Assessment of polycyclic aromatic hydrocarbon (PAH) toxicity in an in vitro lung model

Faculty Mentor: Susan Tilton
Department: Environmental and Molecular Toxicology

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are a class of over 1500 chemicals formed as incomplete combustion products and released into the environment from both natural (e.g. forest fires) or anthropogenic (e.g. burning of fossil fuels, tobacco, charbroiled meats) sources. Significant challenges exist for estimating toxicity and risk from exposure to PAHs in air pollution or waste sites.  Environmental sources of PAHs are subject to weathering and aging processes can contain many structurally diverse PAHs, including alkyl-, N-, S-, and O-substituted forms, along with other unknown chemicals; however, toxicity data exists for only a limited number of PAHs (mostly unsubstituted forms). We propose to measure endpoints for cytotoxicity and oxidative stress in primary human lung cells after short-term exposure to a large screen of PAH chemicals.  We will compare toxicity in cells with the oxidative potential of chemicals, which is a cell-free measure of oxidation that has previously been linked to adverse health effects of air pollutants. Our goal is identify whether oxidative potential correlates with toxicity in lung cells and may be used predict respiratory toxicity to inhaled pollutants.

Project Description

Polycyclic aromatic hydrocarbons (PAHs) are considered a re-emerging class of environmental pollutants due to their persistence and prominence in mixtures of concern.  PAH contamination results from incomplete combustion of fossil fuels (diesel or gasoline exhaust, burning of coal, petroleum or tobacco).  As the demand for energy resources increase world-wide, so are these sources of contamination and exposure for humans. Despite the fact that PAHs were the first class of chemicals identified as chemical carcinogens, we still know very little about the toxicity of many of the over 1500 polycyclic aromatic compounds or about potential mechanisms of toxicity for these chemicals.  In particular, we have very little toxicity data for structurally diverse PAHs that form due to environmental processes of weathering and aging.  To screen toxicity of a broad range of structurally diverse PAHs, we will test chemicals for endpoints of cytotoxicity and oxidative stress using human bronchial epithelial cells.  We propose to test toxicity of over 80 PAH chemicals cultured in 96-well plates by fluorescent assays after exposure to chemicals across a dose-response.  We will then compare toxicity in cells with the oxidative potential for each chemical as measured by the dithiothreitol (DTT) assay, which serves as a cell-free measure of oxidative capacity of chemicals.  While the DTT assay has previously been linked with the health effects of certain chemicals, in particular metals, we don’t know how well these values correlate with toxicity and oxidative stress measured in lung cells.  Based on prior data showing that some PAH chemicals transformed in the environment have higher oxidative potential, we hypothesize that the transformed PAHs will also show higher measurements of cytotoxicity and oxidative stress in our lung cells, indicating the potential for elevated adverse health outcomes for human respiratory disease after exposure.  We will determine how oxidative potential correlates with toxicity in cells for a broad range of PAHS.  Further, we will also explore how these endpoints compare for mixtures of chemicals, which are more representative of real-world exposures, compared to individual PAHs.    

Description of Student Responsibilities

Students will work in a research lab in the toxicology department.  Students will be responsible for cell culture, sample preparation, preparation of stock solutions, autoclaving, setting up experiments, calculating dosing solutions, treating cells, following established protocols for assays.  Students will also be working on computers to analyze data, perform statistical analysis and create visualizations of data in graphing software.

Skills

Students will learn how to maintain a lab notebook, prepare reagents and media, culture mammalian cells using sterile cell culture technique and will learn several molecular biology techniques, including fluorescent-based assays, RNA isolation and quantitative PCR.  Interested students should adhere to established protocols, maintain a laboratory notebook and be familiar with graphing and statistical analysis software.  Students should also be dependable and work well in a team environment.

Learning Outcomes

  • articulate a clear research question or problem and formulate a hypothesis
  • identify and demonstrate appropriate research methodologies and know when to use them
  • know and apply problem solving skills to constructively address research setbacks
  • work collaboratively with other researchers, using listening and communication skills
  • Communicate results confidently and explain their research to others through research presentations
Genomic Testing for Maternal Traits in Beef Heifers

