ABLE 2008
Wednesday June 4, 2008
Christopher J. Harendza, Montgomery County Community College
An Inquiry Based Laboratory Investigation of Eutrophication
Cultural eutrophication is a problem that may be worsening due to increases in development, farming, deforestation and use of chemical fertilizers. Factors affecting cultural eutrophication are dependent upon complex interactions between abiotic and biotic factors of terrestrial and aquatic ecosystems. The concept for this laboratory exercise has been adapted from several existing systems, e.g. Wisconsin Fast Plants (www.fastplants.org), terra-aqua columns (www.bottlebiology.org) and existing published research on eutrophication. Student groups assemble a series of “ecocolumns” where Brassica plants are grown in the “terrestrial” component and Elodea is grown in the “pond” section. In addition, the pond section is inoculated with aliquots of chlorophyte algae, cyanobacteria and protozoa. Students formulate hypotheses on how increasing the fertilizer concentration in various ecocolumns will affect the organisms. Students maintain the ecocolumns for approximately 3-5 weeks, revise hypotheses and analyze the ecocolumns visually and microscopically. Non-majors analyze data primarily by semi-quantitative methods and science majors perform a more in-depth quantitative analysis; e.g. plant size, chlorophyll content, seed number, pH, dissolved oxygen, algal cell counts using hemacytometers. Data is collected and analyzed using MS Excel on laptop computers provided by NSF Grant 0410424. Data is discussed in class and/or online using the BlackBoard™ Wiki function and potential remedies to cultural eutrophication are addressed.
Nicholas Collins, University of Toronto at Mississauga
Dendrochronology
A core of rings from a tree trunk represents a huge amount of information about the experience of an individual plant over many years. That information can easily be related to publicly available weather data and to the growth records from other trees. The cores can be obtained at any time of year, the growth rings can be easily measured by students using public domain image analysis software, and the resulting data provide a particularly good opportunity for thinking about many of the conceptual and practical problems of ecological research. Because the students can participate in every phase of data acquisition and because the ring width and weather measurements are rather simple, concrete, and familiar, students find it easy to recognize how the desire to understand the effects of variables like tree position in a stand, or tree stand characteristics, can be translated into mensurative experiments by proper tree-sampling plans. It’s also easy for them to appreciate how effects of tree age and weather can be translated into experiments by strategic sampling of groups of rings within cores. At the same time students begin to recognize how these mensurative experiments, where “effects” are produced by sampling different times or places, differ from manipulative experiments, where effects are evaluated by randomly assigning subjects to treatments. In this workshop I’ll take you through the process from tree coring to data processing and will survey a number of experimental design and data processing exercises I’ve used to help students understand how ecologists cope with natural variation and mensurative experimental designs. I have used dendrochronology successfully in 3rd and 4th year courses where students have had some exposure to statistics.
Paula Lessem, University of Richmond
Use of Bioinformatics to Investigate β-Lactamase, a Mediator of β-Lactam Antibiotic Resistance
Antibiotic resistance is a major problem today. One group of antibiotics, β-lactam antibiotics (penicillin), has had widespread use and efficacy in mediating bacterial infections. However, due to the emergence of antibiotic resistant bacteria their role has been greatly diminished. Bacterial resistance to β-lactam antibiotics provides the contextual material for a multi-faceted module that includes computer simulations, and bioinformatics. The focus of this workshop is the β-lactamase (bla) gene that encodes the enzyme that is one mechanism bacteria employ to resist β-lactam antibiotics. The workshop will consist of introduction to concepts essential for this module including peptidoglycan biosynthesis, antibiotic resistance, β-lactam drugs, and evolution of β-lactam resistance. Use of computer simulations will provide virtual molecular biological applications using a plasmid that contains the β-lactamase gene. These virtual exercises will investigate primer design for the polymerase chain reaction (of the β-lactamase gene) and restriction digestion of the plasmid with the gene. These protocols can be supplemented by actual “wet laboratories.” The final investigation will be using phylogenetics to demonstrate the evolutionary relationship between penicillin binding proteins and β-lactamase. All materials will be presented such that they can be adapted to a non-science population or biology majors.
