Biotechnology/Bioinformatics Discovery!
Kits for Educators
· ALU*
What it is: Students isolate their own cheek cell DNA and use PCR to amplify a hypervariable site that either has the Alu insert or not. Genotyping done by electrophoresis. Followup bioinformatics activity available.
Credits:
Subject areas: biotechnology.
How long it takes: 2-3 periods.
*Do this lab only after lots of work with electrophoresis and PCR.
· Amax of Bromophenol Blue/Spec 20 Lab *
What it is: Students practice with micropipettors and other volume measuring devices, learn how to make dilutions, make a graph to prepare a standard curve using a spectrophotometer and use with unknown. Accuracy and precision.
Credits: posted with the
permission of Professor John Urbance at
Subject areas: physical science, chemistry, biology, AP biology, mathematics.
How long it takes: one period.
* Do this lab before doing the Amylase Adventure and after doing Micropipetting Techniques.
· Amylase
Adventure: scouting for a biotech
product*
What it is: Students investigate amylase activity using food extracts and then soil samples with starch-agar plates and then cultivate bacterial amylase-producers. Quantify amylase activity using iodine test with spectrophotometer readings.
Credits: derived from Kreuzer and Massey’s Recombinant DNA and Biotechnology
volume as well as the NYSCATE web site and Paul Patev’s
Advanced Biotechnology Education Project at Middlesex CC,
Subject areas: environmental science, biology, biotechnology.
How long it takes: one to four periods depending on how far you pursue the activity.
- Biodegradable Cornstarch Packing Peanuts
What is it: amylase enzyme from soil (microbes) works on biodegradable cornstarch packing peeanuts.
Credits: DeAnn Campbell of OCCC.
Subject areas: environmental science, biology, biotechnology, middle school science.
How long it takes: one class period.
- Bioinformatics (web-based) – four
options.
What it is: An introductory exercise that describes the field of bioinformatics including its career potential, and takes the student through a few simple exercises that use web databases to identify a DNA sequence. Requires computer linked to the internet. One uses zoology examples, second uses biomedical examples. The HIV exercise uses Biology Workbench and is inquiry-based exploration of how HIV evolves over time in the same patient and different patients.
Credits: various sources
including Geospiza and
Subject areas: Biology courses, computer science, biotech, bio II, AP Bio.
How long it takes: Parts I
and II of first two options would take about one period or less. Can use part III to expand to greater or
lesser degree.
Credits: Charlotte Mulvihill of OCCC.
Subject areas: introduction for high school or middle school level in any science class.
How long it takes: less than one class period.
· Bt Corn PCR*
What it is: Students make extracts of corn plant leaves or corn-based food products and use PCR to detect presence of foreign DNA.
Credits: corn material provided through Gary Thull of Education department of Pioneer seeds.
Subject areas: environmental science, biology, horticulture, agriculture, biotechnology, botany.
How long it takes: two-three periods.
* Do Water bath and thermal cycler PCR first.
- Case Study on Huntington's Disease- Less is More
What is it: case study format, the biology of codon-repeats in HD and bioethical dilemmas in gene testing. Includes wet lab with dyes and electrophoresis that simulates the HD lab test.
Credits: organized by Charlotte Mulvihill with extensive use of web resources.
Subject areas: bioethics, biology classes studying genetics.
How long it takes: 3-4 class periods.
- Clinical Trials - the Scientific Method in Action.
What is it: DVD and lesson plans using clinical trials as a model for the scientific method. Parent activity included.
Credits: DeAnn Campbell of OCCC, Brandi Williams of Moore schools, OK.
Subject areas: middle school science, health careers classes.
How long it takes: 3 class periods.
What it is: A class activity simulating restriction enzymes cutting different DNA samples left at crime scene; samples are distributed, cut with restriction enzymes, and data assembled to determine whodunit.
Credits: Sandra Porter of Geospiza.
Subject areas: biology, biotechnology.
How long it takes: one
period or less.
- Demystifying
Electrophoresis – The Technology for DNA Identification.*
What it is: Students explore the process of electrophoresis using pH indicators and dyes, movement by charge and size, to achieve understanding of the basic elements of electrophoresis.
