Category Archives: College of Science

Special Series Covid-19: Finding Clarity and Calm During a Global Pandemic

Amidst the challenges of a global pandemic, the Inspiration Dissemination podcast will strive to be an avenue of human connection and inspiration during a more isolated time. This week, we sit down with Joaquin Rodriquez for the first podcast of a special series covering the COVID-10 outbreak and its impact on the research and lives of our OSU community.

Joaquin Rodriguez; Undergraduate student and researcher in the Barbar lab at Oregon State University.

Joaquin is an undergraduate (soon to be graduate) researcher in the Barbar lab at OSU studying how viruses hijack their hosts. Joaquin’s research allows him to view the coronavirus from a biological perspective that yields him clarity and patience.

Although his studies and research are conducted at Oregon State University, Joaquin calls Lima, Peru home. During an unprecedented time where students are leaving campus to be home with their families, travel restrictions render Joaquin unable to leave Corvallis. Despite the challenges Joaquin faces, he emanates a sense of calm and understanding of the coronavirus and shares with us his experience.

Joaquin explains how misinformation is easy to spread and clear answers are hard to discern during times of fear and uncertainty. Even for those that may have the scientific literacy to understand what a virus is, there can be a great difficulty in comprehending just how a virus works within our bodies. In simplified terms, a virus can be thought of as a piece of genetic material (usually RNA) encapsulated by a protein. Debate on whether or not a virus can even be considered a living thing stems from the fact that viruses themselves do not code for the biological machinery needed for replication, but rather use their host as a means to thrive and reproduce. Upon entering the body, the coronavirus binds to respiratory cells at sites called receptors. Receptors are like doors that only viruses have the keys to, and once binded, they are able to enter the cell and replicate before finally causing the respiratory cell to die. This particular coronavirus eventually causes the disease COVID-19.

Simplified Viral Structure– By domdomegg [CC BY 4.0 (https://creativecommons.org/licenses/by/4.0)], from Wikimedia Commons

The death of respiratory cells as the virus multiplies is inarguably harmful to the body, however, the symptoms we experience from COVID-19 are actually an expression of our immune system response rather than the virus itself. This in part explains why some of those infected by the virus appear to be minimally impacted, while others may develop flu-like symptoms or pneumonia. In fact, the range and lack of predictability of symptoms contribute to the high rate of transmission and success of the virus.

There are many evolutionary trade-offs involved in the overall success of a virus. Aggressive replication within a host may cause the virus to be too deadly and thus lower transmissibility between hosts; the virus is unlikely to become widespread.  For this reason, the deadly virus causing Ebola is not likely to become a global pandemic, whereas the new coronavirus is impacting countries around the world. 

Viral success and transmissibility also relies on mutation rate. At first glance it may seem intuitive that a high rate of mutation would be evolutionarily advantageous. Afterall, a small mutation in the genome of the coronavirus lended its ability to jump hosts from bat to human. However, not all mutations are advantageous. Mutations are random, and the potential of a mutation to be detrimental to the virus’s ability to infect and replicate is high. A high mutation rate is a risk to the success of a virus, but a low mutation rate would yield a stagnation allowing for hosts to more easily adapt immunity. 

Joaquin explains that the coronavirus is successful because it has a relatively low mutation rate compared to other RNA viruses, as well as a high transmissibility owing to a relatively low rate of host death, varying host symptoms, and the utilization of airborne avenues of transmission. He tells us that through a global research effort we are continuously learning about the biology of the coronavirus and using this knowledge to explore treatment options and vaccines. 

While many research labs around the world, including Joaquin’s lab at OSU, are shifting their efforts to contribute to the study of the coronavirus, many researcher’s work has been put on hold. Joaquin now finds himself with extra time to connect with family in Lima or take trips to the coast where he finds comfort surfing. He urges us to stay informed, mindful, and calm, and to find that thing that brings up happiness as we all experience an unusual time united in our isolation.

If you are interested in hearing the full interview with Joaquin, want to keep up with new episodes and our special Covid-19 series, or want to check out past interviews, you can find us on iTunes under Inspiration Dissemination.

Finding a place in policy: where do the scientists fit in?

