Exercise spans two weeks, includes homework, and involves some groups of animals as well as plants. Emphasizes re-interpretation of morphological trait evolution following molecular genetic phylogeny reconstruction

This module assesses the role of wildfire in the eastern US and its impact on bird communities using NEON bird survey data from pre- and post- a major wildfire in the Great Smoky Mountains National Park (GRSM) in November 2016.

E-book in .pdf format and customizable .iba format

Modules to learn big data management, analysis, and hypothesis testing.

Analyzing high-throughput DNA sequence data is a fundamental skill in modern biology. However, real and perceived barriers such as massive file sizes, substantial computational requirements, and lack of instructor background knowledge can discourage faculty from incorporating high-throughput sequence data into their courses. We developed a straightforward and detailed tutorial that guides students through the analysis of RNA sequencing (RNA-seq) data using Galaxy, a public web-based bioinformatics platform. The tutorial stretches over three laboratory periods (~8 hours) and is appropriate for undergraduate molecular biology and genetics courses. Sequence files are imported into a student's Galaxy user account directly from the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA), eliminating the need for on-site file storage. Using Galaxy's graphical user interface and a defined set of analysis tools, students perform sequence quality assessment and trimming, map individual sequence reads to a genome, generate a counts table, and carry out differential gene expression analysis. All of these steps are performed "in the cloud," using offsite computational infrastructure. The provided tutorial utilizes RNA-seq data from a published study focused on nematode infection of Arabidopsis thaliana. Based on their analysis of the data, students are challenged to develop new hypotheses about how plants respond to nematode parasitism. However, the workflow is flexible and can accommodate alternative data sets from NCBI SRA or the instructor. Overall, this resource provides a simple introduction to the analysis of "big data" in the undergraduate classroom, with limited prior background and infrastructure required for successful implementation.

Advances in high-throughput techniques have resulted in a rising demand for scientists with basic bioinformatics skills as well as workshops and curricula that teach students bioinformatics concepts. DNA Detective is a workshop we designed to introduce students to big data and bioinformatics using CyVerse and the Dolan DNA Learning Center's online DNA Subway platform. DNA Subway is a user-friendly workspace for genome analysis and uses the metaphor of a network of subway lines to familiarize users with the steps involved in annotating and comparing DNA sequences. For DNA Detective, we use the DNA Subway Red Line to guide students through analyzing a "mystery" DNA sequence to distinguish its gene structure and name. During the workshop, students are assigned a unique Arabidopsis thaliana DNA sequence. Students "travel" the Red Line to computationally find and remove sequence repeats, use gene prediction software to identify structural elements of the sequence, search databases of known genes to determine the identity of their mystery sequence, and synthesize these results into a model of their gene. Next, students use The Arabidopsis Information Resource (TAIR) to identify their gene's function so they can hypothesize what a mutant plant lacking that gene might look like (its phenotype). Then, from a group of plants in the room, students select the plant they think is most likely defective for their gene. Through this workshop, students are acquainted to the flow of genetic information from genotype to phenotype and tackle complex genomics analyses in hopes of inspiring and empowering them towards continued science education.

Students require a deep understanding of the central dogma before they can understand complex topics such as evolution and biochemical disorders. However, getting undergraduate biology students to apply higher-order thinking skills to the central dogma is a challenge. Students remember and regurgitate the molecular details of transcription and translation but if asked to apply these details, such as how a DNA mutation might affect phenotype, it becomes clear that most students do not deeply understand the central dogma. This lesson is a five-week series of laboratory activities designed to help students transition from applying lower order thinking skills to the central dogma to applying higher-order thinking skills. Over five weeks, students explore the phenotype of Arabidopsis asymmetric leaves 1 (as1) and as2 mutants. Students isolate DNA from wild-type and mutant plants and determine the sequence of the AS1 and AS2 alleles. Students use the DNA sequence data to determine the mutant protein amino acid sequences. They submit the mutant and wild-type protein sequences to a free online server and obtain three-dimensional (3-D) models of the wild-type and mutant proteins. They use free software to analyze and compare the 3-D models to determine the structural differences between the wild-type and mutant proteins. These computer-generated models can be 3-D printed allowing students to better visualize the protein structure. The overall goal is to use student-centered laboratory activities to demonstrate the relationship between DNA sequence, protein structure/function, and phenotype.

