Category Archives: College of Science

Magnet blocks, connect the dots, and the world of modern mathematics

At the Mathematical Sciences Research Institute in Berkely, CA with the Klein quartic sculpture. Photo by Charles Camacho

Charles Camacho, a sixth-year PhD student in the Department of Mathematics at Oregon State University, spends a lot of time thinking about shapes. He describes his research as such: “I study the symmetries of abstract mathematical surfaces made from gluing triangles together.”

Charles explaining his thesis research at the Latinx in the Mathematical Sciences conference at UCLA. Photo by Farida Saleh from the Daily Bruin.

Charles works in a branch of mathematics called topology. Topologists think about shapes and surfaces. There’s a joke among mathematicians that a topologist is someone who can’t tell the difference between a coffee cup and a donut, and there’s some truth to that. It’s not that they can’t see a difference, but that they look past the difference to see the core similarity: both are solid objects punctured with a single hole. Topology as a formal area of mathematics is fairly recent (early 20th century). Topology’s roots go much further back, though, through the streets of Königsberg in the 1700s and to the geometry of the ancient Greeks.

Königsberg bridge problem
There’s a famous puzzle that originated in  Königsberg, Prussia in the 1700s (Königsberg is now Kaliningrad, Russia). The puzzle didn’t originate among mathematicians—but my understanding is that it’s mainly mathematicians that think about the puzzle now. Back then, there were seven bridges crossing the river Preger.

The Bridges of Königsberg (illustration by Leonard Euler, 1736).

The puzzle is this: Is it possible to cross each one of the seven bridges exactly once? (Go on, try it!) In his description of the problem and its solution, Euler said “it neither required the determination of quantities, nor did calculation with quantities help towards its solution.” He was interested in solving this superficially trivial problem because he couldn’t see a way for algebra, counting, or geometry to solve it. This goes against most people’s conception of mathematics—can it really be a math problem if you don’t fill a chalkboard with calculations?

The fact that no one yet had found a way to cross all the bridges without a repeat did not prove that it could not be done. To do that, and thus solve the problem for good, Euler had the insight to try and reduce the problem to its core. Reframing the Königsberg Bridges problem (elements of image from Wikimedia Commons, composited graphic by Daniel Watkins)
Knowing the layout of the city and all of its streets is irrelevant, so we can simplify to a map of just bridges. But even knowing that there is a river and land doesn’t really matter. All we really need is to know is represented in the network on the right (what mathematicians today call a graph). Euler’s solution was this: “If there are more than two regions with an odd number of bridges leading into them, then it can safely be stated that there is no such crossing.” It didn’t matter where the bridges were, it just mattered how many of the possible paths led to each landmass.

With collaborators at a summer research workshop on graph theory. Photo copyright American Mathematical Society

Being a mathematician, Euler wasn’t satisfied just stating a solution to the Königsberg problem. He went further, and generalized: he came up with rules and a solution that would work for any city with any number of bridges. All you have to do is look at the crossings, and note whether there’s an odd number of ways to get there, or an even number of ways. Euler’s method was developed by later mathematicians into graph theory, a branch of mathematics focusing on sets of points and the paths connecting them. Graph theory has a reputation for having many problems that are simple to state, but incredibly difficult to solve conclusively. In this sense, graph theory has a lot in common with geometric toy blocks.

Platonic solids
Charles has a set of magnetic toys in familiar shapes: triangles, squares, pentagons. These shapes are known as regular polygons, which just means that they are shapes composed of straight lines, each of which has the same length. Playing with these, one can hardly help but to arrange them into three-dimensional shapes. Playing with the triangles, you can quickly form a triangular pyramid: a tetrahedron. With six squares, a cube. With eight triangles, an octahedron. And with twelve pentagons, a dodecahedron. Surprisingly, there are only five shapes that can be made this way! Why is this the case? And must this always be the case?

The Platonic Solids: Tetrahedron, Cube, Octahedron, Dodecahedron, Icosahedron. Image copyright Daniel Watkins.

You might notice some other interesting things about these shapes. If you turn a cube while holding the middle of a side, you will see that it looks the same after each turn. It has rotational symmetry. Each of these shapes has multiple axis of symmetry. They can be rotated holding them in different ways and still show symmetry.

