Major Workshops are hands-on opportunities for attendees to experience a laboratory activity that has been developed and implemented for the classroom. Each three-hour workshop is peer reviewed by participants, and ultimately by the editor of our proceedings, Advances in Biology Laboratory Education, 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 registration process. The titles, presenters, and abstracts for each workshop are listed below by day.
Wednesday, June 22
Deconstructing the lab notebook and scaffolding assessments in a CURE
Laura Atkinson, Mount Royal University, Biology Department, Calgary, Alberta, Canada
The pedagogical framework of a course-based undergraduate research experience (CURE) involves having students learn essential experimental techniques, design an experiment, carry out the experiment, interpret data and communicate results (McLaughlin & Coyle, 2016). Common assessments used in a CURE are a research proposal, lab notebook and manuscript/poster/presentation. However, there are several challenges with the use of the lab notebook as an assessment tool. For example, grading of the lab notebook often occurs after an experiment is complete. Errors in understanding or calculations are not caught leading to a waste of reagents and time. Furthermore, finding and assessing information in a lab notebook is extremely time consuming and comments may not be read or understood. To address these issues, I deconstructed the lab notebook into experimental plans and data submissions. Using these assessments, my observations in the lab (echoed in student feedback) are that students come to the lab more prepared, understand the protocol and feel confident in their ability to troubleshoot if something goes wrong. Importantly, the experimental plans can be peer graded in class while the instructor goes over the information. This provides the opportunity for students to ask questions and gain clarification prior to beginning their experiment. In this workshop, participants will be briefly introduced to a semester-long CURE that uses experimental plans and data submissions. Participants will use student-provided examples to peer grade experimental plans (as students) and grade data submissions (as instructors). Participants will be guided through an exercise to prepare grading rubrics for any experimental protocol and the accompanying data submission. Lastly, we will discuss how the use of experimental plans and data submissions allow the scaffolding of assessments for the scientific communication pieces (manuscript/poster/presentation).
Transitioning Students to Researchers: Instructional Baby Steps
Dawn Giesbrecht, University of Saskatchewan, Department Anatomy, Physiology, and Pharmacology, Saskatoon Saskatchewan, Canada; Harold Bull, University of Saskatchewan, Department Biochemistry, Microbiology and Immunology, Saskatoon Saskatchewan, Canada; and Sheryl Mills, University of Saskatchewan, USask Health Sciences, Saskatoon Saskatchewan, Canada
Structuring a course, or part of a course, to include a Course-based Undergraduate Research Experience (CURE) involves both changes in the course format and changes in the instructor’s role and perspective(s). For the past three years we have facilitated authentic research experiences in two ways within the confines of a traditional course structure: (1) by including CURE elements in a traditional lab course and (2) using the CURE format for a complete three credit unit course. In both settings, learners have transitioned from thinking like ‘students’ to thinking, doing, identifying as, and becoming ‘researchers’. This workshop provides the opportunity to move step by step through the process of integrating CURE attributes and principles into a traditional lab course. By the end of this workshop, you will have: (1) a clear understanding of the CURE approach and the related pros and cons, and (2) developed an actionable plan that integrates CURE approaches into your traditional lab course.
Art and the Plight of the Environment: Student-Created Images that Inform and Inspire
Mariëlle Hoefnagels, University of Oklahoma, Department of Microbiology and Plant Biology, Norman, OK, USA; Amanda Boehm-Garcia, University of Oklahoma, Fred Jones Jr. Museum of Art, Norman, OK, USA; Matthew S. Taylor, University of Oklahoma, Department of Biology, Norman, OK, USA
In this three-part activity, students examine, create, and present artistic images to explore the environmental impact of human activities. To begin, students study a work by American artist Patrick Nagatani (1945–2017). The work, called Nuclear Enchantment, contains 40 photographs depicting the damaging legacy of the nuclear industry in New Mexico. During our lab in fall 2021, the photographs were on display at the Fred Jones Jr. Museum of Art (FJJMA), and the class viewed them in person. However, the photographs are also readily available online (patricknagatani.com), so access to the FJJMA is not necessary to complete this activity; in addition, with sufficient notice, FJJMA staff can facilitate a virtual event for any instructor. Regardless of the delivery method, the photographs are combined with discussion questions helping students to understand how Nagatani staged or enhanced elements of the photos to draw attention to social and environmental issues. In the second part of the activity, students have one week to create and modify their own Nagatani-style photo to illustrate an environmental issue of their choice. Along with their image, they submit a written or verbal description of how they constructed their image and what it means to them. In the third part, the lab reconvenes, and groups of students who selected similar issues present their images to the class. Post-lab surveys indicated that students appreciated the opportunity to be creative and to use visual media to explain environmental problems that were important to them. In addition, nearly 75% indicated they would like their image and description to be included as part of the museum’s exhibit, indicating pride and satisfaction in their work. In this workshop, participants will explore Nagatani’s work, create images with their own cameras and computers, and present the images to the rest of the participants.
