These 2-3 hour workshops are hands-on, laboratory sessions during which presenters shared their innovative and successful undergraduate lab exercises with participants. Abstracts are available below, sorted by day of presentation.
Wednesday, June 20, 2012
The Genomics Education Partnership (GEP): Undergraduate Student Analysis of Drosophila Genomes
(Julie A. Emerson, Amherst College, Amherst, MA; S. Catherine Silver Key, North Carolina Central University, Durham, NC; Satish C. Bhalla, Johnson C Smith University, Charlotte, NC; Stephanie Mel, University of California, San Diego, La Jolla, CA; Mary A. Smith, North Carolina A & T State University, Greensboro, NC; Gerard McNeil, York College and The CUNY Graduate Center School of Arts and Sciences, Jamaica, NY)
An effective method for teaching science is to engage students in doing science. The GEP, a group of faculty from over 80 primarily undergraduate institutions, is using comparative genomics to engage students in research within regular academic-year laboratory courses (http://gep.wustl.edu). Using a versatile curriculum that has been adapted to many different class settings (as the core of a research-based laboratory course, as an independent research project, or as a smaller number of activities within the lab of a broader course), GEP undergraduates undertake projects to improve draft genomic sequences and/or participate in annotation of these improved sequences. GEP undergraduates have improved over 2.4 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. An additional goal of the GEP is for students to gain a more sophisticated understanding of eukaryotic gene structure and mRNA processing than is often achieved in lectures. At Amherst College, gene annotation has been integrated into the existing laboratory curriculum of Biology 191 (Molecules, Genes and Cells). This one-semester course is required for biology majors, has a chemistry pre-requisite and is taken primarily by first-semester sophomores; enrollment is ~100 students, who are divided into five lab sections of up to 24 students each. Using one hour of discussion and nine hours of lab time over the last quarter of the semester, students receive training in DNA database searches and complete a gene annotation research project, carefully mapping the protein-coding regions of a putative gene from a recently-sequenced Drosophila species (http://flybase.org/static_pages/species/sequenced_species.html). Participants in the ABLE workshop will work with some of the GEP’s gene annotation training and research tools, to examine both pre-annotated genes and one newly-sequenced, unannotated DNA sequence.
The Size of Living Things
(Kenneth Sossa, Notre Dame of Maryland University, Baltimore, MD)
Most General Biology II courses focus on animal, plant, and fungi taxonomy, while addressing some relevant biological processes, i.e. reproduction, digestion, etc. This procession through the kingdoms of life often leaves biology students unengaged. Here, we present an alternative to teaching this type of course. We base our method on work by biologist John Tyler Bonner (Why Size Matters: From Bacteria to Blue Whales, 2006) and others who illustrate the limitations and advantages of size on life processes within organisms. The laboratory exercises presented guide students as they graph data showing the relationship between size and strength, speed, or complexity. All of these size relationships are proportional with profound significance. While becoming proficient on Excel, students learn biological concepts and scientific literature mining. Using this method, students gladly discover size rules that illustrate the unity and diversity of life.
A Completely Hands-On Paternity Dispute Using DNA Markers and Rapid-Cycling Brassica rapa (Fast Plants Type)
(Douglas Wendell, Oakland University, Rochester, MI)
Students use DNA markers to resolve a paternity dispute resulting when a female has mated with two males and produced a child. The project uses rapid cycling Brassica rapa (a.k.a. Fast Plants) so it can be fully hands-on for the students, but the data generated are of the same type as used in human paternity testing. Students pollinate a plant (Mother) with a mixture of pollen from two other plants (Alleged Fathers). Later they sow the resulting seeds to produce the Child. To obtain genotype data, the students collect leaf tissue from all plants, use it to purify DNA, and then use PCR and gel electrophoresis to determine the plants’ genotype for VNTR-type DNA markers. Multiple child genotypes are possible because one of the Alleged Fathers is heterozygous for each marker used while the other Alleged Father is homozygous. In some cases a clear paternity exclusion can be made, while in others the student must realize that a clear determination cannot be made. Therefore, students must learn not only to trace the inheritance of alleles from parents to offspring but also evaluate the informativeness of their data. The markers used in this lab were designed specifically so that they can be analyzed with the relatively simple equipment that is usually available in a college teaching lab. Mini workshop participants will learn about the DNA markers that we have developed for Fast Plants, practice key points in the methods we have developed to make DNA marker analysis possible in an introductory Biology lab, and perform analysis the data that students can produce.