As a mathematician, Charles thinks about ways to generalize these ideas. We know that the five Platonic shapes are the only solids that can be formed from regular polygons, but what shapes could be formed if you used slightly different definitions? What if, for example, you used arcs of a circle to form the lines? What can we say about different kinds of surfaces? These shapes are defined on flat planes, like a piece of paper, but we know of lots of other surfaces, like the world we live on, that aren’t perfectly flat.  What kind of symmetry do polygons in these geometries show? “Specifically, I wanted to know all the ways that such surfaces can be rotated a given number of times. I generalized previous research on counting symmetries and discovered a formula describing the number of these rotational symmetries,” Charles said.

A topological representation of a four-holed surface with a twelve-fold rotational symmetry (blue arrows indicate which edges are to be glued to make the surface. Graphic copyright Charles Camacho

Tune in to KBVR Corvallis 88.7 FM on Sunday March, 10 at 7 PM to hear more about Charles’s research, his inspirations, and his path to research in mathematics. Stream the show live or catch this episode as a podcast.

Treating the Cancer Treatment: an Investigation into a Chemotherapy drug’s Toxic Product

One of the most difficult hurdles in cancer treatment development is designing a drug that can distinguish between a person’s healthy cells and cancer cells. Cancerous cells take advantage of the body’s already present machinery and biochemical processes, so when we target these processes to kill cancer cells, normal, healthy cells are also destroyed directly or through downstream effects of the drug. The trick to cancer treatment then is to design a drug that kills cancer cells faster than it harms healthy cells. To this end, efforts are being made to understand the finer details that differentiate the anti-cancer effects of a drug from its harmful effects on the individual. This is where the research of Dan Breysse comes in.

Dan a third-year master’s student working with Dr. Gary Merrill in the department of Biochemistry and Biophysics. Dan’s research focuses on a common chemotherapy drug, doxorubicin. Doxorubicin has been researched and prescribed for about 40 years and has been used as a template over the years for many other new drug derivatives. This ubiquitous drug can treat many types of cancer but the amount that can be administered is limited by its toxic effect on the individual. Nicknamed “the red death,” doxorubicin is digested and ultimately converted to doxorubicinol, which in high doses can cause severe and fatal heart problems. However, hope lies in the knowledge that doxorubicinol generation is not related to the drug’s ability to kill cancer cells. These mechanisms appear to be separate, meaning that there is potential to prevent the heart problems, while keeping the anti-cancer process active.

Cancer cells replicate and build more cellular machinery at a much faster rate than the majority of healthy cells. Doxorubicin is more toxic to fast-replicating cancer cells because its mechanism involves attacking the cells at the DNA level. Dividing cells need to copy DNA, so this aspect of doxorubicin harms dividing cells faster than non-dividing cells. It is common for chemotherapy drugs to target processes more detrimental to rapidly dividing cells which is why hair loss is often associated with cancer treatment.

Separately, doxorubicin’s heart toxicity appears to be regulated at the protein level rather than at the DNA level. Doxorubicin is converted into doxorubicinol by an unknown enzyme or group of enzymes. Enzymes are specialized proteins in the cell that help speed up reactions, and if this enzyme is blocked, the reaction won’t occur. For example, an enzyme called “lactase” is used to break down the sugar lactose, found in milk. Lactose intolerance originates from a deficiency in the lactase enzyme. During his time at OSU, Dan has been working to find the enzyme or enzymes turning doxorubicin into doxorubicinol and to understand this chemical reaction more clearly. Past research has identified several potential enzymes, one of which being Carbonyl reductase 1 (CBR1).

Doxorubicin is converted to doxorubicinol with the addition of a single hydrogen atom.

While at OSU, Dan has ruled out other potential enzymes but has shown that when CBR1 is removed, generation of doxorubicinol is decreased but not completely eliminated, suggesting that it is one of several enzymes involved. In the lab, Dan extracts CBR1 from mouse livers, and measures its ability to produce doxorubicinol by measuring the amount of energy source consumed to carry out the process. To extract and study CBR1, Dan uses a process called “immunoclearing,” which takes advantage of the mammal’s natural immune system. Rabbits are essentially vaccinated with the enzyme of interest, in this case, with CBR1. The rabbit’s immune system recognizes that something foreign has been injected and the system creates CBR1-specific antibodies which can recognize and bind to CBR1. These antibodies are collected from the rabbits and are then used by Dan and other researchers to bind to and purify CBR1 from several fragments of mouse livers.