Somewhere, in a local government meeting, an idea is proposed, a policy brief is written, some voting occurs, paperwork is pushed around, money is allocated, and a new highway is built.

In the same region, some bighorn sheep are off trekking in search of their favorite grasses to eat. They come upon a road they can’t cross that wasn’t there before. The sheep stay put and eat the same old grass they were already eating.

Bighorn sheep iImage from Defenders of Wildlife.

When policymakers decided to build this road, it’s unclear whether they considered the consequences of this type of habitat fragmentation on the tiny ecosystems of bacteria that live inside of each bighorn sheep. More importantly, whether they knew their decision might lead to unforeseen consequences for bighorn population health.

We take for granted how intertwined policy and science really are.

Claire Couch is a 5th year PhD candidate in the department of Integrative Biology, studying wildlife disease ecology, but she’s also the president of a new Science & Policy Club at Oregon State University.

Advised by Anna Jolles in the College of Veterinary Medicine, Claire studies the bacteria that live in the guts of large animals like African buffalo, rocky mountain elk, and bighorn sheep. She’s interested in how the gut microbiome can contribute to disease resistance, but separate from her PhD research, she’s interested in how policy can be informed by science, and how science can be impacted by policy.

Claire says she’s always been interested in ecosystem health and fascinated by ecosystem dynamics between big scale (a region the sheep lives in) and small scale (the bacteria living in the gut) ecosystems. Through her research, she’s been exposed to diverse conservation issues for different wildlife species. For example, management and policy shapes where wildlife can reside, and where they are determines the factors that shape the gut microbiome. It became apparent to Claire that most scientists are not typically trained to understand and partake in policy, including herself, even though is it’s critical to all of our research pursuits.

(Left to right) Jane Lubchenco, Karen McLeod and Steve Lundeberg at OSU science policy panel discussion.

Claire started looking for ways to learn more and to become more engaged in science policy, but wasn’t finding exactly what she was looking for. OSU has some science-policy courses and clubs, but they are typically very specific to one type of science. So although she didn’t feel qualified to take the lead on this, she created what she was looking for: a science policy space that is more inclusive and general, with an emphasis on career development and general policy literacy.

In the first year since this group started, they’ve already packed in several activities including:  meetings with OSU faculty who are closely tied to policy, a seminar about how to communicate about controversial topics, a panel talk about how scientists can communicate with the press, a talk from a government agency research organization scientist, and a meeting with House Rep. Peter DeFazio. Finally, the group has an open-source data panel coming up.

House Rep Peter Defazio speaking with OSU Science Policy club. Image from gazettetimes

Claire wants to help scientists make their work relevant, but she hasn’t been doing it all alone. There are currently a few other club officers, and as Claire writes her dissertation, she’s looking to pass on club leadership. In the future, she hopes to see the club become more engaged with the non-OSU community members around us, host bigger events in collaboration with other groups on campus, and start up a mentoring program in which club members would be mentored by policy professionals.

To hear more about this policy club and Claire’s research and future plans, tune in to KBVR 88.7 FM or stream online March 1, 2020 at 7 P.M.

Proteins run the show (except when they unfold and cause cataracts)

Your eye lenses host one of the highest concentrated proteins in your entire body. The protein under investigation is called crystallin and the investigator is called Heather Forsythe.

Heather is a 4th year PhD candidate working with Dr. Elisar Barbar in the Department of Biochemistry and Biophysics. The Barbar lab conducts work in structural biology and biophysics. Specifically, they are trying to understand molecular processes that dictate protein networks involving disordered proteins and disordered protein regions. To do this work, the lab uses a technique called nuclear magnetic resonance (NMR). NMR is essentially the same technology as an MRI, the big difference being the scale at which these two technologies measure. MRIs are for big things (like a human body) whereas NMR instruments are for tiny things (like the bonds between amino acids which are the building blocks of proteins). Heather employed OSU’s NMR facility (which has an 800 megahertz magnet and is on the higher end of the NMR magnetic field strength range) to investigate what the eye lens protein crystallin has to do with cataracts.