Dave L. Robinson and Joann M. Lau, Bellarmine University, Bryony S. Wiseman and Melissa Woodrow, Biotechnology Explorer Program – Bio Rad Laboratories
Modular Cloning and Sequencing Lab: A Six-Week Project in Molecular Biology
Click here for updated lab outline
The objective of this project is to teach principles of molecular biology by having students isolate and characterize the gene for the enzyme Glyceraldehyde 3-Phosphate Dehydrogenase (GAPDH), a major enzyme of glycolysis. This project is appropriate for the laboratory portion of an undergraduate (or early graduate) course in Molecular Biology, Cell Biology, Biotechnology, Recombinant DNA Techniques, or Advanced Plant Biology. It would also be suitable for students doing Independent Research.Students start the project by extracting genomic DNA from a plant species, or cultivar, whose GAPDH has not been previously published. PCR primers specific for GAPDH are then used to amplify a major portion of the GAPDH gene, which is then cloned into a vector prior to transformation into competent E. coli cells. Once screened, putative clones are examined by restriction digestion and then sequenced. In addition to these wet-lab experiences in molecular cloning, students also get the opportunity to analyze the resulting GAPDH contig using various bioinformatic tools, such as BLASTx and CLUSTALW. Students should find significant homology of their amplified GAPDH genes to sequences in public databases. This project differs from other biology lab exercises in that the final data, once annotated, can be published in the NCBI GenBank. The GenBank is a repository for publicly-available DNA sequences and is used daily by researchers throughout the world. This exercise can be repeated year after year, each time with a different plant species, or cultivar. This makes the project provocative for both the student and the instructor, and contributes significantly to the study of GAPDH biochemistry, as well as phylogenetics. This workshop will discuss the basic outline of the six-week project, focusing more on the steps taken to construct the final DNA contig, annotate it for publication, and analyze the DNA and amino acid sequence using publicly-available bioinformatics software.
Janice Bonner, College of Notre Dame of Maryland
A Study of Fermentation by Saccharomyces cerevisiae
Enzyme activity is an important component in many introductory biology courses. However, many protocols for enzyme experiments involve a degree of technical proficiency that is beyond a first-year student. As a result, data that result are problematic and cannot lead into meaningful discussion and analysis. This workshop will present a simple method for investigating fermentation. In the basic reaction, a 7% yeast suspension is combined with 1.0% glucose solution in fermentation tubes—conical centrifuge tubes in which the caps have small perforations. As CO2 is produced, the yeast-sugar solution leaves through the hole. At regular intervals, students mark off the fluid level in the fermentation tubes and measure the concentration of glucose with a diagnostic test strip. A small amount of data manipulation is necessary to obtain the volume of CO2 produced by fermentation. The basic reaction can be carried out within 15 minutes. Once the procedure of the basic reaction is established, the laboratory investigation can be taken in multiple directions. Students can be challenged to develop their own extension of the basic reaction. They might, for example, compare fermentation rates when various carbohydrates are substituted for glucose, or study the effect of temperature or pH. Alternatively, students can be asked to predict the effect of increasing substrate concentration on the rate of CO2 production and then to repeat the basic experiment with multiple glucose concentrations. In either extension of the basic reaction, consistent data are reasonably easy to obtain. Students, therefore, have ample opportunity for more extensive data analysis and deliberation. For example, if students study various carbohydrate substrates, they can address enzyme specificity. If they use various concentrations of glucose as substrate in a series of reactions, they can ultimately construct a graph that shows the effect of substrate saturation on the enzymes.
Robert J. Kosinski and Kaighn Morlok, Clemson University
Challenging Misconceptions about Osmosis
Osmosis is very important for cells and is covered in almost all introductory biology courses, but incorrect explanations of it are common. These include the explanations that water moves into hypertonic solutions because the concentration of water is lower there, or that the concentration of “free” (unbound) water is lower in hypertonic solutions. A less intuitive explanation is van’t Hoff’s Law, which says that osmosis is determined by the number of solute particles only.
This laboratory introduces the concept of water potential (including both pressure and osmotic potential). Then it asks students to estimate the water potential of potato cores with the weight-change method using sucrose, glucose, and NaCl as solutes. The results will show that all three solutes produce the same (correct) estimate of potato water potential, but only if solute concentration is expressed as the number of solute particles per kg of water (osmolality), as predicted by van’t Hoff’s Law. Water concentrations, bound water, and solute concentrations in g/L do not predict osmosis consistently.
A slightly different version of this laboratory was used in 2007 in the introductory biology course for majors at Clemson University, and produced excellent results with 270 students in 12 lab sections. Details of these results (and a literature review that would be included in the Notes for the Instructor) are posted at:http://biology.clemson.edu/bpc/bp/Lab/110/osmosis.htm
Marielle Hoefnagels, University of Oklahoma
Museum ecology: using fine art to reinforce ecological concepts (morning)
This lab takes place entirely in the gallery of a local art museum. Students choose paintings in the museum’s permanent collection and answer questions about ecological relationships they can either see or infer in the artwork. Near the end of the lab, each group of students is assigned one painting about which to answer additional questions. Each group presents its answers about the assigned painting to the entire class at the end of the lab period. The ABLE workshop will use paintings located at the University of Oklahoma’s Fred Jones Jr. Museum of Art, but the activity could easily be adapted to any art museum with a permanent collection of paintings or photographs showing ecological interactions and human impacts on the environment.