Using Gromphadorhina portentosa to teach metabolic and respiratory principles of ectothermic animals
Kenneth G. Sossa, Azusa Pacific University, Biology and Chemistry Department, Azusa, CA, USA
For decades understanding the metabolic differences between ectothermic and endothermic animals has fascinated scientists and students alike. Here we propose to study ectothermic metabolism using the Gromphadorhina portentosa (Giant Madagascar Hissing Cockroach). This large insect model has an extensive tracheal system with a characteristic hiss that is produced when air is forced out through its spiracles. Using an iWorx data acquisition device and software (LabScribe) carbon dioxide production as well as oxygen usage will be recorded over time. These data will be used to plot the Respiratory Exchange Ratio (RER), a measure of metabolic activity. Metabolic differences during periods of high metabolic demand (i.e. exercise) and diet restrictions (i.e. low carbohydrate) will be explored and compared to baseline RER. This lab will underscore ectothermal metabolism and insect respiratory anatomy and physiology.
Who has the flu? Tracing transmission with ELISA and PCR
Callen Hyland PhD, University of San Diego, San Diego, CA, USA and N. Jan Chalupny PhD, Shoreline Community College
With outbreaks in the news and misinformation spreading faster than a virus, immunology and vaccination are urgent topics for high school and introductory college biology. In this engaging, hands-on lab, students will learn how the immune system protects us against disease while tracing an outbreak of influenza in a small community. Students will use real-world molecular techniques to screen a group of individuals with varying vaccination status for influenza infection – enzyme-linked immunosorbent assay (ELISA) to detect antibodies and PCR to detect viral DNA in patient samples. At the conclusion of the lab, students will pool their data and discuss the patterns of infection among vaccinated and unvaccinated individuals and the need to update the influenza vaccine each year on account of the constant evolution of the influenza virus. This lab activity is suitable for advanced high school and early college, but can be adapted for students with different levels of preparation.
Integration of Authentic Research into an Undergraduate Laboratory Course: Design, Synthesis and Testing of a Gene Therapy Vector
Martin Hicks, Victoria DeMarco, Flobater Gawargi; Monmouth University, Biology Department, West Long Branch, NJ, USA
Undergraduate biology students often graduate without exposure to authentic research experiences. Laboratory courses follow a one or two week fail-proof experiment resembling a cookbook recipe, lacking the uncertainty of genuine research. Techniques in molecular biology cover an array of skills essential to succeed in a biotechnological laboratory today. This lab course is based on the teaching of concepts while imparting the skills and applications of modern techniques, providing students with theoretical concepts and laboratory skills. We prepare students to carry-out scientific protocols that can be applied to a future workforce setting. Students are immersed in a 12-week series of labs with the objective to use molecular cloning to make a gene therapy vector; therapies are designed to inhibit the overexpression of oncogenes in brain tumors. Students are introduced to PubMed and Genbank to research the background of a target gene. Students use DNA analysis software, Serial Cloner, as an interactive tool to evaluate DNA sequence motifs and visualize the design of an antisense gene therapy. Using a platform system, students generate a vector with a unique therapy. Students transfect into mammalian tissue culture cells and subsequently collect RNA to verify the effect of the therapy vector on the target gene
Identifying marine fish and estimating fish abundance in underwater community observatories
Mauricio Carrasquilla-Henao, Dave Riddell and Isabelle Cote; University of Victoria, Department, Ocean Networks Canada, Victoria, BC, Canada
Many undergraduate biology students are fascinated by the ocean, marine organisms and how these organisms interact with the environment yet have no access to the marine environment. In this laboratory we bring to students from across the world the opportunity to learn about marine fishes from the Pacific Northwest by collecting data from an underwater camera on one of Ocean Networks Canada’s cabled observatories. In this hands-on activity, students will learn to collect and annotate data from video clips and estimate fish abundance and relative abundance. Students will plot their data against temporal variables (month, season, and time of day) and compare how total fish abundance and species-specific fish abundance vary across these variables.
