Rapid advances in genomics and bioinformatics, the vast amount of data generated by next-generation sequencing, and the penetration of the ‘-omics’ into many areas of biology have created a need for students with hands-on experience with computational and ‘big data’ methods. Additionally, laboratory experience in the isolation, identification, and characterization of unknown bacteria is a vital part of a microbiology student’s training. This lesson is a course-based undergraduate research experience (CURE) focusing on Salmonella enterica, a common and relatively low-virulence foodborne pathogen. In Module 1, students isolate and identify S. enterica strains from stream sediment, poultry litter, or other sources. They conduct phenotypic evaluation of antimicrobial resistance (AMR) and can search for plasmids. Isolates’ whole genomes may be sequenced by the United States FDA or public health laboratories, typically at no charge. In Module 2, students learn basic methods of genome assembly, analysis, annotation, and comparative genomics. They use easily accessible, primarily web-based tools to assemble their genomes and investigate areas of interest including serotype, AMR genes, and in silico evidence of mobile genetic elements. Either module can be used as a standalone learning experience. After course completion, students will be able to isolate and identify Salmonella from natural sources, and use computational analysis of microbial genomic data, particularly of the Enterobacteriaceae. This lesson offers undergraduate microbiologists a genuine research experience and a real-world microbiology application in genomic epidemiology, as well as a valuable mix of field, laboratory, and computational skills and experiences.

Remote learning often requires an alternative to hands-on, student-designed research projects. To this end, we created a package of scaffolded assignments to support introductory students through the research process using datasets from past student projects. These assignments provide opportunities for active practice and feedback on skills in experimental design, data analysis, literature review, and scientific communication. While we created the assignments to be heavily guided and focused on organismal biology to support students in our particular course context, the documents are highly customizable to meet the learning objectives for other course formats, subjects, and levels.

This module contains information for a three part series introducing the venom system in reptiles and discussing it in an evolutionary context. In the first part venom and its ecological roles are defined with a discussion of the diversity of venom structures and venomous lineages, primarily in squamates. Examples are provided of the various ways that venoms may vary among biological scales. In parts 2 and 3, the evolution of venom is discussed. Part 2 focuses on a description of how the venom system arose in squamates and a discussion of the challenges associated with defining "venomousness". Part 3 examines the various genetic mechanisms that produce venom variation using examples from primarily literature that are presented in Part 1. In addition to lecture materials, we include a primary literature based activity and a group activity designed to encourage students to explore the diversity of venomous taxa in reptiles and amphibians.

exercise

The Inside and Outside the Body activity helps students develop a conceptual understanding of anatomical barriers such as skin and mucus membranes that separate internal cells and fluids from the external environment. This short exercise prepares students for lessons in both anatomy and physiology and reflects recommendations from policy documents that suggest teaching core concepts. Understanding processes such as absorption, gradients and flow, and body defenses relies on the core concept of anatomical barriers. Instructors can use the concepts taught in this activity in subsequent discussions of topics such as immune tolerance of the fetus, the devastating impact of burns, and the sites of gas exchange.

The Alliance for the Black Community (ABC) developed a workshop to help faculty at California State University East Bay redesign their syllabi to incorporate anti-racist pedagogical practices.

Presentation on designing accessible STEM learning communities at the 2022 BIOME Institute.

Student Annotation

Meiosis is well known for being a sticky topic that appears repeatedly in biology curricula. We observe that a typical undergraduate biology major cannot correctly identify haploid and diploid cells or explain how and why chromosomes pair before segregation. We published an interactive modeling lesson with socks to represent chromosomes and demonstrated that it could improve student understanding of ploidy (1). Here we present an improvement on that lesson, using DNA paper strips in place of socks to better demonstrate how and why crossing over facilitates proper segregation. During the lesson, student volunteers act out the roles of chromosomes while the whole class discusses key aspects of the steps. Strips of paper with DNA sequences are used to demonstrate the degrees of similarity between sister chromatids and homologous chromosomes and to prompt students to realize how and why homologous pairing must occur before cell division. We include an activity on Holliday Junctions that can be used during the main lesson, skipped, or taught as a stand-alone lesson.

The function of the kidneys is to help maintain a constant internal environment (homeostasis) by regulating the volume and chemical composition of the blood. This regulation occurs via three fundamental processes: filtration, secretion, and reabsorption. Because these three processes all concern transfers between the blood and the pre-urine, inexperienced biology students frequently confuse them with each other and with the related process of excretion. Such confusion impairs understanding of the kidney’s regulatory functions. For instance, the effects of H⁺ secretion and HCO₃^- reabsorption on plasma pH can only be predicted if one knows that secretion entails removal from the blood while reabsorption entails addition to the blood. The enclosed three-part lesson teaches these processes through the use of multiple related examples with clinical relevance. In Module A (“Simple Math”), students define the direction of transfer (blood to pre-urine or pre-urine to blood) for each process, create a simple equation to show how excretion rate depends on these three processes, and solve the equation for missing values. In Module B (“Simple Graphs”), students show qualitatively how the three processes affect the composition of the pre-urine and (by implication) the blood. In Module C (“GFR”), students examine the relationship between glomerular filtration rate (GFR) and plasma levels of solutes like creatinine. By presenting multiple related examples embedded in the framework of Test Question Templates (TQTs), this lesson promotes a solid understanding of filtration, secretion, reabsorption, and excretion that can be applied to any naturally occurring substance or drug.

Primary image: Four urinary system processes. This image visually summarizes the four processes covered in this lesson: filtration, secretion, reabsorption, and excretion.

CFTR variants

This activity guides faculty through analyzing a resource using the Universal Design for Learning Guidelines.

Two activities for introducing Universal Design for Learning to a faculty audience