Faculty Mentor: Michelle Kutzler
Department: Animal and Rangeland Sciences

Abstract

Agricultural genomic testing companies claim that genomic tests are cost effective and will benefit beef producers. Between 2015 and 2016, genomic testing on Angus seedstock increased 45%, to over 1 million cattle in the United States. However, these claims have never been backed up by peer-reviewed publications confirming the effectiveness of genomic testing, and how each trait is expressed in each individual animal. The purpose of the proposed research is to determine if genomic testing is predictive for maternal production traits (age of puberty, first cycle pregnancy rate, calving ease, calf birth weight, maternal behavior, and calf weaning weight [indirect measurement of lactation ability]) in beef cattle. Not only is this beneficial to producers, but for the welfare of the animal as well. If the mother has good maternal traits, she and her calf will be under less stress. In the proposed research, maternal reproductive traits of the cattle will be assessed. Choosing a replacement heifer is a key step in the production of beef cattle, and without a sound replacement heifer, the herd will not be productive. The benefits from this study would be to demonstrate if genomic testing is beneficial for selecting production traits in beef cattle, and if so, which production traits are significantly correlated with genomic testing. Genomic testing is becoming popular in the beef industry because of intense advertising campaigns by the genomic testing companies. The proposed research would confirm if this testing is economically beneficial to beef producers.     

Project Description

The Beginning Researcher will actively participate in all animal studies in which data is collected. In addition, the Beginning Researcher will develop a broad and deep understanding of beef cattle production and genomic testing. The Beginning Researcher will learn how to develop a hypothesis, create an experimental design, analyze data, and summarize results in an abstract, poster and oral presentation. Last, the Beginning Researcher will benefit from a highly diverse and active research laboratory developed on a strong foundation of undergraduate student experiential learning.

Description of Student Responsibilities

On a day-to-day basis, the Beginning Researcher will be responsible for maintaining accurate and complete records of their research in a laboratory notebook. On at least a weekly basis, the Beginning Researcher will meet with the research mentor to discuss accomplishments, setbacks, and future directions for the next week. Twice a month, the Beginning Researcher will meet with the entire laboratory group to share results and learn from other students. At least once a month, the Beginning Researcher will participate with data collection events at the Soap Creek ranch. It is important to mention that the Beginning Researcher does not need to provide their own transportation. Also, the Beginning Researcher will never be asked to participate in an activity in which they do not feel prepared for or safe to participate in.    

Skills

Good record keeping and communication (both oral and written) are required. Honesty and integrity are also values that are required. Previous experience (either hands on or virtual) with beef cattle is a preferred skill. All other skills will be taught by the research mentor and/or other students working in the laboratory.

Learning Outcomes

The learning outcomes for this research include:

  1. Understanding common terminology used in beef production and genomic testing,
  2. Recognizing problems associated with replacement beef heifer selection,
  3. Developing safe habits when working around beef cattle,
  4. Maintaining accurate and complete laboratory records,
  5. Actively participating in laboratory meetings and functions,
  6. Communicating research results to diverse groups (e.g. other students, producer groups, researchers) in a variety of formats (posters, oral presentations).
Olive Production and the Potential for Nursery Container and Field Diseases and Management Challenges in Oregon

Faculty Mentor: Javier Fernandez-Salvador    
Department: Crop and Soil Science - OSU Extension    

Abstract

Olives are an emerging crop in Oregon as growers are beginning to diversify in search of new, nontraditional cropping options. There is currently a small number of olive growers in Oregon and many of these growers anticipate a market for high quality, locally produced oil. Currently, most olives around the world are produced in warmer climates, rather than the mild, wet climate of Oregon. With the expansion of the olive crop, there is a need to understand disease and other potted plant issues, as keeping trees in containers for multiple seasons may be the best option for establishing future fields. Oregon olive growers already face unique challenges regarding plant survival and cold hardiness, in addition to any plant pathogens that may become of importance in the future. There is an increasing need for disease management practices and understanding to be developed for our specific conditions. This project aims to identify and assess potential plant pathogens, as well as explore management plans and strategies for olives potted in nursery containers and transplanted in new fields. The plant pathogen assessment will help start exploration of best practices for prevention of various pathogens. This trial aims to identify pathogens of olives grown in Oregon and explore possible pathogen management practices and control options.

