent amount of rain, the duration of the rainy season is projected to shrink, leading to higher flows earlier in the year and a shift in the timing of the lowest water depth. Currently, low flow and peak summer temperature are separated by time. With the shortening and early arrival of the rainy season, it is more likely that low flow and peak summer temperature will coincide.

A curious trout in one of the experimental tanks.

Francisco is trying to determine how the convergence of these two events will impact the animals inhabiting streams. This is an important question because the animals found in streams are ectothermic, meaning that they rely on their surrounding environment to regulate their body temperature. Synchronization of the peak summer temperature with the lowest level of water flow could raise the temperature of the water, profoundly impacting the physiology of the animals living in these streams.

 

 

How to study animals in stream ecosystems?

Salamander in its terrestrial stage.

Using a simulated stream environment in a controlled lab setting, Francisco studies how temperature and low water depth impact the physiology and behavior of two abundant stream species – cutthroat trout and the pacific giant salamander. Francisco controls the water temperature and depth, with depth serving as a proxy for stream water level.

Blood glucose level serves as the experimental readout for assessing physiological stress because elevated blood glucose is an indicator of stress. Francisco also studies the animals’ behavior in response to changing conditions. Increased speed, distance traveled, and aggressiveness are all indicators of stress. Francisco analyzes their behavior by tracking their movement through video. Manual frame-by-frame video analysis is time consuming for a single researcher, but lends itself well to automation by computer. Francisco is in the process of implementing a computer vision-based tool to track the animals’ movement automatically.

The crew that assisted in helping collect the animals: From left to right: Chris Flora (undergraduate), Lauren Zatkos (Master’s student), Ivan Arismendi (PI).

Why OSU?

Originally from a small town in Washington state, Francisco grew up in a logging community near the woods. He knew he wanted to pursue a career involving wild animals and fishing, with the opportunity to work outside. Francisco came to OSU’s Department of Fisheries and Wildlife for his undergraduate studies. As an undergrad, Francisco had the opportunity to explore research through the NSF REU program while working on a project related to algae in the lab of Brooke Penaluna. After he finishes his Master’s degree at OSU, Francisco would like to continue working as a data scientist in a federal or state agency.

Tune in on Sunday, June 24th at 7pm PST on KBVR Corvallis 88.7 FM, or listen live at kbvr.com/listen.  Also, check us out on Apple Podcasts!

Ocean sediment cores provide a glimpse into deep time

Theresa on a recent cruise on the Oceanus.
Photo credit: Natasha Christman.

First year CEOAS PhD student Theresa Fritz-Endres investigates how the productivity of the ocean in the equatorial Pacific has changed in the last 20,000 years since the time of the last glacial maximum. This was the last time large ice sheets blanketed much of North America, northern Europe, and Asia. She investigates this change by examining the elemental composition of foraminifera (or ‘forams’ for short) shells obtained from sediment cores extracted from the ocean floor. Forams are single-celled protists with shells, and they serve as a proxy for ocean productivity, or organic matter, because they incorporate the elements that are present in the ocean water into their shells. Foram shell composition provides information about what the composition of the ocean was like at the point in time when the foram was alive. This is an important area of study for learning about the climate of the past, but also for understanding how the changing climate of today might transform ocean productivity. Because live forams can be found in ocean water today, it is possible to assess how the chemistry of seawater is currently being incorporated into their shells. This provides a useful comparison for how ocean chemistry has changed over time. Theresa is trying to answer the question, “was ocean productivity different than it is now?”

Examples of forams. For more pictures and information, visit the blog of Theresa’s PI, Dr. Jennifer Fehrenbacher: http://jenniferfehrenbacher.weebly.com/blog

Why study foram shells?

Foram shells are particularly useful for scientists because they preserve well and are found ubiquitously in ocean sediment, offering a consistent glimpse into the dynamic state of ocean chemistry. While living, forams float in or near the surface of the sea, and after they die, they sink to the bottom of the sea floor. The accumulating foram shells serve as an archive of how ocean conditions have changed, like how tree rings reflect the environmental conditions of the past.