Behavioral Priming in Jumping Spiders
(David A. McKinney, University of Georgia, Athens, GA)
Laboratory exercises in behavior are relatively uncommon, and this is in part due to the difficulty of working with most model organisms. Here I propose a novel model organism for teaching behavior, and exemplify its tractability and accessibility with a laboratory exercise in behavioral priming. In this inquiry-focused exercise, students will design behavioral experiments and investigate the concept of behavioral priming in the context of jumping spider communication. The basics of obtaining, maintaining, and manipulating jumping spiders are also described.
Ants as Model Organisms to Study Species Coexistence
(Jonathan Z. Shik, North Carolina State University, Raleigh, NC; Andrea Lucky, North Carolina State University, Raleigh, NC; Mariëlle Hoefnagels, University of Oklahoma, Norman, OK.)
Community ecologists seek to explain species diversity, using experiments to explore the mechanisms regulating species coexistence. Decades of research suggest that niche differentiation plays an important role in allowing ecologically similar species to coexist. In this lab, we will perform a field experiment to explore niche differentiation in an ant (Hymenoptera: Formicidae) community. We will have four main objectives: 1) appreciate ant diversity, 2) test hypotheses about how niche differentiation mediates species coexistence, 3) use ecological methods and analyze data, and 4) participate in School of Ants, a global citizen science initiative based in North Carolina that uses ants to explore biology diversity.
Induction, Purification, Enzymatic Activity and Mutagenesis of Dihydrofolate Reductase
(Joanne M. Lau, Bellarmine University, Louisville, KY)
Dihydrofolate reductase (DHFR) is a key enzyme in the metabolism of folate, catalyzing the reactions for purine synthesis, DNA synthesis, and certain amino acids. The objective of this project is to have students induce expression, purify and enzymatically assay for DHFR activity. In addition, students conducted novel experiments by designing PCR primers for site-directed mutagenesis and examine specific activity of their mutant DHFR product and compare it to the wild-type DFHR gene. Furthermore, students also obtained protein concentrations of their purified DHFR protein product and performed Western blot analysis to detect the glutathione S-transferase (GST) and Histidine (His) tags that were attached to the DHFR gene. In addition to standard biochemical and molecular techniques (e.g. protein purification, PCR amplification, transformation into competent expression cells, restriction enzyme digest, agarose gel electrophoresis, polyacrylamide gel electrophoresis, and Western blotting), students gain experience measuring specific enzyme activity, and bioinformatics skills for primer design and sequence alignment are reinforced.
Outbreak!: Scenario-Based Instruction in Microbiology
(Angela M. Seliga, Jan Blom, Xiaojuan Khoo, and Matthew Walker, Boston University, Boston, MA)
With recent outbreaks of swine flu and the emergence of superbugs it is important to introduce students to the organisms responsible for infectious diseases and how easily they are spread. In this scenario-based learning (SBL) module, students will take part in a simulated epidemic and model the outbreak of an unknown pathogen. Through a six-part series of guided investigations, students will identify the “pathogen” responsible for the epidemic using simple microbiological assays and determine the best treatment to eradicate the infection. The proposed major workshop will present two of these activities and discuss the development of this module.