Thylakoid: An Exciting Game About Photosynthesis
Jennifer Schroeder, Ph.D., Young Harris College, Department of Biology, Young Harris, GA, USA
One of the most challenging and confusing aspects of cellular/molecular biology is understanding how the electron transport chain (ETC) is utilized in cells to create energy. In this game-based activity, students will physically interact with different components of the thylakoid ETC as water is converted to oxygen and stored energy during the light-dependent reactions of photosynthesis. By playing a series of cards that represent different steps, students move electron pieces along a series of graphical representations of photosystems, cytochrome b6/f, and mobile elements to eventually deliver them to NADP+, while also creating a proton gradient that powers the ATP synthase. Additional attack cards also inform on the ways certain mutations and herbicides can impact functions required by the ETC. The level of detail modeled in this game best corresponds to a 2000/3000-level cell biology course, but could be adapted as needed.
Thursday, June 23
Creating Meaningful Professional Development Opportunities for Teaching Assistants Facilitating Course-based Undergraduate Research Experiences (CUREs)
Amie M. Kern, Jeffrey T. Olimpo, and Christina E. D’Arcy; Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX USA
Current national efforts to reform postsecondary laboratory education have emphasized incorporation of authentic research opportunities into science, technology, engineering, and mathematics (STEM) curricula. Within the last decade, course-based undergraduate research experiences (CUREs) have emerged as a viable mechanism to achieve this goal. Evidence within the biology education literature suggests that student engagement in CUREs has the potential to positively impact their development of scientific inquiry and process skills, content knowledge, and affect in the domain. While the majority of studies have focused on student outcomes, few studies have examined instructor outcomes in CURE learning environments. This is especially true for graduate and undergraduate teaching assistants (GTAs/UTAs), who are frequently tasked with teaching CUREs, yet who often receive little, if any, professional development (PD) to improve teaching skills that are vital to this type of instruction. Furthermore, we argue that the ability to equip GTAs/UTAs with the skills necessary to effectively facilitate CUREs is contingent upon likewise providing professional development and education to individuals who lead CURE TA PD at their institution. In this workshop, we will address these needs through the following workshop activities: (i) a brief introduction to existent CURE TA PD literature and programs;(ii) small-/large-group dialogue designed to evaluate novel data which identifies core elements of CURE TA PD(some of which was collected at ABLE 2019); (iii) a brief review of the backward design process, which participants will use to construct their own, individualized CURE TA PD activity for use within their course; and (iv)a gallery walk exercise, which will allow participants to receive feedback on their planned activity from the session facilitators and their peers.
