The Major Workshop is a hands-on opportunity for you to experience a laboratory activity that has been developed and implemented for the classroom. Each three-hour workshop is reviewed prior to approval by the Major Workshop Committee, then peer-reviewed by participants, and ultimately by the Tested Studies for Laboratory Teaching editor before publication.
Most workshops are offered twice daily, morning and afternoon, so participants will have the opportunity to attend two workshops on each of two days, Wednesday and Thursday. Attendee selection of workshop sessions will be done during the conference registration process, as space is limited in each. Titles, presenters, and abstracts for each workshop are below. Click here for workshop materials (members-only).
What does the host institution provide?
For those wishing to do a computer-based lab: All of our undergraduate biology labs (wet and dissection labs) are fitted with integrated computers with internet connections. All rooms are also WiFi-enabled. If you wish to do design a computer lab (e.g. using commercial software like SimBio, an online digital tool of your design, bioinformatics-based exercises, etc.), we can accommodate.
For those wishing to do a wet lab: We have two sorts of labs: traditional bench labs and anatomy/physiology labs with integrated dissection tables. We have the space and equipment needed to store or incubate samples: 4C,-20C, -80C fridges/freezers, liquid nitrogen storage, 4C cold rooms, 37C warm rooms with shakers, fridge style incubators for any range of temp from 4 to 50C, bath incubators, tube incubators, centrifuges, PCR machines (no realtime unfortunately), centrifuges (refrigerated and unrefrigerated for various tube sizes), lab-grade dissection and traditional microscopes with integrated digital cameras (several hundred for each), five epifluorescence microscopes for student use, tissue culture facilities, and all tools and equipment for measuring, transferring, and mixing solutions.
This is not a comprehensive list so the workshop planner can e-mail the hosts to find out more specifically what we have or can do to accommodate.
For those wishing to do a site visit (e.g. field trip): We have a national park (Gatineau Hills) not far from campus to which we take hundreds of students at a time for lab courses focused on ecology. We can at least accommodate workshops that need freshwater ecosystems such as marsh/swamp, lake, stream, and river. There is no zoo in Ottawa but for physiology/anatomy we do have models and have facilities/equipment to do dissections inside. There is an insectarium in Ottawa with whom we could contact to arrange a field trip. Likewise we do have a Museum of Nature with a fossil section.
Personpower: We are going to have a team of student volunteers available. If your workshop needs help, we are collaborating with our community services office to arrange a team of (science-student) volunteers for the conference. Volunteers can be provided to help with the workshops. Most will be upper year students with some ecology-molecular-cellular-physiology lab experiences. So if you need help, we can accommodate.
Wednesday, 19 June
A yeast reporter assay to examine the effect of dietary supplements on gene expression
Quyen Aoh, Gannon University
Oxidative stress is a major regulator of gene expression. Numerous dietary supplements have been reported to counteract the effects of oxidative stress. I have a developed a simple reporter assay that will allow students to test the effects of dietary supplement on gene expression using the yeast Saccharomyces cerevisiae. In this workshop participants will perform an abbreviated version of the assay and use spectrophotometry to examine how gene expression in response to oxidative stress is altered.
Phenotypic characterization of auxotroph mutants obtained by transposon mutagenesis
Sylvie Bardin, Zahra Mortaji, University of Ontario Institute of Technology
The experiments presented in this workshop are part of a semester-long inquiry-based molecular biology laboratory course offered to biological science fourth year undergraduate students. The experiments presented here can however be easily adapted to second or third year level laboratories. In the lab course, E. coli transposon mutants are created using a suicide plasposon (a plasmid containing a transposon). The transposon mutants are then screened for auxotroph mutants and the auxotrophs obtained are further characterized phenotypically and genotypically. This workshop focuses on the isolation and phenotypic characterization of auxotroph mutants. During the workshop, the participants will be introduced to the use of a plasposon, pRL27 (containing Tn5- RL27 transposon), to create random transposon mutation. Participants will then screen for auxotroph mutants, and identify and confirm the phenotype of the mutants using plating techniques. Analysis of the results and ability to adapt the experiment for the screening of other types of mutants will be discussed.
