Beginning Researchers Support Program

Seabird monitoring on the Oregon Coast

Faculty Mentor: Rachael Orben
Department: Fisheries and Wildlife

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 (Uria aalge) 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 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. Some field time would be devoted to monitoring species that are not the focus of the intern’s specific project. This is to ensure 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 work environment

The work environment is primarily fieldwork based on the central Oregon Coast. The student would have access to lab facilities at Hatfield Marine Science Center.

Description of Student Responsibilities

The student's 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 providing 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 (US, 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 field work 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.

Expected start and end date: June 1-Aug 15
Anticipated hours per week: 8 hours/wk
Anticipated hourly wage: $10

Developing a novel contraceptive for wild horses

Faculty Mentor Name: Michelle Kutzler
Faculty Mentor Department: Animal and Rangeland Sciences

Project Abstract

Sperm Protein Reactive with Anti-Sperm Antibody (SPRASA) is present in the granulosa cells and ooplasm of all stages of ovarian follicles in humans, mice, cows, dogs, and cats.  Recently, we demonstrated this to be true in horses as well.  The objective of this study is to produce and purify a sufficient quantity of SPRASA protein in vitro to vaccinate horses for a clinical safety and efficacy trial.

The Job - Project Description

Escherichia coli is an excellent protein expression system. Escherichia coli can be developed and optimized for  induced protein generation in vitro. The protein (SPRASA) will be produced by the E. coli cell concentrate. The bacteria containing SPRASA will lysed, and the resulting supernatant will be clarified to remove ribosomes and other particulate matter. The sample will then be applied to an anion-exchange column to separate SPRASA from cellular contaminants, such as E. coli proteins, nucleic acids, and lipopolysaccharides. The sample will then be further purified through salt precipitation and cation-exchange chromatography, and then concentrated. Finally, the SPRASA protein will be applied to a gel-filtration column to separate it from remaining higher- and lower-molecular-weight contaminants, the purified protein will be stored frozen. This purification protocol is typical for a protein that is expressed in fairly high abundance (i.e., >5% total protein) and accumulates in a soluble state. With these expression levels, only about a 20-fold overall purification is required to obtain pure protein. This process will need to be repeated several times in order to produce enough SPRASA protein to create sufficient antigenic mass for several equine vaccinations.   

Description of work environment

The work environment will be exclusively within a research laboratory on the Corvallis campus.   

Description of Student Responsibilities

The student will be culturing Escherichia coli bacteria and testing batches of bacteria for expression of SPRASA.  The student will also be harvesting the SPRASA protein from the E. coli through cell lysis, centrifugation, anion-exchange column separation, salt precipitation and cation-exchange chromatography. Finally, the student will be purifying the SPRASA protein by gel-filtration column separation. This process will be occurring continuously throughout the project in order to generate enough protein to produce several horse SPRASA vaccines.

Skills

All necessary skills will be taught during this project but will include pipetting accuracy, bacteria propagation, column separation, salt precipitation, and cation-exchange chromatography.

Learning Outcomes

after it is produced by the bacteria, and how to purify the protein so that it is ready to put into a vaccine.

Expected start and end date: July 6 (start), December 6 (end)
Anticipated hours per week: 3-8 hours/week
Anticipated hourly wage: $11.25

Understanding Carbon Storage in the Coastal Rainforest Soils of SE Alaska

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

Project Abstract

Coastal Temperate Rainforests from southeast Alaska to Oregon are among the most carbon dense ecosystems in the world. We need to understand how much carbon is preserved in coastal rainforest soils; a system that is underrepresented in research on global carbon cycling. This project will involve the undergraduate researcher working with a graduate student on soil samples from SE Alaska to measure how much carbon accumulates in soils formed on different types of geologic parent material (sedimentary vs. volcanic bedrock types).

The Job - Project Description

The project will involve extensive work in a soil science laboratory at Oregon State University. The different pools of carbon in the bulk soils will be collected using a density separation technique. The resulting carbon pools will be measured using a carbon-nitrogen elemental analyzer. The undergraduate student will gain experience working in a soil science laboratory and the Central Analytical Laboratory at Oregon State University. The undergraduate student will also gain experience in measuring general soil properties, such as soil color, soil pH, soil texture, and more.

Description of work environment

Primarily campus lab

Description of Student Responsibilities

The day-to-day research responsibilities will involve working with a graduate student in the soil science laboratory on extracting carbon pools from each bulk soil sample. This is done through a density separation process so the student will assist with shaking, centrifuging, filtering, and washing the soil samples using an established protocol. The student will help with grinding and homogenizing the different carbon fractions once they are separated and will likely gain experience working in the Central Analytical Laboratory to determine the percent carbon and nitrogen in each sample.

Skills

Attention to detail; well-organized; patient; laboratory safety (through general science courses with laboratory sections); strong communication; ability to work independently and ask questions when needed

Learning Outcomes

  • Perform density separations on bulk soil samples to obtain soil carbon fractions
  • How to prepare samples for carbon-nitrogen analysis
  • Determine percent carbon and nitrogen on bulk soil samples and carbon fractions
  • Measure soil pH, soil texture, Loss on Ignition, among other general soil analyses

Expected start and end date: 20-Jun
Anticipated hours per week: 10 hours/wk
Anticipated hourly wage: $11.25

Educating veterinarians about diseases and VFDs to improve honeybee health and save lives

Faculty Mentor Name: Michelle Kutzler
Faculty Mentor Department: Animal and Rangeland Sciences

Project Abstract

Since the 1940s, livestock producers (including beekeepers) have used over-the-counter (non-prescription) medicated feeds containing antibiotics to prevent, control, or treat bacterial infections in animals. Some animal producers have never directly consulted a veterinarian or had a veterinarian visit their farm, and may have been unaware that the feed they were purchasing contains antibiotics. However, in January 2017, the Food and Drug Administration (FDA) implemented the Veterinary Feed Directive (VFD) to promote the judicious use of antibiotics in food-producing animals (including honeybees). Honeybees are the only insect listed by the FDA as a food producing animal.

A "veterinary feed directive" is a written statement issued by a licensed veterinarian similar to a prescription that allows the use of an antibiotic in animal feed. Food animal producers (including beekeepers) must have a VFD on file with the feed store, feed mill or online supply company in order to obtain and before the use of any medicated feed containing antibiotics. Animals cannot legally be fed a feed containing antibiotics without a current VFD. Honeybee experts report that many beekeepers are unable to obtain a VFD, and this has had a significant negative impact during the pollination season because of a shortage of bees. Veterinarians who are knowledgeable about honeybee diseases are extraordinarily difficult to find, since bees are not part of the college veterinary curriculum. According to the Honeybee Veterinary Consortium nationwide directory, there is only one veterinary hospital in the entire state of Oregon with veterinarians willing to write VFDs for beekeepers.

The Job - Project Description

A healthy, strong and dynamic beekeeping industry is of immense value to Oregon's agricultural economy. Oregon honeybees pollinate over 90 different crops in Oregon and nearly all of the Oregon commercial beekeepers supply hives to pollinate almonds in California. The economic value of pollination services provided by Oregon honeybees is estimated at $600 million. Keeping colonies healthy and strong for these pollination events is challenging. Stressors include but are not limited to pests, diseases, nutritional stress, and pesticide exposure that can weaken or kill honeybee colonies. Bacterial foulbrood diseases are often treated with antibiotics. American Foulbrood is a rare but serious disease. Untreated colonies will die and the disease is highly contagious to other honey bees within 3-8 kilometer radius. The more common European Foulbrood (EFB) can dramatically impact a colony's growth, strength for pollination, and honey production. In Spring 2019, the prevalence of EFB in Oregon was particularly high and many beekeepers were not able to obtain to find veterinarians willing to write VFDs for the necessary antibiotic treatments to save their bees.

