These 3-hour workshops were hands-on, laboratory sessions during which presenters shared their innovative and successful undergraduate lab exercises with participants. Participants then reviewed these with short form (pdf) or long form evaluations, part of the peer-review process leading to publication of these activities in our annual Proceedings publication.
Wednesday, June 24, 2015
Canceled, but content was offered as a mini-workshop on Friday: The making of a scientist: hands-on, student driven research projects from concept to publication
Jelle Atema and David Minkoff
Utilizing the software package “R” to generate graphs and perform statistical analyses in undergraduate laboratory courses
Michael S. Berger
Many courses in the life sciences require students to graphically present data and use statistical tests to interpret results. Students frequently lack basic skills regarding visual representation of data and processes involved in performing statistical tests. Classroom software is often expensive and can have limitations on graph quality, complexity of graphs generated, or power to perform statistical analyses. I have developed a series of lab exercises that utilizes the software package “R” as a learning tool to improve graphing skills and statistically analyze data. Learning goals are focused on: (1) competency in the visual display of data; (2) using the appropriate statistical analysis based on the question addressed; (3) learning how to use the software package “R”. The software package “R” is an open source script-based software that can be used with a graphical user interface, such as “R Commander”. Students can use this free software to generate high quality graphs and perform numerous statistical tests. The use of a script based software removes the “back-box” effect that can limit conceptual understanding of the components involved in the process of visually representing data or performing statistical analyses. Students were introduced to “R” and provided with step-by-step tutorials that guided them through the process of generating graphs or performing statistical analyses. Workshop participants will use a hands-on approach to learn basic skills that are necessary to use the software package “R” in classroom setting. At the end of the workshop, participants will know how to format data files, generate a line plot with error bars, construct an X-Y-Z contour plot, and run a one-way ANOVA in “R”. The skills developed in this exercise can be adopted for lower or upper division courses across multiple disciplines.
A scaffolded approach to integrating primary literature into a biology laboratory
Janice M. Bonner
This workshop suggests a scaffolded introduction of students to biological literature. Students are presented with deep-lobed and shallow-lobed leaves (Quercus alba) and led to design methods to quantify depth of lobing and determine stomatal density. After students learn that the leaves were obtained from the top and bottom of the same tree, they are asked where each type (deep-lobed/more stomata; shallow-lobed/ fewer stomata) would be located. Finally, students read a journal article in which stomatal density of fossil oak leaves is used to predict paleoatmospheric CO2 concentrations. Students’ familiarity with laboratory procedures facilitates their understanding of the article.
Accessible laboratory and lecture environments for teaching biology
William V. Glider, Christy Horn, Peter Thew, and Amin Makkowy
This workshop will describe a classroom development project that provides a fully inclusive and accessible environment for all students including students with disabilities. Science curriculum has many highly visual and interactive components that have traditionally created barriers to the full participation of disabled students. New technologies have emerged in the teaching of biology in lecture and lab that can assist in creating learning spaces that will enhance student-teacher and student-student interaction and support multiple modes of learning. We will describe a number of accommodation strategies that we have developed over the last ten years to enhance learning for all disability groups focusing on the use of technology as a means to accommodate individual learning challenges.
miR seekers: Finding targets of microRNAs in undergraduate lab courses
Adam Idica, Jordan Thompson, Irene Munk Pedersen, and Pavan Kadandale
microRNAs (miRs) are small, non-coding RNAs that regulate gene expression programs critical for normal development and health. Misregulation of miRs are associated with numerous diseases, and miRs are currently being investigated both as targets for drug design, and as potential therapeutics. Since the precise mechanism by which miRs select their target mRNAs is not known, predictions of targets must be manually verified. The techniques used to validate miR target predictions are relatively straightforward and inexpensive, making this an ideal vehicle to introduce students in undergraduate labs to authentic research experiences. We describe here a 3-session lab module that we have developed that allows students to generate hypotheses about specific miR candidates, and then design and execute experiments to test their predictions. Students will learn the use of bioinformatics tools, biology databases, and literature searches to select a candidate gene of interest. Along the way, they will be faced with the same questions and decisions that scientists tackle, and students will need to evaluate information from a number of different sources in order to pick their gene of interest. They will then use bioinformatics tools to design primers to test expression of their candidate gene. Finally students will extract RNA from cells, and use qPCR to compare expression of their candidate gene in normal cells to expression in miR-overexpressing cells. The module requires students to reproduce their results, and gives them the opportunity to make a real contribution to a cutting edge field of scientific inquiry.