Undergraduates choose your own adventure: Inquiry-based research in plant biology and developmental biology classes
Steven Chatfield, , University of Toronto Mississauga; Georgette Briggs, The University of The West Indies; Chris J Meyer, University of Guelph
We have developed inquiry-based courses in plant biology and developmental biology using readily available resources for the model plant Arabidopsis thaliana. Students “choose-their-own-adventure” in this open-ended course format that allows them to develop skills in critical thinking, experimental design and scientific communication as they simultaneously learn and integrate diverse core biological concepts. During the workshop, each presenter will share their own variations and supporting teaching materials on this format; we will also demonstrate a wet lab from one of the courses focused on characterizing these ‘mystery’ mutants. To identify these mutants, students initially design genetic screen experiments to identify genes involved in a developmental process of their choosing. Within a course students can also choose ‘virtual’ experiments to perform on their mutants and are required to rationalize their experimental choices and set-up (e.g. controls). These virtual experiments allow students to learn from techniques that are usually too time-consuming or costly to perform in undergraduate labs (e.g. genetic cross analysis or next-gen mapping). Students are then provided with the raw data from these virtual experiments, which they must analyze and organize as figures to incorporate into their end of term ‘conference’ or presentation. In this way, students learn how a biological question can be broken down and how diverse experimental and computational methods can be used to answer different aspects of the question. During the workshop, we will provide examples of ‘virtual’ experiments that can be offered to students, allowing them to complete all the component experiments of a research project that they can present as a paper, talk or poster. A course may also include additional labs/tutorials designed to train students in techniques (e.g. image analysis) or online research tools (e.g. ePlant) that will help them complete their research successfully.
Learning basic data analysis skills in intro biology labs using R
Linda Forrester, University of Rhode Island
Having students utilize data visualization and statistical analyses skills in introductory classes (with their own data) allows students to quickly develop an appreciation for digital skills. We wanted to introduce these skills to freshmen with minimal cost, giving all students an equal footing in basic data analysis.
We developed a simple, step-wise introduction using the free, computer program Google Sheets, importing data to the free, data analysis packages R and R-Studio. Our approach through the semester presents students with R-coding templates that they can use for graphing boxplots, scatterplots, and line graphs. Students also use coding language for presenting error bars, t-tests, and best-fit linear regressions. Students responded that this approach was effective in making them feel that they can use a coding language program to analyze and graphically display their data.
This workshop will have participants experience the first two labs of our intro biology course. Firstly, participants will collect data on plankton species diversity with samples from Narragansett Bay (using Sedgewick rafter counting cells and picture keys), sharing their data in wide and long-formats in Google Sheets. Secondly, participants will learn the basic organization of R-Studio, creating variables, creating boxplots, and interpreting their plankton diversity data.
Participants need only bring a laptop computer with internet accessibility. Access to R and R-Studio will be through our University of Rhode Island server, removing the need for students to download programs onto their computers.
Using algae in undergraduate STEM education: A flexible inquiry-based investigation at scale
Dylan Franks, Dr. John F. Stewart, Moria G. Harmon, Dr. Donald P. French, Oklahoma State University
Algae are a diverse group of organisms that influence global biogeochemical cycles, feed millions of people, and inspire myriad entrepreneurial ventures. Any student with a smart phone has likely heard of algae in one or more contexts. Despite all the flash, algae are truly an incredible teaching tool that open inroads towards learning in diverse inter-related topics central to any biology curriculum.
We have developed a laboratory investigation intended for high school and introductory undergraduate education using consumer water bottles, basic equipment and relatively affordable supplies. In this lab, students integrate various biological concepts and applications through inquiry-based, student-driven research. Teams will recognize and apply the basics of photosynthesis and the interplay between fundamental metabolic modes, i.e., cellular respiration and photosynthesis. A number of independent variables such as salinity, nutrients, light quantity and quality, novel additives, and species are alterable for a myriad of multivariate experimental designs, allowing for higher level interpretation and analysis. Students who complete this lab will gain experience in basic microbiology and plant science skills such as sterile technique, cell counting, and pigment extraction. Successful teams will learn to communicate the implications of their findings and provide predictions regarding the effects of climate change on aquatic primary production or the benefits to bio-based industries such as algal biofuels.
While this lab is designed with biofuels in mind, the material herein is flexible and is pertinent in many contexts. Any application focused on generating biomass is within the scope of this framework. However, it would be simple to adapt this investigation to address a number of different applications like bioprospecting, bioassays, community composition, and the fundamentals of water quality.
