Category Archives: science communication

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.

Breaking the Arctic ice

 

Thermal AVHRR image with land masked in black. Can see the lead coming off of Barrow Alaska very bright. The arrows are sea ice drift vectors.

Cascade over mossy rocks near Sol Duc Falls, Olympic National Park, WA.

When you hear about fractures in sea ice, you might visualize the enormous fissures that rupture ice shelves, which release massive icebergs to the sea. This is what happened back in July 2017 when a Delaware-sized iceberg broke off from the Larsen C ice shelf in Antarctica. However, there are other types of fractures occurring in sea ice that may be impacted by atmospheric conditions. Our guest this week, CEOAS Masters student Ben Lewis investigates how interactions between the atmosphere and sea ice in the Beaufort Sea (north of Alaska in the Canadian Archipelago) impact the formation of fractures. His research involves mapping atmospheric features, such as wind and pressure, at the point in time when the fractures occurred and provides insight into the effect of the atmosphere on the formation and propagation of fractures. Utilizing satellite imagery compiled by the Geographical Information Network of Alaska from 1993 to 2013, Ben has conducted a qualitative analysis to determine the location and time when these ice fractures occurred and what type of physical characteristics they possess.

Southern Alps from the summit of Avalanche Peak, New Zealand.

While fractures appear small on the satellite image, the smallest fractures that Ben can observe by are actually 250 meters wide. Fractures can span hundreds of kilometers, and the propagate very quickly; Ben cites one example of a fracture near Barrow, Alaska that grew to 500 kilometers within 6 hours!

Fractures are potentially deadly for people and animals hunting in the Arctic. As weather flux in the fragile Arctic ecosystem has become more erratic with climate change, it has been difficult for people to predict when it was safe to hunt on the ice based on patterns observed in prior seasons. Additionally, it has been problematic to track weather in the Arctic because of its harsh conditions and sparse population. A well-catalogued record of weather is not available for all locations. Modeling atmospheric conditions, such as pressure and wind, based on what has been captured by satelliteimagery, will facilitate better prediction of future fracture events.

Sunset over Sandfly Beach, New Zealand.

While pursuing an undergraduate degree in physics at the University of Arkansas, Ben was able to study abroad James Cook University in Australia, where he gravitated towards environmental physics, while taking advantage of incredible opportunities for nature photography. He also did a semester abroad in New Zealand, where he studied geophysical fluid dynamics and partial differential equations. Ben came to OSU as a post-baccalaureate student in climate science, and while at OSU, he became acquainted with his future PI, Jennifer Hutchings,  and his interest in Arctic research grew. He cites learning about snowball earth, glaciology, and the cryosphere, as providing the basis for his desire to pursue Arctic climate research. Eventually, Ben would like to pursue a PhD, but in the immediate future, he plans to keep his options open for teaching and research opportunities.

 

Using sediment cores to model climate conditions

In the lab of Andreas Schmittner in the College of Earth, Ocean, and Atmospheric Sciences, recently-graduated PhD student Juan Muglia has been developing a climate model to understand ocean current circulation, carbon cycling, and ocean biogeochemistry during the last ice age, focusing on the Southern Ocean surrounding Antarctica.

Juan has developed a climate model using data gathered from sediment cores, which are samples from the ocean floor that provide researchers with a glimpse into the elemental and organic composition of the ocean at different points in time. Scientists can acquire insight into the characteristics of the Earth’s past climate by analyzing the geologic record spanning thousands of years. Modeling the conditions of the last ice age, which occurred 20,000 years ago, allows researchers to better understand how the Earth responds to glacial and interglacial cycles, prompting the transition between cold and warm phases (we are currently in a warm interglacial period).

The process of generating an accurate climate model consists of tuning parameters embedded in the physics equations and fortran code of the model, to reproduce characteristics directly observable in modern times. If researchers can validate their model by reproducing directly observable characteristics, the model can then be used to investigate the climate at points in time beyond our direct observational capacity.

