These 3-hour workshops are hands-on, laboratory sessions during which presenters will share their innovative and successful undergraduate lab exercises with participants. Browse workshop topics and titles below.
Biochemistry
Gaining a structural perspective on the molecular basis of inherited diseases
(Isabelle H. Barrette-Ng and Don MacMillan)
In most undergraduate programs in biology, students are asked to take introductory genetics and biochemistry courses. However, the content presented in these two courses is often not linked, and students are not challenged to apply their genetics knowledge in a more biochemical setting and vice-versa. This prevents students from developing a more cohesive understanding of these fields. We re-evaluated this model and asked whether students’ understanding of biochemistry and genetics concepts could be improved by introducing an inquiry-based laboratory exercise in which students are challenged to explain the root cause of a genetically-inheritable disease by studying protein structure and the effects of mutation on protein function. The implementation of this exercise in a large (>500 students), second-year undergraduate, introductory biochemistry course for biology majors led to a high level of student satisfaction and a more integrated view of biochemistry and genetics.
Comparison of aerobic respiration rates in Zophobas morio larvae and germinated and un-germinated pea (Pisum sativum) seeds using oxygen sensors
(William V. Glider)
This exercise uses insect (Zophobus morius) larvae and Pea (Pisum sativum) seeds to investigate the similarities and differences between aerobic respiration rates of an ectothermic animal compared to the aerobic respiration rates of ectothermal plant seeds in various stages of germination. In addition, students investigate the effect of temperature on rates of aerobic respiration of both organisms. Respiration rates are measured and analyzed using a VernierTM oxygen sensor, Lab Pro data logger, and Logger Pro 3 software linked to a computer. Students also explore the relationship between whole organism aerobic respiration and aerobic cellular respiration. This lab exercise has been used primarily in an introductory biology lab for mixed-majors and non-majors using a directed inquiry approach.
Yogurt making – how does the type of milk sugar affect yogurt chemistry?
(Joanna R. Vondrasek)
This in an inquiry-based lab intended to be used in a majors- or non-majors introductory biology course. There are several published and commercial examples of laboratory activities for biology courses that involve making yogurt or culturing the bacteria isolated from yogurt; however, these labs are typically completely directed or demonstration labs that do not allow for hypothesis generation or experimentation by the student. The main goal of this lab is to allow students to generate hypotheses about what chemical changes will occur to milk substrates during the process of lactate fermentation with Lactobacillus and related microbes. Students are provided with a basic yogurt making protocol and materials to measure pH, glucose (monosaccharide) concentration and consistency. This is a two session lab exercise that requires students (or lab staff) to remove yogurt from incubators after 18-24 hours. The materials are inexpensive, and this lab can be scaled to large enrollment laboratory courses.
Cell Biology
Osmosis and transport
(Carl Stiefbold)[
Red blood cells (RBCs) from rabbits offer several advantages for the study of osmosis and membrane transport. The most important is the absence of internal compartments (nuclei, mitochondria, etc.). In addition, rabbit red blood cells are readily available and their properties are quite stable during storage. This lab exercise is divided into three parts. In Part A students study red blood cells as osmometers, that is, as devices with which they can estimate the relative osmolarity of solutions. The change in refractive index of RBCs as they change size due to changes in the osmolarity of their environment is measured using a spectrophotometer. Students use their results to estimate the water content of RBCs. The other sections of the lab will make use of these results. Part B looks at the relative permeability of RBC membranes to glycerol and the transport of glycerol into RBCs. Part C looks at the facilitated diffusion of electrolytes using the antibiotic valinomycin as a mobile carrier of K+ ions.