Your eye completely forms before birth, and the lens of the eye that helps us see is made of a protein called crystallin. This protein is essential to the structure and function of the eye, but it cannot be regenerated by the body so whatever you have at birth is all you will ever have. However, in the eye lens of someone affected by cataracts, the crystallin proteins become unfolded and then aggregate together. They stack on top of each other in a way that they are not supposed to. A person with cataracts will suffer from blurry vision, almost like you’re looking through a frosty or fogged-up window. While the surgery to fix cataracts (which basically takes out the old lens and puts in a new, artificial one) is pretty straight-forward and not very invasive, it isn’t easily accessible or affordable to a lot of people all over the world. Cataracts is attributed to causing ~50% of blindness worldwide, likely due to the fact that not everyone is able to take advantage of the simple surgery to fix it. Therefore, understanding the molecular, atomic basis of how cataracts happens could result in more accessible treatments (say a type of eye drop) for it worldwide.

This is where Heather comes in. There are different types of crystallin proteins and Heather zeroed in on one of them – gamma-S. Gamma-S is one of the most highly conserved proteins (meaning it hasn’t changed much over a long time) among all mammals, which tells us that it’s super important for it to remain just the way it is. Gamma-S makes up the eye lens by stacking on top of itself, making a brick wall of sorts ensuring that the eye lens retains its structure. However, research prior to Heather’s found that with increased age there is an increase in a modification called deamidation, which occurs in the unstructured loops of the gamma-S protein. Deamidation is a pretty minor change and is common in proteins all over the body, however in the eye lens if too much of it happens it no longer is a minor issue since it starts to disrupt the structure and protein-protein interactions of the eye lens. Heather’s collaborators at Oregon Health Sciences University found that there are two sites on the gamma-S protein (sites 14 and 76) where these deamidation events increase the most in cataracts-stricken eyes. It’s been known for a while that this deamidation is associated with cataracts however we never knew why it is associated with cataract formation because the changes caused by this modification were seemingly minor. This is how the Barbar Lab, and Heather specifically, became connected to this work since they specialize in studying unstructured proteins and protein regions, such as the loops present in gamma-S.

An example of an “1H(x-axis) 15N(y-axis) HSQC” spectra, aka, the fingerprint of a protein. This spectra is of WT gamma-S crystallin.

These deamidation changes are mimicked in the lab by creating two different mutants of the gamma-S protein’s DNA. Heather then compared the two mutants with the normal DNA by putting them through a series of experiments using the trusty NMR. The NMR is basically a large magnet that can make use of the magnetic fields around an atom’s nucleus to determine protein structure and motions. When Heather puts a protein sample into the NMR, the spins of the atomic nuclei will either align with or against the magnetic field of the NMR’s magnet. The NMR spits out spectra, which look like a square with lots of polka dots. This is essentially the fingerprint of the protein, unique to each one and extremely replicable. Heather can analyze this protein fingerprint since the different polka dots represent different amino acids in the gamma-s protein. Heather can compare spectra of the two mutants to the spectra of the normal protein to see whether any of the dots have moved, which would signal a change in the position of the amino acids.

After running experiments which measure protein motions at various timescales, from days to picoseconds, Heather discovered significant changes in protein dynamics when either site 14 or 76 was deamidated, however at different timescales. What this discovery means is that if both of these mutations are associated with cataracts and they are changing the same regions of the gamma-S protein, then these regions are likely central to changes resulting in cataracts. Therefore, research could be directed to target these regions to perhaps come up with solution to prevent and/or solve cataracts in a non-surgical way. The results of Heather’s study were recently published in Biochemistry.

Heather with her dog Piper.

Heather is from Arkansas where she completed her high school and undergraduate education. Living in a single-parent, non-academic home at this time, it took Heather a long time to figure out how to navigate the scientific and college-application scene, as well as even coming to the realization that science was something she was good at and could pursue. Despite receiving scholarships for college, she still had to work multiple jobs while in high school and college to have enough money for car-payments and gas to get to extra-curricular activities and volunteer jobs in the science field; things critical for graduate school applications. As a result, Heather is a strong advocate for inclusivity, striving to make things like science and college in general more accessible to low-income and diverse students. Heather’s decision to leave Arkansas and come to the PNW was inspired by advice she received from her undergraduate advisor who told her “not to go anywhere where you wouldn’t want to live. You will learn to love research, whatever it ends up being, but if you live in an environment that you don’t find fulfilling, then you are going to suffocate.”. Following this advice has lead Heather to where she is now – the senior in her lab where she has become a mentor to undergraduates, makes Twitter-famous Tik Tok videos (see below), goes on adventures with her dog Piper, and publishes cutting edge structural biology research.