Project Description

Production of olives has generally taken place in warmer climates, such as California. Olive production requires specific conditions for optimal plant and fruit development including warm, dry summers and relatively mild winters. Oregon’s climate, featuring colder, wet winters and milder summers, may be considered marginal for what traditionally has been the ideal for olives. However, with shifting climate and weather patterns, the conditions for growing olives in Oregon are unknown, as are the issues and challenges for this growing industry. Olives production in Oregon may have various advantages including quality, potentially local demand for the product and lack of disease issues due to location and climate. Olive growers currently face many challenges, including increasing plant survival and reducing cold damage in winter. The current olive research project is aiming to reduced issues during establishment, by improving plant survival. At the same time, it will be necessary to explore and develop practices for dealing with production problems including pests and disease with the aid of pest and plant pathogen management programs. This study aims to catalog and explore pathogen management and prevention practices for olive production in Oregon. Plants grown in nursery containers and in the field will be surveyed, to identify issues and disease incidence under both production environments. Once the pathogens are identified, the study team will evaluate and prepare a preliminary assessment of control options and management alternatives as needed. The chosen student will actively participate in all parts of the study including assisting lead researchers and graduate students with study design, field activities, sample and data collection, data analysis, and summarizing results. The mentors will provide adequate training on research basics including experimental design, data collection, and field trial management.

Description of Student Responsibilities

The student will be expected to work approximately 10 hours a week on this project and may be given opportunities for more hours if deemed a good fit for the team. The student will have a flexible schedule but will be required to meet with the mentor and the other team members once a week to give progress reports, receive training and conduct project activities. Students will begin work at a rate of $12 per hour. Student will be required to drive and must go through the OSU driver approval process. The position is based out of the North Willamette Extension and Research Center in Aurora.

Skills

Students are expected to have a basic understanding of plant biology, cropping systems and plant pathogens. Previous experience with field research, data collection, and log keeping is preferred, but is not required. Students must be able to work as part of a team as well as independently and must have high attention to detail.

Learning Outcomes

The student will develop a basic understanding of plant pathogens of olives, including their causes and effects. The student will also develop skills in data collection, experimental design, and log keeping. The student should be able to recognize pathogens of olives and understand the effects pathogens have on their host plant.

Organic Strawberry Production and Cover Cropping with Native Species in Aisles

Faculty Mentor: Javier Fernandez-Salvador
Department: Crop and Soil Science - OSU Extension

Abstract

Strawberries for fresh market are commonly grown on raised beds but aisles in between rows are not managed with cover crops or other ground covers. The use of a ground cover between raised beds may improve soil health and nutrient cycling, and positively impact the nutrient status of plants as well as reducing dust incidence for improved fruit quality. This project, will explore the use of native species as cover crops, as they may attract higher rates of native pollinators and beneficial insects. Additionally, soil solarization is being trialed as an organic-compliant pre-planting soil treatment for these inter-rows. Work on the project began in the spring and summer of 2018, with the solarization of select portions of the field already completed. Planting of native cover crop species will commence fall 2018, with strawberry planting and data collection taking place the following spring.
The chosen student will actively participate in the development and management of the research project, assisting with field preparation, trial set-up, planting and field maintenance, data collection, and harvest. The mentor will provide training on research and field trial management basics, study design, and data collection and analysis, as necessary.

Project Description

During the term, the student intern will be expected to spend and estimated total of: (a) 30 hours assisting with the preparation of the study, (b) 40 hours preparing the planting and managing the crop, and (3) 5-10 hours on campus or at the Marion County office giving regular reports on activities conducted and progress. Additional duties include literature review, data collection and analysis, and writing up results.
The student will be expected to work ~10 hours a week on this project from the beginning to the end of the winter/spring 2018 term depending on funding and work availability. Scheduling may need to be adjusted depending on weather and the needs of the project. Most student time can be spent at the OSU Vegetable Crops Farm Organic Certified Berry Project (Corvallis) for field work. Some travel to the Marion County office (Salem) and NWREC (Aurora) may be needed.

Description of Student Responsibilities

The student will start work when selected for the position and continue with the project until the end of spring term 2018 and beyond depending on funding. The student will be expected to work ~10 hours a week on this project and may be given opportunities for more hours if they are a good fit for the team and are interested in more work. The student will have a flexible schedule, but will be required to meet with the mentor and other team members once a week to give a progress report and receive training. Students will be paid $11- 12 per hour depending on qualifications.

Skills

Students are expected to have a basic understanding of plant biology, academic research, and data collection. Previous experience with field research and knowledge of experimental design, note taking and log keeping is preferred, but not required. In addition, student must have an interest in agriculture, especially in the development of new techniques in an organic certified setting.

