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1. Human DNA Fingerprinting by Polymerase Chain Reaction

Mark V. Bloom, DNA Learning Center  [abstract] [full text]

2. Polyacrylamide Gel Electrophoresis (PAGE) of Blood Proteins

John C. Mordacq and Roberta W. Ellington, Northwestern University  [abstract] [full text]

3. Transposon Mutagenesis of Rhodobacter sphaeroides

Timothy Paustian and Robin Kurtz, University of Wisconsin at Madison  [abstract] [full text]

4. Isolating Multiple Strains of Escherichia coli for Coliphage Isolation, Phage-typing, and Mutant Recovery

Richard A. Levin, Oberlin College  [abstract] [full text]

5. Building Molecular Models of DNA, Protein, and Lipids

Anne L. Cordon and Neil A. Straus, University of Toronto  [abstract] [full text]

6. Invertase Activity in Root Growth

Chris J. Perumalla, Johan A. Hellebust, and Corey A. Goldman, University of Toronto  [abstract] [full text: pdf | html]

7. The Hill Reaction: In Vitro and In Vivo Studies

Edward A. Funkhouser and D. E. Balint, Texas A&M University  [abstract] [full text]

8. Determining Hemolymph Volume of the Cockroach

J. J. B. Smith, University of Toronto  [abstract] [full text: pdf | html]

9. The Immune System: Red Cell Agglutination in Non-Humans

Fred W. Quimby, Cornell University, and Nancy V. Ridenour, Cornell High School  [abstract] [full text]

10. An Analysis of Bone/Muscle Movement

Alice C. Jacklet, State University of New York at Albany  [abstract] [full text]

11. Were Dinosaurs Cold- or Warm-Blooded?: An Exercise in Scientific Inference

Grant R. Hurlburt, University of Toronto  [abstract] [full text]

12. Inbreeding Depression and the Evolutionary Advantage of Outbreeding

Christopher G. Eckert, Queen's University  [abstract] [full text: pdf | html]

13. Phylogenetic Systematics: Developing an Hypothesis of Amniote Relationships

Daniel R. Brooks, Deborah A. McLennan, Joseph P. Carney, Michael D. Dennison, and Corey A. Goldman, University of Toronto  [abstract] [full text]

14. Light-Induced Phenotypic Plasticity in Plants

Douglas E. Ryerson and Nancy G. Dengler, University of Toronto  [abstract] [full text]

15. When Do Adaptive Mutants Arise in Yeast?

Michael D. Dennison and Corey A. Goldman, University of Toronto  [abstract] [full text]

16. Predator-Prey Coevolution

Linda R. Van Thiel, Wayne State University  [abstract] [full text]

17. The Evolution of Cooperative Behavior

Alejandro Lynch, University of Toronto  [abstract] [full text]

18. An Investigation of the Behavior of the Pea Aphid, Acyrthosiphon pisum

Joan C. Sharp, Simon Fraser University, and Maydianne Andrade, University of Toronto  [abstract] [full text]

• Appendix A: Abstracts of Mini Workshops
• Appendix B: Author Index, Volumes 1-15
• Appendix C: Subject Index, Volumes 1-15

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Abstracts (Vol. 15)

Laboratory Exercises in Cell and Molecular Biology

1 -- Human DNA Fingerprinting by Polymerase Chain Reaction
Mark V. Bloom  [full text]
Key Words: DNA fingerprinting, polymerase chain reaction, polymorphism.
This experiment uses polymerase chain reaction to demonstrate the polymorphic nature of human DNA. Students obtain samples of their own DNA using a simple mouthwash procedure. PCR is used to amplify a noncoding region of chromosome 1 that contains a repeated DNA sequence. The number of times the sequence repeats can vary from person to person, resulting in a polymorphism. Following amplification, student samples are electrophoresed, stained, and photographed. Each student will see one or two bands in their gel lane, indicating whether they are homozygous or heterozygous for that region of chromosome 1. This experiment is adapted from Advanced DNA Science: An Introduction to Methods of Genome Analysis by Mark V. Bloom, Greg A. Freyer, and David A. Micklos (copyright 1993 Cold Spring Harbor Laboratory and Carolina Biological Supply Company); polymerase chain reaction is covered by patents owned by Hoffman La Roche.

2 -- Polyacrylamide Gel Electrophoresis (PAGE) of Blood Proteins
John C. Mordacq and Roberta W. Ellington  [full text]
Key Words: polyacrylamide, electrophoresis, blood, proteins.
In this laboratory exercise, students utilize differential precipitation and polyacrylamide gel electrophoresis in combination with centrifugation and detergent extraction to fractionate the complex mixtures of proteins found in mammalian red blood cells and mammalian blood plasma and to characterize some of the component proteins. Gels are stained with Coomassie blue and migration distances for the unknown proteins are compared with those of known protein standards. Students then determine the sizes of the unknown proteins, compare their relative abundance, speculate about the identities of the components of the various fractions, and evaluate the efficiency of the fractionation techniques.