Obtaining and analyzing sediment cores

Obtaining these records requires drilling cores (up to 1000 m!) into deep sea sediments, work that is carried out by an international consortium of scientists aboard large ocean research vessels. These cores span a time frame of 800 million years, which is the oldest continuous record of ocean chemistry. Each slice of the core represents a snapshot of time, with each centimeter spanning 1,000 years of sediment accumulation. Theresa is using cores that reach a depth of a few meters below the surface of the ocean floor. These cores were drilled in the 1980s by a now-retired OSU ship and are housed at OSU.

Theresa on a recent cruise on the Oceanus, deploying a net to collect live forams. Photo credit: Natasha Christman.

The process of core analysis involves sampling a slice of the core, then washing the sediment (kind of like a pour over coffee) and looking at the remainder of larger-sized sediment under a powerful microscope to select foram species. The selected shells undergo elemental analysis using mass spectrometry. Vastly diverse shell shapes and patterns result in different elements and chemistries being incorporated into the shells. Coupled to the mass spectrometer is a laser that ablates through the foram shell, providing a more detailed view of the layers within the shell. This provides a snapshot of ocean conditions for the 4 weeks-or-so that the foram was alive. It also indicates how the foram responded to light changes from day to night.

Theresa is early in her PhD program, and in the next few years plans to do field work on the Oregon coast and on Catalina island off the coast of California. She also plans to undertake culturing experiments to further study the composition of the tiny foram specimens.

Why grad school at OSU?

Theresa completed her undergraduate degree at Queen’s University in Ontario, followed by completion of a Master’s degree at San Francisco State University. She was interested in pursuing paleo and climate studies after transformative classes in her undergrad. In between her undergraduate and Master’s studies she spent a year working at Mt. Evans in Colorado as part of the National Park Service and Student Conservation Association.

Theresa had already met her advisor, Dr. Jennifer Fehrenbacher, while completing her Master’s degree at SF State. Theresa knew she was interested in attending OSU for grad school for several reasons: to work with her advisor, and to have access to the core repository, research ships, and technical equipment available at OSU.

To hear more about Theresa’s research and her experience as a PhD student at OSU, tune in on Sunday, June 10th at 7pm on KBVR Corvallis 88.7 FM, or listen live at kbvr.com/listen.  Also, check us out on Apple Podcasts!

Comunicación Científica con Franco

Kristen Finch interviewing Francisco Guerrero for this special episode. (Photo by Adrian Gallo)

This week on Inspiration Dissemination we will be featuring a previous guest: Francisco Guerrero, a PhD student in the Department of Forest Engineering, Resources, and Management. Francisco’s first interview aired on October 18, 2015, and we called him back for a follow-up because he has been selected for the American Association for the Advancement of Science (AAAS) Mass Media Science and Engineering Fellowship. As a fellow, Franco will be writing feature stories about climate change and health for CNN en Español. Part of the fellowship will involve helping with film production, as well. FUN FACT last time Franco was on the show, he told us that he always wanted to be a movie producer. Franco will take this amazing opportunity during the final push for his PhD research to enhance his science communication skills and gain experience in production and video broadcasting.

This special interview will begin at 6:30 pm on May 6, 2018. We will be asking Franco about the application process, his responsibilities as a fellow, and his goals for the fellowship. After our interview with Franco, we will rebroadcast his first interview on Inspiration Dissemination at 7 pm.

Tune in to KBVR Corvallis 88.7 FM at 6:30 pm to hear about the AAAS Fellowship and learn about Franco’s research in the College of Forestry. Not a local listener? No sweat! Stream the show live on line or hear the podcast next week.

Franco wants to hear from you! Tweet him with ideas for CNN Español, specifically stories about Climate Change and Health. 

