Category Archives: Molecular and Cell Biology

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.

The Sweetest Genes

Tonight we have the pleasure of speaking to Natalia Salinas who comes all the way from South America to work on producing more (and delicious) strawberries! Think about how often you see strawberries in the grocery store, but strawberries typically only produce one harvest per year. Some of Natalia’s work focus on identifying if the seeds’ DNA have the perpetual flowering characteristic so there are more potential harvests throughout the year. Just as important as quantity is quality; a second aspect of Natalia’s work is searching DNA markers to try and predict the sugar content in strawberries.

Ideally growers would like many harvests and sweeter strawberries, so tune in tonight at 7PM Pacific time to 88.7FM KBVR Corvallis or stream the show live at http://kbvr.com/listen to find out how Natalia can help your next milkshake be even more delicious!

 

Natalia is working to amplify the DNA sequences in strawberries to identify desirable traits.

Natalia is working to amplify the DNA sequences in strawberries to identify desirable traits.

The fruits of Natalia's labor!!! yum!

The fruits of Natalia’s labor. Yum!

Genomics on the Farm: Breeding A More Resistant Rice

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Photo courtesy the Jaiswal Lab

Tonight Noor Al-Bader of OSU’s Molecular and Cell Biology department joins us on the show to discuss her doctoral research concerning genomics and plant breeding.  Working in Dr. Pankaj Jaiswal’s lab, Noor deals with large data sets of genetic information concerning varieties of Rice and Chia. The goal of her study is to determine which genes relate to the expression of traits implicated in stress resistance and nutritional content. Often the varieties of these crops grown for their value to farmers are susceptible to environmental stressors such as high salinity in water, drought, and high temperatures. These environmental concerns unfortunately promise to be increasing concerns in many areas such crops are grown due to the increasing impact of climate change. Wild types are often hardier, and genetic studies of both types hold promise for producing a “happy medium” capable of producing high yield, nutritious rice and chia that is also highly prosperous under less than desirable environmental circumstances.  These new varieties are not produced via genetic modification in the lab, but bred on the farm, crossing strains generation after generation and recording the results with painstaking attention to detail- the old fashioned way. The contrast between the hands on work of horticulture and the hard science of genetics in the lab may seem a surprising pair, but in this case the genetics research is utilized to facilitate traditional methods of horticulture by simply speeding along a process that could normally take lifetimes. Just like in her research, Noor strives to have the best of both worlds.

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