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.

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.

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: https://twitter.com/SydneyEverhart/status/627546826246221824)

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

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

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.

Allison GickingNot 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.

Navigating Cultural Currents: Sharing Water in Central America

Between the Southeastern portion of the country of Costa Rica and Panama to the south runs the Sixaola River. For almost a hundred miles on its meandering path to the Caribbean the river forms the boundary between these two nations. But the Sixaola has many names. It is shared not only by the two countries to its north and south, but also by countless indigenous peoples who rely on its waters for the valuable resources that make their livelihoods possible.

When determining how the river is to be managed as a valuable resource politics inevitable come into play. This is called “hydro diplomacy“. Waste and chemical pollutants that one group dispose of in the river flow downstream to contaminate the lands of other groups. Complicating the situation is the fact that some of the peoples sharing the river reject the conventions of typical  society: the value of the river is not the same for all peoples along its length.

Dacotah in one of her favorite places: the water.

Dacotah in one of her favorite places: the water.

This is what Dacotah-Victoria Splichalova aims to better understand. As a masters student in Water Resources Policy and Management at Oregon State, Dacotah meets with and interviews many of these peoples to bring their unique cultural values concerning the river into the ongoing governmental discussion of water usage and regulation.

Dacotah’s work differs from other resource management studies in that it is not just about the relationships between people with different points of view, but about the special relationship human beings have with water itself. As a basic resource that all humans need to survive, people have an almost spiritual relationship with water. For Dacotah water is a powerful force for overcoming differences, and a symbol for peace.

You can find more information about her work at http://waterpax.org/

Colonial territories surrounding Lake Victoria in the early 20th Century

Learn the past. Speak the present. Guide the future.

Lake Victoria, sitting just below the equator in eastern Africa, shared between the countries of Kenya, Uganda, and Tanzania is the second largest freshwater lake in the world. To put that into

Early 20th century map of Lake Victoria

Colonial territories surrounding Lake Victoria in the early 20th Century

perspective, at 68,800 square kilometers, Lake Victoria is larger than the country of Switzerland (41,285 sq. km.). Beyond its immense size and grandeur, it is also one of the most important sites on earth for our current understanding of evolution because of one rapidly-diversifying group of fishes: the cichlids, which include both tilapia, an important food source, and aquarium fish such as angelfish.

 

The cichlids in Lake Victoria are especially interesting because that body of water dried out and refilled less than 15,000 years ago. This may seem like a long time, but on a geologic and evolutionary timescale, that’s less than the blink of an eye. Consider that before 1980, itwas estimated that there were over 500 species of cichlids in Lake Victoria. To contrast that with our own timeframe, the speciation time from our last common ancestor with chimps was on the order of millions of years ago. The fish in this lake are evolving at record speeds.

Traditionally haplochromines were harvested and dried as a food source for indigenous peoples Most of these practices were outlawed in 1908 Most subsistence fishing on Lake Victoria today is illegal

Traditionally haplochromines were harvested and dried as a food source for indigenous peoples Most of these practices were outlawed in 1908 Most subsistence fishing on Lake Victoria today is illegal

Today, the populations of cichlids in Lake Victoria have plummeted and many species are either endangered or extinct. The extinction was due to environmental pressures and invasive species such as the nile perch, a large predator game fish with an appetite for a group of small cichlid fish known as Haplochromis. Like many invasive species, the introduction of the nile perch was no accident. It was introduced to stem the overfishing of tilapia in the 1920s. This worked, but at the price of hundreds of species of Haplochromis. Now that the biodiversity in the lake is reduced, there are efforts to protect these species that are informed by scientific inquiry, but who gets a say in how management decisions are made? How did the focus of inquisition change over the past hundred years?

 

Cat. Man. Do.

