Category Archives: Pharmacy

Spaghetti & Networks: Oodles of Nodes

Picture a bowl of spaghetti and meatballs. There are pristine noodles, drenched in rich tomato sauce, topped with savory meatballs. Now imagine you’re only allowed to eat just one noodle, and one meatball. You’re tasked with finding the very best, the most interesting bite out of this bowl of spaghetti. It might sound absurd, but replace spaghetti with ‘edges’ and meatballs with ‘nodes’ and you’ve got a network.

*An image of a network from Nolan’s recent publication. The lines are ‘edges’ and the dots are ‘nodes’.*

Computational biologists like our guest this week use networks to uncover meaningful relationships, or the tastiest spaghetti noodle and meatball, between biological entities.
Joining us this week is Nolan Newman, a PhD candidate in the College of Pharmacy under PI Andriy Morgun. Nolan’s research lies at the intersection of math, statistics, computer science, and biology. He’s looking at how networks, such as covariation networks, can be used to look for relationships and correlations between genes, microbes, and other factors from massive datasets which compare thousands or even of biological entities. With datasets this large and complex, it can be difficult to pare down just the important or interesting relationships – like trying to scoop a single bowl of spaghetti from a giant tray at a buffet, and then further narrowing it down to pick just one interesting noodle.

Nolan is further interested in how different statistical thresholds and variables contribute to how the networks ‘look’ when they are changed. If only noodles covered in sauce are considered ‘interesting’, then all of the sauce-less noodles are out of the running. But what if noodles are only considered ‘sauce-covered’ if they are 95% or more covered? Could you be missing out on perfectly delicious, interesting noodles by applying this constraint?

If you’re left scratching your head and a little hungry, fear not. We’ll chat about all things computational biology, networks, making meaning out of chaos, and why hearing loss prompted Nolan to begin a career in science, all on this week’s episode of Inspiration Dissemination. Catch the episode live at 7 PST at 88.7 FM or https://kbvrfm.orangemedianetwork.com/, or catch the podcast after the episode on any podcast platform.

Finding cancer with sound: the development of nanoparticles to deliver light-to-sound converting agents

“Here I am!” -Cancer

Wouldn’t it be nice if cancer could simply yell out to let us know where it is, and how much of it is there? Anna St. Lorenz, a 4th year PhD student in the College of Pharmacy, is working on just that.

Anna volunteering at Brain Day at OMSI science museum.

Anna’s path to scientific research began when she was 8 years old, on a farm, with some chickens and a candle-lit microscope. Anna spent much of her childhood becoming familiar with the local ecology, as well as the Mendelian laws of genetic inheritance that applied to her family’s chicken breeding. However, her first taste of research was in Death Valley. With funding provided through Smith College associated religious programs, Anna studied arsenic-eating-microbes, but thanks to some giant spiders and allergies, Anna decided field research wasn’t for her and moved to a hospital setting.

In college, Anna’s scientific education expanded further through multiple internships and unique educational opportunities at Novartis Pharmaceuticals, Dana-Farber Cancer Institute and OHSU. Anna obtained a B.A. in Biology with a minor in Neuroscience from Smith College. Receiving a B.A. rather than a B.S. meant that Anna’s science education was interdisciplinary, and incorporated disciplines such as history and the fine arts. Anna’s love of the arts still persists as she frequently paints and creates “bioart,” which she uses as a means to inform and involve the community on her scientific endeavors. She commonly uses her work with her husband, Grey St. Lorenz, in presentations and has previously collaborated with artists in upstate New York for work on display at local universities.

Bioart by Anna. Nanoparticles taken up by an endosome, that then create a pore in the endosome’s membrane to release their payload. It is done in the style of Starry Night and the nanoparticle’s payload matches up with the stars.

After completing her undergraduate degree, Anna received a Master’s in Biomedical Engineering from Rensselaer Polytechnic Institute. While finishing up her Master’s degree, Anna moved to Boston and started working at MIT as a nanoparticle research technician within the Langer Lab. It was at MIT that she learned about a new nanoparticle-specific program being implemented in the OSU College of Pharmacy. This program is now about four years new and Anna has been at the front line of pioneering this program for future graduate students. In addition to navigating a new program and coping with the regular difficulties of being a graduate student, this OSU nanoparticle program is actually based at the Oregon Health & Science University (OHSU) in Portland. Although challenging at times, as a graduate student researching cancer therapeutic technology, OHSU is great place to be.

Anna and the Taratula group.

In this program, Anna works with the Taratula group on ovarian cancer diagnosis. As a disease that is traditionally hard to detect at early stages, it is often only after the cancer has spread to other areas of the body in later stages that diagnosis is able to be made. This metastasis results in a worse prognosis and decreased survival rates. To this end, Anna and other researchers and medical professionals are developing nanoparticles to deliver various iterations of imaging agents. Anna’s role in this process is to design more specific nanoparticles to carry various agents through the bloodstream and allow for specific staining of cancerous tissue.

Bioart by Anna and Grey St. Lorenz demonstrating a nanoparticle (blue) encapsulating a compound (red) and adorned with targeting antibodies (green).

Have you ever used facewash with textured particles in it? Nanoparticles are 1/1000th of that size and are used to envelop or otherwise transport compounds throughout the body and deliver them to more specified regions. This technology can be applied to a variety of compounds to enhance their delivery needs. Solubility issues, tissue or disease specificity, PH, heat, and enzyme specific release are all areas that nanoparticle science delves into to address patient care. So now, the imaging agent, inside of its tiny carrier, can circulate through the body and find the cancerous tissue it’s designed to target.

As tumors are characteristically disorganized tissue whose unregulated growth demands increased nutrients, they develop a leaky vasculature which makes it easier for molecules to permeate the tissue. Once the nanoparticle reaches the tumor, it is able to take advantage of the enhanced permeability of tumors to infiltrate and label the cancer cells. An important characteristic of the works is that the compounds use near-infrared (near-IR) light, which can be administered to excite the delivered agents in a spectral range that is largely unaffected by organic tissue. These agents were specifically screened for their ability to convert this light to acoustic/sounds waves that are detectable by ultrasound imaging. This process allows for an enhanced detection and characterization of ovarian cancer – opening the door for effective screening and improved monitoring of this devastating disease.

Join us Sunday November 4th at 7PM on 88.7FM, or listen live, to learn more about Anna’s exciting journey to graduate school, bioart, sound-making cancer, and nanoparticles.

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.

The way you(r medicine) move(s through you)

When you take medicine for a headache, it goes through your stomach into your bloodstream. The blood with the medicine eventually goes to your head, relieving you of your pain. Of course, on the way to the brain, the medicine also has to move through other organs including your liver and your heart. How is this medicine affecting your body? How is your body affecting the medicine on its journey? How long does the medicine linger in the other parts of your body? These are the questions that Oregon State University graduate student Wenjing Li is trying to answer. Her research combines pharmacology and statistics to create a mathematical model of how medicine travels through the body.

Tonight, at 7PM PST, Wenjing Li will talk about her journey combining her love of math and background in pharmacology to studying pharmacokinetics here at Oregon State University. On the way, we will discuss the opportunities she has encountered and the many challenges she has faced as an international student from China. Listen to the conversation on 88.7FM in Corvallis or stream live at http://kbvr.com/listen