An in silico approach to protease discovery
Pavan Kadandale, Marc Sprague-Piercy, Rachel Martin, Univeristy of California – Irvine
A current area of research in Dr. Martin’s lab is the identification of novel proteases. Based on this, we have developed a simple, 1-2 class activity that allows students to contribute to cutting-edge research as part of the regular curriculum. Using modern software, students view and analyze protein structures, and predict whether an unknown protein might be a protease with novel functionality. Based on the idea that structure and function are related and conserved, students compare structures of predicted proteases to the structure of a known protease and annotate both conserved and novel features. Through this activity, students become conversant with the main secondary structure elements of proteins, and how they fold together. They will learn how to use Chimera to visualize and analyze protein structure. Data generated by the students will be analyzed in Dr. Martin’s lab, potentially identifying interesting new proteases for experimental characterization. In this workshop, participants will work through all the steps of the module, and will have the opportunity to discover a new protease. We will also discuss ideas for how additional exercises can be developed for more advanced students. Participants in this workshop will be required to bring a computer.
Soil respiration
Randi L. Mewhort, Christina Elliott, MacEwan University
This laboratory exercise is an excellent opportunity to demonstrate why ecologists should have a working understanding of chemistry, introduce some of the issues associated with climate change, and expose students to carbon cycling. Students generate a class hypothesis using summarized research and vote on a treatment option: soil type, litter type, water levels or temperature. The chambers incubate for a week, and the amount of CO2 produced over the 7 days is determined the following week. This is an easy, low tech way to teach these concepts, but could be adapted to use probes to measure CO2 directly. It has been our most consistent ecology lab and is nice as it generally takes 1-1.5 hours to set up and about the same time to analyze. We have 3 hour labs and generally combine this with another activity, but this would be excellent in a 2 hour lab time as well. This activity is very adaptable to different skills such as hypothesis testing, statistical analysis and experimental design. In institutions with more space resources this could be easily adapted for more inquiry-based approaches.
Using the novel dipstick DNA extraction technique in a biological barcoding lab
Christof Stumpf, Louisiana State University at Alexandria
This laboratory exercise introduces students to DNA extraction, biological barcoding, and sequence analysis and reinforces the concept of the polymerase chain reaction (PCR). It takes advantage of the dipstick extraction technique that is cheap and fast and allows for DNA extraction and PCR setup on the same day in an 1:50h Introductory Biology lab. Students determine whether local businesses actually use the fish that they advertise, or if cheaper fish are being passed off as the more expensive species in order to boost profits. Different species of fish are collected from local vendors, DNA from their tissues is extracted, and a region from the Cytochrome C Oxidase I gene is amplified. After PCR, results are sent off for sequencing. The following week, chromatograph results are uploaded to NCBI, they are compared to existing genomic datasets, and conclusions are discussed in class.
Protein structure visualization using augmented reality
Swati Agrawal, Washington College
3-D characteristics of protein and DNA molecules are important in aiding student comprehension of almost any biological structure or process that is taught in Introductory biology classes as well as upper level advanced classes such as Cell Biology, Genetics, Biochemistry etc. The following activity was conducted in a Cell biology where students learned about protein structure and function using Augmented Reality (AR) where they visualized protein structures downloaded from pymol as real objects in an AR environment. The immersion and interactivity that this activity brought, significantly changed students understanding of protein structure and led to improved cognition of Cellular Biology core ideas.
Do the write thing: Eight mini-activities to refine students’ writing
Suzanne Thuecks, Washington College
Teaching our students how to improve their writing can be a challenge. It is often difficult for students and teachers to identify what makes one sentence clearer than another, or what causes some writing to flow well and other writing to flow poorly. Students and teachers need a common language, both to identify problems and to suggest solutions for murky writing. Participants will cycle through eight mini-activities or stations, each 10-15 minutes long, that can be used together or as separate activities added to other lab sessions. Each station introduces a strategy for improving students’ technical writing style, and allows students to practice the strategy. This lab is used during the second semester of Washington College’s Introductory Biology sequence, after students have mastered the basics of the lab report and have prepared a draft of their first paper of the semester. This workshop includes some elements that were presented at ABLE 2016 in Madison, but also includes some new activities. Several of Washington College’s other strategies for supporting student writing will be shared; workshop participants will also spend time discussing and sharing strategies for teaching scientific writing effectively. A laptop is highly recommended for this workshop.