For this project, a one-hour program on honeybee disease identification and how to write a VFD will be taught to veterinarians. The training will be held at individual clinics in rural and urban Oregon by Dr. Kutzler and the undergraduate student. The undergraduate student will assist with the selection of veterinary clinics to visit but will be based upon location (no more than 5 veterinary clinics per county) and the veterinarians' willingness to work with beekeepers. After each one-hour training, veterinarians will be asked to complete a survey developed in Qualtrics. To assess the efficacy of this veterinary training effort from the perspective of beekeepers, a survey developed in Qualtrics will be distributed through the Oregon State Beekeepers Association, Central Oregon Beekeepers Association, Southern Oregon Beekeepers Association, Eastern Oregon Beekeepers Association, Willamette Valley Beekeepers Association, Lane County Beekeepers Association, Portland Urban Beekeepers Association, and the Oregon Master Beekeeper Program in October 2020. Data from both surveys will be summarized and analyzed using a Chi-squared test. Confidence intervals will also be calculated. Significant differences will be defined as p<0.05.

Description of work environment

About 50% of the work will be on campus contacting veterinary clinics, scheduling visits, and analyzing survey results. The rest of the work will be traveling with Dr. Kutzler to veterinary clinics around the state to administer the training and the surveys.

Description of Student Responsibilities

Each week the student will travel with Dr. Kutzler to 1-2 veterinary clinics, assist with the delivery of the VFD and honeybee disease identification training to veterinarians, and collect and analyze survey data from veterinarians and beekeepers.

Skills

The student should have good written and verbal communication skills and a valid driver's license.

Learning Outcomes

The student will learn how to examine a beehive and distinguish between the common bacterial infections that occur in honeybees. The student will also learn how to use Excel and Qualtrics for data analysis and survey management, respectively. The student will also meet and network with veterinarians and beekeepers from around the state of Oregon.

Expected start and end date: July 6, 2020 to November 13, 2020
Anticipated hours per week: 5 hrs/wk
Anticipated hourly wage: $11.25

Development of Food Safety RecordKeeping Information System

Faculty Mentor Name: Qingyue Ling
Faculty Mentor Department: Food Innovation Center Experiment Station in Portland   

Project Abstract

OSU Food Innovation Center (FIC) research team is developing a smartphone/mobile device based mobile solution APP and a web based recordkeeping information system to facilitate the Food Safety Modernization Act (FSMA) record keeping requirements for NW specialty crop growers by collaborating with OSU Department of Computer and Electrical Engineering, NW Specialty Crop growers' commissions and association as well as the individual specialty crops fruit, vegetable, and tree nut growers.

This summer project will be part of the development effort to creates a Food Safety Recordkeeping Information System (FSRIS) for NW Fruits and vegetable producers to have a information system that can be accessed and used to store  and manage their food safety records in compliance with FSMA Food Safety Produce Rules.  

If needed, the student may be needed to conduct some food quality analysis and shelf life testing projects

The Job - Project Description

1.  Challenges of Recordkeeping required by FSMA Produce Safety Rule   
 There are over fifteen thousands of specialty crop growers in Northwest states of Oregon and Washington, producing over 250 very diverse specialty crops of fruits, vegetables and tree nuts. It is vital for NW specialty crop growers to produce not only high quality but safe specialty crops to consumers. One of the important steps is to be in compliance with Food Safety Modernization Act (FSMA) Produce Safety Rule.
    Unlike the previous federal food safety regulations, FSMA Produce Safety Rule is mandatory for most of the NW specialty crop growers who are covered by the Rule. One of the most challenging requirements is recordkeeping. It requires basically that all safety related practices in pre and post harvesting has to be recorded and verified for inspection by FDA. According to 21 CFR 112.161, all required records must include:   
    (i)   The name and location of farm;
    (ii)  actual values and observations obtained during monitoring;
    (iii) an adequate description of a commodity, and, when available, any lot number or other
          identifier of covered produce;
    (iv) the location of a growing area or other area; and
    (v)  the date and time of the activity documented.
    Given the intensive and detailed amount of the records required, it is a very challenging task or big burden for each individual growers to create and maintain such recordkeeping system to be in compliance with Produce Safety Rule, especially using the current paper based recordkeeping system, which is often difficult to document and track down in a timely manner. Further more, paper records can be easily miss placed and inaccurate with human errors and also difficult to be accessed when they are needed.  These may discourage growers to actively comply with and delayed the implementation of the FSMA Produce Safety Rule.
    OSU research group proposes to develop a mobile solution tool and web based recordkeeping information system to facilitate effective recordkeeping for the NW specialty crop growers, assisting them in more efficient recordkeeping practices in full compliance with FSMA Produce Safety Rule.

2. Mobile Solution and Web based Recordkeeping Information System
    The proposed mobile solution App and web based recordkeeping information system can bring the following obvious benefits to the NW specialty crop growers:

  • To convert existing paper based produce safety records to electronic records
  • To access and maintain the safety records from anywhere and anytime through mobile devices with flexibility or needed mobility for growers in the field or in production facilities to review, edit and retrieve the desired safety records for the required FDA inspection.
  • To standardize the record forms and documentation format that meet FDA recordkeeping requirements  
  • To be easily adopted and used by the small growers with no or minimum cost.
  • To reduce the regulatory burden by saving the labor and time to create and maintain the needed produce safety records in full compliance with FSMA Produce Safety Rule.

To summarize, this proposed mobile solution APP and web based produce safety recordkeeping  information system will help NW specialty crop growers to produce better and safer specialty crops to their consumers.

3. Overall objectives of this research project
Objective 1: To understand current recordkeeping practices and identify critical needs in developing mobile recordkeeping and web based information system that will be in compliance with FSMA Produce Safety Rule for NW small specialty crop growers/producers through surveys and workshops.
Objective 2: To develop a smart phone/mobile device based recordkeeping APP to facilitate real time record keeping practices for three different specialty groups of fruits, vegetables and tree nuts.
Objective 3: To develop a web based recordkeeping database and information system for management and service of recordkeeping requirements for NW specialty crop growers.
Objective 4: To validate the performance of the developed mobile recordkeeping solution APP and web based database and information system through the participating ender users consisting of small NW specialty crop growers/ growers of representative fruits, vegetable, and tree nuts.
Objective 5: To provide needed education and training to NW specialty crop growers on FSMA Produce Safety Rule and recordkeeping requirements through workshops
Objective 6: To provide the needed user training to NW small specialty crops growers on using and managing the developed smart phone/mobile device based recordkeeping APP and information system.  

Specific objectives of this summer project are mainly covered in the first two objectives above. Specific tasks includes:

  1. Development and conduction of the survey to current recordkeeping practices and identify critical needs of NW fruits and vegetable producers   
  2. Development of standardized recordkeeping forms and documentation for electronic database
  3. Identify effective and low cost methods to convert paper based records and documents to electronic records and documents

Description of work environment

Food Innovation Center (FIC) is one of experiment stations of CAS, located in the downtown of Portland.
It currently has four main programs: (1) food product development; (2) food engineering; (3) Food Safety; and (4) Consumer sensory program.