Heather and her undergraduate mentee performing The Git Up in the lab.

To learn more you can check out the Barbar Lab website and Twitter page.

To hear more about Heather’s research, tune in on Sunday, September 29th 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!

The bacteria living inside us and what they have to say about autism

Trillions of bacterial cells are living within us and they’re controlling your brain activity.

Grace Deitzler is a 2nd year PhD student in microbiology working in Dr. Maude David’s lab on the gut-microbiome and its relation to autism spectrum disorder.

The gut-microbiome is the total population of bacteria living within our digestive tract. These bacteria are critical for digestive health, but also for our immune system and mental health. For example, we harbor bacteria capable of digesting plant fibres we otherwise could not digest. And if you’ve been told that probiotics are good for you, that’s because probiotics can change the gut microbiome in a positive way, allowing for increased bacterial diversity associate with improved health. These bacteria communicate with each other through chemical signaling but also communicate with us. Tryptophan, for example, is an amino acid produced through bacteria metabolism and is a precursor for serotonin, a brain-signaling chemical which causes feelings of happiness.

When the gut communicates with the brain, we call this, the “gut-brain axis”. Grace’s work narrows in on the gut-brain axis and more specifically, how one bacterial species in particular impacts autism spectrum disorder. To further complicate things, the gut-microbiome helps to regulate estrogen levels, and we also know that autism is a disorder found primarily in biological males. Which leads Grace to one of her biggest questions: are the bacteria involved in endocrine system regulation in women, also that responsible for this variation we see. Grace uses a mouse model to elucidate underlying mechanisms at play.

Step one is to feed the mice bacteria that have been found in elevated amounts in people with autism spectrum disorder than in neurotypical peers. These bacteria will colonize in the gut, and mice will go through several behavioral tests to determine if they are exhibiting more behaviors associated with autism. Grace performs three types of tests with the mice: one to test inclination to form repetitive behaviors, one to test anxiety, and one to test social behaviors. One test is a marble-burying test, in which a mouse more inclined to form repetitive behaviors will bury more marbles.

After behavioral testing is complete, the mice are sacrificed and different regions of the gut are taken to look for presence of bacterium. Tissues taken from the mice are used to look for transcriptional markers. The transcriptome is collected for both the mouse and the bacteria present, or the sum total of all genes that are read and converted to RNA. RNA are able to be isolated and sequenced using distinctive markers such as a “poly-A tail”. After this data is collected, Grace can finally move to the computational side of her work which involves combining biological and biochemical data with her behavioral studies.

In addition to her work on autism spectrum disorder, Grace also has a side project working in a honey bee lab, looking at the gut microbiome of honey bees in response to probiotics on the market for beekeepers. But Grace is one very busy bee herself because in addition to her lab work, she’s also involved with an art-science club called “seminarium”. The club is filled with scientists interested in art and artists interested in science. Grace is a painter primarily but is also working on ink illustration. The focus of this group is that art and science are complimentary, not at odds. The group has produced some collaborative projects, including a performance for a lab studying a parasite that effects salmon. The group put together a collage of interpretations of the parasites and had a performance in which one member played piano while someone else drew the parasite live.

Grace moved to Oregon from St. Louis Missouri. She completed her undergraduate degree in biological sciences with minors in chemistry and psychology at a small engineering college, Missouri University of Science and Technology, where she was a radio DJ! Grace first became involved in research during a summer internship in a microbiology lab at Washington University. There she studied the vaginal microbiome and how it effects pregnancy outcomes. Grace went back to this lab for the next couple summers and produced 4 publications! Ultimately, Grace graduated college early after they offered her a full time research position where she worked for a year and a half as a research tech. Through this experience, Grace came to realize that medical school was not her path, canceled her scheduled MCAT and signed up for GRE. Grace looked for schools in the PNW because she knew she wanted to live there, got an interview at OSU, loved it, and here we are!