Testing Hypotheses of Aging in the Nematode Caenorhabditis elegans
(Pliny A. Smith Lake Forest College, Lake Forest, IL)
A common characteristic of many, if not all metazoans, is aging. Countless evolutionary, molecular, and genetic mechanisms have been described that account for aging of creatures as diverse as yeast and man. This laboratory will put some of these factors to the test; participants will develop a hypothesis that explains the interactions between genes and the environment, and design an implement an experiment to test the hypothesis. Students design controlled experiments using the model organisms C. elegans that include variables of environment, food, or genetic background. After completing the experiment, students analyze their data and write a research article-style report.
Authentic Assessment Using Biology Lab Practicals
(Kathy Winnett-Murray and Lori Hertel, Hope College, Holland, MI)
Authentic assessment tasks use real world contexts and are aligned with the assessment and content standards we create. Biology laboratory practicals present a great opportunity to authentically assess individual student achievement of laboratory and field skills. Yet, lab practicals seem to have become less common over the past few decades while science education reform, and most of our colleges and universities, have indicated an increasing need for documenting our assessment strategies over the same time period. Concerned by the challenges of individual accountability among students typically working in lab groups, and by poor retention of skills needed for more advanced biology courses, our department implemented an extensive, integrated program of skills assessment in 2001. We did this primarily by “resurrecting” the lab practicals that had fallen out of vogue decades ago, with a new twist: instead of evaluating student learning of (solely) content-based material, we created practicals in which we directly evaluate each student’s ability to do pre-selected skills that we have collectively identified as being the most important things that all biology majors should be able to do (things such as microscopy, use of various forms of instrumentation, making serial dilutions, preparing graphics with a computer program, handling animals, etc.). A decade and a gigantic database later, we will share what we have learned, from the practical demonstration of “best practices” (planning, set-up and implementation of several of our “favorite” questions, use of TAs, scoring rubrics) to the challenges of tracking and interpreting the data. We will even have some success stories of how our authentic assessment results have enabled our department to make some important curricular and instructional changes.
Thursday, June 21, 2012
Engaging Introductory Biology Students in Critical Analysis and Independent Research
(Jean G. Heitz, University of Wisconsin, Madison, WI)
Numerous studies over the past 20 years have indicated the need to improve both the general level of science literacy among our students and to increase the number of students electing science as a career. A number of these reports have indicated that one mechanism for doing this is to involve undergraduates in research and the earlier the better. As far back as 1989, a Report on the National Science Foundation Disciplinary Workshops on Undergraduate Education noted: “It is clear that the academic community regards the involvement of undergraduate student majors in meaningful research…with faculty members as one of the most powerful of instructional tools.” (NSF, 1989) This was followed in 1995 by publication of the National Science Standards with called for “more ‘science as process,’ in which students learn such skills as observing, inferring and experimenting. Inquiry is central to science learning.” Again in 2003, Bio2010: Transforming Undergraduate Education for Future Research Biologists stated: “To successfully undertake careers in research after graduation, students will need scientific knowledge, practice with experimental design, quantitative abilities, and communication skills…All students should be encouraged to pursue independent research as early as is practical in their education.:” Exactly how science literacy is defined is debatable. My definition of science literacy is having the ability to critically analyze and evaluate information in order to make reasonable decisions. If students are to develop this type of science literacy they must be taught the difference between and analysis and a report. They must also be given multiple opportunities to critically analyze and evaluate information. In our introductory biology 151 and 152 labs we require students to:
- find, review and critically evaluate background literature
- design and conduct experiments
- analyze information gained and
- communicate what they find in scientific format.
These experiences lead up to a semester-long project in either mentored experimental research or a meta-analysis of an open question using data mined from existing literature. In this session I will describe the independent project options available in our Introductory biology 152 course. I will also provide participants with experience using the methods we have developed to teach students how to mine data from the literature and critically analyze it, how to develop a research question and how to effectively find and use peer-reviewed literature in their analyses.