Learning Outcomes

The chosen student will actively participate in the development and management of the entire research project, learning every part involved including but not limited to field preparation, trial set-up, planting and field maintenance, data collection, and harvest. The mentor will provide training on research and field trial management basics, study design, and data collection and analysis, as necessary. There will be additional learning opportunities to prepare and develop educational materials and activities based on the results of the trial.

Phytoremediation of antibiotics and antibiotic resistant genes

Faculty Mentors: Gerrad Jones, Tala Navab-Daneshmand
Mentor Departments: Biological & Ecological Engineering; Chemical, Biological, and Environmental Engineering

Abstract

Worldwide, water shortages are becoming an ever-present threat to crop production systems. To compensate for these shortages, growers increasingly rely on alternative water sources for irrigation, including wastewater effluent, which is rich in essential nutrients. In addition to wastewater effluent, growers increasingly utilize the high volumes of sludge biosolids produced by wastewater treatment facilities. These biosolids are used as fertilizers due to their high nitrogen and phosphorous content. Despite the many benefits to both the agricultural and wastewater treatment communities, an unintended consequence of biosolids and wastewater use in agricultural systems has been the emergence of antibiotic-resistant bacteria in agricultural soils. This increase in resistance is driven by elevated societal use of antibiotics and antimicrobial products and has become one of the largest public health concerns worldwide. Currently, no effective and well-tested management practices are available for reducing the health risks associated with these resources in agricultural soils. Therefore, our objective is to track the movement of both antibiotics and antibiotic-resistant genes in agricultural soils at the Biocycle Farm near Eugene, Oregon. The Biocycle Farm is a poplar plantation that was created to actively manage land-applied biosolids generated from the Eugene-Springfield Regional Wastewater Treatment Facilities. The Biocycle Farm provides a highly unique opportunity to 1) comprehensively study the movement of antibiotics and antibiotic-resistant genes in a full-scale agricultural setting, and 2) investigate how different aged stands of popular trees affect these concentrations in the soil and groundwater.    

Project Description

The selected student will spend approximately equal portions of time performing field work, lab work, and data analysis. Field work will consist of digging shallow groundwater wells and collecting samples. The Biocycle Farm is a 600 acre poplar plantation with 23 shallow groundwater wells; however, within the treed portion of the property, only 4 groundwater monitoring wells are present. In order to augment the sampling locations, the student will use a soil auger to dig additional wells within each of the 3 stands of trees. At monthly intervals, water and soil samples will be collected and taken to the lab for analysis.

Laboratory work will consist of analyzing soil samples for antibiotics and antibiotic resistant genes. Organic chemicals including antibiotics will be processed in Dr. Jones’ lab. Organics will be stripped from soils and water using solid phase extraction. The student will then run the samples at OSU’s Mass Spectrometry Center for quantification. In addition, the student will quantify the prevalence and abundance of antibiotic-resistant genes using quantitative polymerase chain reactions (qPCR) in Dr. Navab-Daneshmand’s lab.

This analysis will contribute significantly to ongoing research  within both labs, so it is expected that the student will contribute to manuscripts that will be submitted for publication and presented at regional and national conferences.

Description of Student Responsibilities

Field work will be conducted off campus at Springfield/Eugene's Biocycle farm. This facility produces class B biosolids, so the student will be required to follow safety procedures outlined by the facility. The student will help identify locations and drill wells on site. The student will collect samples from 10-12 different wells using a geo-pump, and will bring the samples back to the lab immediately. For chemical analysis, samples will be filtered immediately to remove sediments, extracted using solid phase extraction cartridges, and then frozen. Chemical processing takes ~1 week. The student will analyze samples at OSU's mass spectrometer center to quantify the presence of several antibiotics within the water and soil. For microbial analyses,  the student will fix and store collected samples for further molecular analyses. The student will also use DNA extraction kits to extract cellular DNA from stored samples for further gene quantification. With both chemical and microbial data sets, the student will import data from excel into Python or R. The student will develop simple scripts for statistical analysis (e.g., checking for outliers, regression, ANOVA) to identify differences in chemical/microbial composition among the different sites. This analysis will generate results and figures that will be presented in a poster at the end of the project.

Skills

Required Skills- students must be creative, excited, and willing to fail. Research is ~80% problem solving. Most ideas don’t work as originally planned, but with creative out-of-the-box thinking, we can overcome any problem we encounter. It is important for students to be able to take control of the project and think of new ways to tackle a problem. Otherwise, students will not be able to find creative solutions to overcome obstacles.