Norris Armstrong and Peggy Brickman, University of Georgia
Conversion Immersion (afternoon)
Traditional classes frequently present course material as isolated information without strongly linking the concepts being taught to students’ existing knowledge or experiences. Lacking such reference points with which to base their learning, students often resort to memorizing the information rather than truly understanding it. Case-based learning attempts to address this dilemma by presenting course material in the context of an individual or group faced with a problem that must be solved. Students are provided with background information that, with the help of their instructor, they must analyze in order to suggest possible solutions to the problem being faced.
We will hold a “Conversion Immersion” workshop in which instructors can work together to create Cases that can be used to teach basic concepts either in a lecture or a laboratory format. The ideas that emerge from this workshop will be summarized for presentation in the ABLE Proceedings.
Thursday June 5, 2008
Christopher W. Beck, Emory University and Lawrence S. Blumer, Morehouse College
Intraspecific Competition in Bean Beetles
Bean beetles, Callosobruchus maculatus, are agricultural pest insects of Africa and Asia. Females lay their eggs on the surface of beans (Family Fabaceae). The choice of prey bean is the most important choice a female makes for her offspring, as it will influence their growth, survival, and future reproduction. In this study, students design and conduct experiments to evaluate whether female bean beetles respond to the potential for competition among their offspring. The experiments will address three questions: In bean beetle populations, who are potential competitors of a female’s offspring? Do female bean beetles attempt to minimize competition among their offspring? What are the underlying assumptions of the hypothesis that females attempt to minimize competition among their offspring?
Fred Singer, Radford University
Ecology of Dragonflies
Dragonflies are ideal models for community ecology, because they are relatively large, easy to identify, may defend territories or home ranges, and spend a significant amount of time in open areas. Many dragonfly communities will have about five common species, enough for there to be significant differences between species in habitat use, but not too much to frustrate students with identification challenges.
Dragonflies use bodies of water exclusively for mating, as most of their foraging occurs over land. Females oviposit in the water or alongside the shoreline. Males usually defend territories from which they exclude conspecifics – interestingly, some species also exclude other species as well. The characteristics of the habitat can differ between species, and may be the result of an evolutionary history of interspecific competition. A prediction of the interspecific competition hypothesis is that different species will have different behaviors or habitat preferences on a pond that reduce the cost of interspecific competition.
In this lab we explore between-species differences in how high the dragonflies fly, proportion of time in flight and territory size. I chose these variables because they were easy to measure, and were likely to be important factors in the relatively ecologically homogeneous Radford University Wetland. Most of our time will be spent alongside a pond, familiarizing ourselves with the dragonflies, and collecting the same types of data that my students gathered in Fall, 2007. We will discuss how to measure these variables, and some of the challenges associated with making sure that the data are somewhat meaningful. We will also analyze the data at both an introductory and at a more advanced level. We will conclude with a discussion of how this lab activity can be expanded or spun off into investigations of related questions.
Ginny Hutchins, Fort Lewis College and Cathy Silver Key, North Carolina Central University
Gene Knockout/Gene Therapy in Yeast Using Homologous Recombination
The goal of this major workshop is to engage participants/students in learning the concept of homologous recombination by performing a yeast gene deletion/gene therapy experiment. Coupling the engaging concept of ‘gene therapy’ with the complex concept of ‘homologous recombination’, we have developed a laboratory learning module to facilitate student learning by combining three basic teaching approaches: lecture, discussion, and hands-on wet lab. Workshop participants will perform a transformation of S. cerevisiae (baker’s yeast) and observe the resulting phenotypes on selection media plates. Participants will use a hybrid PCR-generated DNA fragment, which contains sequence representing the 5’ and 3’ UTRs of the target gene which flank the coding region of a selection marker gene, to transform yeast. Homologous recombination between the hybrid PCR fragment and the yeast genome results in replacement of the target gene with a selection marker gene. Subsequently, the yeast phenotype is visibly transformed. The targeted gene, ADE2, codes for an enzyme in the purine biosynthesis pathway; loss of the ADE2 gene causes accumulation of purine precursors in the vacuole, giving the yeast colonies a pink/red color. Additionally, since participants will be replacing the ADE2 gene with the TRP1 selection gene in a mutant yeast strain that lacks a functional TRP1 gene, they are simultaneously performing ‘gene therapy’: the yeast will regain the wild-type phenotype of being able to grow on media lacking tryptophan. Participants will also calculate transformation efficiency, solve worksheet problems, and discuss other possible student results. The yeast gene knockout/gene therapy module has been successfully performed by students at multiple institutions; pre-test data, post-test data, and student evaluations have been collected indicating that this is an easy-to-perform, engaging laboratory that increases student knowledge and confidence of targeted concepts.