Photosynthesis in Terrestrial Plant Leaves Using Oxygen Sensors and Data Loggers
(Bill Glider, University of Nebraska, Lincoln, NE)
The relationship between aerobic respiration and photosynthesis in plants is a basic biological concept which is often difficult for students to master. This exercise uses spinach leaves (or most any kind of leaves) to measure the rate of photosynthesis at different light intensities and wavelengths. It also allows the measurement of aerobic respiration rates of the leaves in the dark. This makes it possible to calculate gross and net photosynthesis as well as the light compensation point. The exercise employs the Vernier oxygen sensor, Lab Pro data logger, and Logger Pro 3 software linked to a computer for data collection and analysis. This lab exercise has been used in an organismal biology course for majors and in a general biology course for non-majors, employing both traditional and investigative approaches.
Phylogeny Construction: Primate Skulls and Protein Sequences
(Sarah Deel, Carleton College, Northfield, MN)
Students often have difficulty understanding how phylogenies are made; this lab for introductory biology students leads them through the process of making a phylogeny using primate skull morphological characters. Students complete a practice problem with morphological data collected from dinosaurs before coming to lab, so the tree-building procedures are familiar to them. The students use skull reproductions to collect data on features like the number of teeth, the presence and location of skull structures, and cranial capacity. They then determine whether traits are similar to the outgroup organism (ancestral) or different (derived). They use this information to find the most parsimonious tree for four organisms (fifteen possible trees), requiring the fewest changes from ancestral to derived character states. This portion of the lab is completed by hand, so the students gain a sense of what a computer program might be able to do with more organisms. Different lab groups work with different subsets of primates, and the lab section comes back together to determine how seven different primates might be related to one another. As a follow-up to the lab, students use protein sequences for the same primates to determine evolutionary relationships based on sequence similarities. This is necessary in order to discern the relationships between chimps, orangutans, gorillas, and humans. This computer assignment can be performed during lab or outside of lab, and makes use of free, online resources to collect sequences, generate sequence alignments, and construct phylogenetic trees.
Genetic Variations That May Increase Your Resistance to Malaria
(Ann Yezerski, King’s College, Wilkes-Barre, PA)
There are about 3 million Single Nucleotide Polymorphisms (SNPs) in the human genome. Therefore, it can be calculated that about one in a thousand bases varies across the human population. While most of these single base pair variations have little to no effect on human phenotypes, some contribute to human disease, including the propensity to be infected by pathogens. Malaria, an infection caused by protists from the genus Plasmodium, is the fifth leading cause of death worldwide. However, North Americans rarely consider the implications of this disease because of its low-prevalence in the local population. Therefore, while most biology students are informed of the classic relationship between sickle cell anemia and resistance to malaria, most are unaware of the multitude of other genes that can confer a level of resistance. This exercise explores how minor alleles of four genes, IL-3, Duffy, PKLR, and G6PD have been shown to contribute to malaria resistance. These resistance alleles are not rare in a typical North American population. Students anonymously genotype the class for the frequency of the unique alleles using PCR coupled with differential restriction enzyme digest. They statistically compare the results with the results on HapMap and investigate how these genes could biochemically and physiologically affect susceptibility to malaria. Additionally, students can discuss why these genes do not follow the distribution pattern of sickle cell anemia as well as the important issues of environmental versus genetic resistance to parasites.
Limiting Nutrient and Algal Growth: Designing An Individualized Project
(Kuei-Chiu Chen, Cornell University, Ithaca, NY)
It has been a trend in laboratory education to allow students the flexibility to design their own experiment based on their specific interest. The study of algal growth using nutrient enrichment provides students a self-guided research experience to design an experiment based on the same theme. There are also flexibility in the use of analytical methods to obtain quantifiable results. One type of design in this multi-week lab module is the ‘plant pot’ method in which porous plant pots are filled with agar and nutrient mixer. The plant pots are then placed in clear cups and supplied with pond water. Algal mass is estimated one week later using chlorophyll-a concentration. The other type of design, or the ‘test tube’ method involves growing the algal species of Chlamydomonas reinhardtii in defined media enriched with specific nutrients. The cell density is measured directly using hemocytometer or estimated using spectrophotometry. Depending on the design, students may use one of three statistical tests to analyze their data. The results may be presented in a poster or a paper.