Learned Skills- at the end of this research experience, students will be familiar with general environmental chemistry concepts (e.g., chemical fate and transport) as well as biochemistry laboratory techniques. In addition, students will get exposure to data analysis tools that are easy to code in Python or R. The ultimate goal is to reduce the risk of antibiotic resistance in agricultural systems, so students will use these skills to make sustainable management recommendations that improve human health and safety.

Learning Outcomes

Our primary aim is to determine how the management strategies of the BIocycle Farm affect the abundance of antibiotics and antibiotic-resistant genes in soils and groundwater. With the data that is collected, we anticipate that the student will be able to address this goal. Secondary outcomes include 1) identifying the likely mechanisms triggering antibiotic resistance based on the spatial and temporal patterns of antibiotics and antibiotic resistant genes, and 2) identifying the chemical fingerprints that are indicative of antibiotic resistance within the environment. Finally, the results from this pilot study will serve as the preliminary data for a USDA grant that is to be submitted late in summer 2019.  

There are several student outcomes as well. The student will become proficient in water quality sampling and laboratory analysis in both labs. The student is expected to participate in data analysis and will learn basic statistical analysis tools in either Python or R. Finally, the student is expected to develop presentation skills, and will have the opportunity to present at local-national conferences.

For the project, our primary aim is to determine how the management strategies of the Biocycle Farm affect the abundance of antibiotics and antibiotic-resistant genes in soils and groundwater. Secondary outcomes include testing three different hypotheses proposed for triggering antibiotic resistance based on the spatial and temporal patterns of antibiotics and antibiotic resistant genes, and identifying the chemical fingerprints that are indicative of antibiotic resistance within the environment.

Role of cytokinins in virulence of Agrobacteria

Department: BPP    
Faculty Mentor: Jeff Chang

Abstract

Agrobacteria are plant pathogenic bacteria that have the unusual ability to genetically modify plants. To do so, they often transfer a fragment of their DNA, which encodes proteins that disrupt plant hormone levels to misregulate growth. We recently discovered genes located away from the transferred area, but predicted to have similar functions. We would like to test two competing hypotheses: 1) the genes encodes proteins that synthesize hormones that are secreted and disrupt endogenous plant hormone signaling, 2) the genes encodes proteins that synthesize hormones that remain in the bacteria and regulate bacterial signaling.    

Project Description

The Chang lab studies the interactions between plants and bacteria. We use genomic, molecular, evolutionary, and ecological methods to understand the ecology, evolution, and molecular bases for how bacteria interact with plants. We study both beneficial and pathogenic bacteria. the focus on the project is on pathogenic bacteria and the unusual taxa, Agrobacterium (aka agrobacteria). These bacteria can carry so-called oncogenic plasmids, extra replicons that are not necessary for its survival, but necessary for the ability of agrobacteria to cause disease. The oncogenic plasmids are remarkable and encode proteins that can sense wounded plants, produce a conduit, process a short fragment of itself, and transfer that fragment through the conduit into the plant cell.  Once the fragment integrates into the genome, it expresses proteins that lead to the synthesis of auxins and sometimes, cytokinins. These cause the plant to misregulate its growth and form tumors.

We discovered that in certain types of oncogenic plasmids, that putative cytokinin biosynthesis-encoding genes are located distal to the fragment that is transferred. The questions that this project aims to answer is, "what are these genes doing?" "Are they necessary for full virulence?" Students that elect to tackle this project will learn methods that are standard in molecular biology to generate mutants that lack the genes. Students will also have the opportunity to manipulate agrobacteria and test them for changes in their ability to cause disease.

Description of Student Responsibilities

The student will work with a postdoctoral scientist and learn how to make recombinant DNA molecules, genetic mutants and how to assay agrobacteria for changes in virulence. These approaches are standard molecular biology methods and include PCR, restriction digest, gel electrophoresis, and virulence assays.

Skills

Pre-existing skills: organized, critical thinking, strong oral and written communication skills
Skills acquired: scientific thinking, molecular biology, team-work.