Prior to his time at OSU, Dan obtained a B.S. in Physics with a concentration in Biophysics from James Madison University where he also played the French horn. Realizing he loved to learn about the biological sector of science but not wanting to completely abandon physics, Dan applied to master’s programs specific to biophysics. Ultimately, Dan hopes to go to medical school. During his time at OSU, he has balanced studying for the MCAT, teaching responsibilities, course loads, research, applying to medical schools, and still finds time to play music and occasionally sing a karaoke song or two.

To hear more about Dan’s research, tune in Sunday, December 16th 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!

Infection Interruption: Identifying Compounds that Disrupt HIV

Know the enemy

Comparing microbial extracts with Dr. Sandra Loesgen.

The Human Immunodeficiency Virus, or HIV, is the virus that leads to Acquired Immunodeficiency Syndrome (AIDS). Most of our listeners have likely heard about HIV/AIDS because it has been reported in the news since the 1980s, but our listeners might not be familiar with the virus’s biology and treatments that target the virus.

  • HIV follows an infection cycle with these main stages:
    • Attachment – the virus binds to a host cell
    • Fusion – the viral wall fuses with the membrane of the host cell and genetic material from the virus enters the host cell
    • Reverse transcription – RNA from the virus is converted into DNA via viral enzymes
    • Integration – viral DNA joins the genome of the host cell
    • Reproduction – the viral DNA hijacks the host cell activity to produce more viruses and the cycle continues
  • Drug treatments target different stages in the HIV infection cycle to slow down infection
  • However, HIV has adapted to allow mistakes to occur during the reverse transcription stage such that spontaneous mutations change the virus within the host individual, and the virus becomes tolerant to drug treatments over time.

Faulty Machinery

Due to the highly mutable nature of HIV, a constant supply of new drug treatments are necessary to fend off resistance and treat infection. Our guest this week on Inspiration Dissemination, Ross Overacker a PhD candidate in Organic Chemistry, is screening a library of natural and synthetic compounds for their antiviral activity and effectiveness at disrupting HIV. Ross works in a Natural Products Lab under the direction of Dr. Sandra Loesgen. There, Ross and his lab mates (some of whom were on the show recently [1] [2]) test libraries of compounds they have extracted from fungi and bacteria for a range of therapeutic applications. Ross is currently completing his analysis of a synthetic compound that shows promise for interrupting the HIV infection cycle.

“Uncle Ross” giving a tour of the lab stopping to show off the liquid nitrogen.

Working in Lab with liquid nitrogen.

 

 

 

 

 

 

 

Havin’ a blast

Chemistry Club at Washington State University (WSU) initially turned Ross onto chemistry. The club participated in education outreach by presenting chemistry demonstrations at local high schools and club events. Ross and other students would demonstrate exciting chemistry demos such as filling hydrogen balloons with salt compounds resulting in colorful explosions piquing the interest of students and community members alike. Ross originally made a name in

Collecting Winter Chanterelles in the Pacific Northwest.

WSU’s chemistry club, eventually becoming the president, by showing off a “flaming snowball” and tossing it from hand to hand—don’t worry he will explain this on air. For Ross, chemistry is a complicated puzzle that once you work out, all of the pieces fall into place. After a few undergraduate research projects, Ross decided that he wanted to continue research by pursing a PhD in Organic Chemistry at Oregon State University.

 

 

Tune in this Sunday October 7th at 7 PM to hear from Ross about his research and path to graduate school. Not a local listener? Stream the show live or catch this episode on our podcast.

The Mold That Keeps On Giving

All around us, plants, fungi, and bacteria are waging chemical warfare against one another to deter grazing, prevent against infection, or reduce the viability of competitor species. Us humans benefit from this. We use many of these compounds, called secondary metabolites, as antibiotics, medicines, painkillers, toxins, pigments, food additives, and more. We are nowhere close to finding all of these potentially useful compounds, particularly in marine environments where organisms can make very different types of chemicals. Could something as ordinary as a fungus from the sea provide us with the next big cancer breakthrough?