CRISPRgene technology in Painted Lady Butterflies
Lynn Kee, Department of Biology, Stetson University and Jay Pieczynski, Rollins College, Deland Florida, USA
CRISPR gene technology is ubiquitously used by scientists to investigate gene function and manipulate gene expression and phenotypic outcomes. Moreover, CRISPR technology has been developed for treating genetic diseases like sickle cell anemia and retinal degeneration, as cancer immunotherapy, and even for COVID-19 diagnostic testing. We asked how can we successfully integrate CRISPR technology into undergraduate biology lab curriculum so that students are immersed in current technology and modern research practices? We have previously engaged students in the full process of design, implementation of a CRISPR gene targeting strategy with Vanessa cardui butterflies in a multi-week lab experience. In the lab experience, students targeted a gene called optix that regulates butterfly wing color using CRISPR technology. CRISPR can be used to create a desired gene knockout to deactivate the gene and determine the effect on the gene knockout on butterfly wing color and the nucleotide changes that have resulted from CRISPR targeting in the optix gene. Butterflies are exciting and charismatic to students, and from an instructional perspective provide specific advantages. We can rear V. cardui, commonly known as painted lady butterflies and caterpillars in lab, collect hundreds of butterfly eggs for CRISPR delivery, and the egg size (~1mm) makes CRISPR delivery through microinjection possible in an undergraduate setting. Phenotypic analysis can be conducted three weeks post CRISPR delivery, and the molecular analysis such as Polymerase Chain Reaction and DNA sequencing is relatively simple with both caterpillar hatchlings and butterfly tissue, thus enabling students to make connections between genotypes and phenotypes. In this workshop, I will focus on three specific aspects of the process that other institutions can adapt to their labs: 1) the CRISPR design of targeting the optix gene – how students can design the CRISPR component called the guideRNA to target a specific part of the gene; 2) how to genotype CRISPR mutants using Polymerase Chain Reaction and DNA sequencing; and 3) the analysis of phenotypic and molecular outcomes, specifically, showing how butterfly wings with color changes produced by undergraduates, and demonstrating how to analyze DNA sequencing results of CRISPR-d butterflies.
Using Markdown and Free Tools to Write, Publish, and Share an Open-Source Scientific Writing Guide
A. Daniel Johnson, Wake Forest University, Department of Biology, Wake Forest Road, Winston-Salem NC, USA.
At the 2021 ViABLE conference we presented our “six elements model” for teaching scientific writing in multi-section introductory biology courses. One of our essential tools is a standardized Scientific Writing Resource Guide that students and instructors use across multiple courses. In response to many requests that we share our Resource Guide, it now is available as an open-source book that others can modify to meet their individual needs. To make our Guide easy to maintain and convert to different formats, we wrote it using Markdown. This lightweight markup language is ideal for writing lab materials because authors can write a text once, then output it in a variety of formats such as HTML5 for web pages, or Word/PDF documents for handouts. Groups of Markdown files can be combined to create interactive online books. Markdown takes ~20 minutes to learn, and marked text remains readable. Participants in this workshop do not need any prior technical knowledge beyond basic computer skills. They will learn to use Markdown by editing existing pages from our Guide and creating new pages, which they will convert into formatted Word and HTML5 documents. We will demonstrate how to use R Studio to assemble collections of Markdown documents into books, and how to use GitHub to manage and share writing project files. Participants will leave with a complete copy of our Scientific Writing Resource Guide that they can revise to match their course requirements, the tools for writing and converting Markdown files to their preferred format, and a GitHub account where they can back up their project. Those interested can learn how to launch new book projects of their own, or contribute to our published edition of the Resource Guide.
Snowflake CURE: Isolating microbial DNA from snow for metagenomic analysis to assist undergraduate students with learning molecular and biostatistical tools
Jenean O’Brien, PhD, and Anne Kruchten, The College of St. Scholastica, Biology Department, Duluth, MN, USA
Designed to help undergraduate students gain hands-on experience with molecular biology and to become familiar with bioinformatic analysis of large scale datasets, our Snowflake Course-based Undergraduate Research Experience (CURE) focuses on identifying how microbial populations isolated from different snow samples differ in the types and amounts of species present. In an eight-week course, upper division biology major students isolate and purify DNA from snow samples, amplify microbial 16S DNA by polymerase chain reaction (PCR), purify microbial DNA for metagenomic sequencing, use Excel and R statistical software to analyze sequencing data, and specifically explore the gene Ice Nucleation Protein (inaQ) through PCR, agarose gel electrophoresis and online database analyses. Our goal is that students gain an understanding of what bioinformatics analysis means and hopefully recognition that this skillset is within their abilities. Students are both introduced to and reinforce these molecular and bioinformatic skills in this course. Additionally, students gain experience in writing laboratory notebooks and communicating their science visually and textually through figure development. This course could be easily modified to become a module in a larger course, divided into smaller units to fit into pre-existing courses and/or adapted for any water-based samples.