Thursday, 20 June
Solar panel electricity, efficiency and environmental impacts
Lawrence Blumer, Morehouse College
This is a protocol for a guided-inquiry activity that leads to open-ended course-based research activities using a small solar panel monitored by a digital multimeter that permits students to evaluate solar panel power output. Simultaneously, students may use a digital pyranometer to evaluate the total energy arriving at the solar panel. Thus, the power output of the solar panel may be evaluated at different angles of sunlight incidence and the efficiency of the solar panel may be evaluated. The significance and limitations of using solar panels on our energy use and climate change are the ultimate focus of this work.
Engaging introductory-biology students with the Evolution and Biology of Sex
Sehoya Cotner, Stacey Weiss, University of Minnesota
In response to demands for improved biology education for all students, I created the Evolution and Biology of Sex—an introductory-biology course for non-biology majors. This course, which is currently in its twelfth year, enrolls ~860 students each year and uses evidence-based educational principles in both large-lecture and laboratory settings. The course is accompanied by a semester-long (fourteen-week) laboratory component, in which students work in small (4-person) groups—for two hours each week—to delve deeper into topics such as sexual selection, the adaptive significance of sexual outcrossing, sexually-transmitted-disease transmission, human population growth, and human sperm competition. Using a combination of discussion, demonstration, and hands-on activities, workshop participants will be introduced to several thoroughly assessed laboratory activities, all of which engage students in the process of science through the lens of the evolution and biology of sex. Laboratory materials (sample student materials, equipment lists, and online ancillary materials such as Powerpoints and pre-lab videos) will be available. Note: while many of these laboratories have been implemented in a high-school environment, the overarching sex theme of the course makes several of the labs most suitable for adult students.
FlyBuilder: A multimodal dry-lab curriculum teaches Mendelian genetics through the lens of Drosophila balancer chromosomes
Johanna G. Flyer-Adams, Brandeis University, Belinda Barbagallo, Salve Regina University, Melissa Kosinski-Collins, Leslie C. Griffith, Brandeis University,
The principles of Mendelian inheritance critically inform and support a student’s understanding of genetics. Student labwork with live Drosophila melanogaster (fruit flies) is often used to illustrate Mendelian genetics, but this approach is limited by teacher resources and Drosophila lifecycle. FlyBuilder is a ‘print-and-play’ series of multimodal teaching modules for teaching genetics that overcomes these practical limitations and can be integrated into existing curricula. FlyBuilder uses Drosophila balancer chromosomes with visible ‘marker’ mutations to teach students how to design multi-generational cross schema while incorporating examples of recessive lethality, phenotypic dominance, and Drosophila transgenesis. A ‘paper doll’ style toolkit allows students to ‘build’ flies of specific genotype and phenotype, facilitating their learning with hands-on experience. We piloted FlyBuilder in the introductory Biology laboratory course at Brandeis University in spring 2019, where it yielded a two-fold improvement (40% to 80%, pre-to-post) of progeny prediction and balancer/marker identification. In this workshop, participants will receive a brief overview of the FlyBuilder lecture and background reading modules, and then use the FlyBuilder hands-on toolkit to ‘build’ flies and complete the Module 3 worksheet. Participants will be provided basic tools and resources to integrate FlyBuilder into their own courses.
One fish, two fish, real fish, fake fish: Using free online tools to teach tree thinking
Hans Lemke, Anna Davis, University of Maryland
Tree thinking is a fundamental skill in biology. This workshop highlights two exercises that are designed to provide students with experience interpreting trees and using them to test a hypothesis. Both use a freely available set of web tools (www.phylogeny.fr) to analyze sequences downloaded from Genbank. The first exercise uses molecular data to simulate testing the identity of fish species served in a sushi restaurant. The second is a guided inquiry exercise that allows students to use phylogenetic techniques to test the claims of a simulated advocacy group. In this workshop, we will work through these exercises and then discuss how the techniques can be adapted for other scenarios.
Simulating genetic drift and natural selection
Amy Marion, New Mexico State University
The concepts associated with evolutionary processes can be challenging for students, especially without a way to conduct hands-on experiments about processes that occur in evolutionary time frames. Laboratory simulations make it possible to allow the manipulation of variables that could not otherwise be investigated. This experiment includes two simulations; one to investigate the impact of population size on the degree of genetic drift in a population, and a second simulation to demonstrate the effect of a selective pressure on the evolution of a population. The comparison of results from each simulation allows the processes of genetic drift and natural selection to be clearly delineated from each other.