3 -- Transposon Mutagenesis of Rhodobacter sphaeroides
Timothy Paustian and Robin Kurtz  [full text]
Key Words: transposons, bacteria, conjugation, mutagenesis.
Creation and characterization of mutants is the basis for any genetic analysis. This exercise demonstrates a simple, safe procedure for transposon mutagenesis of Rhodobacter sphaeroides, a purple non-sulfur photosynthetic bacteria. Students perform the mutagenesis by mating a transposon-carrying plasmid from Escherichia coli to R. sphaeroides and then selecting for the drug resistance carried on the transposon. Only R. sphaeroides carrying the transposon in the chromosome survive the selection. Transposon carrying mutants are then scored for various phenotypes. The metabolic diversity of R. sphaeroides allows the isolation of nutritional, photopigment, and photosynthetic mutants. Further analysis of mutants is possible.

4 -- Isolating Multiple Strains of Escherichia coli for Coliphage Isolation, Phage-typing, and Mutant Recovery
Richard A. Levin  [full text]
Key Words: bacteria and coliphage isolation, phage typing, mutant recovery.
Recovery of Escherichia coli from a rectal swab begins a series of procedures combining mastery of technique with productive experiments. After isolating his/her own E. coli strain, each student recovers a unique coliphage from raw sewage and determines its host range, thereby revealing the genetic individuality of each bacterial and viral isolate. Colonies of virus-resistant mutants can often be recovered in regions where sensitive bacteria have been destroyed. After antibiotic sensitivity testing of E. coli isolates, a variety of antibiotic resistant mutants can be recovered, thus yielding genetically marked strains for future bacterial genetics experiments.

5 -- Building Molecular Models of DNA, Protein, and Lipids
Anne L. Cordon and Neil A. Straus  [full text]
Key Words: macromolecular structure, three-dimensional shape and spatial orientation.
Molecular models of DNA, protein (à-helix and B-pleated sheet), and lipids are built to scale. With a minimum of scientific jargon, these laboratory exercises effectively display the important aspects of three-dimensional shape and spatial orientation that are poorly presented in textbook illustrations and demonstrate how the shape of molecules and weak chemical associations like hydrogen bonds and hydrophobic/hydrophilic interactions combine to form the macromolecular associations fundamental to living cells.

Laboratory Exercises in Physiology

6 -- Invertase Activity in Root Growth
Chris J. Perumalla, Johan A. Hellebust, and Corey A. Goldman  [full text: pdf | html]
Key Words: invertase activity, enzyme assay, root growth, anatomy of root tip.
In this exercise students study the interaction between structure and function in the corn root. Students begin by observing a prepared slide of corn root and identifying the regions of cell division, elongation, and maturation of the root tip, and measuring the length of five cortical cells. They then use roots from corn seedlings and determine the activity of the extracellular enzyme, invertase, present in specific 2-mm sections taken from different regions along the corn root. This information is used to later determine how the enzyme activity per cell changes in relation to growth in the corn root.

7 -- The Hill Reaction: In Vitro and In Vivo Studies
Edward A. Funkhouser and D. E. Balint  [full text]
Key Words: photosynthesis, light reactions, herbicides, algae.
For many students, light-driven electron-transport can be abstract and with little utility. To provide additional ways of visualizing this process, this series of exercises is designed (1) to show that the light-reactions of photosynthesis are proportional to light intensity and can be monitored in isolated chloroplast-particles, (2) to demonstrate that chlorophyll, in solution, traps and re-emits light by fluorescence, and (3) to observe increases in chlorophyll fluorescence in intact green-algae when cultures are treated with herbicides that block electron transport. These exercises were adapted from Laboratory Exercises in Plant Physiology by D. E. Balint and E. A. Funkhouser (Ginn Press, 1993).

8 -- Determining Hemolymph Volume of the Cockroach
J. J. B. Smith  [full text: pdf | html]
Key Words: insect circulatory system, hemolymph volume, cockroach, dilution techniques, pipetting.
Insects have slow, low-pressure open circulatory systems that do not carry respiratory gases. The hemolymph (blood) acts as a reservoir of water and metabolites, and its volume can vary considerably. In this exercise students determine cockroach hemolymph volume by injecting a known amount of Amaranth Red dye into a cockroach and measuring its dilution by the hemolymph. They (1) derive a standard curve for dye concentration by a method simulating the dilution by the hemolymph, (2) inject a cockroach with a known amount of dye, (3) extract hemolymph samples at given times, and (4) plot their data and calculate hemolymph volume. A 3-hour exercise that introduces students to laboratory skills is provided as an appendix; including types of pipets, how to pipet, errors in pipetting and weighing, single and serial dilution techniques, and establishing a standard curve.