An introduction to bioinformatics
Robert J. Kosinski
This exercise is used in introductory biology for majors at Clemson University. Students download DNA and protein sequences from a Web site and apply common bioinformatics tools to identifying and researching them. Seventeen sets of sequences (covering common genes) are available for student use, and an eighteenth (the triosephosphate isomerase gene) is used as an example in the exercise. The exercises ask the students to use BLAST to identify a genomic DNA sequence that includes a piece of a gene, to explore their gene’s genomic “neighborhood,” to determine the percent of DNA that is transcribed in this neighborhood, to identify a protein using BLAST, to research this protein using UniProt, to research the role of their gene in disease using PubMed, and finally, to determine if DNA isolates from a mass disease outbreak show evidence of bioterrorism.
Identifying promoter activators and repressors using lacZ transgene expression in Saccharomyces cerevisiae
David A. McDonald, Sarah E. Council, Stephanie C. Schroeder, Ruth S. Phillips, Gail P. Hollowell, and S. Catherine Silver Key
Gene expression is an essential concept to Biology majors. In this 2-week guided inquiry laboratory, students are led to discover the role of promoters in gene expression using colorimetric assay measurable by spectrophotometry. Additionally, the 2-week lab module aims to introduce students to elements of research including iterative skills, data analysis and data interpretation by comparison of their data to assigned figures in primary research papers. Students use a straight-forward protocol to perform the beta-galactosidase assay to analyze 4 Saccharomyces cerevisiae strains carrying the lacZ reporter transgene driven by a eukaryotic wild-type or mutant promoter.
Darwin’s finches: Evolution and natural selection lab
Kimberly Orrell, Laurel Rodgers, and Karen Andersen
This lab is designed to provide students with a hands on activity that demonstrates how changes in environmental conditions can result in the evolution of a species. Students are first introduced to Darwin’s observations on the Galapagos Finches, which provides a framework for understanding natural selection and evolution. Then they are introduced to the later (and still ongoing) research by Peter and Rosemary Grant which describes the rapid evolutionary changes they observed in the ground finches of Daphne Major. Once a basic understanding of evolution and natural selection has been reached, students will become finches, with each student representing one of four beak sizes and shapes. The students make hypotheses about how the different beak types and the seed types available will affect his/her ability to forage for food, and then test those hypotheses by using their beaks to collect seeds. At the end of the lab students organize their data into tables and graphs and evaluate their hypotheses. They then develop their own conclusions, based on the data, about how changes in selection pressure (environmental conditions) can result in differences in survival, and subsequently, in the adaptation and evolution of traits in a population.
