Heavy Digging

Mine Algae!!!

When I think of mining, the first thing that comes to mind is the classic gold rush miners from the mid-1800s. Someone that looks a lot like Stinky Pete from Toy Story 2. I don’t mean to imply that this is, or isn’t, what a miner looks like. However, this does say something about the general lack of thought about mining practices. The EPA certainly isn’t as ignorant about mines as I am; in fact, as of 2014, they had designated over 1,300 sites around the country as superfund sites requiring extensive cleanup efforts. Tullia Upton is also thinking about mines much more deeply than the average person, and she is uncovering some alarming information.

During a road trip through southern Oregon, Tullia was bummed when she was told it was unsafe to swim in a local river, so she decided to dive a bit deeper, figuratively of course. She learned that this area has become dangerously polluted due to waste products of the Formosa mine.

The Formosa mine near Riddle, OR

Mining practices involve extensive digging and extracting of heavy metals which are normally buried in a reducing environment deep down within the earth’s sediment. The process of digging up these heavy metals leaves behind a staggering amount of unused material, known as tailings. Mining also exposes the metals to oxygen and allows them to leach into soils and the watershed. Due to runoff from the tailings and other waste at the Formosa mine, there is now an estimated 18 mile dead zone where no organism can live. The full extent of the damage being done to the local watershed has not been thoroughly mapped though.

Tullia analyzing samples in the lab

As she learned more about the dangerous metals coming from the mine, Tullia immediately got involved as a volunteer and secured research funding to study the pollution occurring at the Formosa mine. Tullia hopes to map the full extent of runoff from the Formosa mine and provide a better picture of the mess for the EPA, and other scientists, working on the cleanup process. When she finishes her Ph.D. here in Environmental Sciences, Tullia hopes to move on to a post-doc and eventually run her own research lab.

Tune in this Sunday, October 9th at 7pm PST to hear more about mine pollution and Tullia’s unique journey to grad school at OSU.

Safety is No Accident

It is no accident that traffic signs are painted with reflective paint to increase visibility at night. It is no accident that some pedestrian crossings in Corvallis are equipped with lighted signals that make noise. And, it is no accident that colored bike lanes are being introduced in Portland to increase driver awareness of cyclists.

Masoud presenting at Cookies and Clubs event as the Vice President of OSU ITE student chapter, Corvallis, Sept. 2016.

But, accidents happen. The city of Portland anticipates that 25% of all daily trips will be accomplished via bicycle by the year 2030, and as bicycle transportation grows in popularity nationally, bicycle fatalities are also on the rise. Recently, the Pacific Northwest Transportation Consortium (PacTrans) teamed up with a group of researchers from Oregon State University to examine the interaction between cyclists and truck motorists in downtown areas. Cyclists are very vulnerable to trucks entering the bicycle exclusive lane, and truck drivers have large blind spots and great inertia. What does a bicyclist do when a truck is in the bike lane? How does a bicyclist react to different configurations of traffic control devices, why do bicycle-truck accidents happen, and what should be done to reduce bicycle fatalities? These are the questions being investigated by PhD student, Masoud Ghodrat Abadi, with the Hurwitz Research Program.

Masoud presenting his research on traffic signal control at Engineering Graduate Research Expo, Portland, Mar. 2016.

Did you know Oregon State University has a cycling and driving simulation lab? We do, and we are one of six in the world! In the lab, a cyclist mounts a stationary bike, dons a pair of goggles that track eye movement, and pedals the bike in front of a screen that provides a 180 degree field of vision. The screen shows a virtual world where the cyclist encounters hazards, and their reactions are monitored. For automobile drivers, the experience is the same except of course the driver sits in a car that tilts as they navigate through the virtual reality. The whole time, Masoud is collecting data, and analyzing the interaction between drivers and cyclists.

Masoud presenting his research at PacTrans PhD Student Research Symposium, Seattle, Aug. 2016.

Although the literal definition of Transportation Engineering is, “the application of technology and scientific principles to the planning, functional design, operation and management of facilities for any mode of transportation in order to provide for the safe, efficient, rapid, comfortable, convenient, economical, and environmentally compatible movement of people and goods.” It is simply the science of making transportation safe and saving lives. We humans need flashing lights, clear signs, and noises to help us avoid accidents. We are not perfect. For Masoud, this intersection between the physics of traffic and human psychology is gripping. Growing up, Masoud always had a talent for math and physics. It was no surprise that he would eventually pursue Engineering. Later when he was earning his Master’s in Transportation Engineering, he found that his field combined his research interests and his fascination with human behavior. This fascination is also influenced and satisfied by his love for teaching. Masoud is constantly learning about effective teaching and how to improve student performance. Masoud comes from a family full of teachers and a nourishing atmosphere at home. For this reason, he decided to pursue a PhD in Transportation Engineering because he wants to become a university professor and “teach for life,” which is rather appropriate considering the research he is pursuing could saves lives.

