Transcript UBL Poster - Cal Poly San Luis Obispo

Facilitating the Integration of Biotechnology Experiences into Diverse Undergraduate Courses
Peter Jankay, Cal Poly, San Luis Obispo, CA
www.bio.calpoly.edu/ubl
UBL was successful. What obstacles did UBL have to
overcome?
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:
 equipment would not be readily available for their course
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.
Cal Poly undergraduate programs prior to UBL (1999)
I.
Very few undergraduate research projects on campus could
address questions that needed basic PCR, DNA sequencing,
or blot sensitivity.
II. The biological sciences department’s molecular bio lab course
essentially ignored sequencing and bioinformatics. Our
vertebrate development lab only looked at prepared slides and
models.
III. Our intro to bio majors course did not address concepts like
PCR. None of the 2K plus non-major students annually were
introduced to concepts like RNA processing.
IV. No student in the Crops Science, Animal Science, and Physics
departments encountered any biotechnology in any class or
research project, and none of these faculty had access to any
biotech tools.
Cal Poly undergraduate programs with UBL
I.
Regardless of their faculty advisors’ time availability, expertise,
or equipment, students now address questions that require
tools like PCR and DNA sequencing, e.g.,
II.
 it would consume considerable time to develop an
appropriate exercise
All of the equipment for a given step (equipment module) can be loaded
onto a cart, and thus can be wheeled literally anywhere on campus.
 experiments would have a high failure rate
As an example, the electrophoresis mobile module contains everything
for making gels (microwave, balance, graduated cylinders, buffer, etc), six
gel boxes, power supplies, pipetors, tips, ethidium bromide, and a gel
documentation system for a class of 24 students. See figure lower left.
 it would take too much to bring themselves up to speed with
the application
 experiments would be at the cost of eliminating traditional
exercises in the course
BIO 111 T8-11
BIO 111 T12-3
BIO 111 T3-6
BIO 111 T7-10
BIO 111 W8-11
BIO 111 W12-3
BIO 111 W3-6
BIO 111 W7-10
BIO 111 R8-11
BIO111 R12-3
BIO111 R3-6
BIO 111 W 8-11
BIO 111 F8-11
BIO 111 F12-3
BIO 151 T/R12-3
BIO 151 T/R3-6
BIO 151 T/R7-10
BIO 151 W/F12-3
BIO 151 T/R8-11
BIO 115 T8-11
UBL technicians train students in use of the equipment and
protocols.
Student needs vary, e.g.,
•Students working on the malaria parasite in lizard
populations had absolutely no skills.
•Their faculty advisor is trained but simply did not have time.
•After training, students are permitted to work independently
in the stationary lab. However, they are free to ask for
additional assistance whenever they get stuck.
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
⇝Fisheries: Identification of rockfish species. (see below
right)
BIO 115 T12-3
BIO 115 W8-11
BIO 115 T3-6
BIO 115 W12-3
BIO 115 W3-6
Each panel shows all the individual students in one lab section.
train faculty and graduate student associates
First, students removed some of their cheek cells and isolated the DNA from these cells.
Second, students used PCR to make millions of copies of a region of chromosome 16 that
may or may not have had a “jumping gene.”
Third, students used gel electrophoresis to separate DNA according to size. Pieces of DNA
without a “jumping gene” would have been 550 bases long. Pieces of DNA containing the
“jumping gene” would have been 850 bases long.
⇝Plant biotechnology: Gene discovery using activation
tagging.
Here are the following genotypes:
BIO 115 R8-11
BIO 115 R12-3
⇝Weed Science: What is the herbicide resistance
mechanism of rye grass?
BIO 115 R3-6
BIO 115 R7-10
Person homozygous with the “jumping
gene”
Person homozygous without the “jumping
gene”
Person who is heterozygous -(one chromosome 16 has the “jumping
gene,”
Applications of DNA Technology in Marine Fisheries Biology
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There are over 59 species along the California coast, many of
which are economically important, both commercially and
recreationally.