Laboratory aquaponics: Bringing fish farming, gardening, and miniature biospheres into the everyday classroom
Peter J. Park, Michael E. Huster, and Catarina Mata
Participants will utilize an aquaponic system to learn principles and concepts in ecology and be trained in skills that can be applied to practical activities (e.g., raising fish, keeping a garden). Aquaponics is a method of keeping/farming aquatic animals (e.g., fish, aquatic invertebrates) and vegetables simultaneously by growing both in an inter-connected system. It is also a form of sustainable farming that can be achieved on very small scales, such as a classroom. An aquaponic system is designed to use nitrogenous wastes generated by fish (or other aquatic animals) as fertilizer for plants growing in a soil-less growing bed that is connected to the aquarium. The plants utilize this fish “waste water” for growth and maintenance, and in the process, filter this water before it is returned to the aquarium. In this workshop, participants will be shown how to direct students to collect weekly data on the growth of red kidney bean (Phaseolus vulgaris) plants and of water chemistry. To assess the quality of plant growth in an aquaponic system, participants will compare their data with that of plants grown in potting soil. Participants will also be instructed on how to construct an aquaponic system of their own and be informed of best practices. As a wrap-up activity, participants will study an ecosphere, which is a fully-enclosed, self-sustaining glass sphere that contains water, brine shrimp, green algae, and nitrifying bacteria. Both the ecosphere and aquaponic system will be used as models of the biosphere. They can also be employed with a variety of exercises that assess knowledge in basic chemistry, photosynthesis, cellular respiration, and understanding of niches. Some examples of such activities will be shared during the workshop. This work was fully supported by an ABLE 2012 Roberta Williams Laboratory Teaching Initiative Grant.
Recent addition: Population Genetics and Behavioral Ecology: Orange, Blue, & Yellow Male Uta stansburiana
Ralph Preszler and Avis James
Populations of side-blotched lizards, Uta stansburiana, have a consistent pattern of variation in male throat color. The variation in throat color among males is associated with variation in male size and mating strategies. Success of alternative mating strategies is dependent on the frequencies of types of males in the population. In this research-based case study, students use population genetics (Hardy-Weinberg Equilibrium), behavioral descriptions of alternative mating strategies, and the results of a behavioral ecology field experiment to explore the evolutionary processes that maintain balanced variation in male throat color. The activity illustrates the use of a sequence of studies to develop an explanation of an interesting field observation. It also provides an example of the maintenance of variation in a population through balancing frequency-dependent selection.
Battle of the bacteria: Characterizing the evolutionary advantage of stationary phase growth
Brian Sato and Karin E. Kram
Providing students with authentic research opportunities has been shown to enhance learning and increase retention in STEM majors. This workshop centers on an investigative microbiology lab module, which focuses on the molecular mechanisms of evolution in E. coli, by examining the growth advantage in stationary phase (GASP) phenotype. The GASP phenotype is illustrated by growing cells into long-term stationary phase (LTSP), and competing them against unaged cells in a fresh culture. This module includes learning goals related to improving student understanding of evolution and strengthening practical laboratory skills. In addition, the students generate novel data regarding the effects of different types of media on GASP and the relationship between evolution, genotypic change, and cell stress. Pairs of students are provided with the experimental background, select a specific aspect of the growth medium to modify, and generate a hypothesis regarding how this alteration will impact GASP. Students explore not only the growth competition between aged and fresh cells, but also how the different types of media impact cell stress and mutation frequency. From this module, we have demonstrated that students are able to achieve the established learning goals and have produced data currently being explored by a research lab. Workshop attendees will be introduced to the GASP phenotype and get hands on experience with the techniques utilized to gather data regarding this phenomenon. We will discuss how to incorporate this module into the lab curriculum at attendees’ institutions, potential pitfalls for both students and instructs, and means to assess student learning.
Genome analysis project
Lori R. Scott, Todd C. Nickle, Katherine Houmiel, Ben McFarland, Jennifer Tenlen, Kimberly Murphy, Andrew Lumpe, and Daihong Chen
The Meiothermus ruber Genome Analysis Project provides an authentic research experience in genome analysis using contemporary bioinformatics and functional genomics tools. The M. ruber project provides a genuine research opportunity for students to study biological processes in M. ruber that have never been studied in this organism. In addition, it is anticipated that much of the work accomplished by students will eventually be published in the primary scientific literature. In this major workshop, participants will be introduced to the online resources for contributing to the M. ruber project. More importantly, however, workshop participants will be shown how to adapt the instructional scaffold provided by the M. ruber project to a new genome analysis project for a microorganism of their choice. The Department of Energy’s Joint Genome Institute sequenced the genomes of 200 microbes from across the Tree of Life as part of the Genome Encyclopedia of Bacteria and Archaea project. Most of these organisms are safe for use in high school and undergraduate laboratories and there is sparse published work on the genetics of their biological processes. The Guiding Education through Novel Investigation (GENI) website at http://www.geni-science.org provides detailed instructions for both instructors and students on select methods in genomics analysis. One of the projects available through the GENI site is the description of how the M. ruber project uses the bioinformatics platform called GENI-Annotation Collaboration Toolkit (GENI-ACT – at http://www.geni-act.org) as a research tool. GENI-ACT is an adaptation of the original Joint Genome Institute’s IMG-ACT system. This platform offers instructions on how to use publicly available bioinformatics tools for making function predictions of putative open reading frames, as well as an online lab notebook for data collection. In this workshop, participants will be shown how the M. ruber genome analysis project uses the GENI and the GENI-ACT platforms in an authentic research experience.