Participation in research provides personal and professional benefits for undergraduates. However, some students face institutional barriers that prevent their entry into research, particularly those from underrepresented groups who may stand to gain the most from research experiences. Course-based undergraduate research experiences (CUREs) effectively scale research availability, but many only last for a single semester, which is rarely enough time for a novice to develop proficiency. To address these challenges, we present the Pipeline CURE, a framework that integrates a single research question throughout a biology curriculum. Students are introduced to the research system - in this implementation, C. elegans epigenetics research - with their first course in the major. After revisiting the research system in several subsequent courses, students can choose to participate in an upper-level research experience. In the Pipeline, students build resilience via repeated exposure to the same research system. Its iterative, curriculum-embedded approach is flexible enough to be implemented at a range of institutions using a variety of research questions. By uniting evidence-based teaching methods with ongoing scientific research, the Pipeline CURE provides a new model for overcoming barriers to participation in undergraduate research.

Engaging and supporting introductory level students in authentic research experiences during required coursework is challenging. Plant bioactive compounds attract students' natural curiosity as they are found in many familiar items such as tea, coffee, spices, herbs, vegetables, essential oils, medicines, cleaning supplies, and pesticides. Over the course of one semester, students work in teams to design experiments in three experimental modules to test whether bioactive compounds have effects on Daphnia heart rate, antibacterial activity, or caterpillar behavior. In a fourth module, they research solutions to an environmental problem. Students are involved in multiple scientific practices as they make their own experimental decisions, analyze data including using statistics to carefully justify their preliminary conclusions, and have the opportunity to improve their experiment and repeat it. Iteration is also emphasized by the fact that students go through the whole process from design to presentation repeatedly for three experiments. In the process, students experience for themselves the real complexity of scientific investigations and what it takes to rigorously show cause-and-effect relationships. The pedagogical focus is on providing introductory students with a supportive structure in a way that empowers them to make informed experimental decisions and be successful. At the end of the semester, the majority of students displayed a strong sense of personal involvement and an appreciation of the difficulties of scientific experimentation in open-ended written reflections. Students reported that statistics was one of the most difficult yet valuable experiences in these labs and demonstrated significant gains on a statistical test.

Primary image: Summary of the Lesson showing that student decide on which bioactive compounds to test in three model organisms (image attributions listed in Acknowledgments).

Laboratory experiences in large-enrollment introductory science courses often utilize “cookie-cutter style” laboratory experiences due to the relative simplicity of setting up the lab stations, as well as a need to teach students particular course content. These experiences rarely offer insights into the way science is done in the research setting, resulting in a lack of understanding of the scientific process. In addition, students enrolled in non-majors introductory science courses often fail to see the relevance between what they are doing in the lab and what they are learning in the lecture portion of their course. To address this gap, we developed a laboratory module for a non-majors Human Biology course that provides students with a hands-on, authentic research experience using the iWorx software and hardware for human physiology. Weekly modules were designed to guide students through the major steps of the research process, including reading current scientific literature, developing a testable hypothesis, designing and performing a physiology experiment, analyzing data and presenting their findings to their peers. The described course framework encouraged students to participate in the scientific process, providing them with the opportunity to engage in an authentic research experience. The model described here could be adapted for use with introductory or advanced students, and could be modified to fit any research model available to the instructor. Utilizing the multi-week format described is recommended for students to gain the full benefit from the research-design-revise process.