Training a Biologists Mind Through an Artist’s Eye
Brett C. Couch, University of British Columbia, Departments of Botany and Zoology, Vancouver BC, Canada; Holly Schmidt, University of British Columbia, Morris and Helen Belkin Art Gallery, Vancouver BC, Canada; and Christine Goedhart, University of British Columbia, Department of Botany, Vancouver BC, Canada
Labs, especially organismal diversity labs, serve a major role within a biology curriculum for developing students’ observational skills. Labs should train students to be active, iterative, patient, and critical observers of the world. Student’s reliance on cell phone cameras to record observations, lack of patience, lack of practice with observational heuristics and lack of skills or confidence in making sketches can limit development of observational skills. In this lab we present multiple fine-arts based observational and mark-making activities that focus on the process of observing as a tool for developing observational skills. These activities could make up a single lab but are envisioned as being woven into the structure of an entire course to provide repeated practice and develop habits of mind. The activities presented here have been used in organismal biology labs at UBC in face-to-face and online formats. The activities were envisioned as being applicable to diverse labs where students make, interpret or record visual observations regardless of the specific organismal focus. Many of the activities involve making sketches as a tool to promote observation. Logically, making an accurate sketch requires structured, repeated, careful, observations as well as the ability to critically evaluate and revise what has been recorded. The focus of these activities is on the process of making observations rather than the product (e.g. a formal scientific drawing). We aim to break students of the habit of being passive recorders of the world through the lens of a cell phone camera and become active observers of material in labs and in the world around them through activities that defy the use of technology for recording observations and require active participation in the process of making, recording and revising observations. Methods of evaluation can include simple participation, reflective activities, evaluation of recorded observations.
Using temperature and light data loggers to drive an inquiry-based environmental science field lab
Michael S. Berger, School of the Environment and School of Biological Sciences, Washington State University Vancouver, USA
Engineering design principles were applied to the development of a modular, inquiry-based introductory (100-level) environmental science lab. Engineering design focuses around addressing a problem through an iterative process that acknowledges constraints in the system and optimizes the outcome for success. The laboratory exercise was designed for students to work through the process of designing an experiment, given realistic constraints of the system. While the research question they asked was relevant contextually, the lab was not focused on the merit of the question students developed. Learning goals were focused on: 1) developing a testable question and appropriate experimental design; 2) collecting data, organizing data, and applying an appropriate data analysis methodology; 3) reflecting on the experimental design and system constraints to address the research question. Each group of students were provided with two temperature and light data loggers and then assigned the problem of designing an effective experiment that addressed a novel environmental science question of interest to the students. Students were asked to consider the following in their experimental design: 1) treatments tested; 2) frequency of sampling; 3) replication. One focus of this lab was for students to critically reflect on the design process and use an iterative approach to refine their experimental design. Following data collection in the field for one week, students were tasked with summarizing their data in a meaningful way, to help evaluate the effectiveness of their experimental design. At the end of this modular lab, students reflected on what aspects of their experimental design worked, limitations in their experimental design, and major constraints encountered. Workshop participants will be able to develop a question, design an appropriate experiment, deploy data loggers in the field, collect data using a mobile device, organize data, and reflect on the experimental design process.
Using Genome Annotation Projects to Teach Eukaryotic Gene Structure and to Engage Students in Genomics Research
Maria S. Santisteban1, James Godde2, Anya L. Goodman3, Charles R. Hauser4, Don Paetkau5, Catherine Reinke6, Wilson Leung7, Cindy Arrigo8, Nathan T. Mortimer9, and Laura K. Reed10
1 University of North Carolina at Pembroke, Department of Biology; 2 Monmouth College, 700 E Broadway, Monmouth, IL, USA; 3 California Polytechnic State University, Chemistry and Biochemistry Dept., San Luis Obispo CA, USA; 4 St. Edward’s University, School of Natural Science, 3001 South Congress, Austin, TX; 5 Saint Mary’s College, Notre Dame, IN, USA; 6 Linfield College, Biology Department, 900 SE Baker Street, McMinnville OR, USA; 7 Washington University in St. Louis, Department of Biology, Campus Box 1137, One Brookings Drive, St. Louis MO, USA; 8 New Jersey City University, Department of Biology, 2039 Kennedy Blvd., Jersey City, NJ, USA; 9 Illinois State University, School of Biological Sciences, Box 4120, Normal IL, USA; 10 University of Alabama Tuscaloosa, Department of Biological Science, Tuscaloosa, AL, USA