Neuroprogenitor cell differentiation in culture
(Olga Miakotina)
Neuroprogenitor cells are capable of differentiating in cell culture to give rise to neurons, astrocytes, and oligodendrocytes. This experiment for an upper level laboratory allows students to get an opportunity to obtain hands-on experience in sterile tissue culturing, to observe and comprehend factors stimulating neuroprogenitor cell differentiation, to recognize neural cell types in culture, and to explore the influence of co-culturing on neuroprogenitor differentiation and cell fate. Students are provided with progenitor cells in suspension, and endothelial cell culture on tissue plate inserts. During this unit students prepare substratum for cell attachment, make medium and filter-sterilize it, triturate cells, set up a co-culture of neuroprogenitors and endothelial cells, perform live imaging of differentiating cells, fix cells, and stain cells on coverslips using double fluorescence staining for neurons and astrocytes and DAPI nuclear counterstaining. As an outcome of the project, students count cells of different cell types in control with neuroprogenitors only and experimental condition which was co-cultured with endothelial cells, summarize, analyze and present results in the format of a scientific manuscript. In order to upgrade this laboratory to inquiry lab, we restructured the exercise and made the following changes: a) eliminated time-table with listed procedures performed each week and closely nurtured by the instructional staff; b) formed groups according to out-of-class time availability and group assessments aimed to reveal problems within groups which facilitates formation of collaborative groups; c) added quizzes with peer instruction; d) laboratory record book evaluations; e) group interviews to monitor group progress; f) introduced performance-based assessments to verify skills on fluorescence microscope handling and sterile techniques skills; and g) allow students to develop their own plan of experiment, and share load between group members. Even in format of classical type of laboratory, students gave great evaluations for this unit, and instructors were impressed with the high quality of final lab reports.
Ecology
Extremophiles in my backyard? Enhancing analytical and math skills with a simple inquiry-based lab
(Lakshmi Chilukuri and Lorlina Almazan)
What lives in your compost? What grows in a sulfur hot spring? What survives the extreme conditions in a hydrothermal vent? Can you make money from the organisms living in your local pond? Curiosity is a powerful tool in teaching. In our microbiology lab, we harness that interest in a guided inquiry based laboratory exercise that promotes critical and analytical thinking and reinforces math skills.
Using standard lab resources, students conduct authentic research, setting up enrichment assays for soil organisms with special capabilities such as cellulose hydrolysis, casein degradation, and survival of extreme conditions of temperature, salt, and pH. In the process, they apply concepts such as the relationship between the physical and chemical environment of a natural environment and the types of microorganisms that it might support, the use of selective and differential media, dilution and viable counts, and the appropriate use of controls. In collaboration with their classmates, they collect, evaluate, and analyze numerical data, and present their findings in scientific format. We will present one of the enrichment assays done in our classrooms, that of thermophiles from a soil sample. This workshop also discusses an extension of this project, the use of metagenomics and bioinformatics to identify the microorganisms in the enrichment.
This project has been invaluable in contextualizing science in our classrooms and is a flexible model that adapts easily to many questions. Attendees will collaborate in designing similar exercises and devising assessments.
Sex determination and mating strategies of the bluehead wrasse, Thalassoma bifasciatum
(Karen L. Haberman)
In this workshop, participants will explore the mating strategies of the bluehead wrasse, Thalassoma bifasciatum, a coral reef fish with socially-mediated determination of initial sex and of female-to-male sex reversal later in life. The bluehead wrasse’s social system is ideal for examining key concepts in behavioral ecology including proximate and ultimate causes of behavior, phenotypic plasticity, and female choice. Participants will conduct role-play simulations of competitive and mating interactions of the bluehead wrasse on different reef sizes as well as with and without female choice. Then, they will calculate and compare the reproductive success among fish with differing strategies for the different scenarios. Finally, they will develop proximate and ultimate hypotheses related to initial sex ratios and to female-to-male sex reversal. The workshop will culminate in a discussion of how instructors can adapt this lab to work effectively at any level, from lower-division introductory courses to more advanced courses in animal behavior, ecology or evolution.
Ecology in a three module format
(M. Carmen Hall and Sheryl Shanholtzer)
The choice between depth and breadth is a common dilemma in most courses. We found that to be particularly true when developing our environmental science labs. The students in our environmental science classes are primarily non-science majors who may not have taken another science course before enrolling in this class. We developed the labs to work as stand alone modules that take place over the course of three weeks. In this workshop we introduce you to the ecology module. We begin our exercise by mapping a study area using Google Earth and using digital resources to explore the study area. From our information we identify two different habitats within our study area. Our exercise is continued by conducting a plant and animal survey in the two habitats. We conclude our exercise by comparing the importance values (plants) and diversity (animals) in the two habitats.