Thursday, June 25, 2015
Conducting authentic collaborative research in undergraduate biology courses using the open science framework
Anne B. Allison
This workshop will lead instructors through initial set-up of the Open Science Framework (OSF, https://osf.io/) for their individual authentic research projects. Participants will learn how to create and use an OSF account. They will learn about file editing, version control, and storing as well as how to customize settings for public and private information sharing. A case study from a 200-level laboratory course in cell biology will be presented. This month-long research project involved using immunofluorescence microscopy to measure mitotic index in a population of HeLa cells depleted of the Arf6 GTPase protein. We will discuss how this project—and specifically the implementation of the OSF as a research management tool—enhanced student understanding of best scientific practices such as the following: statistical considerations in experimental design, preregistering hypotheses and methods prior to the experimental stage, blind data collection, record preservation, and sharing raw data in a transparent way. Participants of this workshop will also spend time planning their own individual research projects into their existing laboratory curricula, in part by creating a Fink’s castle-top diagram to map the work students would execute inside and outside the laboratory during a multi-week research project. Finally, we will discuss persisting barriers to conducting authentic research with undergraduates as well as the benefits that drive continued efforts to provide these meaningful opportunities to as many students as possible.
Choosy worms to teach experimental design
Megan Cole
In this module students learn core concepts in experimental design, data analysis and the ‘messiness’ of biological research by designing and analyzing their own research project using C. elegans, various chemicals, potential bacterial food sources or pathogen, and a simple behavioral assay. Participants in this workshop will design and carry out their own experiment and discuss the potential learning gains for students. This module can easily be adapted for a single period or a multi-week module and can be used in intro classes for majors/non-majors or ecology labs.
Laboratories for integrating bioinformatics into the life sciences—Part II
Garry Duncan, William McClung, Letitia Reichart, Dawn Simon, William Tapprich, Neal Grandgenett, and Mark Pauley
Bioinformatics is a well-established and rapidly-emerging discipline integrating mathematical and computational techniques with biological knowledge to analyze genetic information. The essential nature of bioinformatics is well-recognized in graduate programs, research consortia, and biotechnology industries, but exposure to bioinformatics has been slow to reach life sciences undergraduates, and bioinformatics-focused laboratories are not yet widely available. The goal of this workshop is to present a bioinformatics-focused laboratory that has been developed and implemented by the authors at three universities in Nebraska. The laboratory can be used in a variety of classes. A similar workshop covering different laboratories was presented at ABLE 2014.
Bean beetle nutrition and development lab: An inquiry-based introduction to experimental design
Julie Laudick and Christopher Beck
In this lab, students formulate a novel hypothesis about bean beetle nutrition and development, and design an experiment to test it. When presented with gelatin capsules full of bean flour, the female beetle will lay her eggs on the capsule. Larvae burrow down into the flour where they grow and develop, just as they would in a natural bean. Students will add a nutrient of interest to flour made from a bean that is naturally deficient in that nutrient. After a few weeks of development, students compare larval mass in their experimental capsules to positive and negative controls.