Matt his cat work on writing Matt’s thesis

Our guest, Matt McConnell, is trying to answer these questions and trying to understand how communication between scientists and non-scientists affect how science is done. As a Masters Student in the History of Science department or Oregon State University, he is digging through the archives, trying to understand the changing scientific values surrounding Lake Victoria in the 20th century. Is the lake important as a resource or as a haven for species? Why should we care? Our current notion of science is that it is objective, but as we look into its history, science is value-driven, which is culturally laden; the question is, who’s culture is asking the questions and who’s culture is affected? In our current time, we are hearing about resource management and those are informed by scientific inquiry. Science is the answer, but it affects farmers and fishermen and their opinions are often denigrated in favor of science. Science is considered an objective measure, but it is really a cultural decision. Practitioners of science not only need to communicate their values, but they need to listen.

Matt and the 2016 History of Science cohort enjoy a day in the sun in Seattle at an Environmental Humanities Conference

Matt and the 2016 History of Science cohort enjoy a day in the sun in Seattle at an Environmental Humanities Conference

Tune in Sunday, July 3rd at 7PM PDT on 88.7FM or live stream to hear Matt talk about his journey with the history of science and science communication.

The hurdles for a college education are not the same for all students

The majority of college students today had the privilege of transitioning from high school to college in a year or less, making the transition to higher education easy. I think it’s safe to say our freshman-selves would’ve argued with the term “easy transition”. But what happens if you needed a gap year to decide what major to pursue, or needed to work and save money so you could even pay for college. Unfortunately, this gap year (often years) for many students leads them to pursue a career without a higher education limiting their potential achievements in the long-run. Furthermore, many in disadvantaged socio-economic backgrounds don’t even consider the possibility of obtaining a college degree because it’s fiscally impossible, or they simply don’t know anyone who has a higher degree so they can’t relate to anyone. A college education has become a necessity in the job market, and in order for everyone to have a fair fight towards the American dream we need to level the playing field.

Our guest tonight focuses on how social policy influences the accessibility of higher education to people of lower incomes, non-traditional, and first generation students. Terese Jones, a 4th year Ph.D. student in the College of Public Health and Human Sciences, explores the institutional and personal hurdles that prevent many people from obtaining a higher education. Imagine trying to pay for college when most scholarships are geared towards the younger demographic, or trying to adjust to a rigorous 10-week quarter system from a “9-5” job. You begin to see a picture of why going back to school after a career, or even a few years away from school, can become difficult to transition back into.

Terese and Quinlan painting together at the 2016 Bring Your Kid to Campus Day. Terese chairs the Student Parent Advisory Board at OSU, and works with the office of Childcare and Family Resources to advocate for affordable and accessible childcare for OSU students. There are many benefits to having children on college campuses, for both kids and college students.

One of the theories Terese is exploring is called the cumulative advantage theory as a potential explanation for why students of lower socioeconomic status do not succeed to the same degree as their more affluent counterparts. Think about moving to an entirely new city where you don’t know anyone and need to find a job. If you have money in the bank you can get an apartment and start looking for a job in your field; however if you’ve moved with no money you’re likely to take the first job coming your way to pay for an apartment before you ever think of looking for a job you will enjoy. 30 years later the person who had money has advanced in their career far quicker compared to the person who arrived empty handed. The benefits of a small advantage at the beginning of ones life, produces a disproportionate benefit through their life-course when compared to someone who did not have the small advantage at the beginning.

Terese also remembers her mother going back to school to finish her GED when she was only 12, but the difficulty her mom had with finishing school while maintaining a full household was extremely challenging. Even though Terese has extensive experience with the social system working in Chicago with the homeless, and Seattle at a women’s shelter, she still found that some applications and processes were just plain confusing and hard to fit into her schedule. This troubling experience led her to realize even though she’s familiar with the paperwork, the process was not trivial which gave her the motivation to pursue a higher degree at Oregon State.

Quinlan and Terese, after completing the Turkey Trot! The family that runs together gets leg cramps together!

Quinlan and Terese, after completing the Turkey Trot! The family that runs together gets leg cramps together!

Tune in tonight to hear this terrific story of how Terese aims to continue helping others as she focuses on some programs at Linn-Benton Community College can increase the chances students attend and finish a college degree. You can listen online here or on 88.7FM at 7PM!