This authentic research experience lesson teaches the core concept of systems and the competencies of quantitative reasoning, communication, and the ability to apply science. The research is student driven, the results are unknown, and the students engage in an iterative process to gather data, collaborating with classmates.  It is designed for first-year biology majors, in a class size of 15-30 students who can work in groups of three.  Students will learn to properly design an experiment, work as teams, analyze data, evaluate conclusions, and communicate findings to others. Additionally, this lesson also incorporates self-reflection and peer assessment when students produce a poster as a summative assessment. Over a five–week period, students will explore how an abiotic factor affects growth, reproduction, and survival of Daphnia.  Students are asked to compare their results to published literature. By the end, students should have a better understanding of science as an ongoing process where results are being updated and furthering the state of knowledge.

Growing calls in science education reform have emphasized wide-scale engagement of first-year undergraduate students in authentic research experiences; however, large course enrollments, inadequate student experience, limited resources and departmental inertia often create obstacles to reaching this goal. To help overcome these obstacles, the Department of Biology at James Madison University (JMU) has developed a cost-effective, scalable, and transferable semester-long (14-week) course-based undergraduate research experience (CURE) designed for large enrollment introductory biology labs. In this series of labs, first-year students use DNA barcoding to engage in authentic research practices drawn from the fields of ecology, molecular biology, and bioinformatics. These labs enable students to identify local species of plants, fungi, and invertebrates using student-generated DNA barcode sequences, which are then shared through a public database. Since their implementation at JMU in 2016, students in these labs have created and shared over 1,500 unique DNA barcode sequences and documented over 300 local species of plants, fungi, and invertebrates. These data are being used in an ongoing project comparing the biodiversity of forest edge versus forest interior habitats, but the labs are adaptable to almost any habitat or taxonomic group. In this article, we provide detailed descriptions of the content, logistics, and implementation of this 14-week series of labs. To our knowledge, this is among the largest-enrollment CUREs being offered to first-year undergraduates in the United States, and we hope that it can be useful to other institutions interested in documenting biodiversity and engaging introductory biology students in authentic research.

In order to introduce students to the concept of molecular diversity, we developed a short, engaging online lesson using basic bioinformatics techniques. Students were introduced to basic bioinformatics while learning about local on-campus species diversity by 1) identifying species based on a given sequence (performing Basic Local Alignment Search Tool [BLAST] analysis) and 2) researching and documenting the natural history of each species identified in a concise write-up. To assess the student’s perception of this lesson, we surveyed students using a Likert scale and asking them to elaborate in written reflection on this activity. When combined, student responses indicated that 94% of students agreed this lesson helped them understand DNA barcoding and how it is used to identify species. The majority of students, 89.5%, reported they enjoyed the lesson and mainly provided positive feedback, including “It really opened my eyes to different species on campus by looking at DNA sequences”, “I loved searching information and discovering all this new information from a DNA sequence”, and finally, “the database was fun to navigate and identifying species felt like a cool puzzle.” Our results indicate this lesson both engaged and informed students on the use of DNA barcoding as a tool to identify local species biodiversity.

Primary Image: DNA Barcoded Specimens. Crane fly, dragonfly, ant, and spider identified using DNA barcoding.

We have designed three laboratory modules for an introductory organismal biology course with an emphasis on quantitative reasoning and data analysis skills. Module 1 tests for dimorphism in crayfish chelae using a paired statistical design. Module 2 tests for allometric growth of tapeworm hook structures using a regression model. Module 3 tests for differences in stomatal densities between two groups of plants using a two-sample statistical approach. For all three modules, we emphasize the use of confidence intervals to draw statistical conclusions about hypotheses. Knowledge about the basic biology of animals and plants is required, including arthropods, platyhelminths, and vascular plants. Background reading on dimorphism, allometry, and transpiration provides the necessary foundation to develop questions and hypotheses. Some familiarity with R is necessary for both students and instructors, although the activities can be modified for analysis with Excel or another statistical package. These modules can be taught independently or together as a unit within a course. As stated in the AAAS document, Vision and Change: A Call to Action, the ability to use quantitative reasoning is a core competency that must be developed by all biology students. These modules address the call for instruction in quantitative reasoning and provide a hands-on active introduction to key tools that will be required to build students’ statistical repertoire in more advanced courses.