Lastly, Masoud would tell you to wear a helmet and stop listing to music while you bike. Everyone can learn to be safe.

Please tune into 88.7 FM KBVR Corvallis this Sunday at 7 pm to hear more from Masoud Ghodrat Abadi. You can also stream the show live.

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

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

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

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

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

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

Paul does it all: Is there hope for the amphibian taxa?

Everyday there is a constant battle between healthy immune systems and parasites trying to harass our bodies. In the case of buffalos in South Africa they cannot simultaneously fight off a tuberculosis infection and a parasitic worm. Their immune system has to choose which of the adversaries it will fight; this decision has consequences for the individual and the health of the entire population of buffalos it encounters. This situation is not unlike those for humans. We are not fighting one immunological disease at a time, but many at once and they can interact to influence how we feel. Our guest this evening specializes in disease ecology, which focuses on how the spread of pathogens interacts with humans and non-human organisms.

Paul while working as the Ezenwa Lab manager at the University of Georgia

Paul Snyder has worked on tiny ticks in New York to wild buffalo in South Africa, but he’s had a very colorful life before beginning his studies at OSU. Even though he loved everything science and technology growing up, there was limited exposure to those fields in high school and he never thought of being a scientist as a career path. To put things in perspective, he wasn’t allowed to buy any video games growing up; instead he programmed his first working computer game at the ripe age of 6, yes six, years old! Paul continued his illustrious career as a 13-year old paperboy, then burger flipper, and eventually working his way up through the ranks to the manger of a Toys R Us store. He realized he wanted to focus on science and pursued his schooling at University of South Florida doing research on the interaction of parasites and tadpoles, then New York counting ticks, and finally University of Georgia as a lab manager. Oh yeah, somewhere in-between he successfully mastered the bass guitar with his band mates and learned how to program virtual reality simulations, but I digress.

In his downtime Paul works on virtual reality apps for us to enjoy

Back in the world of science, Paul is working with Dr. Blaustein’s Integrative Biology lab group in the College of Science that he first became aware of from his work with South African buffalo’s. Rather than beginning his disease ecology research with human trials, Paul is focusing on the #1 declining vertebrate taxa in the world. Amphibians have been sharply declining since the 1980’s and there have been no shortage of guesses, but sadly few answers as to why this is happening. Paul’s current project has identified a species-virus interaction (e.g. the number of species present impacts how the infection spreads). But Paul’s real interest and ongoing research lies in the very young field of ecoimmunology: how do the immune systems of organisms change over time in response to the environment they experience.

You’ll have to tune in to hear how he plans to rectify the molecular-scale view of immunology, with the large-scale controls from the environment. You can listen tonight September 18^th 2016 at 7PM on the radio at 88.7FM KBVR Corvallis, or stream live at 7PM.

Religion and Spirituality at Work

Most adults spend the majority of their time at the workplace and organizing their lives through or around their occupations. While work is often portrayed as not personal or political, social science research continues to highlight how gender, race, and sexuality play an important role in organizing work and occupations. Recently, scholars are beginning to demonstrate that like gender, race, and sexuality, religion and spirituality are also deeply rooted in occupations and their organizations, the identities of workers, and the interactional dynamics at work. This week we ask, how does religion and spirituality shape work, and vice versa, and what do identities (gender, race, and sexuality) and inequalities have to do with it?

Our guest this week, Andres Lazaro Lopez PhD student in Applied Anthropology, is interested in the interplay between religion/spirituality and intersecting identities (gender, race, class, and sexuality) at and around work, especially for queer professionals. Andres’ focus is on Lived Religion, which centers on people’s choices about their relationship with religious practices, the spiritual language and communities that help filter the meaning of the religions they engage with, and the actual daily uses that result from both. How do people bring religion to work? How do individuals and groups make spiritual meaning out of their work and workplaces? What makes a location, activity, or object sacred? This is based on the idea that religion and spirituality is not contained within or limited to activities within a church or its organizations.