Since it’s not possible to directly measure temperature or nutrient composition of the ocean during the last ice age, Juan uses an indirect signature that serves as a proxy for direct measurement. Three isotopic sediment tracers, including 15Nitrogen, 14Carbon, and 13Carbon, are incorporated into Juan’s climate model as proxies for biological productivity and current circulation in the ocean. Investigating changes in the elemental composition of the ocean, also known as biogeochemistry, is important for understanding how climate and biology have transformed over thousands of years. The ocean serves as an enormous reservoir of carbon, and much more carbon is sequestered in the ocean than in the atmosphere. The exchange of carbon dioxide at the interface of the ocean and atmosphere is important for understanding how carbon dioxide has and will continue to impact pH, ocean currents, and biological productivity of the ocean.

Even as a kid, Juan dreamed of becoming an oceanographer. He grew up near the ocean in Argentina, surrounded by scientists; his mom was a marine botanist and his dad is a geologist. During his undergraduate studies, he majored in physics with the goal of eventually becoming a physical oceanographer, and his undergraduate thesis consisted of building fortran code for a statistical physics project. After finishing his post-doctoral studies at OSU, Juan plans to return to his hometown in Argentina, where he hopes to develop a model specific to the Argentinian climate.

Searching for viruses that make plants sick

Ripening sweet cherries in Mosier, Oregon. Photo credit: Lauri Lutes

When plants get sick, they can’t be treated or cured in the same way as people who receive medicine for an illness.  Plants require specialized care by scientists who are uniquely equipped to study and treat their diseases.  As a graduate student in the lab of Dr. Jay Pscheidt in the Department of Botany and Plant Pathology, Lauri Lutes is a plant doctor looking for viruses that infect sweet cherry trees in Oregon. She is able to identify an infected sweet cherry tree by looking at symptoms, including yellow rings or discolored mottling on the leaves, or fruit that is smaller than normal. To pinpoint the identity of the virus, further tests in the lab are performed.

Mottling and ringspot symptoms on sweet cherry, Prunus avium, in Umpqua Valley, Oregon. Photo Credit: Jay W. Pscheidt

Sweet cherries are one of Oregon’s top commodities, with 12,300 acres of sweet cherry production near the Dalles and Hood River, and 3,200 acres in the Willamette valley. There are a few viruses that the Oregon Department of Agriculture looks for each year, including Plum pox virus, a quarantine pathogen in the United States. However, if sweet cherry trees are infected with something other than the most common or most damaging viruses, they may never receive a diagnosis! Lauri works with the Oregon Sweet Cherry Commission to determine where diseased sweet cherry trees are located in Oregon. During her time at OSU, Lauri has discovered a virus infecting sweet cherry trees in the Dalles region that had never been reported in Oregon!

Lauri Lutes collecting leaf samples from sweet cherry trees in The Dalles, Oregon. Photo credit: Lauri Lutes

As an undergraduate student majoring in biology at Indiana University South Bend, Lauri discovered her passion for plant biology after taking a plant systematics course. Her undergraduate research consisted of studying fungal pathogens in a native waterleaf plant that grows in the forest floor of Indiana. Lauri attributes her positive experiences in undergraduate classes and research to female professors who provided encouragement and strong mentoring. After the birth of her daughter during her senior year of college, Lauri’s path toward attending grad school diverged, and she began working at a plant pathogen diagnostics company, Agdia, Inc. There, she used magnetic particles to purify viruses from plant material and co-developed a Technical Support Department. Curiosity driven, she found that she still wanted a deeper foundation in plant pathology, which led her to pursue graduate work at OSU.

View of Mount Hood from sweet cherry orchard in Parkdale, Oregon. Photo credit: Lauri Lutes

In addition to her work with sweet cherry tree viruses, Lauri is enrolled in the Graduate Certificate in College and University Teaching (GCCUT) program, and is active in science communication, having recently been selected to attend ComSciCon-PNW (Communicating Science Conference) in Seattle. After grad school, Lauri is considering teaching at the university level and continuing her involvement in science communication. As the first person in her family to complete an advanced degree, she hopes to inspire and expose her daughter to educational opportunities she might not have had otherwise.

Please join us this Sunday, April 2nd on KBVR Corvallis 88.7FM at 7 pm PST, to hear much more about Lauri’s journey through grad school, and her research about sweet cherry tree viruses. 

You can also stream this episode live at www.kbvr.com/listen.

View from a sweet cherry orchard in the Hood River, Oregon. Photo credit: Lauri Lutes