Learning Outcomes

  • Domain knowledge (plant biology, microbiology, plant pathology)
  • Disciplinary skills (molecular biology)
  • Personal and professional skills (see above)
Role of PPARgamma in milk fat syntehsis in goat

Faculty Mentor: Massimo Bionaz
Department: Animal and Rangeland Sciences

Abstract

Prior data indicated that Peroxisome Proliferator-activated Receptor gamma control milk fat synthesis in ruminants; however, goat has a very weak response to PPARgamma synthetic agonists and a conclusive proof of PPARgamma controlling milk fat synthesis is lacking. To address that gap in knowledge, we will isolate mammary epithelial cells from the milk of 4 goats. Cells will be transfected with a gene reported plasmid to measure PPAR activation. Cells will be treated with several PPARgamma synthetic agonists at increased dose to assess the PPARgamma response. Cells will be treated with the agonist and dose that maximize PPARgamma activation and lipid synthesis will be assessed. We expect increase activation of PPARgamma enhances lipid synthesis in goat mammary epithelial cells.    

Project Description

Nutrigenomics is a scientific branch of nutrition that studies how molecules contained in feedstuff can modify the biology of the organism by changing the expression of specific genes. The study of nutrigenomics is very important because, once deciphered the effect on the transcription of genes of a molecule present in the feed, we can use such effect to fine-tune the biology of an organism by increasing (or decreasing) the amount of that specific compound in the diet. Considering the milk production, the study of the nutrigenomics effect of compounds in feedstuff can allow to have a powerful, although cheap, means to improve efficiency of production and/or quality of the milk.

It is becoming evident that fatty acids can affect the expression of genes. They can do this by binding and activating proteins in cells that turn on or off specific genes. It is known that fatty acids, especially saturated ones (e.g., palmitate or stearate), have a positive effect on milk fat production when added into the diet. Part of the milk fat increase is due to the augmented availability of fatty acids from the diet. However, recent data seem to suggest a nutrigenomics effect of saturated fat on milk fat synthesis. Mammary epithelial cells treated in vitro with palmitate and stearate showed an increased expression of genes involved in milk fat synthesis. Data indicated that the saturated fatty acids were partly acting through the peroxisome proliferator-activated receptor gamma (PPARg), a nuclear receptor that works as transcription factor controlling expression of genes. This protein plays a very important role in controlling the metabolism of lipid in mammals and seems extremely promising in increasing butterfat. PPARg is known to be very abundant and the main regulator of fat production in the adipose tissue. Recent it was observed that expression of PPARg increases from pregnancy to lactation in mammary tissue of dairy cows suggesting an association with the increase of milk fat synthesis. This was then supported by in vitro studies in mammary cells of cows and goats, where the use of the PPARg synthetic agonist rosiglitazone (the active principle of the human drug Avandia used for the treatment of Type II Diabetes) increased the expression of genes involved in milk fat synthesis. However, the role of PPARγ in controlling milk fat synthesis need to be confirmed by proof-or-principle experiments where lipid syntehsis is also measured (besides expression of genes). Prior data from our lab also indicated that PPARg in goats does not have a strong response to PPARg agonists. However, it is unknown if synthetic agonists developed for monogastric animals have the same potency in ruminants. Our hypothesis is that goats mammary cells respond to very high dose of PPARg synthetic agonists iand PPARg contorl milk fat synthesis

Using mammary epithelial cells (MEC) isolated from goat milk, the objective of the present study are: 1) to identify teh dose of several synthetic agonists with the highest activation of PPARg and 2) determine if activation of PPARg increase lipid syntehsis in MEC.

For the project MEC will be isolated from the milk of 4 goats using a protocol established in our laboratory for bovine mammary cells. Cultured cells will be transfected with a gene reporter plasmid containing a luciferase driven by a PPAR response element. Transfected cells will be treated with increased dose of rosiglitazone or pioglitazone plus PPARalpha and PPARdelta inhibitor (to isolate activation of PPARg). Once the dose that maximize PPARg activation is determined, cells will be treated with that dose plus a control and triglycerides synthesis in cells will be assessed by Oil Red O while excreted triglycerides will be assessed using a  commercial kit. Data will be analyzed using GLM for the dose effect and ANOVA for the effect of PPARg activation on triglycerides synthesis.

Description of Student Responsibilities

For this project, the student intern will be expected to spend 15-20 hours per week on an indoor lab to aid a visiting scholar to accomplish the above project..    

Skills

Not specif background is required    

Learning Outcomes

Student will learn isolation and cultivation of cells; molecular biology techniques, especially gene reporter assay; and statistical analysis of data.