Induction of the Lambda Lysogen
(Carrie Doonan and Lynley Doonan, Carnegie Mellon University, Pittsburgh, PA)
In this experiment, students will examine gene regulation in bacteria – the production of lambda phage particles that occurs when the lysogenic relationship between a bacterial cell and its quiescent prophage is disrupted. The lysogenic state in the bacterial cell is maintained by a repressor protein specified by the lambda virus; deactivation of the repressor results in de-repression of the regulated genes and production of lambda phage. Normally, the lysogenic state is indefinitely stable once established and a lysogenic bacterial cell produces lysogenic progeny cells, but no free viruses. The particular strain of lambda we are using in this experiment has a temperature sensitive mutation (857) in the repressor gene (cI) that results in an altered repressor protein that can be inactivated by a shift to 42 °C. Therefore, we can easily initiate the lytic or reproductive cycle of phage lambda in an entire population of lysogenic bacteria and follow the events of phage production. Students are given a lysogenic culture of CM58 bacterial cells that they will shift to 42 °C. They will take aliquots of the culture after de-repression and measure the production of lambda phage particles by pour plating with E. coli C600 host cells on agar plates. The phage produced will form a clear area called a plaque upon infection of the host cells. Students will observe the lysis of the lysogenic culture, and the production of lambda phage after de-repression.
The “Anti-Cookbook Laboratory”: Converting “Canned” Introductory Biology Laboratories to Multi-Week Independent Investigations
(James J. Smith, Kendra Cheruvelil, Cori Fata-Hartley, Douglas B. Luckie, Cheryl Murphy, and Gerald Urquhart, Michigan State University, Lyman Briggs College, East Lansing, MI)
Workshop participants will be guided through the process that we used in the Lyman Briggs Biology program to convert a series of typical, one-week, “canned” biology labs into a smaller number of multi-week, guided-inquiry laboratory investigations. The “Teams and Streams” model has been implemented in both our Introductory Organismal Biology and our Introductory Cell and Molecular Biology courses. Students work in research “Teams” of 3-5 students on multi-week, guided-inquiry experimental “Streams”. Each faculty member in our Biology group has interpreted the Teams and Streams model in her/his own way, inventing Streams ranging from a five-week long Ecology Stream that culminates in a formal poster presentation to a 12-week long PCR Stream that leads to the production of a journal-quality manuscript. The PCR Stream, which will serve as the model for our workshop session, may challenge some participants to move out of their “comfort zones” and explore a learning space where students are asking questions that are as yet unanswered (like real science!). We will model several aspects of the PCR Stream, including: i) how we guide students’ development of testable hypotheses and the experimental framework in which these are tested; ii) how productive and cooperative group interactions within Teams are promoted; and iii) some of the activities that we use in the laboratory, including assessments. Participants will explore the learning objectives associated with multi-week investigations and see how these can differ from (and be richer than) objectives associated with single-session labs. With a “Teams and Streams” model, more emphasis can be placed on troubleshooting experimental procedures, working with data and its analysis, summarizing data in tables and figures, and communicating research results to peers. Participants will be challenged to think of ways to modify their own labs to incorporate elements of the “Teams and Streams” model.
Using Phylogenetic Trees as an Investigative Tool in an Introductory Biology Course
(Janice M. Bonner, Notre Dame of Maryland University, Baltimore, MD )
Although cladograms and phylogenetic trees are included in college biology textbooks more and more regularly, students frequently have little idea of how these structures are developed or of how they function as experimental tools for biologists. This session will describe a laboratory exercise in which students are presented with experimental phylogenetically-based questions. For each question, students use morphological characters provided by the instructor to develop a cladogram. The cladogram then serves as their hypothesis which they test by developing a phylogenetic tree using either a protein or nucleic acid database in Biology WorkBench. The session will also explain how instructors can use primary literature to design additional questions that can be incorporated into the laboratory exercise.