Fishing for Improvements

Movies have a way of portraying ecology as a battle between tree-hugging scientists and the large corporations that want to destroy the natural world. The companies are shown with their giant boats and nets full of fish or with a tree removal machine ripping apart a forest in the blink of an eye. Meanwhile, the scientists and environmentalists are putting their own lives on the line in protest. While this image of the battle for the environment isn’t totally inaccurate, it certainly doesn’t represent the experience Alex Avila has had in her life and she’s working to make sure both the fisherman and the environment can live in harmony.

IMAG0923

Alex helping out with Salmon sorting for the ODFW

 

Alex grew up in the Andes mountains of Ecuador. When you ask Alex about her childhood, the first thing she brings up are her family trips to the ocean. She talks about the fisherman and watching them unload their full nets of fish and pick through the day’s catch. These experiences played a large role in defining Alex’s path. After moving to the United States from Ecuador, Alex’s life and work has continued to revolve around the water. She pursued a degree in coastal studies and environmental policy at Hood College in Maryland and went on to work many, many, many different jobs for the park service and other government research organizations. All of these experiences have cycled back around, and Alex is now researching fish populations to help the fisherman she grew up watching on the coast of Ecuador.

Avila_rockfish

Alex getting to know her study specimen, the rockfish

During her master’s research, Alex returned home to Ecuador to study the grouper population off the western coast. Her master’s research led to a better understanding of how the grouper population was distributed in this area, and inform the local fisherman of better fishing practices. Alex is now a Nancy Foster Scholar, part of the Office of National Marine Sanctuaries, pursuing her Ph.D. in the Department of Fisheries and Wildlife with Scott Heppell. She is working to understand the distribution of rockfish off the coast in the pacific northwest. By recognizing how the ocean currents affect the rockfish distribution along the coast, we can better inform fisherman how, when, and where to fish. This type of collaboration between scientists and fisherman mean that both the fishing industry, and the rockfish, can keep thriving for generations to come.

Tune in Sunday, June 19th at 7pm on KBVR Corvallis to hear all about how Alex is working to making fishing sustainable. We will also have a special guest, Meryl Mims, on at 6pm to talk about the transition from PhD to Postdoc to PI.

Go With The Flow

If you get the chance to meet Emily Khazan, you’ll probably learn a thing or two about damselflies. You can think of them as smaller versions of dragonflies whose wings can fold back

Emily attempting to collect ants off of baited trees in Costa Rica

Emily attempting to collect ants off of baited trees in Costa Rica

when they perch. They need bodies of water to breed and live, and sometimes, water caught in the leaves of a plant is all that’s needed for survival. For her Masters degree, she worked with damselflies that lived in old growth forests in Costa Rica. She would wade through thick underbrush, collecting data, trying to understand how damselflies were affected by a highly impacted landscape throughout a biological corridor that was designed for restoration of habitat for a large-bodied, strong-flying bird.

 

These days, you’ll find her stooped over the bank of a river in the desert, collecting the various insect inhabitants that live there. Working in the David Lytle lab, she wants to understand how these aquatic invertebrate communities are affected by climate change by seeing how they respond to the changing river flow. Why does it matter? Because aquatic invertebrates not only serve as a food source for fish, and a good indicator for water quality, but because our world is interconnected, biodiversity matters.

 

One of Emily's current study sites: the lower Salt river outside of Phoenix, AZ

One of Emily’s current study sites: the lower Salt river outside of Phoenix, AZ

So, how does one go from research in the tropics to the arid lands of the American southwest? For Emily, its a story where she continuously reinvents herself as she moves across the landscape. This Sunday, you can hear her journey from her first ecology course at the University of Michigan, to persevering through an underfunded Masters degree fueled by her weird love of damselflies and their environment, to leading a research station in Costa Rica, and finally coming to OSU to study aquatic invertebrates.

Tune in Sunday, June 12, 2016 at 7PM PST on KBVR 88.7FM or stream live at http://kbvr.com/listen

View of the Costa Rican coast line from the Caño Palma Biological Station (http://www.coterc.org/)