Seabird monitoring on the Oregon Coast

Department: Fisheries and Wildlife
Faculty Mentor: Rachael Orben

Abstract

Because of their reliance on the marine environment for food, seabirds can be used as indicators of marine ecosystem health. By monitoring the reproductive success and diet of seabirds we can understand changes in the marine resources they depend on. OSU researchers from the Seabird Oceanography Lab monitor common murres, cormorant (spp.), and western gulls that nest on the Oregon coast. We have been collecting reproductive data for one of the largest colonies of common murres in Oregon at Yaquina Head Outstanding Natural Area (YHONA) since 2007, providing the long-term perspective that is critical for ecological understanding. In addition to prey regulation of seabird populations, predators such as bald eagles can impact breeding success. As part of our efforts, we quantify predator disturbances to the breeding colonies, in order to gain an understanding of how bottom-up and top-down regulation of seabird populations alters over time.  We also monitor the foraging ecology and reproductive success of western gulls at two colony sites, and isolated nests in Newport.

Project Description

The intern would participate in our monitoring efforts of murres, cormorants and western gulls. Roughly one day a week would be devoted to monitoring species that are not the focus of the intern's specific project. This is to insure that methods are similar between species and to broaden exposure to a variety of methods, seabirds, and to build a cohesive monitoring team. The intern is expected to focus on a specific research question that uses the long-term monitoring datasets and/or field data collected specifically for the purpose of the project. Projects could include the comparative reproductive ecology of urban versus rural western gulls, disturbance impacts on murres and cormorants, or nest attendance of pigeon guillemots.

Description of Student Responsibilities    

The student would be expected to spend 2-4 days a week on the Oregon coast monitoring seabirds (June-Aug). A typical field day is likely to be 3-5 hours and begins at sunrise. Much of the time is spent looking through binoculars or a scope at marked nests to identify their contents. Nests are selected early in the season and marked on photographs to ensure that the same nests are followed throughout the season. The work requires attention to detail and patience in order to spot when birds move to provide a glimpse of their egg(s) or chick(s). Data is routinely entered and proofed. Work conditions are typically windy, rainy, and cold. The intern is responsible for following the monitoring schedule, communicating with others on the team, and following monitoring protocols. The intern is also responsible for working with the PI to develop an independent research project focused on a research question of mutual interest.

Skills

Required

  • Valid driver's license (U.S., any state)
  • Team player, good communicator, excellent attention to detail
  • Enthusiasm for field work in all weather conditions
  • Physical ability to lift 30 lbs, climb several flights of stairs, use optical equipment

Preferred:

  • Background in wildlife/animal sciences/biology/marine biology or related field
  • Prior experience with databases (e.g., MS Access) and spreadsheets (e.g., MS Excel)
  • Interest in learning basic programming (e.g., R)

Learning Outcomes

  • The intern will gain fieldwork skills including observation, data entry, data visualization, and interpretation.
  • The intern will be part of a small team of scientists and will learn communication and team skills.
  • The intern will gain a basic understanding of seabird ecology.
  • The intern will lead a focused research project to answer a specific research question. Within the scope of this project, the intern will learn critical thinking, problem-solving skills, communication skills, data management, and analysis and interpretation.
Small-scale microcosms to assess silver nanoparticle toxicity

Department: Environmental and Molecular Toxicology
Faculty Mentor: Stacey Harper

Abstract:

With the immense growth in silver nanoparticle (AgNP) nanotechnologies, there is significant interest in understanding which features can be modified to maintain efficacy while reducing impacts to off-target species. Discrepancies over the relative contribution of Ag+ to AgNP toxicity remain prevalent in the literature primarily due to differences in study design. Commercial AgNP products are often proprietary, not well-defined, and undergo rapid surface oxidation and dissolution of Ag+ making their assessment difficult to study. Consequently, there is a gap in our understanding of the specific inherent AgNP features that drive nanoparticle stability, nanomaterial-biological interactions (NBI), biouptake, and ecotoxicity.  Mesocosms and microcosms are now widely accepted as a useful tool for investigating the ecotoxicity of a substance since they are constructed to simulate integrated parts of natural aquatic ecosystems.  Such studies are advantageous since they take into account relevant aspects from a simulated ecosystem such as bioavailability, indirect effects, biological compensation and recovery, as well as community level effects and the potential for trophic transfer and biomagnification.  However, traditional micro/mesocosm studies are time-intensive and require a large amount of material for testing.  To overcome these critical limitations, our overall objective is to use our newly established novel, small-scale simulated ecosystems with reliable reference conditions and sufficient cost-effective replicates to address community response to AgNP exposure. 