Credits: various sources
including Access Excellence and
Subject areas: physical
science, biology, chemistry, AP biology, biotech .
How long it takes: One period to practice and then run electrophoresis and discuss results and brainstorm; one more period to try out hypothesis on other samples.
*This lab is prerequisite for DNA Patterns and Seafood Forensics and PCR.
- DNA is Everywhere - DNA
Extractions from food sources
What it is: We have protocols that show that you can extract DNA from many common food sources: raw wheat germ, a fruit smoothie, kiwi, spinach, as examples. The protocol is rapid and easy and chemicals are harmless.
Credits: various sources including Access Excellence and Shoestring Biotech Project.
Subject areas: Biology (genetics), general science.
How long it takes: Assuming prior introduction to DNA, procedure can be done in part of period, then rest of period for brainstorming and planning other extractions. Part of second period to test hypotheses.
What it is: Students do electrophoresis of precut DNA samples; samples provide different patterns; describes use of restriction enzymes and plasmid maps. Unknown provided. Exercise to determine molecular weights available.
Credits: DNA Learning center, OCCC biotechnology program.
Subject areas: AP biology, biotechnology.
How long it takes: two periods.
*Prerequisite: Demystifying electrophoresis.
**Prerequisite: Demystifying electrophoresis and Making Gels.
· Exploring
World of Biotechnology Including Careers (web based)
What it is: web based activity focusing on careers in biotechnology.
How long it takes: one
period or homework assignment.
What it is: collection of labs and activities that we support which can be made into a unit on forensics, both at basic and more advanced levels.
Subject areas: biology, general science, anatomy-physiology, biotechnology.
Time it takes: variable
lengths of time, depending on which activities chosen.
- The
Human Genome Project (web
based)
What it is: science literacy would not be complete without some knowledge about the Human Genome Project. Medical implications included. Students access two web sites about the HGP to find out about it. Requires internet access.
Credits: occc.
Subject areas: Biology (genetics), general science, anatomy-physiology, biotechnology.
How long it takes: One
period.
- ImmunoAssay Simulation (with forensic twist)
What it is: Perform a simulated immunoassay to detect whether a mock protein sample came from one of four animal sources. The exercise can be integrated into a “crime scene” forensic exercise, or used to demonstrate antigen-antibody interactions. Uses agar plates and harmless inorganic chemicals. Students will conduct assay and then design further experiments with the technique.
Credits: Shoestring Biotechnology project, NABT
Subject areas: General science (forensics), Anatomy-Physiology (immunology), Biology (diffusion).
How long it takes: Assuming prior introduction to the subject matter, one period to conduct protocol, part of next period to discuss results, brain storm new ideas, and design experiments. Third period to perform student-designed experiments.
·
Introduction to
Column Chromatography
What it is: Students are introduced to the basics of chromatography by making an extract of beet leaves and stem, and running the extract through a column of play sand as matrix.
Credits: NABT Shoestring Biotechnology project, OCCC biotechnology program.
Subject areas: biology II, AP biology, biotechnology.
How long it takes: one period.
Making Agarose Gels*
What it is: protocol for making and casting agarose gels for electrophoresis.
Subject areas: AP biology, biotechnology
Time it takes: one period.
*This exercise required before doing DNA Patterns for biotech classes only.
· Micropipetting Exercise and Techniques*
What it is: Students learn correct usage of variable volume micropipettors, make measurements in metric system, do graphs, learn about accuracy and precision.
Subject areas: biology, biotechnology.
How long it takes: One period or less.
*This exercise required
before doing transformation lab, Amax and PCR labs.
What it is: Students work with power supply and gel box to derive Ohm’s law from their observations.
Credits: The Gene Connection project of San Mateo County Biotechnology Education Partnership.
Subject areas: biology, biotechnology, physical science, physics.
How long it takes: one
period.
What it is: Students perform electrophoretic analysis of crabmeat extracts to determine if crabmeat is fake or real. Presented in the context of a mystery to solve.
Credits: Shoestring Biotechnology project, NABT.
Subject areas: Biology, Honors biology (proteins, electrophoresis), biotechnology, bio II.