Using the citizen-science app, “iNaturalist” as a lab tool for hypothesis-testing
Joe Newsome, San Diego State University
Interest in citizen-science projects in the college lab has risen dramatically recently. iNaturalist, https://www.inaturalist.org is a free app that facilitates the collection of observations of macroscopic organisms world-wide can be thought of as a pathway to a CURE (course-based undergraduate research experience) for organismal biology, natural history, and even biodiversity. This app allows users to enter photographs, propose identifications, solicit expert identifications, and log location, time, and date data. When species are ultimately identified the aggregate data facilitates testing hypotheses about presence/absence in specific locations, frequency, and annual timing. Participants will receive a short introduction to both the use of iNaturalist and to its project construction features and then will go to a local natural preserve, Gatineau Park, http://ncc- ccn.gc.ca/places-to-visit/gatineau-park/conservation-at-gatineau-park to collect observations. Upon return to campus the participants will construct and discuss hypotheses to test, and see the collective data set built from this single observation outing. We will also discuss the feasibility of including a single-week iNaturalist lab versus a longer project.
How do you like them apples? Cellulose scaffolds seeded with mammalian cells.
Alp Oran, Karine Loiselle, Cindy Lesage-Pelletier, Lucille Joly, University of Ottawa
The following workshop proposal represents a thesis project designed and written by an undergraduate biology student (K.L.) under the supervision of a lab course coordinator (A.O.) in cell biology looking to include novel approaches in a cost- and time-effective fashion. The project was inspired by previous published work involving apple slices stripped of their fruit cells and replaced with animal cells (Modulevsky et al., 2014). K.L. successfully modified the protocols outlined in the aforementioned study, adapting the experiments to fit into the structure of an upper-level lab course focused on myogenesis. The protocols herein allow students the ability to decellularize various 3D cellulose scaffolds from different varieties of fruit and vegetables before re-seeding with the mouse myoblast cell line, C2C12. Participants in this workshop will benefit from the hands-on experience with some of the key experiments including preparing plant sections for decellularization, preparing sections for mammalian cell seeding, slide mounting and chromogenic staining for visualization using common lab equipment and inexpensive reagents. Finally, although we outline a specific approach, we will discuss workarounds and share other insights learned since the first iteration of this project.
Sequence analysis: A paper and computer-based exercise in cloning
Laurel Rodgers, Shenandoah University
The process of cloning is critical for scientists to study the relationship between the structure of a protein and its function. However, the development of the cloning vectors needed for such studies can be very time consuming and not necessarily practical in the constraints of a 3hr lab that meets once a week. My post doctorate research project was focused on deleting each functional domain from the tight junction scaffolding protein, Zonula occludens (ZO-1), in order to determine the role of each domain in the formation and function of the tight junction within epithelial cells. This “dry” lab walks students through key points of the process I used to develop the plasmids used to express the altered ZO-1 proteins within epithelial cells. During this lab students practice finding and labeling protein domains and enzyme restriction sights within the ZO-1 gene and plasmid DNA sequences. They also learn about some of the methods researchers use to put their DNA sequence of interest into expression vectors. This lab can be used as a stand-alone unit on tight junctions, protein-structure function, and cloning or it can be used as the final exercise of your favorite cloning wet lab. This lab is recommended for a 300 or 400 level cell and molecular biology type course.
Using foldscopes for offline exploration in online biology courses
Jennifer Van Dommelen, Jacob Fletcher, Dalhousie University
A FoldscopeTM is a portable microscope that is assembled from paper and a small lens; it can be used alone or in combination with a smartphone or tablet camera. FoldscopesTM can magnify up to 140X with a resolution of 2 microns, producing images comparable to those obtained with a basic light microscope. FoldscopesTM can provide students with direct access to the microscopic world via a safe, inexpensive activity that they can participate in without supervision, which makes them especially useful for online courses where students may not have access to standard laboratory equipment. In our online introductory courses for mixed majors, we use FoldscopesTM to observe chloroplasts in plants and algae and pigmented epidermal cells in red onion (Allium cepa), and guide students to consider the evolutionary and physiological significance of their observations. In the workshop, participants will assemble their own FoldscopesTM, work through our students’ activities, and provide suggestions for using FoldscopeTM in other contexts (such as field work, experimental work, face-to-face settings, and with other organisms); these suggestions will be included in the revised workshop manuscript.