Paige Mandelare with one of the many marine bacteria she works with

Paige Mandelare thinks so. As a fourth-year PhD student working for Dr. Sandra Loesgen in OSU’s Chemistry department, she has extracted and characterized a class of secondary metabolites from a marine fungus, Aspergillus alliaceus, isolated from the tissues of an algae in the Mediterranean Sea. After growing the fungus in the laboratory and preparing an extract from it, she tested the extract on colon cancer and melanoma cell lines. It turned out to be cytotoxic to these cancer cells. Further purification of this mixture revealed three very similar forms of these new compounds they called allianthrones. Once Paige and her research group narrowed down their structures, they published their findings in the Journal of Natural Products.

Next, she grew the fungus on a different salt media, replacing bromine for chlorine. This forced the fungus to produce brominated allianthrones, which have a slightly different activity than the original chlorinated ones. Her lab then sent two of these compounds to the National Cancer Institute, where they were tested on 60 cell lines and found to work most effectively on breast cancers.

The recent publication of Paige in her story of the allianthrones from this marine-derived fungus, Aspergillus alliaceus.Like many organisms that produce them, this wonder mold only makes secondary metabolites when it has to. By stressing it with several different types of media in the lab, Paige is using a technique called metabolomics to see what other useful compounds it could produce. This will also give insight into how the fungus can be engineered to produce particular compounds of interest.

A native Rhode Islander who moved to Florida at the age of ten, Paige has always been fascinated with the ocean and as a child dreamed of becoming a marine biologist and working with marine mammals. She studied biology with a pre-med track as an undergraduate at the University of North Florida before becoming fascinated with chemistry. Not only did this allow her to better appreciate her father’s chemistry PhD better, she joined a natural products research lab where she first learned to conduct fungal chemical assays. Instead of placing her on a pre-med career path, her mentors in the UNF Chemistry department fostered her interest in natural products and quickly put her in touch with Dr. Loesgen here at OSU.

Paige enjoying her time at the Oregon Coast, when she is not in the research lab

After finishing her PhD, Paige hopes to move back east to pursue a career in industry at a pharmaceutical company or startup. In the meantime, when she’s not discovering anticancer agents from marine fungi, she participates in a master swimming class for OSU faculty, trains for triathlons, and is an avid baker.

To hear more about Paige and her research, tune in to KBVR Corvallis 88.7 FM this Sunday July 15th at 7 pm. You can also stream the live interview at kbvr.com/listen, or find it on our podcast next week on Apple Podcasts.

When Fungus is Puzzling: A Glimpse into Natural Products Research

Ninety years ago, a fungal natural product was discovered that rocked the world of medicine: penicillin. Penicillin is still used today, but in the past ninety years, drug and chemical resistance have become a hot topic of concern not only in medicine, but also in agriculture. We are in desperate need of new chemical motifs for use in a wide range of biological applications. One way to find these new compounds is through natural products chemistry. Over 50% of drugs approved in the last ~30 years have been impacted by natural products research, being directly sourced from natural products or inspired by them.

Picture a flask full of microbe juice containing a complex mixture of hundreds or thousands of chemical compounds. Most of these chemicals are not useful to humans – in fact, useful compounds are exceedingly rare. Discovering new natural products, identifying their function, and isolating them from a complex mixture of other chemicals is like solving a puzzle. Donovon Adpressa, a 5th year PhD candidate in Chemistry working in the Sandra Loesgen lab, fortunately loves to solve puzzles.

Nuclear Magnetic Resonance (NMR): an instrument used to elucidate the structure of compounds.

Donovon’s thesis research involves isolating novel compounds from fungi. Novel compounds are identified using a combination of separation and analytical chemistry techniques. Experimentally, fungi can be manipulated into producing compounds they wouldn’t normally produce by altering what they’re fed. Fungi exposed to different treatments are split into groups and compared, to assess what kind of differences are occurring. By knocking out certain genes and analyzing their expression, it’s possible to determine how the compound was made. Once a new structure has been identified and isolated, Donovon moves on to another puzzle: does the structure have bioactivity, and in what setting would it be useful?