Assessing biodiversity with forest plots
Shannon Mallison and A. Daniel Johnson
This workshop will demonstrate how we teach biodiversity estimation in a non-majors lab course. The pre-lab homework introduces biodiversity assessment, and leads students through the mathematical models will use. In the field, participants use standard dendrology techniques to sample 1+ small plots containing woody vegetation. Back in lab, they use multiple indices to estimate relative diversity. The core exercise can be adapted to woody flora of almost any location. The core procedures are extremely simple, requiring only wooden stakes, flagging tape, a long rope or tape to measure plots, and cloth or plastic tape measures. While we designed and use it as a one-week exercise, the core exercise can be adapted easily into a two-week inquiry lab suited to majors or upper level courses. It also can anchor a group of labs on other topics, such as plant identification, conservation, bioremediation, etc. Participants and presenters will share ideas for expanding the lab, and their suggestions will be incorporated into the final published workshop.
Reflex functions and other physiology principles: Active learning and real time analysis
Elizabeth McCarthy, Parthena Sanxaridis Mantis, and Angela Seliga
At Boston University, we have two large enrollment physiology courses; one for health and rehabilitation and one for pre-medical students. Both courses use equipment from iWorx, which allows students to record and analyze human and animal data in real time. This laboratory module was designed to address misconceptions about reflexes and learned responses by comparing patellar tendon reflexes it to a tactile learned response. Participants can also explore our other laboratory modules to demonstrate the breadth of physiology concepts we explore with this equipment, as well as to facilitate discussions on how to develop or adapt these modules.
Introduction to systems biology using Cell Illustrator
Rebecca L. Murphy, Juan Rodriguez, and Tom Ticich
Over the past decade, advances in high throughput technologies have allowed scientists to collect unprecedented amounts of data in a single experiment. The ability to collect genomic, transcriptomic, and proteomic information has also brought biology to the cusp of a new era where all of life’s building blocks will have been characterized. Moreover, rapid and relatively inexpensive genome sequencing has resulted in the advent of personalized medicine, allowing patients to be treated in an individualized way never realized before. The unprecedented level of data collection has also revealed that the information flow between DNA and proteins is not straightforward. Rather, information follows networks of complex interweaving DNA, RNA, and protein pathways. Understanding this level of biological complexity is the focus of the emerging field of systems biology. Many biologists are beginning to turn to modeling programs created by systems biologists to analyze pathway data in a functional way that allows the user to make quantitative predictions. Because the use of these programs is becoming more prevalent in all areas of biology as well as in medicine, it has become essential that students be trained in their use. The primary objective of this workshop is to provide participants instructional resources that introduce students to Cell Illustrator, a simple systems biology program that illustrates and analyzes interacting molecular pathways. Specifically, the workshop will walk participants through activities designed to introduce students to Cell Illustrator and systems biology, first by modeling simple chemical kinetics commonly discussed in introductory chemistry classes, then gradually working up to more complex molecular systems, such the lac operon presented here. Moreover, the level of access to this program can be chosen that fit the educational and budgetary needs of each institution: temporary trial access can be acquired by students for free, simulations can be performed in class using the free version of Cell Illustrator Player, ten classroom licenses can be purchased for $1300 a year, or individual professional level access can be obtained by requesting a quote.
Pazmo bugs: An old-fashion paper simulation for a modern genetics lab
Dale Pasino and Daphne Schatzberg
Inspired by fruit flies, this original simulation has been used successfully in biology labs for nearly 25 years to help teach and illustrate a variety of concepts related to genetics. The simulation simultaneously tracks genotype and phenotype of 12 Mendelian traits through successive generations. The simulation consists of two phases: (1) data collection and (2) data analysis. During data collection, working in small groups, each student generates a unique population of pazmo bugs through mating; genotype, phenotype, and parents are known for each individual of the population. Data can be easily analyzed at four different population levels – individual student populations, small group populations, lab section populations, and/or entire course population. Concepts routinely illustrated using the mating procedure and through data analysis include meiosis and gamete formation, independent assortment, effects of population size and inbreeding on allele frequencies, natural selection, and pedigrees. The simulation is adaptable and can be modified slightly to illustrate other concepts as well. This simulation is an effective teaching tool. It is interactive, involves multiple modalities, allows students to get results in real time, and gives students an opportunity to work with a large data set. Further, students can “see” how the processes work. Because of its simplicity and breadth, this simulation is generally the first thing done in the genetics portion of our lab. Afterwards, it serves as a point of reference or foundation for introducing additional or more advanced concepts.