All four programs have two components of research and industrial client service.  this summer project will be carried out under the food engineering program under the supervision of Dr. Qingyue Ling

Description of Student Responsibilities

To fulfill the required tasks of this summer student position, here are the list of the main responsibilities:

  •  To come to work at FIC provided office space with a 8:00 - 5:00 working hours schedule from Monday to Friday
    • Working from home may be allowed if approved by the supervisor.   
  • To communicate with fruits and vegetables producers through emails, phone call, and internet conferences
  • To work with your supervisor and develop industrial survey questions
  • To conduct surveys through educational workshop, online surveying tool, and emailing
  • To identify and acquisition of the record and document converting tools from paper based to electronic based systems  
  • If needed, to conduct food quality analysis of pH, Water activity and assisting in shelf life testing lab work.

Skills

  • Effective oral and written communication skills
  • Office software of WORD, EXCEL, POWERPOINT

Learning Outcomes

  • 'How to effectively communicate with industrial world
  • Collaborative Team work
  • Knowledge of Food Safety Modernization Act Food Produce Rules and Recording Keeping Requirements
  • How to conduct industrial Surveys
  • Knowledge of Information systems
  • How to convert paper based information system to an electronic based information system.
  • Some basic skills of shelf life testing and food quality analysis

Expected start and end date: 10 weeks from the thrid week of of June to the first week of September    
Anticipated hours per week: 20 to 40 hrs depending on the availability of student summer time and the needs of the research project and lab testing   
Anticipated hourly wage: $12.50

The origin and evolution of a sex chromosome in wild strawberry.

Faculty Mentor Name: Aaron Liston
Faculty Mentor Department: Botany & Plant Pathology

Project Abstract

Almost all animals have sex chromosomes, but separate sexes are found in only about 5% of flowering plants.  My lab has documented the earliest stages of sex chromosome evolution in the wild ancestors of the cultivated strawberry, and shown that the sex determining region (SDR) has moved among chromosomes at least twice in these species. We are now evaluating alternative hypotheses for why the SDR has moved.

The Job - Project Description

The undergraduate researcher will be involved in characterizing the sex determining region in new accessions of wild strawberry. The work will involve DNA extraction, PCR amplification, and sequencing of amplicons using Nanopore technology.

Description of work environment

The work will be conducted in a lab at the OSU Research Way Laboratory Building (RWLB), located approximately 2 miles south of the main campus. The Department of Botany & Plant Pathology will be temporarily relocated there during the renovation of Cordley Hall.  BPP will operate a van shuttle to and from campus every 30 minutes, Corvallis Bus #3 also serves the location twice an hour. Together these will provide transportation every 15 minutes. There will also be covered bicycle racks and free parking at the RWLB.

Description of Student Responsibilities

DNA extraction, PCR amplification, gel electrophoresis, Nanopore library preparation, Nanopore sequencing.

Skills

The student will acquire skills using standard molecular biology procedures. Preferred skills includes careful attention to detail and course work in Plant Genetics.

Learning Outcomes

  • Following protocols for molecular biology.
  • Troubleshooting molecular biology procedures.

Expected start and end date: September 16, 2020 to Dec. 15, 2020
Anticipated hours per week: 8-10 hours/wk
Anticipated hourly wage: $12

Evaluation of mycotoxins in Florida forages

Faculty Mentor Name: Jennifer Duringer
Faculty Mentor Department: Environmental & Molecular Toxicology

Project Abstract

Concerns over livestock health issues that recently developed in cattle, equine and wildlife in the state of Florida, USA lead to questions surrounding the safety of pasture forages that those animals were consuming. A collaboration was formed between extension agents and researchers that resulted in a project whose objective is to survey common Florida grass forages for mycotoxins and the fungi that produce them across the state, and at multiple times of the year. My group is responsible for utilizing an LC-MS/MS multi-mycotoxin method to evaluate the presence and quantity of 50 mycotoxins. Grass species include bahiagrass, bermudagrass, limpograss and smutgrass. Students will gain experience in grinding grass samples, extracting with organic solvents, and preparation for analysis by mass spectrometry. Students will be operating the mass spectrometer and its associated software and analyze samples against standard curves for the mycotoxins under investigation. Relationships between mycotoxin concentration, grass species, sampling location and date will be delineated with correlative statistics. This work will contribute to developing more targeted investigations as to whether or not the mycotoxins/fungi identified are associated with the reduction in animal health and performance that are being observed on Florida ranches, and if so, what the mechanism may be.

The Job - Project Description

Safety training as maintained by our laboratory and the guidelines of OSU will be the first priority. Once the student has completed safety training, we will begin with the project described. The student will be working with myself to process approximately 100 samples for analysis of mycotoxins via liquid chromatography-mass spectrometry. I will train and be with them every step of the way; work flow will include sample grinding, weighing, extraction with organic solvents, separation via centrifugation, drying down to concentrate under nitrogen, reconstitution in mobile phase, injection onto the mass spectrometer, analysis of sample data by comparing to standards for quantitation, processing of data into Excel or statistical programs, and summary of the data for reporting to collaborators. This project will allow the student to gain skills in analytical chemistry, with a project that encompasses toxicology, food safety and livestock health. This project will be performed on the Corvallis campus of OSU.

Description of work environment

The work environment is primarily in an analytical chemistry laboratory.

Description of Student Responsibilities

Students will first undergo all appropriate safety training for working in the laboratory. Then they will begin working with samples, performing the duties of grinding, organic extraction, concentration, preparation for mass spectrometry analysis, data interpretation and statistical analysis. It is best to do each of those tasks in time chunks of at least 3 hours. If two 4 hour shifts per week could be arranged, that would be ideal. In general, we will progress through each of those tasks one at a time, with my oversight every step of the way. Students will also be expected to perform tasks that keep the lab operational such as dishes, taking out the trash, general lab clean-up, maintenance of instrumentation they are using and other related operations.

Skills

Skills required

  • Willingness to learn and excitement about food safety and toxicology.
  • Punctual, ability to work independently but communicate when help or advise is needed.

Skills acquired

  • Wet laboratory bench skills including pipetting, weighing, operation of small lab equipment such as centrifuges, chemical extraction apparatus, and nitrogen evaporator
  • Organization of samples and data
  • Chemical extraction
  • Analysis of samples via mass spectrometry including data interpretation and quantitation
  • Integration of data into Excel and statistical programs for summary information

Learning Outcomes

Students will gain skills in analytical chemistry, toxicology and food safety and gain a broader understanding of how all of those components are interrelated. Students will also relate what we do in the lab to agriculture in general and how all of the pieces depend on and work together to make it a viable industry.

Expected start and end date: July 6-mid September
Anticipated hours per week: 5-10 hours/wk
Anticipated hourly wage: $12

Using GPS-activated shock collars to prevent cattle grazing of burned rangeland.

Faculty Mentor Name: Juliana Ranches
Faculty Mentor Department: Animal and Rangeland Science - EOARC (Burns)

Project Abstract

Traditional fencing is expensive, timing consuming, and often delayed by procedural and logistical barriers (e.g., NEPA, archeological clearances, contracting, etc.).  Recent technology using behavioral modification based on GPS-activated shock collars (i.e. virtual fencing) may offer a less expensive and less logistically challenging alternative to traditional fencing as well as allow grazing to occur on the unburned portions of burned pastures in the absence of additional fencing.
 
Virtual fencing can be defined as a structure serving as an enclosure, a barrier, or a boundary without a physical barrier. Usually, animals in virtual fencing receive an auditory warning cue followed by an electric stimulus if they trespass the determined boundary (Umstatter, 2011). A recent study conducted in Europe (Campbell et al., 2018) demonstrated that virtual fences are highly effective at keeping heifers at designated locations after heifers were trained to respond to the GPS-activated shock collars. However, it has been observed in other studies (Lee et al., 2009) a high variation in how individual animals respond to cues, including animals that shows undesirable responses as running forward after an electric stimulus.