The Genomics Education Partnership (GEP; https://thegep.org) began as a consortium of 16 faculty in 2006 with a goal of providing students with Course-based Undergraduate Research Experiences (CUREs) in genomics. Today, GEP has over 200 faculty from more than 180 institutions and engages more than 3,900 undergraduates in authentic genomics research annually. These faculty joined and continued to participate in the GEP for many reasons, including the collaborative nature of the research, the well-established infrastructure, and the supportive network of like-minded colleagues. Faculty implement GEP materials in diverse settings — ranging from short modules (2–8 weeks) within a course, to a standalone full-semester course, to independent student research. GEP students show significant gains in scientific knowledge and attitudes toward science. In addition to improving their understanding of the research process and how new knowledge is created in the field, GEP students acquire desirable and transferable skills essential for future participation in the workforce, such as problem solving, independence, application of knowledge, team-work, and collaboration. Students also gain competence in the use of computational algorithms to analyze large biological datasets — thereby preparing students for a growing need of a workforce trained at applying statistics and computational tools to analyze large datasets. In addition, GEP students and their faculty mentors are eligible to be co-authors on the scientific publications that are based on their work. In this workshop, we will provide an overview of the GEP community, a hands-on guided tour of our introductory curriculum aimed to teach gene structure, transcription, translation, and processing, and a step-by-step walkthrough that illustrates the protocol for annotating a protein-coding gene in Drosophila. Participants will receive information on how to join the GEP community and receive training and resources to enable their implementations.
Molecular Parasitology CURE: Understanding the apoptosis pathway in kinetoplastid parasites.
Swati Agrawal, University of Mary Washington, Department of Biology, Fredericksburg, VA, USA
Embedding inquiry driven research in undergraduate courses allows integration of core concepts and competencies necessary scientific thinking and develop lab skills. These are critical skill for undergraduates to be successful in science careers and for admission into graduate school. However, there are only a handful of examples of collaborative CUREs in Biology where students have an opportunity to connect with a network of researchers outside of their own institution, and none in the field of parasitology. In Spring 2021, we piloted a mini-CURE where student groups from University of Mary Washington and Georgia State University collaboratively completed research projects as part of a research-intensive course on Molecular Parasitology. The benefits of this approach were immediately obvious as students interacted across institutions, learned from each other’s disciplinary expertise while informing their own research with data collected by their collaborators. It provided enrichment to the course by adding networking opportunities as well as cross-disciplinary knowledge sharing. We present here our CURE model as a way for other educators to design and implement similar cross-institutional inter-disciplinary CUREs that can be modified to align with their research expertise.
Fetal Pig Dissection Lab with Detailed Images
Beth Cantwell and Laurel Rodgers, Shenandoah University, 1460 University Drive, Winchester, VA, USA
This lab provides students with detailed dissection instructions of the fetal pig, including the digestive, respiratory, cardiac, urinary, and reproductive systems. Color pictures are provided for each step to help students ensure that they are removing the correct tissues and making the correct incisions. Information is provided throughout the lab about the function of each organ students observe. This lab was written for a non-majors, general education course. However, we have provided additional materials in the appendix in order for instructors to expand the lab for a Biology majors course.
A Rich Independent-Project-Based Enzymology Lab Using Plant Mitochondrial Succinate Dehydrogenase
Jonathan E. Moore, Ross N. Pringle, and David Becker, Pomona College, Biology Department, Claremont CA, USA
For well over twenty years, we have successfully run a half-semester inquiry-based enzymology lab at the introductory/ intermediate level. In successive weeks, students use black-eyed pea (Vigna unguiculata) plants to make a crude mitochondrial purification, hone their pipetting skills with a Bradford protein concentration assay, construct a Lineweaver-Burk plot to determine Km and Vmax of succinate dehydrogenase (complex II) in their experimental conditions, consult with their instructor about their independent project proposal, execute their plan, and then write up their results. The literature on SDH is quite diverse, and accordingly the independent projects are quite diverse in nature. Along the way, they learn about differential centrifugation, accurate pipetting, spectroscopy, systematic errors, outliers, and mining the literature. This lab could be easily scaled back to a two-week lab with simpler learning goals.