Growing up with two older masculine heterosexual brothers, Andres learned about code switching at an early age – how to use language and behavior differently for varying groups and audiences. As a young person making sense of his queerness, the practice of code switching taught him how masculinity and sexuality can shape interactions. His background led to his Bachelor’s in Sociology from Xavier University in Cincinnati, Ohio. His senior thesis was an empirical analysis of how college-aged men felt restricted by their masculinity.

After a short break from academia, Andres earned a Master’s degree in sociology from the University of Missouri – Kansas City. This is when the topics of religion and masculinity became intertwined for Andres; he studied the largest men’s ministry organization in the U.S., asking why men would join an all-men’s religious ministry and what motivated them to be regular participants.

Andres’ life has certainly shaped his career path. Now in the Oregon State program of Applied Anthropology, Andres is truly forging his own path in the field by approaching the intersection between identities, culture, and inequalities, and how they affect the performance of gay men in and around professional work. Tune in Sunday September, 11 at 7 pm to hear more or stream the show live.

Can You Hear Me Now?

A mutation in the otoferlin gene causes inherited hearing impairment. The otoferlin gene codes for the massive otoferlin protein, which is in the part of the inner ear called the cochlea. Otoferlin is responsible encoding the sound and proposed to act as a calcium sensor for neurotransmission in inner hair cells of the cochlea. Murugesh Padmanarayana, PhD student in Biochemistry and Biophysics here at OSU, has been working on functional characterization of this protein in order to understand how it works and what it does to encode sound faithfully.

A photo of Murugesh in the lab.

Why is it important to know the function of a protein and the functions of all of its parts? Different parts of proteins perform different tasks, and otoferlin’s most important parts are called C2 domains that bind calcium, lipids and other proteins. If there is a mutation in the otoferlin gene that affects the C2 domains, it abolishes neurotransmitter release and no sound will be detected. Murugesh has discovered that it is possible that only two functioning C2 domains are enough to rescue hearing. This is ground breaking because if only two parts are really necessary for hearing than proteins that look and act like otoferlin but are smaller may be able to restore hearing function to a person with inherited hearing impairment. Otoferlin at its complete size with six C2 domains is far too big to be administered through gene therapy. Murugesh hopes that his research may lead to further development of this protein as a potential treatment for inherited hearing impairment.

Murugesh came from a small village called Bagoor in India. There he is one of the few people to have attempted to or succeeded at obtaining a graduate degree, but Murugesh was a good student and he pushed himself to go farther. He graduated with a bachelor’s in Pharmacy from Rajiv Gandhi University of Health Sciences in India. After college, Murugesh worked at a pharmaceutical company for two years where he decided to pursue a career in medicinal chemistry. Murugesh left India and earned a master’s in Drug Design and Biomedical Science from Edinburgh Napier University in the United Kingdom where he was first involved in research. After working for two years in the protein science department of Agilent Technologies, he decided he wanted to return to graduate school for a PhD.

In his spare time Murugesh loves three antidepressants: nature, reading, and biking.

Murugesh contacted professors from 15 schools, based on their positive reply he applied to 7 schools, and we are fortunate that he chose Oregon State University and the Biochemistry and Biophysics Department where he works with Dr. Colin Johnson. Murugesh will continue working in protein biochemistry or protein engineering after his time here at OSU.

We are so thrilled to have Murugesh on the show this weekend, and we are excited to talk to him about his research with protein otoferlin. Be sure to listen to KBVR Corvallis 88.7 FM at 7 pm on Sunday, August 21 to hear from Murugesh, or stream the show live.

We Answer to the Nucleotide Chain Gang

This week on Inspiration Dissemination our featured guest is our very own Zhian Kamvar aka DJ CATGAG the co-host and co-founder of our weekly broadcast. Before his radio and phytopathological fame, Zhian was an eager biologist and a DJ by a different name! All will unfold during this week’s episode, but I will supply some teasers to get the oospore rolling.

Zhian got interested in biology while in high school in California where he wanted to become a mortician…yes we all were very surprised (but not really) to learn this. Like any aspiring mortician, Zhian used the internet to find out how he should focus his studies and achieve his goal. Anatomy and Physiology were high on the list. Zhian was fascinated with many aspects of human biology particularly respiration and circulatory processes that “just happen.” For example, the human heart pump blood throughout the body 80 times per minute with no conscious intention of the individual. That was only the tip of the iceberg and his enthusiasm continued to grow while in his first genetics course in college at Truman State University in Kirksville, Missouri. This is when everything changed for Zhian and he decided to forgo his dream of becoming a mortician and focus on genetics. After a rough start at scaling the learning curve, Zhian aced Advanced Genetics and began an undergraduate research project investigating the that genes are responsible for making cultivars of corn grow and develop differently. A pivotal and proud moment for Zhian was presenting a poster at a national conference; this was only one of the many conferences that would follow.