The folks behind the episode: Francisco Guerrero, Kristen Finch, and Lillian Padgitt-Cobb. (Photo by Adrian Gallo)

Exploring a protein’s turf with TIRF

Investigating Otoferlin

Otoferlin is a protein required for hearing. Mutations in its gene sequence have been linked to hereditary deafness, affecting 360 million people globally, including 32 million children. Recently graduated PhD candidate Nicole Hams has spent the last few years working to characterize the activity of Otoferlin using TIRF microscopy. There are approximately 20,000 protein-coding genes in humans, and many of these proteins are integral to processes occurring in cells at all times. Proteins are encoded by genes, which are comprised of DNA; when mutations in the gene sequence occur, diseases can arise. Mutations in DNA that give rise to disease are the focus of critical biomedical research. “If DNA is the frame of the car, proteins are the engine,” explains Nicole. Studying proteins can provide insight into how diseases begin and progress, with the strategic design of therapies to treat disease founded on our understanding of protein structure and function.

Studying proteins

Proteins are difficult to study because they’re so small: at an average size of ~2 nanometers (0.000000002 meters!), specific tools are required for visualization. Enter TIRF. Total Internal Reflection Fluorescence is a form of microscopy enabling scientists like Nicole to observe proteins tagged with a fluorescent marker. One reason TIRF is so useful is that it permits visualization of samples at the single molecule level. Fluorescently-tagged proteins light up as bright dots against a dark background, indicating that you have your protein.

Another reason why proteins are hard to study is that in many cases, parts of the protein are not soluble in water (especially if part of the protein is embedded in the fatty cell membrane). Trying to purify protein out of a membrane is extremely challenging. Often, it’s more feasible for scientists to study smaller, soluble fragments of the larger protein. Targeted studies using truncated, soluble portions of protein offer valuable information about protein function, but they don’t tell the whole story. “Working with a portion of the protein gives great insight into binding or interaction partners, but some information about the function of the whole protein is lost when you study fragments.” By studying the whole protein, Nicole explains, “we can offer insight into mechanisms that lead to deafness as a result of mutations.”

Challenges and rewards of research

Nicole cites being the first person in her lab to pursue single molecule studies as a meaningful achievement in her graduate career. She became immersed in tinkering with the new TIRF instrument, learning from the ground up how to develop new experiments. Working with cells containing Otoferlin, in a process known as tissue culture, required Nicole to be in lab at unusual hours, often for long periods of time, to make sure that the cells wouldn’t die. “The cells do not wait on you,” she explains, adding, “even if they’re ready at 3am.” Sometimes Nicole worked nights in order to get time on the TIRF. “If you love it, it’s not a sacrifice.”

Why grad school?

As an undergraduate student studying Agricultural Biochemistry at the University of Missouri, Nicole worked in a soybean lab investigating nitrogen fixation, and knew she wanted to pursue research further. She had worked in a lab work since high school, but didn’t realize it was a path she could pursue, instead convinced that she wanted to go to medical school. Nicole’s mom encouraged her to pursue research, because she knew that it was something she enjoyed, and her undergraduate advisor (who completed his post-doc at OSU) suggested that she apply to OSU. She feels lucky to have found an advisor like Colin Johnson, and stresses the importance of finding a mentor who is personally vested in their graduate student’s success.

Besides lab work…

In addition to research, Nicole has been actively involved in outreach to the community, serving as Educational Chair of the local NAACP Chapter. Following completion of her PhD, Nicole intends to continue giving back to the community, by establishing a scholarship program for underrepresented students. Nicole remembers a time when she was told and believed that she wasn’t good enough, and while she was able to overcome this discouraging dialogue, she has observed that many students do not find the necessary support to pursue higher education. Her goal is to reach students who don’t realize they have potential, and provide them with resources for success.

Tune in on December 3rd  at 7pm to 88.7 KBVR Corvallis or stream the show live right here to hear more about Nicole’s journey through graduate school!