We hypothesized that GPS-activated shock collars will be an efficient tool for cattle being managed in rangeland. Thus, our intent is to test the efficacy of this technology for excluding cattle from specific areas, such as burned areas. Additionally, cattle behavior and performance data while on virtual fencing is scarce and therefore will be evaluated in this study.

The Job - Project Description

The main objective of this study is to determine the efficacy of GPS-activated shock collars for excluding cattle from burned sagebrush steppe. A second objective of this study is to evaluate cattle behavior, and performance when using GPS-activated shock collars.

Procedures:

Cattle Conditioning:  Cattle (dry cows) will be conditioned to GPS-activated shock collars during the spring of 2020. In order to condition and accurately measure cattle learning behavior two tests will be conducted using 12 naïve cows. Cows that successfully learn how to positively respond the GPS-activated shock collars will be subsequently used in the grazing trial. Tests will be performed in a testing arena where an attractant will be positioned in different locations (exclusion areas) to stimulate cattle displacement within the testing arena. Prior to the beginning of each test cows will be familiarized with the testing area. Each test will be performed at least three times for each individual cow. Each repetition of the test is called session, which will last 10 minutes. We will consider that cows were successfully conditioned (i.e to not cross/enter the exclusion area) when measures taken at the initial session to the final session differ by approximately 75%. For example, if a cow received 10 sensory cues during the initial to, she will be considered successfully conditioned if at the final session she receives 2.5 or less sensory cues.

Grazing Trial: This portion of the study will employ a single factor randomized block design, with two treatments, replicated 3 times (i.e. 3 blocks) during the mid-growing season 2020. Experimental units will be adjacent 5-acre pastures located in big sagebrush steppe at the Northern Great Basin Experimental Range near Riley, Oregon.  Treatments will be non-activated shock collars and activated shock collars set to exclude animals from the burned portion of a pasture. Vegetation within pastures consists primarily of a native perennial bunchgrass understory (Stipa spp., Pseudoroegneria spicata, Poa secunda), and an overstory dominated by Wyoming big sagebrush (Artemisia tridentata subsp. wyomingensis). Behavior data will be compared between cattle using non-activated shock collars and cattle using activated shock collars to evaluate if sensory cues provided by the collar will change cattle behavior. Behavioral data will be collected at cow's placement in each designated pasture and on days 1, 2, 3 after being placed in the pasture. Live behavioral observations will be conducted by 2 trained observers from 0800 to 1200 h and from 1300 to 1700 h using instantaneous scan sampling strategy, which will result in 8 scan observations per group per day. Behavior will be recorded using the same measures used during the "Conditioning Phase" and also based on a pre-established ethogram considering the following activities: stand, walk, ruminate, drink, rest, play, grooming, allogrooming, agonistic behavior, and animal-environment interactions.  Additionally, collars will be set to record cattle location, which will provide data to estimate time spent near to virtual fencing, cattle attempt to move out of the virtual fencing limits, and time spent out of the virtual fencing limits.  

To determine percent utilization of standing herbaceous biomass we will clip unburned herbaceous biomass every 3 days during the trial within 10 randomly located 1m2 quadrants in each pasture; dry sample weights will be compared to those of ungrazed (from small utilization cages) vegetation.

Description of work environment

The study will be conducted at the EOARC  during the summer of 2020.
The EOARC is one of the branch experimental stations of OSU, which is located in Burns (eastern Oregon). Here the student will have the opportunity to interact with other students, as well as range scientists and technicians as the EOARC also house scientists from USDA and TNC, providing the student with great opportunity to enhance the network.

Description of Student Responsibilities

The study will be conducted at the EOARC (Burns, OR) during the summer of 2020. The study will be conducted in two parts, (1) Cattle conditioning and (2) Grazing Trial.

During part (1) the student will be responsible for cattle training to the use of GPS collars and will be responsible for collecting all the animal behavior data. In part (2) the student will be responsible for collecting animal behavior data and also forage consumption data.

Skills

No pre-existing skills are required. A student participating in this research project will gain skills in cattle management and handling. Additionally, students will be able to gain skills in the use of technologies (GPS Collar)  in the livestock industry, which is an area of great development.

Learning Outcomes

It is anticipated that the student responsible for the behavioral data collection will improve knowledge towards beef cattle behavior and welfare. Additionally, it is expected that great knowledge regarding the use of new technologies in livestock operation will be obtained.

Expected start and end date: May/June 2020
Anticipated hours per week: 20
Anticipated hourly wage: $13

Pruning, Staking, and Shading to Improve Fruit Quality in Dry Farmed Tomato Production

Faculty Mentor Name: Alexandra Stone
Faculty Mentor Department: Horticulture

Project Abstract

Dry farmed tomato production in the Willamette Valley has been associated with high levels of the physiological disorder blossom end rot. It has been hypothesized that pruning + staking and shading may decrease incidence of blossom end rot. Replicated research trials will be conducted to determine the efficacy of these treatments on dry farmed tomato outcomes.   

The Job - Project Description

Dry farming is the production of crops during a dry growing season without any irrigation. Farmers who lack adequate water rights or are interested in reducing irrigation water use are exploring dry farmed tomato production. In addition, dry farmed tomatoes are prized for their improved flavor. However, dry farmed tomatoes in the Willamette Valley are susceptible to blossom end rot, a physiological disorder that can lead to crop failure. Research into methods of mitigating blossom end rot will be necessary to develop a commercial dry farmed tomato market in the Willamette Valley. Pruning, staking, and shading may improve dry farming outcomes. Pruning and staking allow for farmers to get their crops off of the ground and to control vegetative growth. Shading may reduce evapotranspiration, resulting in decreased plant water demand. This research project will evaluate the impact of pruning, staking and shading on yield and fruit quality in Early Girl tomatoes.

Description of work environment

Work will primarily be conducted at the Vegetable Research Farm next to Trysting Golf Course just outside of Corvallis.

Description of Student Responsibilities

The student will be expected to lay out and plant a research trial in mid May, maintain the trial from May to the end of September including weeding around tomatoes and pruning and staking tomatoes, and collect weekly data on tomato yields and incidence of blossom end rot. After the conclusion of the field season, the student will conduct statistical analysis on their results, write a report, and present their findings.

Skills

Attention to detail is critical when conducting any sort of research activity and preference will be given to students who have demonstrated this skill. Additional skills include the ability to work outside in inclement conditions and to maintain a small field plot. Student will learn to prune, stake and shade tomatoes and design and analyze simple field experiments.

Learning Outcomes

We expect that students will learn about field experimental design, how to work in the field in the heat, how to maintain a research trial, and how to perform statistical analysis. In addition, the student will gain an understanding of plant ecophysiology, ecosystem ecology, and horticultural science.

Expected start and end date: May 15-October 15
Anticipated hours per week: 2 - 8 hours/wk for an average of 4 hours a week
Anticipated hourly wage: $15

Parasite ecology in freshwater stream food webs, with implications for canine and human health

Faculty Mentor Name: Ivan Danilo Arismendi   
Faculty Mentor Department: Fisheries and Widllife   

Project Abstract

The trematode parasite Nanophyetus salmincola is infectious to humans and causes Salmon Poisoning Disease in dogs and wild canids. This project will use Juga snails as a model system to answer questions about the impact of land-use changes on parasite diversity and abundance, and the importance of environmental variability as a driver of parasite community dynamics. Aspects of this project will allow undergraduate researchers to develop skills in field sampling, study design and experimental methods, parasite ecology, parasitological dissection and identification, and science communication. This is a great opportunity for undergraduate researchers who wish to develop their own project that is relevant to the framework of this study, and present their research at conferences and/or prepare their research for publication. Although this project is open to all, we are particularly interested in supporting students from underrepresented backgrounds, especially those who identify as LGBTQIA2+ and are seeking mentorship from graduate researchers in this community.