Charlotte Omoto, Washington State University
Diffusion
Diffusion is a fundamental physical process that is important in biology. Textbooks commonly explain diffusion as movement of solutes from region of higher concentration to a region of lower concentration. Thus students think of diffusion only in the context of a concentration gradient. The key concept that diffusion is due to random movement due to thermal energy, and is a power function, not a linear function, is often overlooked. Thus, many mistakenly use the term diffusion rate, not recognizing that diffusion cannot be described as rate that is constant over time and distance. In this very simple laboratory exercise, students measure how much time it takes for diffusion to cover various distances. By graphing this data, they see the
power relationship between diffusion over distance and thus the time that it takes. So although the exercise is simple, it conveys a very important aspect of diffusion that is difficult to understand. Once the student understands the power function aspect of diffusion, it is much easier to recognize why, diffusion on the scale of single cells is very fast and efficient whereas diffusion over relatively short but macroscopic distances is much too slow for many biological processes.
Kathy Winnett-Murray and Lori Hertel, Hope College
BioOp Corporation: An Investigative Interdisciplinary Case Study on the Eye
Authors of Exercise: Christopher C. Barney, Dept. of Biology and Catherine M.Mader, Dept. of Physics, Hope College, Holland, MI
This exercise consists of a case study on biological solutions to optical problems that was specifically designed by members of our Biology and Physics departments to encourage our second semester introductory biology majors to become better equipped to draw learning connections between these two disciplines. In this case study, students examine the physical and biological properties of vision as employees of an imaginary company, BioOptics Corporation. There are two main components of the case study – 1) A laboratory component on optics using optical benches to investigate various physical aspects of visual systems based on pinholes, mirrors, and lenses, and 2) An out of lab component in which students research information on visual systems and then propose solutions to one of three visual problems: 1) improving visual acuity, 2) improving visual (light) sensitivity, and 3) expanding the range of wavelengths that can be detected in color vision. These proposed solutions, along with the background research information, are then presented to each laboratory section as an oral presentation.
Sarah E. Jardeleza, University of Georgia
Systematics Lab
Systematics is the classification and study of organisms with regard to their evolutionary history. It is fundamental to all modern biology and all science students should and will see phylogenetic trees at some point in their education. However, there are few opportunities for students to understand the science behind systematics and its importance. Systematics is essential to many branches of science and technology including: human health, pharmaceuticals, agriculture, as well as understanding and conserving biodiversity. Projects such as the Human Genome Project (HGP) are based on systematic analyses and the growing database of genomic data represents a multi-billion dollar investment of resources. This lab is designed to serve as an introduction to the concepts of how to unfold the information phylogenetic trees impart to us as well as the processes that go into making the trees themselves from databases such as the HGP and Genbank. For the latter part of the lab we will utilize the user-friendly program “Geneious” that “combines all the major DNA and protein sequence analysis tools into one revolutionary software solution!” Helping our students on the road to learning the systematics language and understanding what goes into an analysis increases their appreciation for the importance of systematics and how it affects not only science but also their lives.
Norris Armstrong and Peggy Brickman, University of Georgia
Conversion Immersion (morning)
Traditional classes frequently present course material as isolated information without strongly linking the concepts being taught to students’ existing knowledge or experiences. Lacking such reference points with which to base their learning, students often resort to memorizing the information rather than truly understanding it. Case-based learning attempts to address this dilemma by presenting course material in the context of an individual or group faced with a problem that must be solved. Students are provided with background information that, with the help of their instructor, they must analyze in order to suggest possible solutions to the problem being faced.
We will hold a “Conversion Immersion” workshop in which instructors can work together to create Cases that can be used to teach basic concepts either in a lecture or a laboratory format. The ideas that emerge from this workshop will be summarized for presentation in the ABLE Proceedings.
Marielle Hoefnagels, University of Oklahoma
Museum ecology: using fine art to reinforce ecological concepts (afternoon)
This lab takes place entirely in the gallery of a local art museum. Students choose paintings in the museum’s permanent collection and answer questions about ecological relationships they can either see or infer in the artwork. Near the end of the lab, each group of students is assigned one painting about which to answer additional questions. Each group presents its answers about the assigned painting to the entire class at the end of the lab period. The ABLE workshop will use paintings located at the University of Oklahoma’s Fred Jones Jr. Museum of Art, but the activity could easily be adapted to any art museum with a permanent collection of paintings or photographs showing ecological interactions and human impacts on the environment.