Facilitating the Integration of Biotechnology Experiences into Diverse Undergraduate Courses

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Facilitating the Integration of Biotechnology
Experiences into Diverse Undergraduate
Courses Peter Jankay, Cal Poly, San Luis Obispo,
CA pjankay_at_calpoly.edu
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 BioRads 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

www.bio.calpoly.edu/ubl
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 TAs.
Introduction 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, UBLs 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
  UBLs 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.,

• 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.
• 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.
• 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.
• 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 class. In contrast, the mobile laboratory
  can simultaneously serve different classes at
  different locations. The mobile laboratory,
  therefore, makes equipment readily available in a
  highly efficient manner.
• The user need not even have a sink. See figure
  lower left of middle  partially showing a
  classroom set up for freshmen.

• equipment would not be readily available for
  their course
• it would consume considerable time to develop an
  appropriate exercise
• experiments would have a high failure rate
• 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

• Cal Poly undergraduate programs prior to UBL
  (1999)
• Very few undergraduate research projects on
  campus could address questions that needed basic
  PCR, DNA sequencing, or blot sensitivity.
• The biological sciences departments molecular
  bio lab course essentially ignored sequencing and
  bioinformatics. Our vertebrate development lab
  only looked at prepared slides and models.
• 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.
• 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
• Regardless of their faculty advisors time
  availability, expertise, or equipment, students
  now address questions that require tools like PCR
  and DNA sequencing, 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.
• 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.
• 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.
• Sometimes students need help only in trouble
  shooting a protocol or help with optimization,
  e.g., PCR conditions.

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
• training
• 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

• 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
  Three-Dimensional Self-Assembly using DNA Linkage

• 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.

• Freshman majors and non-majors bio courses Alu
  polymorphism (see figure to the right)
• Fisheries Identification of rockfish species.
  (see below right)
• Plant biotechnology Gene discovery using
  activation tagging.
• Weed Science What is the herbicide resistance
  mechanism of rye grass?

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.
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 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. 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 )
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gloves
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.
buffer
gel doc system
goggles spatulas flasks tongs
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.
microwave
Blue rockfish (S. mystinus)
Can you see the three distinct banding patterns
for the three species?
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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 Royden Nakamura Peter
Jankay Acknowledgements National Science
Foundation Cal Poly Plan Southwest
Fisheries Science Center (National Marine
Fisheries Service / NOAA)
tips
gel boxes
agarose
power supplies
balance
pipetors
pneumatic wheels