The Job - Project Description

This project will use Juga snails as a model system to answer questions about the impact of land-use changes on parasite diversity and abundance, and the importance of environmental variability as a driver of parasite community dynamics. Aspects of this project will allow undergraduate researchers to develop skills in field sampling, study design and experimental methods, parasite ecology, parasitological dissection and identification, and science communication.

Description of work environment

Field work to collect samples and lab work in Nash Hall

Description of Student Responsibilities

This is a great opportunity for undergraduate researchers who wish to develop their own project that is relevant to the framework of this study, and present their research at conferences and/or prepare their research for publication.

Skills

Aspects of this project will allow undergraduate researchers to develop skills in field sampling, study design and experimental methods, parasite ecology, parasitological dissection and identification, and science communication. Reponsabilities will include conducting short-term experiments, data collection and assistance during field work.

Learning Outcomes

This is a great opportunity for undergraduate researchers who wish to develop their own project that is relevant to the framework of this study, and present their research at conferences and/or prepare their research for publication. Although this project is open to all, we are particularly interested in supporting students from underrepresented backgrounds, especially those who identify as LGBTQIA2+ and are seeking mentorship from graduate researchers in this community.

Expected start and end date: June-mid November
Anticipated hours per week: 5-10 hours/wk
Anticipated hourly wage: $12

Database development for aquatic invertebrate interactions and food web modeling

Faculty Mentor Name: Ivan Arismendi
Faculty Mentor Department: Fisheries and Wildlife    

Project Abstract

This project will require scientific literature review of diet interactions between aquatic invertebrate taxa in the northwest, in addition to data entry, database management and formatting for R Studio software. Extensive stream community data was collected across three paired watershed studies in the Oregon Coast Range over a 10-year period. For the food web modeling and analysis of these data, we are looking for someone to help compile previously observed diet interactions between taxa and to cross reference/manage existing interaction database.

The Job - Project Description

This project will require scientific literature review of diet interactions between aquatic invertebrate taxa in the northwest, in addition to data entry, database management and formatting for R Studio software. Extensive stream community data was collected across three paired watershed studies in the Oregon Coast Range over a 10-year period. For the food web modeling and analysis of these data, we are looking for someone to help compile previously observed diet interactions between taxa and to cross reference/manage existing interaction database.

Description of work environment

This project will require scientific literature review of diet interactions between aquatic invertebrate taxa in the northwest, in addition to data entry, database management and formatting for R Studio software. Extensive stream community data was collected across three paired watershed studies in the Oregon Coast Range over a 10-year period.

Description of Student Responsibilities

For the food web modeling and analysis of these data, we are looking for someone to help compile previously observed diet interactions between taxa and to cross reference/manage existing interaction database.

Skills

We are looking for someone interested in food web modeling, stream ecology, aquatic invertebrates and forest harvest disturbance. Candidates for this position will need to have experience working with excel spreadsheets, be self- motivated and have an understanding of the literature review process. Experience working with R Studio is a plus!

Learning Outcomes

Learning outcomes this project include database management, learning to format data for statistical analysis, an introduction to R coding and modeling and further experience researching literature and working with excel.

Expected start and end date: June-mid November
Anticipated hours per week: 5-10 Hours/wk
Anticipated hourly wage: $12

Soil moisture release curves across the NEON network

Faculty Mentor Name: Stephen Good
Faculty Mentor Department: Biological And Ecological Engineering   

Project Abstract

The National Ecological Observation Network (NEON) consists of a group of ~50 research sites across the United States operated by the National Science Foundation. A wide variety of research groups from around the country are using data from these sites to address questions in biology, ecology, hydrology, meteorology, and agriculture. Soil water is a critical component of many of these studies, however, the relationship between the volumetric soil water content (theta) and the soil water potential (psi) is not known at these sites. The relationship between theta and psi is known as the soil moisture release curve. A student on this project will work with a team of researchers to collect and analyze soil samples throughout the NEON network to develop soil moisture release curves.

The Job - Project Description

The student research on this project will be tasked with making highly precise measurements of volumetric water content and soil water potential for a large number of soil cores from across the NEON network. Field work may involve visiting many sites across the Unites States to collect new soil samples. The student will also be tasked with reviewing published literature for information about study sites.   

Description of work environment

Work in a lab on campus, potential opportunity to conduct field work at sites across the United States.   

Description of Student Responsibilities

Student will work with the research team to develop a work flow for measurements. Student will prepare pressure vessels for measurements. Student will carefully weigh each soil sample after equilibrium conditions are satisfied. The student will create a detailed record of all measurements.

Skills

Student should be detail oriented and good with taking lab notes. Knowledge of soil properties a preferred qualification.

Learning Outcomes

Student will learn about soil properties and how to make detailed measurements of soil water content and pressure.

Expected start and end date: June 15, 2020 to August 21, 2020
Anticipated hours per week: 8 hours/wk
Anticipated hourly wage: $12

Assessing nutrient uptake and accumulation in hop production

Faculty Mentor Name: Betsy Verhoeven   
Faculty Mentor Department: Crop and Soil Science

Project Abstract

This project aims to improve our understanding of hop nutrient uptake and accumulation. Through this work nutrient accumulation curves for all macro and micronutrients will be generated and expressed relative to a range of plant development metrics designed to give growers a better idea of uptake in relation to plant development. We will look at nutrient accumulation in relation to days since pruning, days since training, growing degree accumulation (GDD), growth development stage (BBCH scale) and distance to trellis wire. Understanding nutrient accumulation rates for hops over time will allow growers to better time and adjust in-season fertilization thereby optimizing yield, disease and pest control, quality and environmental outcomes. This work will also examine the relationship of current in-season nutrient status testing methods (petiole tissue, petiole sap and soil tests) to nutrient uptake and critically examine the variability in petiole tissue and soil tests as indices of plant nutrient status.

The Job - Project Description

The primary duties of this job will be in assisting with fieldwork and processing of samples in preparation for laboratory analysis. Fieldwork will be conducted as part of a team, with a minimum of two people in a field at a time. This work will consist of harvesting hop biomass sample at various growth stages (~ 6 times in the course of the summer) and sampling of soil and hop petioles for nutrient analysis. Attention to detail and good observation skills are necessary. Processing of plant biomass sample will consist of separating the hop plant into lateral and main stem tissue and further separating cones from the rest of plant tissue. Samples will then be carefully sub-sampled and the tissue ground for nutrient analysis. This work will not be in the field but will be in a field laboratory setting and/or a combination of facilities centered around campus (USDA-ARS facility, campus lab in ALS, or Hyslop field station. Possibility for sample processing at North Willamette Research Station upon discussion with the project team). Processing of petiole and soil samples will consist of sub-sampling, drying for moisture content, and carefully labeling and packaging for off-site analysis.