Urban ecology: Inquiry‐based and experiential laboratory exercises for urban ecosystems
Nathan Rycroft, Angela Seliga, Tristan Lubinski, Derek Stefanik, and Ashley Jennings
Many universities are located within urban areas, not commonly recognized as complex and dynamic ecosystems. This module was created to introduce students to these ecosystems, provide them with techniques used commonly by ecologists to assess ecosystem diversity and health, and gain a better understanding of both positive and negative human impacts on urban environments. Originally designed as a 3–‐hour laboratory module, it has since been expanded into a three–‐day, 18—hour module, and includes indoor contingencies in case of inclement weather. The proposed major workshop will present activities from the module that can be easily implemented into both high school and undergraduate biology courses. The workshop will also include a discussion regarding the development and implementation of this module elsewhere.
Flipping virtual labs into team-based learning tools
Andrew R. Whiteley, Ellie Steinberg, and Eli Meir
Team-Based Learning (TBL) is one form of ‘flipped classroom’ wherein the majority of instruction occurs via inquiry-based team activities with very little lecture content. Support is growing for TBL as an effective way to promote student learning and engagement with material. We demonstrate how interactive simulations in virtual labs can be incorporated into the TBL framework. We use as an example three SimBio Virtual Labs (Darwinian Snails, Mendelian Pigs, and Genetic Drift & Bottlenecked Ferrets) that one of the authors has adapted to use in a TBL Conservation Genetics course at the University of Massachusetts Amherst. The SimBio labs provide a mix of structured and open-ended inquiry, which facilitates this approach. For each lab, students complete a set of initial exercises on their own outside of class. They complete a final open-ended exercise in class as part of a team project. After all exercises have been completed, each student individually answers a set of final questions that are part of the SimBio lab. (Note: we demonstrate the use of these modules in a 300-level course, but the same labs are commonly used in introductory Biology courses.)
Antibiotic properties of spices
Maria Burnatowska-Hledin, Sasha Balcazar, Kathy Winnett-Murray, and Lori Hertel
Spices have been used for centuries to make food taste better, add nutrients, and retard spoilage. Scientists have recently proposed that spices may also kill micro-organisms, inhibit their growth, or suppress their production of toxins, implying that the development of spice use in ethnic cuisines may have been used historically to protect consumers from illness caused by pathogens (Sherman and Flaxman 2001). A variety of laboratory exercises designed to test spices for antimicrobial effects have been developed. Few of these emphasize evolutionary themes, and even fewer capitalize on the rich potential that a multitude of unique combinations of spices, microbes, solvents, and preparations can provide for an array of student-directed hypothesis-testing. Worldwide, there is tremendous variability in the use of different spices. This suggests that, if there is a relationship between spice use and antimicrobial benefits, this relationship has been realized multiple times in different cultures in the development of ethnic cuisines. This theme is inherently intriguing to many undergraduates, who may be curious about “who” uses what types of spices, and why. In this lab, we allow students to construct an investigation, including submission of a group research proposal, arising from their own personal interest in certain spices. We equip students with a standard protocol (the Kirby-Bauer disc method) to test their own unique hypotheses; the shared protocol facilitates lab management, resource use, and interpretation of outcomes, while allowing for a significant range of student-generated experiments. Students are also encouraged to compare the effectiveness of their spice extracts with other antibiotics (e.g. penicillin, erythromycin) on a target microbe (either Escherichia coli or Staphylococcus epidermidis). An extension allows students to document evidence of the microbial response through mutations – evidence of the evolution of antimicrobial resistance.