Author Archives: Lillian Padgitt-Cobb

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.

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

Mosquito soup in the Brazilian rainforest

Fieldwork in the Brazilian Amazonia meant continuously trying to outsmart their savviest opponents…ants!

Fieldwork in the Brazilian Amazonia meant continuously trying to outsmart their savviest opponents…ants!

Deforestation in Brazil due to cultivation of monoculture crops, such as soybean, has profoundly impacted wildlife populations. In the lab of Taal Levi in the Department of Fisheries and Wildlife, wildlife biologist Aimee Massey has adopted a quantitative approach to studying this impact. During her first and second year of graduate school, Aimee traveled to Brazil for fieldwork and data collection, collaborating with researchers from Brazil and the UK. During this trip, she collected 70,000 biting flies, including mosquitoes and sandflies, by engineering 200 fly traps constructed from 2-liter soda bottles, netting, and rotting beef. Aimee installed biting traps throughout 40 individual forest patches, which are regions delineated by their physical characteristics, ranging approximately in size from the OSU campus to the state of Rhode Island.

Who knew fieldwork could be such a balancing act?!…especially when trying to avoid poisonous insects and thorns. Let’s hope the next branch Aimee reaches for is not of the slithering snake kind!

Who knew fieldwork could be such a balancing act?!…especially when trying to avoid poisonous insects and thorns. Let’s hope the next branch Aimee reaches for is not of the slithering snake kind!

Subsequent DNA analysis on biting flies provides a relatively unbiased source of wildlife tracking, since mosquitoes serve as a repository of DNA for the wildlife they have feasted upon. DNA analysis also provides information regarding diseases that may be present in a particular patch, based on the bacterial and viral profile. For example, sandflies are carriers of protozoa such as leishmania, which cause the disease leishmaniasis. To analyze DNA, Aimee uses bioinformatics and metabarcoding, which is a technique for assessing biodiversity from an environmental sample containing DNA. Different species of animals possess characteristic DNA sequences that can be compared to a known sequence in an online database. By elucidating the source of the DNA, it is possible to determine the type of wildlife that predominates in a specific patch, and whether that animal may be found preferentially in patches featuring deforestation or pristine, primary rain forest.

Learning about human/wildlife interactions while drinking tea with camel’s milk in Laikipia, Kenya.

Learning about human/wildlife interactions while drinking tea with camel’s milk in Laikipia, Kenya.

Aimee completed her undergraduate studies at University of Maine, where she quickly discovered she wanted to study biology and chemistry in greater depth. She planned to attend med school, and was even accepted to a school in her junior year; however, an introductory fieldwork course in Panama spent exploring, doing fieldwork, and trekking made a deep impression on her, so she decided to apply to graduate school instead. Aimee completed a Masters degree in environmental studies at the University of Michigan, during which time she spent 4 months at the Mpala Research Centre in the middle of the Kenyan plateau, just north of the Masai Mara. Following completion of her Masters degree, Aimee spent a year as a research assistant at the University of New Hampshire working with small mammals. Before beginning her PhD studies at OSU, Aimee spent two months in Haines, Alaska doing fieldwork with her future PI, Taal Levi. After she finishes her PhD, Aimee plans to focus on conservation work in New England where she is originally from.

Having fun after fieldwork; Aimee’s eulachon fish catch of the day in Haines, Alaska. One is better than none!

Having fun after fieldwork; Aimee’s eulachon fish catch of the day in Haines, Alaska. One is better than none!

Tune in on October 23rd, 2016 at 7PM on the radio at 88.7FM KBVR, or stream live, to hear more about Aimee’s adventures in Brazil, and why her graduate work is shaping our understanding of how deforestation impacts biodiversity.

 

Heat and oxygen exchange at the interface of ocean and atmosphere.

 

Jenessa aboard OSU's vessel the R/V Oceanus during a cruise for a field work course. She is deploying a vertical microstructure profile attached to a large winch: fishing for the big one!

Jenessa aboard OSU’s vessel the R/V Oceanus during a cruise for a field work course. She is deploying a vertical microstructure profile attached to a large winch: fishing for the big one!

As a physical oceanographer in the College of Earth, Ocean, and Atmospheric Sciences, Masters candidate Jenessa Duncombe is investigating how the movement of water impacts heat and oxygen exchange at the interface of the ocean and atmosphere. Combining analytical and modeling approaches in the labs of Roger Samelson and Eric Skyllingstad, Jenessa uses linear stability analysis to predict the circulation of water in the upper 300 feet of the ocean.  Jenessa focuses on regions in the ocean with high rates of ocean and atmosphere exchange; those areas are common throughout the ocean, typically occurring near river mouths, along upwelling regions, or along strong surface currents, like the Gulf Stream. These regions can be thought of as the lungs of the ocean, responsible for the majority of oxygen and carbon dioxide uptake into the ocean. Jenessa’s goal for her research is to improve how surface ocean circulation is accounted for in global climate change models, hopefully making model predictions more accurate.

Satellite sea surface temperature image of the Gulf Stream. The red colors show the warm Gulf Stream waters traveling from the Gulf of Mexico, along the east coast, then traveling out into the Atlantic. Whirlpools of warm and cold water, called eddies, pinch off as the Gulf Stream becomes unstable heading into the Atlantic Ocean. Ocean eddies are (in Jenessa’s opinion) the coolest type of ocean circulation! For a dynamic look at ocean surface currents, check out this video from NASA called Perpetual Ocean. You can see the Gulf Stream and other strong currents, as well as whirlpools of warm and cold water spinning up in the ocean!

Jenessa’s interest in earth science began during middle school with encouragement from an inspirational teacher.  During her undergraduate studies at Wesleyan University in Connecticut, Jenessa decided to major in earth science after becoming acquainted with other earth science majors who shared her interest in hiking. Structural geology and a physics course on the topic of waves and oscillations were among her favorite courses. In particular, waves and oscillations provided insight and clarity into her realization that visual patterns can be described by a mathematical equation. Jenessa cites a summer REU (Research Experiences for Undergraduates) at the University of Maryland through the NSF as a critical introduction to research. During the summer after finishing her undergraduate studies, Jenessa worked at Sandia National Laboratories in New Mexico, acquiring experience in research related to harnessing power generated from wave energy. After finishing her Masters degree, Jenessa plans to pursue a career in science writing.

Tune in on September 25th 2016 at 7PM to hear more from Jenessa about her research related to the movement of water in the ocean and the role it may play in climate change. You can listen on the radio at 88.7FM KBVR Corvallis or by streaming live.