Facilitating the Integration of Biotechnology Experiences into Diverse Undergraduate Courses Peter Jankay, Cal Poly, San Luis Obispo, CA [email protected]
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Facilitating the Integration of Biotechnology Experiences into Diverse Undergraduate Courses
Peter Jankay, Cal Poly, San Luis Obispo, CA [email protected]
3. B. Stationary Laboratory This laboratory houses a complete set of equipment that duplicates mobile equipment (e.g., thermocycler, gel boxes, gel documentation system, balance), as well as non-mobile equipment like the ABI 377 DNA sequencer, and BioRad’s Fluorimager. The stationary laboratory supports, development of course specific exercises, training, and undergraduate research activities.
UBL was successful. What obstacles did UBL have to overcome?
Teaching loads are heavy, and research expectations are increasing.
Limited budgets since 1985 left the department with little biotech equipment.
Faculty (new and "seasoned") were quite reluctant to incorporate biotechnology into their classes even if they had the expertise, and even if the department were to acquire equipment. Probable reasons include perceptions like:
2. Training. UBL trains faculty and graduate student TAs how to teach course specific exercises. Trainees learn the techniques, are required to perform each step, are given basic theory for each step, are given proven logistics for the classroom, are given lessons learned by others who have taught the course. Last year alone we trained four faculty, and 21 graduate student TA’s.
Biotechnology is pervasive in applied and basic science and its impact on society is great. The undergraduate biotechnology laboratory (UBL) was created to facilitate the appropriate integration of biotechnology into the undergraduate curriculum.
How does UBL facilitate undergraduate research?
In an outreach approach, UBL’s director talks with faculty about their research interests and about interests and ideas their students have had. This led to undergraduate projects not previously even considered. Awareness about UBL’s services are also spread by word of mouth.
UBL director discusses the project with the student's advisor.
Students make appointments with the UBL technicians for equipment use and assistance.
UBL technicians train students in use of the equipment and protocols.
Student needs vary, e.g.,
How did UBL overcome the obstacles and get faculty involved?
It was obvious that whether or not faculty had recent molecular experiences, faculty needed:
considerable assistance to develop exercises, encouragement, and assurance that the exercises will work in the classroom without extraordinary efforts on their part and without losing too much of the previous course content
readily available equipment
1. Course specific exercises. UBL had to be proactive.
First we had to identify courses whose topics result from basic or applied research making use of biotech tools.
Individual faculty were contacted and encouraged to work with UBL to develop objectives that focus on questions/issues important to their course
UBL then adapts and rigorously tests protocols for higher probability of success in classroom. This includes anticipating common mistakes, and misuses by students who often have limited or no biotech experience.
UBL troubleshoots problems when they arise
Examples of exercises are:
The UBL Technicians
Two undergraduate students are hired each year who can each make a ten-hour/week commitment from September through June, and who have had a course like Molecular Biology Laboratory. These undergraduate students play very important roles for UBL. They
develop, and trouble shoot course specific exercises
quality test solutions to be used by various courses
train faculty and graduate student associates
train and assist undergraduates in the pursuit of their research projects that involve biotech applications.
operate the ABI 377 DNA sequencer for students working on independent projects and for classes who have completed the cycle sequencing. Especially for classes, the technicians give instruction on loading the gel comb, the technicians “drop the loaded gel comb in,” and using existing gel files they give abbreviated theory and a tour of the operation the sequencer.
operate the real time PCR machine for classes, and for students working on independent projects.
Applications of DNA Technology in Marine Fisheries Biology
There are over 59 species along the California coast, many of which are economically important, both commercially and recreationally.
Some of these species have undergone precipitous declines in recent years.
In solving these problems, marine biologists need to be able to estimate population size and make projections of long term trends.
A traditional way of doing this is to systematically sample the ocean for eggs and newly hatched young with devices such as plankton nets.
The marine resources of California include a large group referred to as “Rockfishes” that belong to the Scorpionfish family.
Canary rockfish (Sebastes pinniger )
Black rockfish (S. melanops )
Initial Funding. This project was started with funding from a Cal Poly grant, an NSFCCLI grant, and a CSUPERB grant.
Continued fundingSalaries. Cal Poly colleges, Science and Mathematics, and Agriculture jointly fund the two undergraduate student technician positions. The director works receives an occasional pat on the back.
Expendables. Costs of expendables for course exercises can be rather significant. It is estimated that it costs about $6 per student to perform the Alu polymorphism exercise; note that approximately 2,000 students perform this exercise annually.
The enlightened Administration has approved a three-tiered course fee system for courses that use one or more biotechnology application.
Quillback rockfish (S. Maliger )
Redbanded rockfish (S. babcocki )
Fin tissue samples were taken and analyzed by gel electrophoresis to distinguish variations in the fish DNA.
The life history of rockfishes is very complex and includes early planktonic stages that are difficult to identify to species.
The results show clear separation of the three species on the basis of gel banding patterns.
Modern molecular biology has provided new ways to distinguish the planktonic stages of the various rockfish species.
The following graphics demonstrate the application of RFLP (Restriction Fragment Length Polymorphism) analysis of three species of rockfish. The work was performed in the Fisheries Science and Conservation course (BIO 423) during the winter quarters of 2000 and 2001.
gel doc system
Olive rockfish (S. serranoides)
Yellowtail rockfish (S. flavidus)
1) Genomic DNA was isolated from fin tissue.
2) The sequence was amplified using PCR (Polymerase Chain Reaction).
3) PCR products were digested with an endonuclease
4) The digested PCR was resolved using gel electrophoresis.
Blue rockfish (S. mystinus)
Can you see the three distinct banding patterns for the three species?
With this technology a marine biologist can now make a positive identification of rockfish larvae sampled of the California coast.
Continuing work on gene sequencing and microsatellite analysis on these species could provide additional information on important and often controversial questions such as:
Do populations associated with coastal marine preserves contribute significantly to the conservation of fished populations?
Does an individual rockfish come from a large, single, genetically homogenous, population distributed along the Pacific coast?
The curriculum in the Marine Biology and Fisheries Concentration exposes students to both theoretical and applied aspects of marine science, including current issues and controversies.
Poster: Todd Olive
Acknowledgements: National Science Foundation
Cal Poly Plan
Southwest Fisheries Science Center (National Marine Fisheries Service / NOAA)