Join us at 7 pm on Sunday, August 11th, 2019, to hear more about Grace’s research and her journey to OSU. Stream the show live on KBVR Corvallis 88.7FM or check out the episode as a podcast after a few weeks.

Micro structures and macro support

Our guest this week, Shauna Otto from the Department of Biochemistry and Biophysics, is a member of the lab of Dr. Colin Johnson. The focus of the Johnson lab is a group of proteins called ferlins. The ferlin family of proteins have many different functions, and many are involved in the fusion of vesicles to cell membranes in a process called, “exocytosis.” Another example is the protein otoferlin which fuses vesicles carrying neurotransmitters to the cell membrane of neurons in the inner ear that play a crucial role in hearing. See more about otoferlin from past guests from the Johnson lab, Murugesh Padmanarayana and Nicole Hams.

Shauna loading a sample for Cobalt-60 irradiation at the Notre Dame Radiation Laboratory.

Shauna studies dysferlin, another ferlin protein, which helps mend membrane tears in muscle cells. Mutations in the dysferlin gene lead to Muscular Dystrophy II. Through her work, Shauna has characterized portions or “domains” of the large dysferlin protein via Nuclear Magnetic Resonance (NMR). NMR is a process by which the magnetic field around the nuclei of atoms in a protein domain are excited, and by recording the magnitude of that disruption, Shauna can learn the structure of the domain. Her focus domain putatively binds other proteins that join dysferlin in a protein complex that initiates muscle cell membrane repair. However, the mechanism by which dysferlin bind repair proteins is unclear. Through her explorations with dysferlin, Shauna has found that an increase in Calcium leads to the stabilization of the dysferlin domains that might initiate repair. Right now, it is unclear if this stabilization initiates muscle cell repair, but if it does the next question is how and when such stabilization occurs.

Shauna and husband (Kris Hill) backpacking in Yosemite

Shauna’s academic journey was wrought with hardship, and we are grateful to her for being willing to share her story with us on air. Shauna started undergraduate with an interest in marine biology, but found that college is cost prohibitive. After a two year break, she went back to University of California Long Beach to major in Chemical Engineering, but finally landed on biochemistry. She had a knack for chemistry and loved solving complex puzzles in cellular biology through the lens of protein interactions and biochemical pathways. She began undergraduate research, but her work took a turn as she struggled with homelessness. Homelessness is a growing problem for college students, and has prompted bills targeting the problem of home insecurity for students in California and Washington. However, for Shauna, homelessness was not discussed among fellow students and officials when she attended school. Rather, instead of resources to alleviate her financial hardship, she was met with policy allowances such as permission to sleep in her research lab.

Shauna and her daughter in a bookshop.

Since beginning her PhD at OSU, Shauna has found support here on campus from mentors and her department who have listened and replied with support in the form of University Resources and Services to help her succeed academically, financially, and in personal wellness. Given her past, Shauna now knows the questions to ask about support when seeking the next job, and she is a resource for undergraduates and graduate students who are going through similar life experience.

Hear more about Shauna’s research and personal story this Sunday June 2, 2019 at 7 pm on KBVR Corvallis 88.7FM. Stream the show live or catch the episode as a podcast in the coming weeks.

Zebrafish sentinels: studying the effects of cadmium on biology and behavior

Cadmium exposure is on the rise

There’s a good chance you might have touched cadmium today. A heavy metal semi-conductor used in industrial manufacturing, cadmium is found in batteries and in some types of solar panels. Fertilizers and soil also contain cadmium because it is present in small levels in the Earth’s crust. The amount of cadmium in the environment is increasing because of improper disposal of cell phone batteries, contaminating groundwater and soil. This is a problem that impacts people all over the world, particularly in developing countries.

Plants take up cadmium from the soil, which is how exposure through food can occur. Leafy greens like spinach and lettuce can contain high levels of cadmium. From the soil, cadmium can leach into groundwater, contaminating the water supply. Cadmium is also found in a variety of other foods, including chocolate, grains and shellfish, as well as drinking water.

Cadmium has a long half-life, reaching decades, which means that any cadmium you are exposed to will persist in your body for a long time. Once in the body, cadmium ends up in the eyes or can displace minerals with similar chemical properties, such as zinc, copper, iron, and calcium. Displacement can cause grave effects related to the metabolism of those minerals. Cadmium accumulation in the eyes is linked to age-related macular degeneration, and for people in the military and children, elevated cadmium is linked to psychosocial and neurological disorders.