Diversity in microcosms for introductory biology
(Mary Ann McLean)
Diversity is an important component in our Introductory Biology sequence, however, bringing home the idea of biodiversity can be a challenge. Students relate biodiversity with programs on Discovery channel and have little concept of their local biodiversity. The creation of Winogradsky columns during the first week of labs in the fall allowed students to investigate their local diversity of microbes and invertebrates over the next 8 months. Each student constructed a Winogradsky column from soil and water and included sources of carbon, sulfur, and other minerals. Columns were maintained on the lab windowsill throughout. Column communities and diversity differed significantly depending on the source of the original soil and water, the nutrients supplied and the proportion of masking on the column. During the year, the students sampled their columns for bacteria, cyanobacteria, protists, algae, fungi, moss, plant seedlings and small invertebrates (egnematodes, mites, insect larvae, rotifers, crustaceans, earthworms). Not only did each student observe a wide diversity of organisms in their own column, they also observed a different suite of organisms in other students’ columns. These columns also permitted discussions of food webs and ecological communities. For each student, the value of their own personal Winogradsky column using their own garden or local soil was tremendous in terms of knowledge and enthusiasm.
HHMI stickleback evolution virtual lab
(Peter J. Park and Laura Bonetta)
The goal of the Stickleback Evolution Virtual Lab is to introduce students to the science and techniques used to analyze the forms and structures of organisms. This online lab focuses on pelvic structures of the threespine stickleback fish (Gasterosteus aculeatus). Stickleback are ancestrally marine or sea-run but have repeatedly established freshwater populations across the Northern Hemisphere, an ecological process that still occurs today. In some lake populations, almost all stickleback possess a pelvis consisting of sharp spines that are used for protection. However, in other lake populations, stickleback without pelvic spines are more prevalent. U sing three virtual experiments, students will explore in this species the impact of natural selection as it relates to pelvis evolution. In the first experiment, students will investigate the patterns of pelvic reduction using stickleback from living populations. Students will analyze the data they collect using a chi-square test, which is built into the virtual lab interface. In the second experiment, students will study pelvis evolution in past populations using the real fossil record of stickleback. Students will analyze the data they collect using linear regression, which is built into the virtual lab interface. In the last experiment, students will explore the genetic mechanisms underlying stickleback pelvic reduction and infer if the same gene(s) is involved in limb loss of other vertebrates (e.g., snakes, whales). Learning from each experiment will be assessed using quizzes that are built into the virtual lab interface. There is one quiz per experiment, one per statistical analysis, and one cumulative final quiz (9 quizzes in total). This virtual lab will encourage students to inquire about why such patterns in nature exist and how they can be measured. (v-lab url: http://www.hhmi.org/biointeractive/vlabs/stickleback/index.html)
Genetics
Teaching genetic principles with dogs
(A. Daniel Johnson and Sabrina D. Setaro)
In 2012 we launched the open-access project, “Teaching Genetics With Dogs” (TGD), to explore, develop, and disseminate materials for teaching undergraduates. In this workshop, participants will use TGD resources to create new genetics problems that demonstrate basic and advanced principles of inheritance. Participants with all levels of background knowledge in genetics are welcome.
There are many advantages to using dogs (Canis familiaris) as teaching models. They are familiar, and innately interesting and engaging for students. Class lessons are reinforced every time students walk by a purebred or pet a mixed terrier on campus.
Using currently available data students can explore the genetic basis of morphology, physiology, intelligence, behavior, and disease. Scientists have identified the roles of specific genes, alleles, and proteins in determining many of a dog’s distinctive physical features. This knowledge makes it easier for students to identify connections between genotype, phenotype, and protein activity. In addition, phenotypes of dogs can be scored easily from color photographs or direct observation. Canine alleles exhibit various inheritance patterns including: autosomal dominant/recessive, sex-linked/hemizygous, codominance, epistasis, gene dosage effects, pleiotropy, and allelic series. Dogs can be used to explain DNA regulation and mutation mechanisms, plus advanced topics like medical genomics, population genetics, phylogenetic reconstruction, and quantitative trait loci mapping.
Participants will learn which physical traits have simple Mendelian inheritance (leg length, coat length and texture, muscle structure) versus more complex inheritance (overall size, coat color). Working in pairs, they will create 1-2 genetics teaching problems and get feedback from other participants. They can choose to publish their revised problems in the TGD library and will have continued site access after the workshop.
Participants also will explore resources available for advanced courses, such as NCBI’s bioinformatics tutorials on dog phylogeny, and the OMIA database of canine genetic diseases.