Description of work environment

All field work will take place in Marion Co. around Mt. Angel and Woodburn, approximately 1-1.5 hrs from campus. Over the course of the summer, the number of full days in the field is anticipated to be around 12-15. These may be long days, as the include driving to the sites from campus.  The remainder of the work will take place on or near campus and will mainly consist of partitioning biomass samples and grinding in preparation for nutrient analysis. Basic lab work may be included and would consist of soil and plant tissue moisture analysis. There may be the possibility to carryout biomass sample processing at North Willamette Research Station if the project team decides this will be less travel for all. The main adviser for this project is located at the Marion Co. Extension office in Salem, OR. A student based our of the Salem area or greater Marion Co. would be welcome. The student could be based out of Salem or Corvallis.  While daily instructions and check-ins will occur, these may be by phone. The student must be able to work independently and injunction with one or two other students. Student must have a valid driver license and able to drive a motor pool vehicle.

Description of Student Responsibilities

  • Daily responsibilities could include a combination of the following:
  • Checking - in with adviser
  • fieldwork: plant and soil sampling
  • sample processing: partitioning biomass, grinding plant tissue, labeling and data recording
  • driving to field site(s)
  • measurement of soil moisture
  • packaging and tracking samples
  • petiole sap nutrient analysis

Skills

Ability to follow instructions and work independently, with an expectation, that if something is not clear - please ask! Asking for clarification is never a bother. Experience with plant / biomass sampling preferred. Experience with fieldwork on commercial farms preferred.  Experience with soil sampling preferred.

Learning Outcomes

The student will learn about experimental design, conducting fieldwork on commercial farms, plant and soil sampling. The student will learn about hop production practices and plant physiological development. The student will also learn about methods for in-season nutrient analysis of hop tissue.

Expected start and end date: 6/15/2020-9/15/2020
Anticipated hours per week: 20 hours/wk
Anticipated hourly wage: $11.50

Orchard Management and Plant Development of Olives in Oregon's Climate

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

Project Abstract

Olives are an emerging crop in western Oregon. The Olea Olive Project was launched in 2017 to research topics related to small-scale orchard establishment, including on-farm propagation, overwintering and transplanting young trees, and cultivar evaluation for varieties best adapted to Oregon's climate. Additionally, work is being done to track vegetative and floral development timelines, and instances of winter cold damage in this region. This project is based at the North Willamette Research and Extension Center (in Aurora) with occasional work at the Woodhall Vineyard (in Alpine). The chosen student will assist with the overwintering and transplanting study, which includes managing young trees currently out in the field, as well as potted trees in a greenhouse setting. Tasks will include assisting with fertility, irrigation, weed and pest management, and data collection. Additionally, the student will help conduct literature reviews, draft handouts and PowerPoint presentations, and learn data entry, analysis, and summary techniques. The student will be expected to collaborate and communicate with the entire team, and is highly encouraged to continue longer term with the project if it is a good fit.

The Job - Project Description

The Olea Olive Research Project was established to explore olive production in Oregon, and topics relevant to the establishment of a new tree fruit industry in Oregon, including propagation, orchard planting and management, and cultivar evaluation for cold hardiness. The overwintering and transplanting study is exploring the hypothesis that young trees will have increased growth and survival rates if first grown for multiple years in a greenhouse setting prior to field transplanting. The project consists of two field sites (NWREC/Aurora, and Woodhall/Alpine), each with two established fields reflecting different management approaches. As of summer 2020, the spring planted/raised bed fields will have been completely planted with all experimental replicates, with plantings still in progress in the fall planted fields.

Description of work environment

We seek a student to assist with both the day to day field and greenhouse management, as well as research and data collection aspects of this trial (primarily at the research station but also on campus). Student tasks would include helping with fertility and irrigation, weed and groundcover management, scouting and spraying for pests and/or applying beneficial microbial products, as well as data collection. Data collection takes place multiple times a year in regards to quantifying tree growth, while tracking tree vegetative and floral development is conducted throughout the growing season. Additionally, students will have the opportunity to learn methods of data entry, statistical analysis, and reporting and writing up results for both a grower and scientific audience. Finally, students will have a chance to contribute to other aspects of the Olea Olive Research Project, including propagation, cultivar evaluation, and grower collaborator trials, and participate in Extension educational events, field days, and workshops.

Description of Student Responsibilities

The student will be expected to work between 5 and 20 hours a week on this project from the beginning of Summer 2020 term to the end of the Fall 2020 term depending on funding and work availability. This will consist of fieldwork, greenhouse work, computer tasks, and involvement in Extension and outreach events. Duties will include assisting with both management and data collection and analysis for all fields and collections of trees involved in the overwintering/transplanting trial.  The student may be given opportunities for more hours and more specific training if they are a good fit for the team and are interested in more work. Field and greenhouse work will take place at either the North Willamette Research and Extension Center (Aurora, 1 hour drive from campus), or Woodhall Vineyard (Alpine, 30 minute drive from campus). The team typically coordinates carpooling at the start of each term; however if team schedules do not align, students will be responsible for their own transportation to and from the research site. The student will have a flexible schedule; however it is HIGHLY encouraged that students have at least one half day per week (ideally one full day) available for work at the field station in order to complete their tasks. Additionally, students will be required to meet with the mentor and other team members once a week to give a progress report and receive training. Scheduling may be adjusted depending on weather and the needs of the project.

Skills

Students are expected to have a basic understanding of plant biology and the scientific method. Previous experience with agriculture (organic or otherwise), nursery/greenhouse management, field research, statistics, and technical writing is preferred, but not required. Good organization, time-management, communication, and problem-solving will be critical to student success.

Learning Outcomes

The chosen student will develop skills relevant to both agricultural production and field-based research. They will gain an understanding of an emerging cropping system in Oregon, as well as basic skills in fertility and irrigation, pest management, working with data, and communicating results with the public. The mentor will provide training on research and field trial management basics, organic agriculture, and data collection and analysis, as necessary. Students will have the opportunity to learn how to operate a range of equipment, ranging from hand tools and backpack sprayers, to tractor driving.   

Expected start and end date: June 15th OR Sept 21st, 2020 (Summer or Fall start date possible) through December 11th, 2020. Highly encouraged to continue as a winter-spring student researcher.
Anticipated hours per week: 10-20 hours for the first 2-3 wks, then 20-40 hours/wk once the team schedule for the term is established (summer or fall)
Anticipated hourly wage: $12

Organic Strawberry Season Extension Under Low Tunnels

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

Project Abstract

Strawberries in Oregon are a high-value product that provides high-quality, local, flavorful fruit. This project will focus on production of Organic day-neutral strawberries for the fresh-market. This will contribute to the larger work of the Berry Research Initiative, which conducts research to assist our Oregon growers in developing better production practices for Oregon berries. Students have the option to develop a research project focused on a specific aspect of Strawberry crop biology, cultural production practices, or pest management. The student will work in the field at the North Willamette Research and Extension Center (in Aurora) on an Organic strawberry plot with low tunnels. The chosen student will develop their research project and experimental design in early Summer; they will manage the project and collect data during late Summer and Fall term. The student will be expected to collaborate and communicate with the entire team, and is highly encouraged to continue as a student researcher for the rest of the academic year if it is a good fit.

The Job - Project Description

Strawberries for fresh market are commonly grown on raised beds in plasticulture to achieve better weed management, temperature regulation, and water drainage. These strawberry cultivars are “day-neutral” and therefore produce fruit all season long, beginning in late-May and continuing through early October depending on the season's weather conditions. This harvest period can be extended, and the fruit quality improved, through the use of angled beds, low tunnels for frost and precipitation protection, and optimized pest-management practices. Growers who use Organic practices can achieve significant price premiums on their fruit, as the demand for local, Organic strawberries remains high and the production does not meet the levels of demand. We seek a student to help manage a project related to the production of Organic Strawberry in the Willamette Valley. We currently have one established field with low tunnels, and are planting a second field for the 2020 season. Potential projects could focus on biological management practices including fertilizer application, the use of cover crops in aisles, bed-shaping, or renovation timing for plant renewal and optimized yield; cultural practices including low tunnel type; and pest management including Organic methods for lygus bug (bug vacuum, pesticides). Students will have the ability to include cultivar as a treatment, selecting among common Oregon day-neutral varieties (e.g. Sweet Ann, Seascape, Albion).