Primary Image: A highlight of the three modules used in our introductory organismal biology course, including the use of calipers to test for dimorphism in the size of crayfish chelae (upper right), a leaf impression (lower right) from a hydrangea plant (lower left) used to test hypotheses about stomata densities, and the image of an Echinococcus tapeworm (upper left) to test hypotheses about allometry.  

This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.

A collection of materials related to Molecular Case Net – NSF RCN with Shuchi Dutta

This collection shares my work on Black representation in science.

This module introduces action potentials in the context of understanding nerve impulses. It is intended for an introductory biology audience.

In this module, students use data from natural history collections to look at range shifts related to climate variables over different time periods.

As instructors of introductory biology courses for majors and non-majors, we have struggled with teaching the concept of cell structure and function in an engaging way.  However, this is a foundational concept that most biology instructors would agree is vital for all students to know. The overall objective of this teachable unit is to help non-major introductory biology students learn the names and functions of the basic components of eukaryotic cells and, at the same time, understand the connection between cellular structure and function using active learning approaches. The key component of this teachable unit is a group exercise termed Cell Engineer/Detective. In this exercise, students work in groups to design a cell that is well suited for a function that is provided to them by the instructor (Cell Engineer). The groups then exchange their cells with classmates and try to guess the function of their classmates’ cells (Cell Detective). This exercise helps students visualize how the organelles of a cell work together to perform a specific function, allows instructors to clarify misconceptions regarding cell structure, guides students away from that quintessential but unrealistic model cell found in most biology textbooks, and reinforces the central biological connection between form and function.

Read the Essay Article about how author HN Tinsley adapted this lesson for online in "Online Adaptation of the Cell Engineer/Detective Lesson"

With the publishing of the Vision and Change report, we know it is best practice to include authentic research experiences in our undergraduate science lab classes. One big challenge in teaching so-called "wet lab" classes is figuring out a way to make sure students come to lab prepared to successfully complete their experiments. Molecular biology protocols are particularly challenging as they are typically long, detailed, and have multiple steps to complete. The most successful teaching practice I have tried is having students prepare for lab by hand-drawing flowcharts of the lab protocols. Drawing is a proven way to increase scientific understanding and requires students to engage with the lab materials before class. These flowcharts are due when students walk in to lab and more importantly, students use their flowcharts during lab. This teaching tool is easy to teach to students, simple to assess, and does not rely on any pre-existing knowledge of molecular biology or artistic skill. I have had great success using flowcharts as a teaching tool in both upper division and lower division classes as well as with both life science major and non-major students. Flowcharts have many potential applications beyond undergraduate "wet lab" classes including discussion courses and graduate research projects.

A long-standing tradition uses strings of poppit beads of different colors to model meiosis, especially to show how segments of paired homologous chromosomes are recombined. Our use of orthodontic latex bands to model cohesion of sister chromatids, and plastic coffee stirrers as microtubules, extends what can normally be achieved with ‘standard’ commercial kits of beads, so emphasizing the importance of four key elements of meiosis: (a) the role of chromosome replication before meiosis itself begins; (b) pairing and exchange (chiasma formation) of homologous chromosomes during meiosis I; (c) centromere (kinetochore) attachment and orientation within/on the spindle during meiosis I and meiosis II; and (d) the differential loss of arm and centromere cohesion at onset of anaphase I and anaphase II. These are essential elements of meiosis that students best need to visualize, not just read and think about. Bead modeling leads them in that direction, as our gallery of figures and accompanying text show.

Primary image: Unassembled components of ‘PoppitMeiosis’ – a poppit bead exercise aimed at student learning of meiosis. Beads are snapped together to model bivalent chromosomes (on the right side), with double-stick tape (top) representing the synaptonemal complex, orthodontic latex bands representing cohesion rings, and coffee stirrers representing microtubule bundles that connect centromeres to the spindle poles.