Read more about cadmium in the food supply:



Using zebrafish to study the effects of cadmium

Delia Shelton, a National Science Foundation post-doctoral fellow in the Department of Environmental and Molecular Toxicology, uses zebrafish to investigate how cadmium exposure in an individual affects the behavior of the group. Exposing a few individuals to cadmium changes how the group interacts and modifies their response to novel stimuli and environmental landmarks, such as plants. For example, poor vision in a leader might lead a group closer to predators, resulting in the group being more vulnerable to predation.

Zebrafish

As part of her post-doctoral research, Delia is asking questions about animal behavior in groups: how does a zebrafish become a leader, how do sick zebrafish influence group behavior, and what are the traits of individuals occupying different social roles? These specific questions are born from larger inquiries about what factors lead to individual animals wielding inordinately large influence on a group’s social dynamic. Can we engineer groups that are resilient to anthropogenic influences on the environment and climate change?

Zebrafish

Zebrafish are commonly used in biomedical research because they share greater than 75% similarity with the human genome. Because zebrafish are closely related to humans, we can learn about human biology by studying biological processes in zebrafish. Zebrafish act as a monitoring system for studying the effects of compounds and pollution on development. It is possible to manipulate their vision, olfactory system, level of gene expression, size, and aggression level to study the effects of pollutants, drugs, or diseases. As an added benefit, zebrafish are small and adapt easily to lab conditions. Interestingly, zebrafish are transparent, so they are great for imaging. Zebrafish have the phenomenal ability to regenerate their fins, heart and brain. What has Delia found? Zebrafish exposed to cadmium are bolder and tend to be attracted more to novel stimuli, and they have heightened aggression.

Read more about zebrafish:

ZFIN- Zebrafish Information Network – https://zfin.org/
Zebrafish International Research Center in Eugene Or – http://zebrafish.org/home/guide.php



What led Delia to study cadmium toxicity in zebrafish?

As a child, Delia was fascinated by animals and wanted to understand why they do the things they do. As an undergrad, she enjoyed research and pursued internships at Merck pharmaceutical, a zoo consortium, and Indiana University where she worked with Siamese fighting fish. She became intrigued by social behavior, social roles, and leadership. Delia studied the effects of cadmium in grad school at Indiana University, and decided to delve into this area of research further.

Delia began her post-doctoral work after she finished her PhD in 2016. She was awarded an NSF Postdoctoral Fellowship to complete a tri-institute collaboration: Oregon State University, Leibniz Institute for Freshwater Ecology and Inland Fisheries in Berlin, Germany, and University of Windsor in Windsor, Ontario. She selected the advisors she wanted to work with by visiting labs and interviewing past students. She wanted to find advisors she would work well with and who would help her to accomplish her goals. Delia also outlined specific goals heading into her post-doc about what she wanted to accomplish: publish papers, identify collaborators, expand her funding portfolio, learn about research institutes, and figure out if she wanted to stay in academia.

Research commercialization and future endeavors

During her time at OSU, Delia developed a novel assay to screen multiple aspects of vision, and saw an opportunity to explore commercialization of the assay. She was awarded a grant through the NSF Innovation Corps and has worked closely with OSU Accelerator to pursue commercialization of her assay. Delia is now wrapping up her post-doc, and in the fall, she will begin a tenure track faculty position at University of Tennessee in the Department of Psychology, where she will be directing her lab, Environmental Psychology Innovation Center (E.P.I.C) and teaching! She is actively recruiting graduate students, postdocs, and other ethnusiatic individuals to join her at EPIC.

Please join us tonight as we speak with Delia about her research and navigation of the transition from PhD student to post-doc and onwards to faculty. We will be talking to her about her experience applying for the NSF Postdoctoral Fellowship, how she selected the labs she wanted to join as a post-doc, and her experience working and traveling in India to collect zebrafish samples.

Tune in to KBVR Corvallis 88.7 FM or stream the show live on Sunday, April 7th at 7 PM. You can also listen to the episode on our podcast.

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.