Zhian seems very normal and boring, but wait!

Zhian poses with a petri dish containing a cultured specimen of the plant destroyer Phytophthora syringae. (Photo Credit: Lindsey Thiessen)

During his time at Truman State University, Zhian stumbled upon and promptly crashed into a gig as a radio DJ for the Truman State College Radio Station-KTRM “The Edge”. Zhian’s shows hosted the metal, vinyl, and classical genres. One of Zhian’s shows was a morning show called “Up Late with a Vampire,” a classical music hour for your morning commute in nowhere Missouri. Thus began our own DJ CATGAG’s life as a radio DJ subjecting us to his diverse musical taste. Zhian is not only a music connoisseur, from the common to the obscure, but also Zhian made and produced some of his own music, OH YES we have samples to play this Sunday! First, Zhian mixed electronic tunes as…wait for it…DJ Poopslice! Then his sound truly took form as Not Jeremy Jones where he explored harsh noise and “poplematic” (problematic pop) music.

Also, worth mentioning that after graduating from Truman State Zhian took a solo trip to Daegu, South Korean where he taught English for 3 years. In South Korea, Zhian did a lot of reading in his free time and decided he really missed participating science and research. He decided it was then time to apply to graduate school.

Zhian demonstrating functionalities of his software package, poppr, to a workshop at the American Phytopathological Society meeting in 2015 (Photo Credit: Sydney Everhart) (From twitter)

Lucky for us, (and I mean that sincerely) he was accepted to Oregon State University Department of Botany and Plant Pathology. Zhian is part of the lab of Nik Grünwald where he studies the population genetics of plant destroyers in the genus Phytophthora, specifically Phytophthora syringae and Phytophthora ramorum (this one is the pathogen responsible for Sudden Oak Death). These organisms are fungi-like and usually reproduce asexually, but they do have sex when conditions are good. His dissertation focuses on diversity of Phytophthora populations. Basically, if a population is very diversified than the effect of the pathogen on the plants involved is going to be harder to manage; whereas a population of clones may be taken out uniformly. In addition to interpreting population genetics, Zhian has been working to develop software tools that will help others to analyze data to study the genetics of other organisms. His R package called poppr allows users to analyze and visualize the distribution of genetic diversity in a population. Zhian does very great work, and we are sad to know that soon he will finish his dissertation and leave the Inspiration Dissemination team.

This is an episode you will not want to miss. Tune in at 7 pm on Sunday, August 14 to KBVR Corvallis 88.7FM or stream the show live.

Get out and Play with Friends!

As the Rio Olympics gets underway we are reminded just how far a human being can push their body to shave off ¼ second, or jump the extra inch; we tend to envision exercise for purely physical benefits such as burning calories, bigger muscles, and a stronger heart. Think about how much more enjoyable it is to play basketball with friends or run with a buddy instead of trudging through mile after mile by yourself.

Our guest this evening sees the physical benefits of exercising, but wants to remind us of social bonding and psychological well-being that can be produced from exercising with a group of people. Jafra Thomas is a Ph.D. student in the College of Public Health and Human Sciences focusing on how health should be viewed as a social phenomenon, instead of purely an anatomical process. Not only is Jafra interested in the effects of exercise on the individual, but also how these activities can strengthen the social fabric with our peers, how values can develop from these experiences, and how this can promote a positive personal identity.

Think back to your (probably very awkward) early high school days, some may have been on the dance team, band group, or some other sports team. Your very first practice was really scary because you were not physically ready and you’re surrounded by lots of new people you don’t know! Fast-forward to the end of high school you realize what you learned about team-bonding, inclusion, perseverance, and hopefully developed a life-long personal identity through those long and grueling practices.

Jafra Thomas is currently a PhD student in the College of Health and Human Sciences

While going through his undergraduate degree at the University of Pacific in California, Jafra spearheaded a program to encourage community members of diverse backgrounds to participate on a rowing team. This rowing program helped the participants overcome some of the many barriers that often limit participation in these unique sports. The program made sure to provide equally accessible events and create an inclusive environment so kids can learn more about themselves and others. This is the kind of healthy development we should be promoting in tandem with the physical benefits of exercising.