How long it takes: One period to practice and prepare gels (can skip and use ready-made), one period to prepare extracts of samples, another period to load and run gel (instructor stains and destains gels); one period to discuss results and design further experiments; one period to run further experiments (as on different kinds of fish or meats).
* Prerequisite: Demystifying electrophoresis.
Using Salts and Gel Box to Explore Chemical Concepts
Subject areas: Chemistry, biotechnology.
How long it takes: 4 periods if all exercises are done.
- Sickle Cell Anemia
What it is: Students learn something about the molecular, genetic aspects of sickle cell anemia, explore databases for more information and explore the technology of genetic testing for this disorder. Includes wet lab with electrophoresis.
Credits:
Subject areas: Biology (various levels) and Anatomy-physiology (blood).
How long it takes: about 3-5 class periods.
· Transformation
with pGREEN plasmid*
What it is: A culture of E. coli is transformed with plasmid that makes green fluorescent protein, turning the transformed colonies visibly green.
Credits: protocol and plasmid
derived from
Subject areas: biology II, AP biology, biotechnology.
How long it takes: one period to perform transformation, look at results in second period.
*Prerequisite: Micropipetting techniques.
· Plasmid
MiniPrep of pGREEN plasmid*
What it is: A colony of transformed E. coli from transformation experiment is grown, and the plasmid is recovered, and identified with electrophoresis.
Credits: protocol and
plasmid derived from
Subject areas: biology II, AP biology, biotechnology.
How long it takes: one
period to recover plasmid.
*Prerequisites: Demystifying electrophoresis, Micropipetting Techniques and
Transformation expt.
·
Restriction
Analysis of pGREEN
What it is: A miniprep plasmid is identified by restriction digest and electrophoresis.
Credits: protocol and
plasmid derived from
Subject areas: biology II, AP biology, biotechnology.
How long it takes: one
period to digest; one period for electrophoresis.
*Prerequisites: Demystifying electrophoresis and
transformation expt. and plasmid miniprep.
·
Recovery
and Purification of GFP by Chromatography.
What it is: Students use hydrophobic interaction chromatography to extract and purify GFP from E. Coli MM294 transformed by pGREEN.
Credits: protocol and
plasmid derived from
Subject areas: bio II, biotechnology.
How long it takes: one-two
periods, depending on skill of students in packing columns.
*Prerequisites: Introduction to chromatography.
· PCR Basics *
What it is: Students use PCR beads, primer/loading dye mix, and Lambda DNA to amplify fragment of Lambda genome. Water bath & thermal cycler versions.
Credits:
Subject areas: biology II, AP biology, biotechnology.
How long it takes: two periods, one for cycling, one for running gel.
*Prerequisites: Micropipetting
techniques and Demystifying electrophoresis.
- PCR Human Taste PTC
What it is: Students use PCR beads, primer, and their own DNA to amplify the part of their genome that codes for PTC taste and distinguish tasters versus non-tasters via restriction digest and electrophoresis analysis.
Credits: DNA Learning Center.
Subject areas: biotechnology.
How long it takes: four periods, one to prepare DNA, one for cycling, one for digest, one for running gel. *Prerequisites: Micropipetting techniques, Demystifying electrophoresis and Water Bath PCR.
What it is: Introduce your students to a biotechnology product called Beano. Beano is an enzyme (alpha-galactosidase) that breaks down the complex carbohydrates that otherwise cause gas production in humans when consumed. Students will monitor digestion and design experiments to test the enzyme activity under various conditions.
Credits: Shoestring Biotechnology project, NABT
Subject areas: Biology (enzymes), Anatomy-Physiology (enzymes and digestion).
How long it takes: Assuming prior introduction to the subject matter: One period to conduct protocol, part of next period to discuss results, brainstorm new ideas, and design experiment. Third period to perform student-designed experiments.
For more information please contact:
DeAnn Campbell, Project Coordinator, 682-1611 x7765 dacampbell@occc.edu or
Charlotte Mulvihill, PI, 682-1611 x7225 cmulvihill@occc.edu
Funding provided in part by the National Science
Foundation and the National Institutes of Health