Thanks for reading!

You can download Nicole’s iTunes Podcast Episode!

Earlier in the show we discussed current events, specifically how the tax bill moving through the House and Senate impact students. Please see our references and sources for more information.

Elucidating protein structure with crystals

Kelsey in the lab pipetting one of her many buffers!

Proteins are the workhorse molecules of the cell, contributing to diverse processes such as eyesight, food breakdown, and disabling of pathogens. Although cells cannot function without helper proteins, they’re so small that it’s impossible to view them without the aid of special tools. Proteins are encoded by RNA, and RNA is encoded by DNA; when DNA is mutated, the downstream structure of the protein can be impacted. When proteins become dysfunctional as part of disease, understanding how and why they behave differently can lead to the development of a therapy. In Andy Karplus’ lab in the Department of Biochemistry & Biophysics, PhD candidate Kelsey Kean uses a technique known as protein x-ray crystallography to study the relationship between protein structure and function.

Protein crystals. On the left, each blade making up this cluster is an individual crystal that needs to be separated before we can use them.

Protein diffraction. An individual crystal is placed in front of an x-ray beam and we collect the diffraction resulting from the x-ray hitting each atom in the protein crystal . Using the position and darkness of each spot (along with some other information), we can figure out where each atom in the crystal was originally positioned.

An electron density map. After collecting and processing our diffraction images, we get an electron density map (blue)- this shows us where all the electrons for each atom in the protein are- and this guides us in building in the atomic coordinates (yellow) for each part of the protein. It’s like a puzzle!

Crystallization of protein involves many steps, each of which presents its own unique challenges. A very pure protein sample is required to form an ordered crystal lattice, and hundreds of different buffer solutions are tested to find the ideal crystallization conditions. Sometimes crystals can take weeks, months, or a year to grow: it all depends on the protein. Once a crystal is obtained, Kelsey ships it to the synchrotron at Lawrence Berkeley National Laboratory, which provides a source of ultra powerful x-ray light beams. Exposure of the protein crystal to x-ray light results in a diffraction pattern, which is caused by the x-ray light diffracting off of all the atoms in the crystal. A map of electron density is generated from the diffraction pattern, and then the electron density map is used to determine where the atoms are located in the protein, like a complex puzzle. X-ray protein crystallography is really amazing because it allows you to visualize proteins at the atomic level!

In addition to her lab work, Kelsey is extensively involved in teaching and STEM outreach. For the past 3 summers, she has organized a week-long summer biochemistry camp through STEM Academy, with the help of a group of biochemistry graduate students. Kelsey has also been involved in Discovering the Scientist Within, a program providing 150 middle school girls with the opportunity to perform science experiments, including isolation of strawberry DNA and working with mutant zebrafish.

Kelsey completed her undergraduate degree in biochemistry with a minor in math at the University of Tulsa, where she was also a Division I athlete in rowing. She attributes her work ethic and time management skills to her involvement in Division I athletics, which required a significant commitment of time and focus outside of lab and coursework. During one summer when she wasn’t busy with competitive rowing, she performed experiments related to protein crystallography at the Hauptman-Woodward Medical Research Institute associated with the University at Buffalo.

Kelsey knew she wanted to pursue science from an early age. She grew up surrounded by scientists: her mom is a biochemist and her dad is a software engineer! She recalls playing with Nalgene squirt bottles as a kid, and participated in the Science Olympiad in middle school, where she engineered a Rube Goldberg machine. She cites early exposure to science from her family as one reason why she feels strongly about STEM outreach to students who might not otherwise receive encouragement or support. In the future, Kelsey would like to teach at a primarily undergraduate institution.

Please join us this Sunday, April 23rd on KBVR Corvallis 88.7FM at 7 pm PST  to hear much more about x-ray protein crystallography, STEM outreach, and to hear an awesome song of Kelsey’s choosing! You can also stream this episode live at www.kbvr.com/listen.