Detecting genetic polymorphisms in different populations of bean beetle (Callosobruchus maculatus)
(Jennifer M. Smith)
Differences at the DNA sequence level are intrinsically important in helping molecular biologists categorize groups of organisms with respect to each other. This exercise for an introductory majors laboratory aims to introduce students to DNA extraction and basic PCR techniques, with which they will compare genomes from different populations of bean beetles (Callosobruchus maculatus). Using primer sets determined from the recently reported Callosobruchus genome, students extract and amplify DNA from different populations of bean beetles, and compare the amplified DNA via gel electrophoresis. The specific regions of DNA selected for amplification by these primer sets have been identified as containing microsatellites, or Short Tandem Repeats. These microsatellite alleles often contain numerous polymorphisms, which may be useful in assessing genetic similarities. The present experiment challenges students to consider how separation of populations over time and/or geographical distances may affect changes at the DNA level. This exercise offers students the opportunity to participate in a relatively unexplored research topic, which may also help contribute to our understanding of bean beetle molecular genetics.
Instructional Methods
Uncooking the lab: laboratory designs for engaging students in the process of science
(Jean Heitz)
We all know that the study of biology, or any other science, involves more than assimilating factual information. It also involves learning how to effectively use that information for problem solving, posing hypotheses, conducting experiments, and interpreting experimental results. Given this, if we want our students to understand what science is, we need to provide them with both conceptual knowledge and we need to give them opportunities to actively practice science.
The question then becomes: How do we do this? One solution – design our student lab activities to provide experiences similar to what goes on in actual research labs.
The “Research Project” labs I have designed:
–are all offshoots of what were previously cook book-type labs
–last more than one week
–mirror real-life research problems
–are open-ended (do not have known or expected outcomes)
–allow students the opportunity to learn from their “mistakes”
–are inexpensive to run with a just few students or with as many as 1200 students per year
In this session participants will:
1) Get a brief introduction to the types of labs I developed including what worked and what didn’t.
2) Experience one of my investigative labs – Gravitropism in the Hypocotyl.
3) Have time to brainstorm how cook book-type labs can be modified to be more open-ended.
Using a comparative endocrinology model to recruit future scientists
(Mary Beth Hawkins and Miriam Ferzli)
Students in an undergraduate research program, called Research PackTrack (RP), are investigating the structural and functional evolution of the three estrogen receptors (ERs) found in a teleost fish, Micropogonias undulatus. This well-characterized neuroendocrine model introduces students to the value of scientific inquiry through a comparative, evolutionary approach via a three credit-hour course for RP sophomores that offers hands–on experience in a working research laboratory. Students in RP come into this class after taking a basic research skills course that introduces them to the process of scientific inquiry and discourse. Lab times are highly flexible, vary from week to week, and depend on individual progress. Students use a robust experimental protocol, in vitro bacterial expression of the ER and subsequent competitive binding assays, to test their novel hypotheses about the effects of site-directed gene mutations on ER-ligand interactions. This course allows for hypothesis-driven authentic research projects that are loosely based on the laboratory model rather than standardized laboratory exercises. In this workshop, we will learn about the three-estrogen receptor system, and then participants will form a hypothesis similar to those that students would test in the course. Through this process, we will identify the aspects of this model that allow for the formation of unique hypotheses by large numbers of students who have a broad range of backgrounds and interests. We will discuss the elements of a research question that are best suited to this approach, and then brainstorm to identify suitable projects that could be implemented by participants at their institutions. We will discuss the pros and cons of the Studio Lab concept, including research productivity, laboratory logistics and student evaluations. We will discuss our current findings to date on student attitudes about science and their success in finding research opportunities after participating in the RP program.
Molecular Biology
From bugs to barcodes: Using molecular tools to study biodiversity
(Madeline Butler, Stephanie Mel and Heather Henter)
Biodiversity refers to the variety of organisms within an ecosystem or a defined geographic region. Earth’s biodiversity remains incompletely documented and our lack of knowledge about the species around us is particularly troubling at a time when human activities are impacting virtually every organism on the planet. DNA barcoding is a method that uses a specific region in an organism’s DNA as a genetic marker to identify its species. The goal of the Consortium for the Barcode of Life (CBOL), an international collaboration between museums, biological repositories and academic and commercial institutions, is to compile DNA barcodes of known and newly discovered plant and animal species and to establish a public library of sequences. Students at any academic institution can join this barcoding project and contribute novel sequence to the CBOL database.