Donovon’s interest in chemistry sparked in community college. While planning to study Anthropology, he took a required chemistry course. Not only did he ace it, but he loved the material. The class featured a one-week lecture on organic chemistry and he thought, ‘I’m going to be an organic chemist.’ However, there were no research opportunities at the community college level, and he knew he would need research experience to continue in chemistry.

At Eastern Washington University, Donovon delved into undergraduate research, and got to work on a few different projects combining elements of medicinal and materials chemistry. While still an undergrad, Donovon had the opportunity to present his research at OSU, which provided an opportunity to meet faculty and see Corvallis. It all felt right and fell into place here at OSU.

As a lover of nature and hiking in the pacific northwest, Donovon has always had a soft spot for mycology. It was serendipitous that he ended up in a natural products lab doing exactly what interested him. Donovon’s next step is to work in the pharmaceutical industry, where he will get to solve puzzles for a living!

Tune in at 7pm on Sunday, March 18th to hear more about Donovon’s research and journey through graduate school. Not a local listener? Stream the show live.

Aquatic Invertebrates: Why You Should Give a Dam

Rivers are ecosystems that attract and maintain a diversity of organisms. Fish, birds, mammals, plants, and invertebrates live in and around rivers. Have you considered what services these groups of organisms provide to the river ecosystem? For example, river invertebrates provide numerous ecosystem services:

Dragonfly larvae caught in in the waters of a small stream flowing into the Grand Canyon.

  • Insects and mussels improve water quality by fixing nutrients, such as those from agricultural runoff.
  • River invertebrates are food resources for fish, bats, birds, and other terrestrial organisms.
  • Grazing insects can control and/or stimulate algal growth.
  • Mussels can help to stabilize the bed of the river.

High school students are the best helpers for sampling aquatic insects!

And the list continues. These invertebrates have adapted to the native conditions of their river ecosystem, and major disturbances, such as a change in the flow of a river from a dam, can change the community of organisms downstream. If dams decrease the diversity of invertebrates downstream, then they may also decrease the diversity of ecosystem services offered by the invertebrate community.

Our guest this week, Erin Abernethy PhD candidate from the department of Integrative Biology, is investigating the community structure (or the number of species and the number of individuals of each species) of freshwater aquatic invertebrates downstream of dams. Specifically, Erin wants to know if invertebrate communities near dams of the Colorado River are different than those downstream, and which factors of dams of the Southwest US affect invertebrate communities.

Getting to field sites in the Grand Canyon is easiest by raft! It’s a pretty float, too!

Erin’s dissertation also has a component of population genetics, which examines the connectivity of populations of mayflies,populations of caddisflies, and populations of water striders. The outcomes of Erin’s research could inform policy around dam operation and the maintenance of aquatic invertebrate communities near dams.

“One must dress for sampling success in the Grand Canyon!” said this week’s guest, Erin Abernethy, who is pictured here.

Growing up, Erin participated in many outdoor activities with her parents, who are biologists. She became interested in how dams effect ecology, specifically fresh water mussels, doing undergraduate research at Appalachian State University. After undergrad, Erin completed a Master’s in Ecology from University of Georgia. She was investigating the foraging behavior of animals in Hawaii. This involved depositing animal carcasses and monitoring foraging visitors. Check out Erin’s blog for photos of these animals foraging at night! Erin decided to keep going in academia after being awarded a Graduate Research Fellowship, which landed her a position in David Lytle’s lab here at Oregon State. After she completes her PhD, Erin is interested in working for an agency or a nonprofit as an expert in freshwater ecology and the maintenance of biodiversity in freshwater ecosystems.

 

Tune in at 7 pm this Sunday February, 25 to hear more about Erin’s research and journey to graduate school. Not a local listener? Stream the show live.

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.

Motor proteins—and people—can change directionality

It took three years of adventures after college—including stints as a ski instructor, barista and a commercial chemist—before Andrew Popchock knew that he wanted to return to the lab to pursue a PhD at OSU’s Department of Biochemistry and Biophysics.

Two microtubules slide across each other by the walking of motor proteins sandwiched between them

Andrew’s research takes place at Dr. Weihong Qiu’s Single-Molecule Biophysics Laboratory and focuses on kinesin-14s—motor proteins found in eukaryotic cells. These motor proteins in cells travel along microtubules to create and maintain the mitotic spindle, which are macromolecular structures that are responsible for chromosome segregation during cell division.