Description of work environment

Work will primarily be field work and greenhouse work (~80%) at the North Willamette Research and Extension Center (NWREC), with some computer-based data entry and analysis (~20%) on campus. NWREC is in Aurora, a 1 hour drive from campus. The team typically schedules 3-5 work days per week at NWREC during the summer, and 1-2 work days per week at NWREC during the fall, coordinating carpooling at the start of each term. Students must have a valid driver's license, and it is preferred that they have their own method of transportation.

Description of Student Responsibilities

The student will be expected to work ~32-40 hours/week on this project during the Summer 2020 term and ~10 hours/week during the Fall 2020 term, depending on funding and work availability. During this time, the student will be expected to spend an estimated total of: (a) +/-50 hours assisting with the preparation of the study, (b) 220 hours preparing the planting, managing the crop, and collecting data, and (3) 70 hours on campus giving regular progress reports at team meetings and collaborating with student coworkers. Additional duties include literature review, data collection and analysis, and writing up results.  The student 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. Scheduling may need to be adjusted depending on weather and the needs of the project.

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. Good organization, communication, and problem-solving will be critical to student success. In addition, the student must have an interest in agriculture, especially in the development of new techniques in a Certified Organic setting.

Learning Outcomes

The chosen student will actively participate in the development and management of the entire research project, including but not limited to: field preparation, trial set-up, planting and field maintenance, data collection, harvest, analysis, and write-up. 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. Students will likely learn to use hand tools, power tools, and learn strawberry production methods.

Expected start and end date: Start date - June 15th, 2020. End date - Dec 11th, 2020. Highly encouraged to continue as a winter-spring student researcher.
Anticipated hours per week: 32-40 hours/wk during the summer, 10 hours/wk during the Fall
Anticipated hourly wage: $12.00

Optimizing Strawberry Management for Production in Substrate

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

Project Abstract

Strawberries in Oregon are a high-value product that can maximize profits through off-season production of local fruit for fresh market. In Europe, growers achieve year-long production through vertical, soilless systems under protection. This project will focus on improving the growth and development of strawberries in alternative systems to develop methods for production in Oregon. This will contribute to the larger work of the Berry Research Initiative, which conducts research to assist our Oregon growers in developing better production practices for Oregon berries. The student will have the option to help develop a research project focused on a specific aspect of Strawberry growth, development, fertility, or production practices using alternative systems. The student will work in the greenhouses at the North Willamette Research and Extension Center (in Aurora). The chosen student will develop their research project and experimental design in early Summer; they will manage the project and collect data during late Summer and Fall term. The student will be expected to collaborate and communicate with the entire team, and is highly encouraged to continue as a student researcher for the rest of the academic year if it is a good fit.   

The Job - Project Description

Strawberries for year-long fresh market production are commonly grown in vertical, soilless systems in other parts of the world. These practices help avoid the build-up of soil-borne diseases, reduce labor costs, and enable the efficient and precise control of nutrients and other inputs. The strawberry industry in Oregon is extremely interested in the potential of these systems to produce local Oregon fruit during the times of year when the price premiums are highest and currently only California berries are available. We seek a student to help develop a project related to the production of Strawberry in Oregon using table-top substrate systems. We currently have a demonstration planted and many table-top benches constructed that are ready for the upcoming trial. The student will participate in creating additional clothesline bag-growing systems. Potential projects could focus on comparing conventional and Organic fertilizer, different substrates and mixes (e.g. peat and coco coir), fertigation and irrigation timing, or tray size and arrangement. Students will have the ability to include cultivar as a treatment, selecting among common Oregon day-neutral varieties (e.g. Sweet Ann, Seascape, Albion). This project will allow students to assist in the development of new and exciting production techniques.

Description of work environment

Work will primarily be field work and greenhouse work (~80%) at the North Willamette Research and Extension Center (NWREC), with some computer-based data entry and analysis (~20%) on campus. NWREC is in Aurora, a 1 hour drive from campus. The team typically schedules 3-5 work days per week at NWREC during the summer, and 1-2 work days per week at NWREC during the fall, coordinating carpooling at the start of each term. Students must have a valid driver's license, and it is preferred that they have their own method of transportation.

Description of Student Responsibilities

The student will be expected to work ~32-40 hours/week on this project during the Summer 2020 term and ~10 hours/week during the Fall 2020 term, depending on funding and work availability. During this time, the student intern will be expected to spend an estimated total of: (a) 50 hours assisting with the preparation of the study, (b) 220 hours preparing the planting, managing the crop, and collecting data, and (3) 70 hours on campus giving regular progress reports at team meetings and collaborating with student coworkers. Additional duties include literature review, data collection and analysis, and writing up results.  The student 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. Scheduling may need to be adjusted depending on weather and the needs of the project.

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. Good organization, communication, and problem-solving will be critical to student success. In addition, the student must have an interest in agriculture, especially in the development of new techniques in organic and conventional settings.

Learning Outcomes

The chosen student will actively participate in the development and management of the entire research project, including but not limited to: field preparation, trial set-up, planting and field maintenance, data collection, harvest, analysis, and write-up. 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. Students will likely learn to use hand tools, power tools, and learn strawberry production methods.

Expected start and end date: Start date- June 15th, 2020. End date Dec 11th, 2020. Highly encouraged to continue as a winter-spring student researcher.
Anticipated hours per week: 32-40 hours/wk during the summer, 10 hours/wk during the Fall
Anticipated hourly wage: $12.00

Activation of PPAR by fatty acids in liver tissue from cows

Faculty Mentor Name: Massimo Bionaz
Faculty Mentor Department: Animal and Rangeland Sciences

Project Abstract

The object of this project is to assess the activation of Peroxisome Proliferator-activated Receptors (PPAR) by fatty acids in bovine liver tissue cultivated in vitro. For the purpose, liver biopsy will be collected from 5 cows to obtain liver slices. Those will be cultivated in vitro and treated with a mixture of fatty acids previously determined to activate PPAR. The mixture will be provided at 3 increased doses. A mixture composing a commercially available fat supplement for dairy cows will be sued as control. Expression of 10 putative PPAR target genes will be assessed using RTqPCR to determine the activation of PPAR. Results from the study will provide for the first time proof that fatty acids can activate PPAR in liver of bovine.

The Job - Project Description

Peroxisome Proliferator-activated Receptors (PPAR) are nuclear receptors that play a major role in controlling main metabolisms and immune system in mammals, including dairy cows. The PPAR are known to be activated by fatty acids (FA) in monogastrics. Preliminary evidence obtain from our laboratory confirm this to be the case for dairy cows as well. However, the results were obtained using in vitro immortalized cells. Data from several laboratory, including data from our laboratory, indicated that the liver from dairy cows is resilient to the effect of FA on PPAR when synthetic PPAR agonists are used. However, we have determined a mixture of FA that is 5-fold more potent than synthetic PPAR agonists to activate PPAR in bovine. Thus, we hypothesized that this mixture of FA is potent enough to activate PPAR in the resilient liver of dairy cows. For the purpose, we will perform biopsy of the liver from 5 mid-lactating cows. Liver slices will be obtained and cultivated in vitro and treated with 3 increased doses of the mixture of FA that activate PPAR plus a negative control (i.e., untreated control) and a positive control (i..e., the composition of FA found in a commercial fat supplement for cows - Megalac-R). After 18 h of treatment, RNA will be extracted from the tissue and media will be saved. RT-qPCR will be sued to assess the expression fo 10 putative PPAR target genes. The level of FA oxidation and triglycerides formation in media and tissue will be assessed using commercially available kits. Fatty acid composition of the media will be also assessed to determine uptake of each FA. Results form the experiment will be essential to inform futureh in vivo studies.