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Canary rockfish (Sebastes pinniger )
Black rockfish (S. melanops )
Quillback rockfish (S. Maliger )
Redbanded rockfish (S.
babcocki )
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The life history of rockfishes is very complex and
includes early planktonic stages that are difficult to
identify to species.
Some of these species have undergone precipitous
declines in recent years.
train and assist undergraduates in the pursuit of their research
projects that involve biotech applications.
the other chromosome 16 does not)
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.
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.
Initial Funding. This project was started with funding from a Cal Poly
grant, an NSFCCLI grant, and a CSUPERB grant.
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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.
Fin tissue samples were taken and analyzed by gel electrophoresis to
distinguish variations in the fish DNA.
The results show clear separation of the three species
on the basis of gel banding patterns.
Olive rockfish (S. serranoides)
goggles
spatulas
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.
flasks
microwave
Students make appointments with the UBL technicians for
equipment use and assistance.
•Sometimes students need help only in trouble shooting a
protocol or help with optimization, e.g., PCR conditions.
The marine resources of California include a large group referred to as “Rockfishes” that
belong to the Scorpionfish family.
buffer
gel doc system
Winter 2002 Alu Polymorphism
Examples of exercises are:
⇝Freshman majors and non-majors bio courses: Alu
polymorphism (see figure to the right)
5
gloves
middle partially showing a classroom set up for freshmen.
UBL troubleshoots problems when they arise
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IV. The Animal Sciences department developed an animal
biotechnology course. The Crops department developed lab
exercises for their intro students that use PCR to answer real
questions important to the discipline, e.g. “Did Dr. Phillips
illegally plant Round-up Ready cotton?” Both departments
hired faculty with considerable biotech expertise.
UBL director discusses the project with the student's
advisor.
•UBL technicians trained the students with how to: obtain
blood samples, use the DNA isolation kit, determine DNA
quality and quantity, calculate primer dilutions, perform
PCR, electrophoresis, print and digitally save gel for later
annotation.
The user need not even have a sink. See figure lower left of
1. 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
2. training
3. readily available equipment
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.
III. About 1K freshman science majors and about 2K freshman
non-science students annually each isolate DNA from their own
cheek cells, and perform PCR and electrophoresis to determine
their own pv92 genotype. As part of the exercise, students
address questions regarding PCR technology, gene structure
and regulation, RNA processing, and the significance of
transposable elements.
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.
So how is the mobile laboratory concept any better than a traditional
molecular laboratory? The traditional laboratory has all necessary
equipment located in a single room, e.g., a molecular laboratory. When
being used by one class, none of the equipment is available to any other
How did UBL overcome the obstacles and get faculty involved? class. In contrast, the mobile laboratory can simultaneously serve different
classes at different locations. The mobile laboratory, therefore, makes
It was obvious that whether or not faculty had recent molecular experiences,
faculty needed:
equipment readily available in a highly efficient manner.
Individual faculty were contacted and encouraged to work with UBL to
develop objectives that focus on questions/issues important to their course
The molecular bio lab course now sequences plasmid inserts,
and uses Lasergene software, and NCBI databases. UBL is in
the beginning phase to help develop an exercise for the
vertebrate development course that uses qPCR to address
patterns of gene expression.
How does UBL facilitate undergraduate research?
3. A. Readily available equipment – Mobile Laboratory
Common to most protocols from diverse biotech applications are three
distinct steps: DNA isolation, PCR, and gel electrophoresis.
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.
Created a gene construct to be used for
phytoremediation of oil contaminated soil.
Determined if he inherited his mother's
breast cancer gene.
Tetrahedral Photonic Bandgap Crystal: ThreeDimensional Self-Assembly using DNA Linkage
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.
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.
Teaching loads are heavy, and research expectations are increasing.
Introduction
[email protected]
tongs
Continued funding Salaries. 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.
Blue rockfish (S. mystinus)
Can you see the three distinct banding patterns for the three species?
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Poster: Todd Olive
Royden Nakamura
Peter Jankay
tips
Acknowledgements: National Science Foundation
Cal Poly Plan
Southwest Fisheries Science Center (National Marine Fisheries Service / NOAA)
gel boxes
agarose
power supplies
pipetors
pneumatic wheels
balance
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.
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.