Category Archives: College of Science

Mosquito soup in the Brazilian rainforest

Fieldwork in the Brazilian Amazonia meant continuously trying to outsmart their savviest opponents…ants!

Fieldwork in the Brazilian Amazonia meant continuously trying to outsmart their savviest opponents…ants!

Deforestation in Brazil due to cultivation of monoculture crops, such as soybean, has profoundly impacted wildlife populations. In the lab of Taal Levi in the Department of Fisheries and Wildlife, wildlife biologist Aimee Massey has adopted a quantitative approach to studying this impact. During her first and second year of graduate school, Aimee traveled to Brazil for fieldwork and data collection, collaborating with researchers from Brazil and the UK. During this trip, she collected 70,000 biting flies, including mosquitoes and sandflies, by engineering 200 fly traps constructed from 2-liter soda bottles, netting, and rotting beef. Aimee installed biting traps throughout 40 individual forest patches, which are regions delineated by their physical characteristics, ranging approximately in size from the OSU campus to the state of Rhode Island.

Who knew fieldwork could be such a balancing act?!…especially when trying to avoid poisonous insects and thorns. Let’s hope the next branch Aimee reaches for is not of the slithering snake kind!

Who knew fieldwork could be such a balancing act?!…especially when trying to avoid poisonous insects and thorns. Let’s hope the next branch Aimee reaches for is not of the slithering snake kind!

Subsequent DNA analysis on biting flies provides a relatively unbiased source of wildlife tracking, since mosquitoes serve as a repository of DNA for the wildlife they have feasted upon. DNA analysis also provides information regarding diseases that may be present in a particular patch, based on the bacterial and viral profile. For example, sandflies are carriers of protozoa such as leishmania, which cause the disease leishmaniasis. To analyze DNA, Aimee uses bioinformatics and metabarcoding, which is a technique for assessing biodiversity from an environmental sample containing DNA. Different species of animals possess characteristic DNA sequences that can be compared to a known sequence in an online database. By elucidating the source of the DNA, it is possible to determine the type of wildlife that predominates in a specific patch, and whether that animal may be found preferentially in patches featuring deforestation or pristine, primary rain forest.

Learning about human/wildlife interactions while drinking tea with camel’s milk in Laikipia, Kenya.

Learning about human/wildlife interactions while drinking tea with camel’s milk in Laikipia, Kenya.

Aimee completed her undergraduate studies at University of Maine, where she quickly discovered she wanted to study biology and chemistry in greater depth. She planned to attend med school, and was even accepted to a school in her junior year; however, an introductory fieldwork course in Panama spent exploring, doing fieldwork, and trekking made a deep impression on her, so she decided to apply to graduate school instead. Aimee completed a Masters degree in environmental studies at the University of Michigan, during which time she spent 4 months at the Mpala Research Centre in the middle of the Kenyan plateau, just north of the Masai Mara. Following completion of her Masters degree, Aimee spent a year as a research assistant at the University of New Hampshire working with small mammals. Before beginning her PhD studies at OSU, Aimee spent two months in Haines, Alaska doing fieldwork with her future PI, Taal Levi. After she finishes her PhD, Aimee plans to focus on conservation work in New England where she is originally from.

Having fun after fieldwork; Aimee’s eulachon fish catch of the day in Haines, Alaska. One is better than none!

Having fun after fieldwork; Aimee’s eulachon fish catch of the day in Haines, Alaska. One is better than none!

Tune in on October 23rd, 2016 at 7PM on the radio at 88.7FM KBVR, or stream live, to hear more about Aimee’s adventures in Brazil, and why her graduate work is shaping our understanding of how deforestation impacts biodiversity.

 

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.

Kean on Science!

This evening on our special pre-Inspiration Dissemination interview, we had a wonderful conversation with Kelsey Kean, a PhD candidate in the department of Biochemistry & Biophysics. While discussing the Tsoo King Lecture series, we stumbled into a myriad of tangential topics including CRISPR/Cas9 and Peter Walter’s discovery machine. As promised, we’re including some links to more information here. Click away for some awesome reading, watching, and listening!
TsooKingFlyer

Tsoo King Lectures with Peter Walter; Vilcek Award winner on the unfolded protein response

CRISPR-Cas9, revolutionary tool for genome editing.

 

Looking For the Link Between Centromeres and Cancer

DNA, the “building blocks of life”, can be bent and broken. While it is the source code for every creature on the earth, DNA is also the source of some of the most difficult diseases that plague humanity. Tonight at 7PM PST, Steve Friedman joins us from the department of Biochemistry and Biophysics to discuss characterizing centromeres of a filamentous fungi called Neurospora crassa. Centromeres, the part of the chromosome that is targeted by proteins that aid in cell division, are studied to understand how genetic mutations and resulting abnormalities in cells can lead to genetic disease and cancer.

Flasks containing strains of Neurospora crassa

Flasks containing strains of Neurospora crassa

Fungi serve as a model organism for the study of centromeres in Steve’s work because their genetic code is more complex than the yeast (Saccharomyces cerevisiae) that have been used in older studies, but still easier to study and understand than the complicated human genome.

Understanding how the human genetic code controls the production of proteins that are implicated in diseases like cancer, and how these proteins relate to centromeres that are crucial parts of a natural and healthy process of cell division, is the long term goal of such research.

To learn more about Steve and his work, tune in at 88.7 KBVR FM, or stream the show live!

microscopy images of GFP/RFP tagged centromere proteins (taken in Galya Orr's Lab at PNNL)

Microscopy images of GFP/RFP tagged centromere proteins (taken in Galya Orr’s Lab at PNNL).

Steve enjoys some time away from the lab

Steve enjoys some time away from the lab