Project Description:

Given the critical need to identify factors leading to AgNP toxicity, we have partnered with researchers at Portland State University to design well-defined AgNPs with tightly-controlled size and shape that are tuned for Ag+ release is of significant interest. assess the potential ecotoxicity of the suite using a novel microcosm assay. The hypothesis to be tested is that the surface coverage of AgNPs determines their environmental disposition, biological uptake and bioavailability, and biomagnification through food chains. Our approach is to use HSI to visualize AgNP biodistribution among bacteria, algae, crustaceans and fish from community exposures in the small-scaled freshwater ecosystem assay.  Morbidity and mortality of the organisms will be determined in addition to the assessment of overall community health.  The justification for the proposed research is that it will address significant information gaps in our understanding of the risks posed by AgNP exposure by defining the relationships between their physicochemical properties, their environmental fate and complex biological and ecosystem responses to their exposure.  The overall outcome is expected to be a wide range of biological response variables and measures of community effects that will be analyzed for correlation to AgNP physicochemical properties or environmental disposition.   Collectively, the use of well-characterized AgNPs tuned for Ag+ release will allow us to tease apart the relative contribution of the AgNP and Ag+ to biouptake, toxicity, and potential for environmental impacts.

Description of Student Responsibilities

Student will work directly with graduate students and the laboratory research coordinator to assist in microcosm set-up, maintenance and evaluations of impacts at the end of a study.  Students will learn about data management and data analysis and will prepare summaries of data acquired with graphs and statistical analyses.  The student is not expected to be entirely independent but should work well as part of a research team.

Student Skills and Tasks:

No prior skills or experience is necessary, just an interest in the environment and research.

Student Learning Outcomes:

As part of our research team, students will learn how to design an experiment, collect and record data, analyze data and present their data.  Students will gain experience in dynamic light scattering, microscopy, animal husbandry, dilutions, nanoparticle characterization, and flow cytometry. 

Soils of Alaska: From Coastal Rainforest to Permafrost-Affected Landscapes

Faculty Mentor: Rebecca Lybrand
Department: Department of Crop and Soil Science

Abstract

Our Alaska Soils project spans active research assessing soil carbon storage and mineral weathering in the coastal rainforests outside of Juneau, Alaska to understanding how soil-landscape relationships impact permafrost stability in the Arctic regions of Alaska.

Project Description

Students will be helping with sample processing in the laboratory including preparing samples for mineralogical analysis and measuring percent carbon and nitrogen on Alaska samples. Students will also have the opportunity to develop an undergraduate research project with graduate students on the research team who are working on samples collected in Alaska. There are options for students to work on soils projects related to greenhouse gas emissions/incubations, mineralogical analysis, and better understanding soil carbon storage mechanisms. Students will also be offered the opportunity to travel to the Pacific Northwest National Laboratory to assist with additional research activities specifically focused on using microscopy, x-ray computed tomography, and other innovative instrumentation to analyze samples collected in Alaska.

Description of Student Responsibilities

Student responsibilities will include grinding soil samples in preparation for carbon and nitrogen analysis, grinding soil samples in preparation for mineralogy analysis, removing organic matter from samples prior to analysis using chemical pre-treatment techniques, extracting nutrients from the samples using different types of chemical extraction techniques, and more. Furthermore, the student will be trained on performing the analyses on his/her own undergraduate research project as needed. The student will be offered the opportunity to travel to the Pacific Northwest National Laboratory to assist with sample analyses under the direction of graduate student mentors and chief scientists at the national lab.. Depending on the timing of the project, there may also be funds available to support field outings for the student to collect additional samples or to work in the field.

Skills

Laboratory analysis skills (safely performing soil sample processing and analyses in the lab environment), verbal and written communication skills as well as working with collaborative team of graduate students, faculty, and national lab scientists. It is preferred that students have taken basic science courses in biology, chemistry, or other science with hands-on laboratory sections. It would be helpful (but not required) if the student had completed a basic soils course as well.

Learning Outcomes

  • Perform sample analyses in a laboratory environment (soil pH, extracts, particle size analysis, preparation for mineralogy/total carbon and nitrogen content measurements)
  • Communicate and collaborate with graduate students and faculty in a professional research environment
  • Learn how to use innovative instrumentation through a visit to the Pacific Northwest National Laboratory
  • Develop initial project with graduate student mentor and perform basic sample analyses to address question
  • Learn basic soil-landscape description techniques through training in the laboratory and potentially in the field