This workshop will guide participants through all of the steps from sample collection to DNA sequence analysis. We will grind up insect legs, then learn how to extract DNA from the insect samples and amplify the DNA barcoding region using Polymerase Chain Reaction (PCR). Participants will purify the PCR product from agarose gels and analyze sample DNA sequences using several bioinformatics programs. We will identify the insect species and also compare insect sequences, noting any DNA polymorphisms within species. The methods are all straightforward and inexpensive, and require only basic molecular biology lab equipment.
Mutation and selection: an exploration of antibiotic resistance in Serratia marcescens
(Laurel L. Hester and Mark A. Sarvary)
Often the key to success in biology labs is giving the ownership of a research project to the students and allowing them to design and analyze their own experiments. The challenge is finding that balance between providing structure and giving enough freedom to students who may have just learnt the steps of experimental design. This three-week laboratory module aims to give students hands-on experience with mutation and selection in bacteria using the topic of antibiotic resistance. In the first two weeks students observe the pattern of de novo streptomycin-resistance mutations and compare classwide mutation patterns with those found by Luria and Delbruck in their classical experiment showing that mutations are spontaneous rather than induced. Related topics such as bacterial growth, positive and negative controls and the difference between mutation rate and mutation frequency are also addressed. In the second and third weeks students design and implement their own experiments related to antibiotic resistance. Students will have semi-guided experiments, in which they can choose from several variables we provide them, but they have the freedom to form their hypotheses, come up with predictions, identify confounding factors, design an experiment and analyze their data using statistical software. Technical skills learned in this lab module include pipetting, preparing serial dilutions, using a spectrophotometer and becoming familiar with sterile technique. Students also practice scientific communication skills by writing a scientific paper or presenting a poster on their group’s experiment. Students enjoy this module because it both teaches them basic technical skills and provides a balance between initial structure followed by guided freedom in designing their own experiments.
Pedagogy and Assessment
Building rubrics for graded lab assignments: a helping hand up a steep slope
(Hans D. Lemke and Michael J. Keller)
Assessment of student comprehension and performance in the biology teaching lab inevitably involves written assignments or other “constructed” items such as drawings or graphs that must be graded and given a score. This is a difficult task for most instructors under the best circumstances, and can be a daunting exercise for novice teaching assistants faced with even the simplest assignment. Graders understand that they should be fair, consistent, and objective with their grading, but may find these standards elusive in practice because of the diversity of issues encountered in a stack of student writing assignments. Enter the rubric – a tool that defines grading standards and guides their application to make assessments as uniform, transparent, and valid as possible even with multiple graders. In this workshop we will discuss what a rubric is (and what it is not), the benefits and pitfalls of using rubrics, and best practices for building rubrics. A universally approachable problem, the judging of chocolate chip cookies, will be employed to model the rubric development process and lead into a discussion of how to approach building rubrics for real lab assignments. Following this, participants will work in small groups to develop a rubric for a lab assignment.
Physiology
Biomechanical analysis of a vertebrate foot
(Janice M. Bonner)
While studying the skeletal system, students learn that various bone systems are examples of three classes of lever systems. They memorize the origin and insertion of various muscles, but often with little appreciation for their connection to concepts of levers. They study bones from a variety of vertebrates, but don’t understand the reasons for the differences in skeletal structure that they observe. In this workshop (a revival of one presented at the second ABLE conference in 1981) participants will work with a biomechanical model of a skeletal foot and determine how modifications in the length of the calcaneus or the length of the actual foot can determine whether the foot can maximize either strength or speed. They will then apply the principles derived from the foot analysis to an examination of particular animal skeletons.
Teaching Assistant Training
GTA boot camp: a training program to prepare first-time graduate student teaching assistants
(Carly Jordan, Angela M. Seliga and Elizabeth A. Flaherty)
We tested two different intensive training models to prepare graduate teaching assistants (GTAs) for their first experience teaching laboratory sections. In the first model, GTAs attend two 4-hour training sessions for inquiry-based teaching, Socratic questioning, applying Bloom’s Taxonomy, and providing the GTAs with opportunities to practice using each of these pedagogical techniques. In the second model, GTAs attend one six-hour training session to practice teaching by role-playing prepared scenarios. At ABLE, attendees will receive an introduction to both models with opportunities to practice using our training activities.