9 -- The Immune System: Red Cell Agglutination in Non-Humans
Fred W. Quimby and Nancy V. Ridenour  [full text]
Key Words: antibody, lymphocytes, hemagglutination, complement, Rh-factor, hemolytic disease of the newborn.
This exercise presents the concepts of immunology from biochemical, evolutionary, and adaptive standpoints. While all organisms have developed some mechanism of defense against external agents, vertebrates have the most complex immune responses capable of exquisite specificity and long duration. This affords a distinct advantage to species with a relatively long life span and low fecundity. This exercise explores the relationship between immunologic stimulation of the host with foreign antigens and antibody production. The principles of species specificity, primary and secondary immune responses, cross-reactivity, and complement-mediated cell lysis are demonstrated using the red cell agglutination assay. Agglutination occurs when a single antibody molecule binds simultaneously to a surface antigen on two red cells a principle used daily in the diagnosis of viral infections and blood groups incompatibility in humans and other animals.

10 -- An Analysis of Bone/Muscle Movement
Alice C. Jacklet  [full text]
Key Words: skeletal system, muscle system, kinematic model, evolution, biological levers.
By manipulating a simple kinematic model representing the leg and foot, students can get hands on information about the interaction of bones and muscles in humans. Having worked with the model, they then are able to predict and analyze the properties of bone/muscle systems in other vertebrates and understand how these systems have become modified during the course of evolution for a particular life style. By the end of the exercise, students have learned both traditional information (cellular structure, names of bones, taxonomy of vertebrates) and how to project the knowledge they gained from working with a model to the biological world.

11 -- Were Dinosaurs Cold- or Warm-Blooded?: An Exercise in Scientific Inference
Grant R. Hurlburt  [full text]
Key Words: dinosaur, thermal regulation, allometry, relative brain size.
Both metabolic rates and brain masses are approximately 10 times as great in modern terrestrial warm-blooded animals (birds and mammals) as in cold-blooded terrestrial animals (reptiles) of the same body mass. This is one of several lines of evidence scientists have used to infer the mode of thermal regulation of dinosaurs and other extinct amniotes. In this exercise each student is assigned one of a number of dinosaurs. Students estimate brain mass from a drawing of a cranial endocast and body mass from a plastic model. They determine relative brain size and compare this to relative brain sizes of modern vertebrates. Students combine this application of allometry with information about Mesozoic environments and thermal physiology to infer the mode of thermal regulation of their assigned species.

Laboratory Exercises in Evolution, Ecology, and Behaviour

12 -- Inbreeding Depression and the Evolutionary Advantage of Outbreeding
Christopher G. Eckert  [full text: pdf | html]
Key Words: Brassica rapa, Fast Plants, genetic load, heterosis, mating-systems, self-fertilization, self-incompatibility, sex.
The harmful effects of inbreeding constitute a major selective force maintaining outbreeding in plants and animals. This long-term laboratory experiment examines the negative effects of inbreeding on fitness in fast-cycling populations of self-incompatible Brassica rapa (Brassicaceae). Components of survival, growth, and flowering are compared between experimentally self- and cross-fertilized offspring. A quantitative estimate of inbreeding depression is then calculated and used to predict whether outbreeding is evolutionarily stable. In completing this experiment, students become familiar with basic ideas in reproductive ecology, population genetics, and experimental design.

13 -- Phylogenetic Systematics: Developing an Hypothesis of Amniote Relationships
Daniel R. Brooks, Deborah A. McLennan, Joseph P. Carney, Michael D. Dennison, and Corey A. Goldman  [full text]
Key Words: phylogenetic analysis, reconstructing phylogenetic relationships, cladistics, phylogenetic reconstruction of amniotes.
Biodiversity studies begin with patterns of evolutionary diversification, made possible by phylogenetic systematics. Phylogenetics clusters species into groups depicting their common ancestry based on shared derived characters unique to that group. It is quantifiable, reproducible, and scientifically testable, and has three assumptions: evolution has occurred, there is a single phylogeny of life resulting from evolutionary diversification, and characteristics are passed from generation to generation, modified or unmodified, during evolutionary descent. This exercise acquaints students with the terminology and methodology of phylogenetics, and permits them to reconstruct the phylogenetic relationships among major amniote groups using characteristics they observe themselves.

14 -- Light-Induced Phenotypic Plasticity in Plants
Douglas E. Ryerson and Nancy G. Dengler  [full text]
Key Words: phenotypic plasticity, plant growth, leaf anatomy, chlorophyll, t-test.
Phenotypic plasticity is the ability of an individual organism to alter its physiology or morphology in response to changes in environmental conditions. This ability is particularly important for the non-motile vascular plants that are unable to move when environmental conditions become unfavourable. This exercise compares morphological and anatomical characteristics of two plant species after 6 weeks of growth under two differing levels of irradiation. Measurements of leaf area, weight, thickness, and anatomy are used to test the hypothesis that species that colonize more variable habitats will show considerable phenotypic plasticity in contrast to species from stable, shaded habitats that show little plasticity.