Jafra has already received some prestigious awards, and in the future plans to become university professor who hopes to strike a balance between research, teaching and service. In the mean time, he’s keeping himself busy by being a part of the Black Graduate Students Association (BGSA), Graduate Certificate in College and University Teaching Program (GCCUTP), and recently got back into rowing through the Corvallis Rowing Club.

Tune in Sunday, August 7th at 7PM PDT on KBVR, 88.7 FM or stream live at http://www.orangemedianetwork.com/kbvr_fm/ to hear Jafra’s story.

A Softer Side of Robots

Do me a favor: close your eyes for a few seconds and think of a robot, any robot, real or imaginary.

Done? Good. Now, that robot you thought about, what did it look like? What did it do? What was it made of? The answers to the first two questions will likely be different from person to person: perhaps a utilitarian, cylindrical robot that helps with menial tasks like cleaning and homework, or a humanoid robot, hell-bent on crushing, killing, and/or destroying humans. I’m willing to bet, however, that the majority of the answers to the last question is one word: “metal”.

Most of our images of robots, droids, and automatons (i.e. R2-D2, The Cybermen, or Wall-E), including robots that we encounter in day to day life, are made of metal, but that might change in the future. The future of robotics is not simply to make robots harder, better, faster, or stronger, but also softer. For robots that must interact with humans and other living or delicate things, they must have the capacity to be gentile.

Samantha works on the jumping spider model that mimics a jumping spider by using an air hockey table with a tethered puck with a consistent starting speed

Researchers like Samantha Hemleben are beginning to explore the world of soft robotics, creating robots that are made out of soft materials, acting through changes in air pressure. These robots could be used for tasks where a light touch is needed to avoid bruising such as human contact or fruit picking. Currently, the technology to create soft robots involves making a 3D-printed mold and then casting the silicone robot parts in those molds. If you need a robot that has both soft and firm parts, it must be designed in separate steps, reducing efficiency and effectiveness.

This is where Samantha comes in; she’s trying to optimize this process. When she started her undergrad at Wofford College, she tried out Biology, Pharmacy, and Finance, but didn’t feel challenged by them. Switching to mathematics with a computer science emphasis allowed her creativity to flourish and she was able to secure a Research Experience for Undergraduates here at OSU, modeling a robot that mimics the movements of jumping spiders. This experience heavily influenced her decision to get her Ph. D. at OSU.

Samantha is now a 2nd year Ph. D. student of Drs. Cindy Grimm and Yiğit Mengüç in Robotics (School of Mechanical, Industrial, and Manufacturing Engineering). Her research is focused on trying to understand the gradient between hard and soft materials. That is, she’s creating mathematical models of this gradient so that the manufacturing process can be optimized, and soft robots will be able to stand on solid ground.

Tune in on Sunday, July 24th at 7PM PDT on 88.7FM or stream live at http://www.orangemedianetwork.com/kbvr_fm/

Walk Like a Kinesin

To the naked eye, plants don’t move around a whole lot. Take a closer look, inside of a plant cell, and a whole new world is opened. From cytoplasmic streaming to mitosis (cellular division), a cell is a bustling city with a plethora of different molecules and organelles being moved all around so it can grow and survive. And how are these molecules and organelles moving about? How are they getting to their very important destinations to ensure that vital signals or nutrients are delivered on time? The answer is molecular motor proteins. Molecular motors are proteins that all cells have. They have feet, can walk, and carry stuff. These proteins are the workforce of the cell, moving along the cytoskeleton (fibrous protein bundles that give the cell structure), carrying precious cargo from one place to another.

Not all of these microscopic walkers are created equal, however, some can walk farther or faster than others and Allison Gicking wants to know why and how this happens. She is using a particular kind of microscopy called TIRF (Total Internal Reflection Fluorescence) to put a spotlight on individual protein molecules so she can observe the unique ballet of life dancing on minuscule tightropes. Because these proteins are important for cell division, her work on understanding the movements of these proteins could have implications in cancer remedies or even drug delivery.

A 4th year Ph. D. student in the department of Physics, Allison has always had a passion for science. From high school to college, she was constantly looking for ways to blend her love of physics and biology. In a time when fewer than 20% of physics degrees are awarded to women, Allison is using her experience to advocate for women in science by being involved in science communication and co-organizing the Conference for Undergraduate Women in Physics here at OSU.

Tune in Sunday, July 17th at 7PM PDT on KBVR, 88.7 FM or stream live at http://www.orangemedianetwork.com/kbvr_fm/ to hear Allison’s journey.