By using an imaging technique called TIRF microscopy, a team of researchers from Dr. Qiu’s lab discovered that a kinesin-14 found in fungus cells called KlpA can change direction along its cytoskeleton tracks. KlpA is the first motor protein of its kind that researchers have discovered that demonstrates this type of bidirectional movement. The results of their study were recently published in Nature Communications.

Total Internal Reflection Fluorscence (TIRF) microscopy image of two microtubules sliding across each other

The motor protein that Andrew studies could be important in helping researchers understand cancer growth. This could have implications for drug treatment therapy, potentially guiding the creation of motor protein-based molecular devices for more controlled drug delivery in cancer treatments.

 

Andrew on the Oregon Coast

Growing up, Andrew was interested in physics and biology, but it wasn’t until he worked in a lab under the direction of a graduate student at Washington State University that he began to consider graduate studies. While working as a chemist in Idaho, he realized that he quickly reached the limit of his creative capacity and that returning to a laboratory as a graduate student at OSU would help him continue to develop his skills as a researcher.

To learn more about Andrew’s research and his path to graduate school, tune in to hear our conversation on Sunday, May 14th at 7:00 pm on 88.7 FM KBVR Corvallis or listen live online.

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.

Just keep swimming or don’t! Curiously following Zebrafish

People often think of science as focusing on very specific questions or rigorous hypothesis testing. However, some of the most exciting advancements were the result of general curiosity of seemingly disparate ideas, and a sprinkle of creativity. For example, the beginnings of how electricity was discovered started by poking frog legs with different types of metals. The modern zero-calorie sugar (saccharin) was discovered by playing creative-chef with coal tar products in the 1870’s when the chemist accidentally tasted his chemical concoction.

Sarah Alto

Our guest this week is using young zebrafish to investigate how environmental factors affect their behavior, and whether behavioral changes can be attributed to specific brain activity. Why zebrafish you may ask? They are a model organisms or they tend to be well studied, relatively easy to breed and maintain in lab settings, and as vertebrates, they share some characteristics with humans. The more we know about zebrafish, the more clues we may have into our own neurobiology. Sarah Alto is exposing these model organisms to different levels of oxygen and carbon dioxide stress. She monitors their swimming with infrared cameras and examines their brain to get an idea of how they respond to stress physically and mentally. This is no easy task because the young zebrafish are only a few millimeters long!

Oxygen, nitrogen, and carbon dioxide gas is bubbled into the tank holding the larvae.
The entire set-up is enclosed in a light-tight box so the larval behavior is more connected to the environment changes and not human interaction.

Curious Sarah is asking: Are low oxygen or high carbon dioxide concentrations changing the swimming behavior of zebrafish? What happens in the brain of a zebrafish when it experiences environmental stress? What can we learn about how environmental factors shape the brain’s connections and influence behavior? Sarah has a long road ahead of her, one that is unpaved with many junctions, but she is performing the exploratory work that may inspire future investigations into the affects of stress on the brain.

The second part of Sarah’s research will be investigating the neural activity when the larvae are exposed to the same gas concentrations as studied in the behavioral experiments.
Image courtesy of Ahrens et al. (2013)

Prior to Sara’s interest in biology, she was always drawn to art as an escape and a method of expression. When choosing which colleges to attend, she didn’t want to choose between art and science. So she chose to pursue both! Sarah enrolled at UC Berkeley as double major including Molecular and Cellular Biology, as well as Practice of Art. The San Francisco art scene was highly accessible, and Berkeley is a top-flight university for the sciences. Needless to say she flourished in this environment and her love of science grew but her love of art continues to this day. Finishing her schooling she began working at UC San Francisco, a premier medical research university, investigating the role of stem cells in facial development to for possible medical treatments for facial reconstruction. She was involved in a variety of projects but her gut feeling led her to continue schooling at Oregon State.

Sarah is now a part of Dr. James Strother’s lab in the College of Science within the department of Integrative Biology focusing the behavioral neurobiology of zebrafish. Be sure to tune in Sunday April 9th at 7PM PST on 88.7FM or listen live.