Description of work environment

The work will includes:

  • work with dairy cows at OSU Dairy Center for the  liver biopsies
  • work in BIonaz's laboratory in Weniger Hall 536-538
  • work in the laboratory of Gita Cherian, Withycombe Hall..

Description of Student Responsibilities

The student will be responsible to:

  • be trained by a PhD student in in vitro tissue cultivation
  • be trained to perform RTqPCR and other in vitro assays
  • set up and help during biopsies
  • obtain liver slices and treat them in vitro for 18 h
  • extract RNA and conduct RTqPCR
  • perform in vitro assays
  • analyze data
  • write the final abstract or manuscript.

Skills

  • Prior experience in handling cattle is desirable
  • Excellent pipetting skills
  • Good knowledge of chemistry and lab procedures
  • Ability to analyze data

Learning Outcomes

The student swill learn about PPAR and regulation of gene expression. The student will acquire skill on tissue culture, lipid metabolism, RTqPCR and other in vitro assays. The student will also learn how to communicate science professionally.

Expected start and end date: May 20-flexible end date depending on project needs
Anticipated hours per week: 10 hours/wk
Anticipated hourly wage: $11.50

Carcinogen-Induced DNA Mutations Identified Through Genome-Scale Sequencing

Faculty Mentor Name: Andrew Buermeyer
Faculty Mentor Department: Environmental and Molecular Toxicology

Project Abstract

The accumulation of DNA mutations is a significant driving force underlying the development of human cancer. Correctly assessing the types of mutations (where they occur and at what frequency) induced by environmental chemicals across the whole genome is important for assessing human cancer risk. Traditional studies of chemically-induced mutation utilize a single gene as a "target for mutation, requiring very high doses of the chemical and a measurable change in cellular behavior to identify the rare cells in which a mutation has "hit" the target gene. Such studies have relatively poor sensitivity for mutation detection and limited utility for cancer risk assessment. We are working to develop an alternative approach that harnesses the power of high throughput, genomic-scale DNA sequencing (HTS) for detection of carcinogen-induced mutation in human cells. Our approach will increase the target size for mutation, obviate the need for measureable behavioral changes and will significantly enhance the accuracy of mutation assays. Students will learn how to grow human cells in culture, safe handling of chemicals and chemical exposure in cell culture, genomic DNA isolation and preparation for sequencing, and the bioinformatic analysis of the DNA sequencing data. In addition, students will participate in a professional development workshop during the summer 2020.

The Job - Project Description

Development of human cancer is characterized by the accumulation of multiple mutations in the genomic DNA of otherwise normal cells. Such mutations affect the biochemical pathways that control cell growth and behavior, and specific combinations of mutations affecting different pathways are needed for cancer development in different cell types. Many environmental chemicals, both known and suspected causes of human cancer (so-called carcinogens), act as mutagens, causing the accumulation of mutations in genomic DNA. Exposure to mutagens increases cancer risk by increasing the likelihood that the specific combination of mutations necessary for cancer development accumulates in a given cell type. Accurately predicting the increased cancer risk to individuals from exposure to specific carcinogens or combinations of carcinogens requires the ability to quantitatively and qualitatively link the development of specific cancers to specific carcinogens. However, traditional studies of chemical-induced mutation have relied on experimental approaches that are limited in their applicability to human cancer risk assessment. In particular, there remains no general understanding of the effect of chronic, low-dose chemical exposure on the induction of mutations across whole genomes. Such data gaps in the understanding of mutation at the whole genome scale associated with exposure to environmental chemicals, especially at environmentally relevant low doses, has limited the effectiveness of human cancer risk assessment. Indeed, even the hypothesis that a significant percentage of human cancers arise from exposure to chemical mutagens in the environment remains controversial.

Technological advances in genome scale DNA sequencing (high-throughput DNA sequencing or HTS) provide an opportunity to address the data gap in understanding chemical-induced mutagenesis. HTS allows for the measurement of genome wide mutation rates (i.e. rates averaged across the whole genome, including sites with potentially higher and lower mutation), and facilitates the identification of true “hot” and “cold” spots for mutation (e.g. specific genes, or regions of the genome with higher or lower than expected mutation rates). Furthermore, HTS is predicted to increase the sensitivity of the measurement, such that significant numbers of individual mutations should be detected at greatly reduced levels of chemical exposure. Our goal is to develop a new experimental approach that uses HTS to measure mutations on a genome-wide scale caused by exposure to environmental chemicals. Initial experiments will measure chemically-induced mutation by using HTS in a well characterized human cell line grown in cultures in the laboratory and exposed to known human cancer-causing mutagens. HTS will sequence all the genes within the genome, so-called “exome sequencing”, to measure chemically-induced mutation rates, which will be compared to more traditional measurements of mutation. We expect to identify mutations with dramatically increased sensitivity and precision, supporting additional experiments to development the assay further with lower exposure doses, different combinations of mutagen/carcinogens, and expanding the HTS to cover the whole genome, not just the known genes. Students will learn how to grow human cells in culture, safe handling of chemicals and chemical exposure in cell culture, genomic DNA isolation and preparation for sequencing, and the bioinformatic analysis of the DNA sequencing data.

Description of work environment

This project will be conducted in an indoor laboratory on campus over the summer in 2020. Students will be expected to complete the necessary laboratory safety training, and work up to 40 hours per week in the laboratory. There will be opportunities for matching funds to support a full-time internship for up to 10-12 weeks. In addition, students will participate in the Department of Environmental and Molecular Toxicology Undergraduate Research Professional Development Workshop that consists of weekly meetings throughout the summer engaged with graduate students and faculty in the department in various professional development activities, including an exploration of graduate student experiences and training in the scientific presentations.

Description of Student Responsibilities

Daily research activities will include the growth and care-taking of cultured mammalian cells, design and execution of chemical exposure experiments along with assays to detect, quantify and analyze mutations induced in the genomic DNA. Analysis will largely utilize bioinformatic (computer software) approaches following DNA isolation and preparation for sequencing. Students will participate in weekly discussions of research progress and journal clubs in which current literature is discussed.

Skills

Required prerequisite skills include familiarity with general laboratory safety training such as is available through undergraduate Biology and Chemistry laboratory courses. Prior completion of undergraduate Biochemistry and Organic Chemistry are preferred but not required. Students will become familiar with the procedures associated with growth of mammalian cells in culture, isolation and analysis of genomic DNA, and interpretation and presentation of scientific data, results, and interpretation.

Learning Outcomes

With completion of this project students will: (1) be familiar with general laboratory safety procedures and preparation of common use laboratory chemicals and solutions, (2) be able to successfully culture mammalian cells, (3) design, execute, and interpret results from chemical exposures in mammalian cells appropriate to measuring induction of genomic mutations, and (4) be able to organize, prepare and successfully communicate the results of scientific studies in this area using different oral and written communication forms.

Expected start and end date: Summer term 2020
Anticipated hours per week: 40 hours/wk
Anticipated hourly wage: $12.50