15 -- When Do Adaptive Mutants Arise in Yeast?
Michael D. Dennison and Corey A. Goldman  [full text]
Key Words: baker's yeast, spontaneous mutations, replica plating, copper-tolerant mutants.
This exercise examines when adaptive mutations arise in a population. Students prepare cultures of baker's yeast on normal agar media and then transfer the exact spatial pattern of these colonies to agar plates containing copper using the replica-plating technique. They compare the pattern of mutant colonies on the two replicate plates to test when copper-tolerant mutants arose. If the colony positions match then the mutants pre-existed in the original population (spontaneous mutation). If colonies do not match then this supports a hypothesis that mutants were induced by exposure to the copper. Students learn skills such as preparing agar plates, the sterile technique, replica-plating, and the use of pipets and dilutions.

16 -- Predator-Prey Coevolution
Linda R. Van Thiel  [full text]
Key Words: predator, prey, natural selection, phenotype morphs, reproductive advantage, coevolution.
Through natural selection, two interacting populations of predators and prey can change with respect to one another. Some prey individuals display characteristics that decrease their chance of capture; they have a reproductive advantage and produce more offspring. Other individuals display negative characteristics that result in a greater chance of being captured; their numbers decrease as they fail to reproduce. Predators are similarly affected. This exercise examines the change in numbers of individuals of three predator morphs and four prey morphs over four generations. Students actively participate as predators and capture prey morphs, simulating the feeding needed to support reproduction.

17 -- The Evolution of Cooperative Behavior
Alejandro Lynch  [full text]
Key Words: cooperation, evolution, game theory, reciprocity, Prisoner's Dilemma.
In this exercise students investigate the possibility of cooperative behavior to arise among unrelated individuals even in the presence of selfish individuals or individuals that do not care for the well- being of other organisms with which they interact. Is it possible for individuals to obtain the benefits of mutual cooperation but at the same time protect themselves from cheaters? Students play a game among themselves where they use a number of different strategies that are either cooperative or selfish. They will learn basic concepts of game theory and use these to examine the evolution of cooperative behavior. A computer simulation is available where students can expand the range of possibilities that are offered to them during the laboratory exercise.

18 -- An Investigation of the Behavior of the Pea Aphid, Acyrthosiphon pisum
Joan C. Sharp and Maydianne Andrade  [full text]
Key Words: aphid, behavior, pheromone, life cycle, parthenogenesis, introductory biology.
The pea aphid, Acyrthosiphon pisum, is a versatile laboratory organism. This experiment investigates the response of pea aphids to an alarm pheromone normally produced in response to predator attack. The responses of aphids feeding on good quality and on poor quality long bean plants will be compared and discussed in terms of the costs and benefits of antipredator behaviors. The life cycle of the pea aphid is demonstrated and information about obtaining, rearing, and working with pea aphids is provided.

Mini Workshops

 [full text]

• Identification of an Unknown Plasmid (Todd M. Bennethum)
• Tissue Printing: A New Way to Look at Plant Structure (Graham R. Kent and Philip D. Reid)
• A Student-Built Cell Counting Chamber (Robert B. Ketcham)
• An Economical Method for Generating and Delivering an Even Flow of CO₂ Gas (Angélique G. L. Gloss and Evelyn J. Stillwell)
• Teaching Spectrophotometry and Graphing Using Red Cabbage Extract and pH Buffers (Frances G. R. Kennedy)
• Some Effects of pH on Living Systems (Sherry K. Brooks)
• Ecological Interactions: Testing Prey Distribution Patterns (Jane M. Beiswenger)
• Succession in a Sub-Alpine Forest (Karen E. Bedford and Ruth St. John)
• Ecological Crisis 2050 A.D. (Nancy L. Goodyear)
• Majors Biology: An Evolutionary Synthesis (Joan C. Sharp)
• A Semester-Long Research Problem Approach to Senior Undergraduate Laboratories in Ecology (Thomas D. Nudds)
• The Methods of Science: Properties of Life as Observed in a Slime Mold (Carolyn S. Ogren)
• From Hypothesis to Manuscript: Small Group Research Projects in Ecology for Introductory Biology and Ecology Courses (David Lasenby, Erica Nol, and Kate Frego)
• The Eyes Have It: Ideas for Undergraduate Student Research (Kathleen A. Nolan, Adam Splayer, Matthew Gottlieb, and David Azizian)
• Making and Using Computer Animations to Teach Biology (Alan W. Day and Robert L. Dean)
• Procuring and Preserving Animals for Biological Instruction (Raymond O. Flag